Supercomputing Institute for Digital Simulation and Advanced Computation

2006 Annual Research Report 2006 Annual Research Report of the Supercomputing Institute for Digital Simulation and Advanced Computation

Visit us on the Internet: www.msi.umn.edu Supercomputing Institute for Digital Simulation and Advanced Computation University of Minnesota 599 Walter 117 Pleasant Street SE Minneapolis, Minnesota 55455

This report was prepared by Supercomputing Institute researchers and staff. Editor: Tracey A. Bartlett

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contains a minimum of 10% postconsumer waste Table of Contents Introduction Overview ...... 2 Digital Technology Center ...... 2 Supercomputing Institute Resources and Programs Core Resources ...... 3 Research Laboratories Basic Sciences Computing Laboratory ...... 5 Computational Genetics Laboratory ...... 6 Digital Technology Computational Biology Laboratory ...... 7 Laboratory for Large-Scale Data Analysis ...... 8 Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory ...... 9 Scientific Data Management Laboratory ...... 10 Scientific Development and Visualization Laboratory ...... 11 Graduate Programs Scientific Computational Graduate Program ...... 12 Computational Neuroscience Program ...... 12 Partnerships Computational Life Sciences Program ...... 13 Grid and BlueGene Computing Block Grant ...... 14 Laboratory for Computational Science and Engineering ...... 15 Research Scholarship Program ...... 16 Undergraduate Internship Program ...... 17 Researchers and Administration Fellows of the Institute ...... 18 National Advisory Board ...... 19 Administrative Staff ...... 19 Technical Support Staff ...... 20 Committee and Panel Members ...... 22 External Support ...... 24 Events Sponsored Symposia Bioinformatics: Building Bridges ...... 34 VLab Workshop ...... 35 Outreach Programs Environmental Science Career Days ...... 36

2006 Annual Research Report of the Supercomputing Institute i Table of Contents (continued) Ongoing and Recently Completed Research Projects From January 1, 2005 Through March 15, 2006

University of Minnesota–Duluth College of Science and Engineering Department of Chemical Engineering ...... 39 Department of Chemistry and Biochemistry ...... 39 Department of Computer Science ...... 41 Department of Physics ...... 42 Natural Resources Research Institute ...... 43 Medical School Department of Anatomy, Microbiology, and Pathology ...... 44 Department of Biochemistry and Molecular Biology ...... 44

University of Minnesota–Hormel Institute The Hormel Institute ...... 47

University of Minnesota–Twin Cities Academic Health Center Cancer Center ...... 60 Center for Computational Genomics and Bioinformatics ...... 61 Center for Drug Design ...... 61 Stem Cell Institute ...... 62 College of Agricultural, Food, and Environmental Sciences Department of Agronomy and Plant Genetics ...... 63 Department of Animal Science ...... 66 Department of Entomology ...... 67 Department of Horticultural Science ...... 67 Department of Plant Pathology ...... 68 Department of Soil, Water, and Climate ...... 71 College of Agricultural, Food, and Environmental Sciences and College of Human Ecology Department of Food Science and Nutrition ...... 72

ii 2006 Annual Research Report of the Supercomputing Institute Table of Contents (continued) College of Agricultural, Food, and Environmental Sciences and Institute of Technology Department of Biosystems and Agricultural Engineering ...... 72 College of Biological Sciences Biotechnology Institute ...... 73 Department of Ecology, Evolution, and Behavior ...... 74 Department of Plant Biology ...... 77 College of Biological Sciences and Medical School Department of Biochemistry, Molecular Biology and Biophysics ...... 82 Department of Genetics, Cell Biology, and Development ...... 95 College of Education and Human Development Institute of Child Development ...... 101 College of Liberal Arts Department of Economics ...... 101 Department of Geography ...... 102 Department of Sociology ...... 103 College of Natural Resources Department of Bio-based Products ...... 103 College of Pharmacy College of Pharmacy ...... 104 Department of Experimental and Clinical Pharmacology ...... 105 Department of Medicinal Chemistry ...... 107 Department of Pharmaceutics ...... 112 College of Veterinary Medicine Department of Veterinary and Biomedical Sciences ...... 113 Department of Veterinary Population Medicine ...... 118 Curtis L. Carlson School of Management Department of Human Resources and Industrial Relations ...... 118 Department of Information and Decision Sciences ...... 119 Department of Operations and Management Science ...... 119 Hubert H. Humphrey Institute of Public Affairs Hubert H. Humphrey Institute of Public Affairs ...... 120

2006 Annual Research Report of the Supercomputing Institute iii Table of Contents (continued) Institute of Technology Department of Aerospace Engineering and Mechanics ...... 121 Department of Astronomy ...... 125 Department of Biomedical Engineering ...... 126 Department of Chemical Engineering and Materials Science ...... 129 Department of Chemistry and Chemical Physics Program ...... 142 Department of Civil Engineering ...... 158 St. Anthony Falls Laboratory ...... 164 Department of Computer Science and Engineering ...... 167 Department of Electrical and Computer Engineering ...... 173 Department of Geology and Geophysics ...... 179 Department of Mechanical Engineering ...... 180 Department of Physics ...... 190 Theoretical Physics Institute ...... 195 School of Mathematics ...... 195 Institute For Mathematics and Its Applications ...... 199 Medical School Department of Dermatology ...... 200 Department of Laboratory Medicine and Pathology ...... 200 Department of Medicine ...... 207 Department of Microbiology ...... 217 Department of Neurology ...... 223 Department of Neuroscience ...... 224 Department of Neurosurgery ...... 229 Department of Orthopaedic Surgery ...... 230 Department of Otolaryngology ...... 230 Department of Pediatrics ...... 232 Department of Pharmacology ...... 235 Department of Physical Medicine and Rehabilitation ...... 237 Department of Physiology ...... 238 Department of Psychiatry ...... 239 Department of Radiology ...... 239 Department of Surgery ...... 241 Department of Therapeutic Radiology ...... 243 Department of Urologic Surgery ...... 244 School of Dentistry Department of Developmental and Surgical Sciences ...... 246 Department of Diagnostic and Biological Sciences ...... 246 School of Public Health Division of Biostatistics ...... 250 Division of Environmental Health Sciences ...... 251 Division of Epidemiology and Community Health ...... 252

iv 2006 Annual Research Report of the Supercomputing Institute Table of Contents (continued) Bethel University College of Arts and Sciences Department of Chemistry ...... 254

Macalester College Department of Chemistry ...... 254

Mayo Clinic College of Medicine Advanced Genomic Technology Center ...... 256 Department of Molecular Pharmacology and Experimental Therapeutics ...... 256 Department of Neuroscience and Neurology ...... 257 Department of Orthopedic Research ...... 257 Department of Physiology ...... 258 Division of Cardiovascular Disease ...... 258

Metropolitan State University College of Arts and Sciences Department of Information and Computer Sciences ...... 260

Minnesota State University, Mankato College of Business Department of Management ...... 262 College of Science, Engineering, and Technology Department of Computer and Information Sciences ...... 262 Department of Mechanical and Civil Engineering ...... 263

St. Cloud State University College of Science and Engineering Department of Chemistry ...... 265 Department of Computer Science ...... 265

University of St. Thomas School of Engineering ...... 267

2006 Annual Research Report of the Supercomputing Institute v Table of Contents (continued)

Index and Bibliography

Index of Principal Investigators ...... 270 Bibliography of Research Reports for January 2004–May 2006 Aerospace Engineering and Mechanics ...... 276 Agronomy and Plant Genetics ...... 277 Astronomy ...... 277 Bio-based Products ...... 278 Biochemistry, Molecular Biology and Biophysics ...... 278 Biomedical Engineering ...... 280 Biostatistics ...... 281 Cancer Center ...... 281 Center for Drug Design ...... 281 Chemical Engineering and Materials Science ...... 281 Chemistry ...... 286 Civil Engineering ...... 299 Computer Science and Engineering ...... 301 Ecology, Evolution, and Behavior ...... 305 Diagnostic and Biological Sciences ...... 305 Economics ...... 305 Electrical and Computer Engineering ...... 305 Epidemiologyand Community Health ...... 307 Experimental and Clinical Pharmacology ...... 307 Genetics, Cell Biology, and Development ...... 307 Geology and Geophysics ...... 308 Laboratory Medicine and Pathology ...... 311 Management ...... 311 Mathematics ...... 312 Mechanical Engineering ...... 312 Medicinal Chemistry ...... 315 Medicine ...... 316 Microbiology ...... 316 Molecular Pharmacology and Experimental Therapeutics ...... 317 Neuroscience and Neurology ...... 317 Operations and Management Science ...... 317 Pharmaceutics ...... 317 Pharmacology ...... 318 Physical Medicine and Rehabilitation ...... 318 Physics ...... 319 Physiology ...... 321 Plant Biology ...... 321 Soil, Water, and Climate ...... 322 Surgery ...... 322 Veterinary and Biomedical Sciences ...... 322

vi 2006 Annual Research Report of the Supercomputing Institute Introduction Introduction

Overview Founded in 1984, the Supercomputing Institute is an make displays more informative, and add multimedia interdisciplinary research program spanning all colleges value to communications and work environments. In of the University of Minnesota. The Supercomputing many cases, these research activities may involve research Institute provides supercomputing resources and user aimed at the design or evaluation of high-performance support to faculty and students and is a linchpin pro- computing hardware, operating systems, networking, and gram in the University’s broad-based digital technology general-purpose algorithms and software. effort. The mission of the Supercomputing Institute is The Supercomputing Institute’s resources are available supercomputing research. This includes all aspects of to researchers at the University of Minnesota and other high-performance computing and scientific modeling post-secondary educational institutions in the State of and simulation, as well as graphics, visualization, high- Minnesota. In addition, the Supercomputing Institute performance network communications, informatics, and organizes and hosts symposia, workshops, and seminars, data mining. and coordinates other educational and collaborative Supercomputing research is defined broadly to include activities to promote supercomputing research, increase a variety of research activities from many disciplines. This university–industry collaboration, and promote technolo- research involves the use of high-performance computing gy transfer. environments to address problems in science and engi- Hardware resources include both core resources and neering that could not otherwise be attempted. Such laboratories. In addition to hardware and software, the efforts often result in domain-specific algorithms and Institute provides an extensive program of user support codes that exploit the available computing environments and training. as well as visualization techniques to enhance insight,

Digital Technology Center

The Supercomputing Institute plays a central role in the Center. This $63.4 million renovation brought state-of- University of Minnesota’s digital technology initiative. the-art hardware and user support to the center of the This initiative includes technologies based on computers, campus. The Supercomputing Institute joined the electronics, telecommunications, digital design, computa- Digital Technology Center in 2001 and moved to the tional biology, systems recognition and verification, home of the Digital Technology Center in Walter Library graphics and visualization, databases and data mining, in March 2002, where it is located on the fifth floor and networks, storage, artificial intelligence, robotics and part of the fourth floor and basement. vision, signal processing and wireless technology, and electronic commerce. Key to this initiative was the renovation, completed in 2002, of Walter Library on the University’s East Bank Campus into a Digital Technology

2 2006 Annual Research Report of the Supercomputing Institute Supercomputing Institute Resources and Programs

Core Resources In 1981, the University of Minnesota was the first of memory each and 1.5 GHz Power4 proces- American university to acquire a supercomputer (a Cray- sors. 1B). The Supercomputing Institute was created in 1984 • Eleven 8-processor p655+ nodes with 16 GB of to provide leading-edge, high-performance computing memory each and 1.7 GHz Power4 processors. resources to the University of Minnesota’s research com- The interactive node is one of the 8-processor p655+ munity. The supercomputing resources offered to the 1.7 GHz nodes, and there are four 4-processor P655+ University of Minnesota research community have nodes used as file servers. There is 17.3 TB of disk space included a Cray-2, an ETA 10, a Cray X-MP, an IBM shared across all 32 nodes. 3090, a Cray M90, a Cray T3D, a Cray C90, a Cray The Institute’s Linux Cluster consists of 76 2-proces- T3E-900, an IBM SP based on Silvernodes, two SGI sor Netfinity nodes from IBM. Characteristics of the Altix 3800s, an ES7000 Orion 230, a QuantumCube nodes are: cluster, an IBM SP based on WinterHawk and • Twelve 2-processor nodes with 1.5 GB of mem- NightHawk nodes, an IBM Power4 with p690+ ory and 2.6 GHz Intel Pentium 4 processors (Regatta) and p655+ nodes, a Linux Cluster, an SGI (Gigabit Ethernet). Altix 3000, and an ES7000 Orion 430. • Sixty-two 2-processor nodes with 3.25 GB of The Supercomputing Institute has continued the memory and 1.26 GHz Intel Pentium III strong tradition of providing University of Minnesota processors (Fast Ethernet and Myrinet). researchers with leading-edge, high-performance comput- • One 2-processor node with 2 GB of memory ing technologies and diversified programs that comple- and 1.13 GHz Intel Pentium III processors (Fast ment these technologies. In addition, the Institute has Ethernet and Myrinet) (interactive node). developed a strong program of user support, including • One 2-processor node with 2.6 GB of memory tutorials and applications support across the physical, and 2.66 GHz Xeon processors (Fast Ethernet biological, mathematical, and computer sciences, engi- and Myrinet) (server node). neering, and other disciplines that use high-performance Sixty-nine nodes are available for computation computing, informatics, and data mining. through a queuing system, three nodes are for interactive The Institute’s IBM SP supercomputer, which consist- use, and the remaining four nodes are file servers. The ed of 91 shared-memory nodes with a total of 356 nodes are connected using Gigabit Ethernet, Fast processors and 695 GB of memory, was retired on March Ethernet, and Myrinet, as noted above. A cluster file sys- 13, 2006. tem provides 2.5 TB of disk that is shared by all nodes. The IBM Power4 system is a constellation of several The SGI Altix Cluster consists of 11 shared-memory shared-memory nodes. The operating system is AIX, machines: IBM’s brand of the Unix operating system. The nodes • One 256-processor compute server with 512 GB are either pSeries 690+ nodes (called Regatta nodes) or of memory and 1.6 GHz Intel Itanium 2 proces- p655+ nodes. All nodes are connected with IBM’s HPS sors. switch for faster interprocess communication and file • One 48-processor compute server with 96 GB of access. The detailed characteristics of the nodes are as fol- memory and 1.3 GHz Intel Itanium 2 proces- lows: sors. • One 32-processor Regatta node with 128 GB of • One 4-processor interactive machine with 12 memory and 1.7 GHz Power4 processors. GB of memory and 900 MHz Intel Itanium 2 • One 32-processor Regatta node with 64 GB of processors. memory and 1.7 GHz Power4 processors. • Eight 16-processor Altix 350 compute nodes • One 32-processor Regatta node with 64 GB of with 32 GB of memory and 1.5 GHz Intel memory and 1.3 GHz Power4 processors. Madison processors. • One 24-processor Regatta node with 24 GB of All machines run the Linux operation system and memory and 1.3 GHz Power4 processors. share 4.5 TB of disk space. An additional 4.5 TB of disk • Thirteen 8-processor p655+ nodes with 16 GB space is dedicated to local scratch spaces on the nodes.

2006 Annual Research Report of the Supercomputing Institute 3 Supercomputing Institute Resources and Programs

Core Resources (continued) On September 15, 2005, the Unisys ES7000 Orion Planning Committee 430 was designated a core resource. It had previously Donald G. Truhlar, Chemistry, Chemical Physics, been used for the Laboratory for Large-Scale Data Nanoparticle Science and Engineering, and Analysis, which has been closed. This machine has six- Scientific Computation, chair teen Intel Itanium 1.5 GHz processors and 32 GB of Graham V. Candler, Aerospace Engineering and memory. A Fiber Channel EMS Clarion CX400 Raid Mechanics and Scientific Computation provides 0.7 TB of disk space. The ES7000 runs the Jiali Gao, Chemistry and Scientific Computation RedHat Linux AS 3 operating system. This machine pro- Yiannis Kaznessis, Chemical Engineering and vides both interactive and batch resources. Materials Science The Institute has purchased an IBM BladeCenter H* Vipin Kumar, Computer Science and Engineering Linux Cluster from IBM with 275 LS 21 nodes. Each and Scientific Computation node has two dual-core 2.6 GHz AMD Opteron proces- David J. Lilja, Electrical and Computer Engineering sors sharing 8 GB of memory. This gives a total of 1,100 and Scientific Computation cores on the system. The system will have approximately Krishnan Mahesh, Aerospace Engineering and 40 TB of disk space. The BladeCenter is scheduled to be Mechanics delivered in late summer 2006. Alon V. McCormick, Chemical Engineering and The major supercomputing resource program and Materials Science long-term planning at the Institute are guided by the Douglas H. Ohlendorf, Biochemistry, Molecular Institute’s Planning Committee. Biology, and Biophysics Yousef Saad, Computer Science and Engineering and Scientific Computation George L. Wilcox, Neuroscience and Scientific Computation

4 2006 Annual Research Report of the Supercomputing Institute Supercomputing Institute Resources and Programs

Basic Sciences Computing Laboratory Since 1996, the Supercomputing Institute has provided This laboratory was overseen and guided during high-performance graphics and visualization workstations 2005–06 by the following people: to the University of Minnesota research community through the Basic Sciences Computing Laboratory Laboratory Manager (BSCL). The BSCL is located in Nils Hasselmo Hall on the East Bank of the Twin Cities campus. The unique Benjamin Lynch mixture of computational servers, workstations, visualization tools, software, and technical consulting resources Executive Committee offered through the BSCL are made available to all Douglas H. Ohlendorf, Biochemistry, Molecular University researchers. With its location in Hasselmo Biology, and Biophysics Hall, the research at the BSCL is heavily focused on such Donald G. Truhlar, Chemistry, Chemical Physics, areas as biomedical engineering and structural biology (x- Nanoparticle Science and Engineering, and ray crystallography and nuclear magnetic resonance). Scientific Computation Linux, Unix, and Windows computing and visualization systems from Dell, IBM, SGI, and Sun are housed Steering Committee at the BSCL. These resources include multiple graphics workstations and a visualization/computation system Carrie M. Wilmot, Biochemistry, Molecular Biology purchased through a National Institutes of Health Shared and Biophysics, chair Instrumentation Grant. The visualization/computation Timothy J. Griffin, Biochemistry, Molecular Biology, system consists of a 48-processor SGI Altix, a 16-proces- and Biophysics sor SGI Onyx4, and a large (4 ft. by 6 ft.), high-resolu- Tongbin Li, Neuroscience tion screen for stereo viewing. David H. Live, Biochemistry, Molecular Biology, and Biophysics David D. Thomas, Biochemistry, Molecular Biology, and Biophysics and Scientific Computation Kylie J. Walters, Biochemistry, Molecular Biology, and Biophysics

2006 Annual Research Report of the Supercomputing Institute 5 Supercomputing Institute Resources and Programs

Computational Genetics Laboratory The Computational Genetics Laboratory (CGL) of the This laboratory was overseen and guided during Supercomputing Institute is managed jointly with the 2005–06 by the following people: Center for Microbial and Plant Genomics and the Biomedical Genomics Center. The laboratory is located Laboratory Manager in the Cargill Microbial and Plant Genomics Building on the St. Paul campus. In addition, the laboratory has a Zheng Jin Tu secondary home in Nils Hasselmo Hall. The laboratory is designed to meet the emerging computational needs of Executive Committee the computational biology community, especially in the Ronald L. Phillips, Agronomy and Plant Genetics areas of bioinformatics, computational genomics/genet- Ashley T. Haase, Microbiology ics, and proteomics. Donald G. Truhlar, Chemistry, Chemical Physics, The CGL is equipped with many state-of-the-art Nanoparticle Science and Engineering, and computers, including one 16-CPU, one 8-CPU, and two Scientific Computation 4-CPU Sun servers, two Sun workstations, two SGI workstations, one IBM Linux workstation, five Dell Steering Committee Windows computers, and a Macintosh G5. In addition, users can access the supercomputers at the Institute. Vivek Kapur, Microbiology, chair The CGL has more than 90 popular software pack- John V. Carlis, Computer Science and Engineering ages for bioinformatics (BLAST, GCG, EMBOSS, Scott C. Fahrenkrug, Animal Science PHRED/PHRAP, DNASTAR, MACVECTOR, and others), Arkady Khodursky, Biochemistry, Molecular Biology, evolution (PHYLIP, PAUP, PAML, and others), microarray and Biophysics data analysis (EXPRESSIONIST, GENETRAFFIC, Kenneth D. Vernick, Microbiology GENESPRING, SPOTFIRE, and others), and proteomics Gary L. Nelsestuen, Biochemistry, Molecular (MASCOT, PEAKS, SCAFFOLD, PRO ID, PRO QUANT, and Biology, and Biophysics others). The laboratory also has numerous local biologi- Gary J. Muehlbauer, Agonomy and Plant Genetics cal databases available, including GENBANK and many genome databases. Statistic packages such as SAS and SPLUS are available and can be used for biological data analysis. Furthermore, there are numerous bioinformatics database projects hosted at the CGL.

6 2006 Annual Research Report of the Supercomputing Institute Supercomputing Institute Resources and Programs

Digital Technology Computational Biology Laboratory The basic objective of the Digital Technology Compu- This laboratory was overseen and guided during tational Biology Laboratory is to provide computing 2005–06 by the following people: resources to faculty members and students involved in computational biology. Laboratory Manager While computational biology faculties have full access to all Institute resources, this laboratory is dedicated to Yuk Sham computational biology in a way that allows special and focused stimulation of interdisciplinary and interdepart- Executive Committee mental digital technology collaboration among Hans G. Othmer, Mathematics and Scientific University of Minnesota faculties and their research Computation, chair groups. The goal of the laboratory is to encourage collab- Donald G. Truhlar, Supercomputing Institute oration and high-performance computing research within Director, Chemistry, Chemical Physics, the computational biology community at the University Nanoparticle Science and Engineering, and of Minnesota as well as with other academic and indus- Scientific Computation trial organizations in the state of Minnesota. The laboratory also provides user support, training, and knowledge Steering Committee sharing services. The laboratory is equipped with an 8-processor Hans G. Othmer, Mathematics and Scientific Compaq ES40 with a processor speed of 500 MHz and 8 Computation, chair GB of memory. Jiali Gao, Chemistry and Scientific Computation Alexander Y. Grosberg, Physics and Astronomy and Scientific Computation

2006 Annual Research Report of the Supercomputing Institute 7 Supercomputing Institute Resources and Programs

Laboratory for Large-Scale Data Analysis The Laboratory for Large-Scale Data Analysis was For 2005, the Laboratory for Large-Scale Data designed to provide a computational environment that Analysis was overseen and guided by the following peo- encouraged experimental use of the Unisys Orion super- ple: computer for large problems that demand high capabilities of the equipment and software. The goal of the Laboratory Manager Supercomputing Institute–Unisys partnership was to foster the growth of research that took advantage of the Yuk Sham unique capabilities of the hardware and operating system of the Unisys supercomputing platform. The key hard- Steering Committee ware in this laboratory was a 32-processor Intel Itanium Yiannis Kaznessis, Chemical Engineering and 1.5 GHz ES7000 Orion 430 supercomputer with 64 GB Materials Science, chair of memory. The machine was configured into two parti- Wei-Shou Hu, Chemical Engineering and Materials tions running the 64-bit Windows Datacenter 2003 Science operating system on one partition and Red Hat Fumiaki Katagiri, Plant Biology Enterprise’s Linux AS operating system on the other. Vipin Kumar, Computer Science and Engineering Microsoft SQL SERVER and ORACLE were installed on the and Scientific Computation machines, which enabled researchers to carry out data- Michael J. Olesen, Digital Technology Center, ex base-oriented or data-mining-intensive types of research officio member projects. Friedrich Srienc, Bioprocess Technology Institute On September 15, 2005, the Unisys equipment was and Chemical Engineering and Materials Science converted to a core resource, and the laboratory was closed.

8 2006 Annual Research Report of the Supercomputing Institute Supercomputing Institute Resources and Programs

Medicinal Chemistry/Supercomputing Institute Visualization-Workstation Laboratory The Medicinal Chemistry/Supercomputing Institute This laboratory was overseen and guided during Visualization–Workstation Laboratory (VWL) is co- 2005–06 by the following people: sponsored by the Department of Medicinal Chemistry and the Supercomputing Institute. The laboratory is Laboratory Manager located in Weaver-Densford Hall, home of the College of Pharmacy and the Center for Drug Design. Being within Yuk Sham the University’s Academic Health Center campus, the laboratory is heavily used by biomedical researchers. Executive Committee While the scope of studies carried out within the labora- Yusuf J. Abul-Hajj, Medicinal Chemistry tory is very broad, some of the main focuses of the labo- Donald G. Truhlar, Chemistry, Chemical Physics, ratory include structure determination of pharmaceutical Nanoparticle Science and Engineering,and compounds and the design of potent drugs for treatment Scientific Computation of cancer and HIV (human immunodeficiency virus). The laboratory contains a wide variety of Sun, SGI, and Steering Committee Linux workstations, Windows PCs, and state-of-the-art commercial software applications. The laboratory is avail- Carston R. Wagner, Medicinal Chemistry, chair able to all University of Minnesota researchers and their Elizabeth A. Amin, Chemistry collaborators. David J. W. Grant, Pharmaceutics (deceased, December 2005)

2006 Annual Research Report of the Supercomputing Institute 9 Supercomputing Institute Resources and Programs

Scientific Data Management Laboratory The Scientific Data Management Laboratory (SDML) is This laboratory was overseen and guided during designed to meet the evolving data management 2005–06 by the following people: demands of University faculty and researchers. The SDML provides access to software, computational, and Laboratory Manager storage resources necessary to develop and support high- profile research related data applications. This centralized Zheng Jin Tu database infrastructure is available for all applicable research projects. Steering Committee The SDML currently houses a 4-processor Sun V490 Timothy J. Griffin, Biochemistry, Molecular Biology database server with 8 GB of memory, a Web server and Biophysics, chair (PERL, PHP, JAVA through TOMCAT, APACHE, etc.), a sys- Yiannis N. Kaznessis, Chemical Engineering and tem for interactive logins (database and Web interface Materials Science development), and 6.4 TB of disk space. The available Mohammed F. Mokbel, Computer Science and hardware will continue to evolve with demand. Engineering The SDML provides users access to a variety of data- Gary L. Nelsestuen, Biochemistry, Molecular Biology base management systems including MYSQL and and Biophysics ORACLE. Other database management systems and relat- Nathan M. Springer, Plant Biology ed software can be installed upon request, dependent on Jaideep Srivastava, Computer Science and availability. Engineering and Scientific Computation Carrie M. Wilmot, Biochemistry, Molecular Biology and Biophysics

10 2006 Annual Research Report of the Supercomputing Institute Supercomputing Institute Resources and Programs

Scientific Development and Visualization Laboratory The Supercomputing Institute’s Scientific Development For 2005–06, the Scientific Development and and Visualization Laboratory (SDVL), which is located Visualization Laboratory was overseen and guided by the in the Supercomputing Institute’s facilities on the fifth following people: floor of Walter, provides Institute researchers with access to SGI, Sun, and Linux workstations, an 8-processor sys- Laboratory Manager tem with PQS nodes known as QuantumCube, Mac- intosh workstations, PCs, hardware and software for the Seema Jaisinghani production of short videos, and associated software and technical support. The SDVL also hosts a Windows Steering Committee Application Server that provides remote access to win- Alon V. McCormick, Chemical Engineering and dows software at the Institute. Materials Science, chair Researchers use workstations for code development, Thomas W. Jones, Astronomy and Scientific submission and monitoring of jobs on the Institute’s Computation supercomputers, and workstation queues. SDVL Krishnan Mahesh, Aerospace Engineering and machines support various computer engineering applica- Mechanics tions, scientific computing, and visualization software. Gary W. Meyer, Computer Science and Engineering The SDVL also serves as a permanent facility to hold P. Paul Ruden, Electrical and Computer Engineering tutorials and hands-on workshops offered regularly by the Institute. The Institute’s summer undergraduate internship program activities are organized in the laboratory premises, turning it into a vibrant hub for partici- pants.

2006 Annual Research Report of the Supercomputing Institute 11 Supercomputing Institute Resources and Programs

Scientific Computation Graduate Program The graduate degree program in scientific computation vides a new combination of studies for solving today’s encompasses coursework and research on the fundamen- scientific computational problems. It is a degree program tal principles necessary to use intensive computation to that builds on the strength of existing programs at the support research in the physical, biological, and social University of Minnesota in formulating real problems sciences and engineering. There is a special emphasis on based on the physical system or the traditional discipline, research issues, state-of-the-art methods, and the applica- and it augments field-specific work relating to the mathe- tion of these methods to outstanding problems in sci- matical and numerical modeling with state-of-the-art ence, engineering, and other fields that use numerical techniques for scientific computation in an integrated analysis, symbolic and logic analysis, high-performance manner. computing tools, parallel algorithms, supercomputing The Scientific Computation Program offers Ph.D. and and heterogeneous networks, and visualization. M.S. degrees. The current Director of Graduate Studies Scientific Computation is gradually emerging as an is Jiali Gao of the Department of Chemistry. important field of its own in academia and industry. In the last decade, it has become clear that solving a given scientific problem often requires knowledge that straddles several disciplines. This interdisciplinary program pro-

Computational Neuroscience Program The Computational Neuroscience Program is an interdis- Program Director is Timothy J. Ebner, Neuroscience, ciplinary pre-doctoral fellowship program that integrates and the Program Co-Director is Donald G. Truhlar, training in neuroscience with physical-computational Chemistry, Chemical Physics, Nanoparticle Science and studies. Fellows pursue the Ph.D. degree with a major in Engineering, and Scientific Computation. graduate programs in Biomedical Engineering, Chemis- The fellowship program began in 1998 with funding try, Computer Science, Mathematics, Neuroscience, from a National Science Foundation Integrative Physics, or Scientific Computation. Those fellows major- Graduate Education and Research Traineeship (IGERT) ing in Neuroscience pursue a minor of supporting pro- grant. It is now funded by a National Institutes of Health gram in computation or physical science, and those Neuro-Physical-Computational Science Training Grant, majoring in any of the other disciplines minor in awarded in September 2004. Other support is provided Neuroscience. Participating faculty include representa- by the Department of Neuroscience, the Graduate tives from Biomedical Engineering, Chemistry, School, the Institute of Technology, the Medical School, Computer Science and Engineering, Mathematics, and the Supercomputing Institute. Neuroscience, Scientific Computation, and Physics. The

12 2006 Annual Research Report of the Supercomputing Institute Supercomputing Institute Resources and Programs

Computational Life Sciences Program The Computational Life Sciences Program is an initiative • Both IBM and the University benefit from the of the University of Minnesota Supercomputing Institute development of the software expertise needed to that is intended to foster the growth of research in com- take advantage of IBM’s DiscoveryLink software putational biology. This program has been formed in • The Supercomputing Institute makes space order to: available to IBM staff members in exchange for • Focus and enhance the resources, software, and additional technical support in the area compu- technical support we provide to the University of tational biology, specifically including tutorials Minnesota computational biology research com- and seminars munity To complement its partnership with IBM, the • Foster and develop the use of the Institute’s Supercomputing Institute has also established an affiliates resources, software, and technical support among program that provides an opportunity for Minnesota the biological sciences community industry and other Minnesota research institutions with To fulfill these goals, the Supercomputing Institute interests in the area of computational biology to have has entered into a special partnership with IBM. This access to these computational resources, software, and relationship is mutually beneficial, with the following technical support. Participating affiliates receive the fol- mutual benefits: lowing benefits: • IBM receives feedback through personal com- • They are able to use computational, software, munications of user support and systems staff and technical support resources for the develop- and through the Supercomputing Institute’s ment of seed projects research report series • They are able to establish relationships with • University of Minnesota/IBM partnership activi- University of Minnesota faculty, Supercom- ties with researchers, including joint efforts with puting Institute staff, and IBM staff affiliates, are fostered The current affiliates are Cargill, the Hormel Institute, • The Supercomputing Institute continues to serve and the Mayo Clinic College of Medicine. the high-performance computing resource needs Further information about this program is available at: of the entire University of Minnesota high-per- www.msi.umn.edu/general/Programs formance computing research community while /uofmibm/index.html also meeting the emerging computational needs of the biology community • The Supercomputing Institute makes a large amount of additional computer storage available to University of Minnesota researchers through the leverage of a Shared University Research (SUR) grant from IBM

2006 Annual Research Report of the Supercomputing Institute 13 Supercomputing Institute Resources and Programs

Grid and BlueGene Computing Block Grant The following committee explored new opportunities in the areas of grid and BlueGene computing:

Block Grant Committee for 2005–06 Thomas W. Jones, Astronomy and Scientific Computation, chair Graham V. Candler, Aerospace Engineering and Mechanics Jiali Gao, Chemistry and Scientific Computing Sean C. Garrick, Mechanical Engineering William B. Gleason, Laboratory Medicine and Pathology J. Woods Halley, Physics Yiannis Kaznessis, Chemical Engineering and Material Science Vipin Kumar, Computer Science and Engineering and Scientific Computation Krishnan Mahesh, Aerospace Engineering and Mechanics Robert Numrich, Supercomputing Institute Yousef Saad, Computer Sciences and Engineering and Scientific Computation Renata M. Wentzcovitch, Chemical Engineering and Material Science David A. Yuen, Geology and Geophysics and Scientific Computation

14 2006 Annual Research Report of the Supercomputing Institute Supercomputing Institute Resources and Programs

Laboratory for Computational Science and Engineering The Supercomputing Institute partners with the The cooperative program was overseen and guided by Laboratory for Computational Science and Engineering the following people in 2005: (LCSE). Through this partnership, Supercomputing Institute researchers are able to participate in the LCSE Executive Committee for the program. Cooperative Program The LCSE encourages the participation of Supercomputing Institute researchers with applications Donald G. Truhlar, Chemistry, Chemical Physics, that demonstrate or test new technologies under active Nanoparticle Science and Engineering, and development, applications requiring very large online Scientific Computation data sets, particularly if they must be accessed at very Paul R. Woodward, Astronomy and Scientific high bandwidth, and applications requiring very high- Computation resolution visualizations, particularly if image animations are needed. Distributed computing applications with Program Committee for the Cooperative tight coupling of computing resources on a fast network Program are also encouraged. The Supercomputing Institute cooperative program Paul R. Woodward, Astronomy and Scientific with the LCSE ended on June 30, 2005. Computation, chair Baoquan Chen, Computer Science and Engineering David H. Du, Computer Science and Engineering Thomas W. Jones, Astronomy Ernest F. Retzel, Center for Computational Genomics and Bioinformatics David A. Yuen, Geology and Geophysics and Scientific Computation

2006 Annual Research Report of the Supercomputing Institute 15 Supercomputing Institute Resources and Programs

Research Scholarship Program The Supercomputing Institute offers a Research Research Scholarship Peer Review Scholarship Program that provides grants to enhance the Panel for 2005-2006 supercomputing research programs of University of Minnesota faculty. These grants, which are peer reviewed Renata M. Wentzcovitch, Chemical Engineering and and competitively awards, are for the partial support of Materials Science, chair research associates who work closely with Alexander Y. Grosberg, Physics and Astronomy and Supercomputing Institute principal investigators on their Scientific Computation research projects. Over the past 14 years, the Krishnan Mahesh, Aerospace Engineering and Supercomputing Institute has awarded 207 Research Mechanics Scholarships. These Research Scholarships have provided Douglas H. Ohlendorf, Biochemistry, Molecular an important opportunity for the creation and pursuit of Biology, and Biophysics research projects that might not have otherwise been Heinz G. Stefan, Civil Engineering attempted. David D. Thomas, Biochemistry, Molecular Biology, and Biophysics and Scientific Computation

Research Scholars, 2004-2005 Research Scholars, 2005-2006 Divesh Bhatt, University of California, Berkeley, Olalla Nieto Faza, Universidade de Vigo, Vigo, California Spain Yuhua Duan, Department of Chemical Pablo César Jaque Olmedo, Catholic University Engineering and Materials Science of Chile, Santiago, Chile Daniel Goldstein, University of Colorado, Suzanne Shontz, Department of Computer Boulder, Colorado Science and Engineering Ahren Jasper, Department of Chemistry Roshan Shrestha, Kyoto University, Kyoto, Japan Benjamin Lynch, Department of Chemistry Magdalena Stolarska, School of Mathematics Shuha Ma, Department of Chemistry Rosendo Valero, Leiden University, Leiden, The Murilo Tiago, University of California, Berkeley, Netherlands California Jean-Francois Vinuesa, St. Anthony Falls Taku Tsuchiya, Department of Chemical Laboratory Engineering and Materials Science Irina Vlasova, Department of Microbiology Koichiro Umemoto, Department of Chemical Yuegang Zhang, Department of Pharmeceutics Engineering and Materials Science Jean-Francois Vinuesa, St. Anthony Falls Laboratory

16 2006 Annual Research Report of the Supercomputing Institute Supercomputing Institute Resources and Programs

Undergraduate Internship Program The Supercomputing Institute provides an Undergrad- Undergraduate Internship Committee uate Internship Program for undergraduate students for 2005-2006 throughout the country. The focus of the program is the application of computational approaches and visualiza- Victor H. Barocas, Biomedical Engineering and tion methods to supercomputing research. Faculty from Scientific Computation, chair various disciplines have contributed projects and super- Donald G. Truhlar, Chemistry, Chemistry, Chemical vise the undergraduate students in their daily work. This Physics, Nanoparticle Science and Engineering, program provides an opportunity for a challenging and and Scientific Computation enriching educational experience for undergraduate students interested in pursuing graduate or professional education. The program has sponsored 477 interns in its 16 years of existence.

Undergraduate Interns, Summer 2005 Joshua W. Allen, University of Minnesota, Carl G. Peterson, University of Minnesota Karli J. Anderson, University of Minnesota Thomas J. Preston, University of Maine, Orono, Lee B. Ballard, Purdue University, West Lafayette, Maine Indiana Scott J. Reckinger, University of St. Thomas, St. Gretchen L. Beebe, University of Minnesota Paul, Minnesota Philip W. Bransford, University of Minnesota Ekaterina Shukh, University of Minnesota Adam R. Burr, University of Minnesota Evgenia (Jane) Shvelidze, University of Minnesota Monica D. Christiansen, University of Minnesota Mark B. Sielaff, Carleton College, Northfield, Stephen A. DeSalvo, University of Minnesota Minnesota Benjamin J. Dodson, University of Pennsylvania, Benjamin A. Sowell, Carleton College, Northfield, Philadelphia, Pennsylvania Minnesota Blayne A. Field, University of Minnesota Yang Bee Vue, Massachusetts Institute of Technology, Ian R. Haken, Texas Academy of Mathematics and Cambridge, Massachusetts Science Anthony A. Widboom, University of Minnesota Benedict L. Hanrahan, University of Minnesota Michael R. Frasca, Bucknell University, Lewisburg, Kara B. Johnson, Stanford University, Stanford, Pennsylvania California Nicholas J. Voshell, University of Minnesota Benjamin J. Kadlec, University of Minnesota Shuo Mark Wang, University of Minnesota Caroline E. Newcombe, Arizona State University, Tempe, Arizona

2006 Annual Research Report of the Supercomputing Institute 17 Researchers and Administration

Fellows of the Institute, 2005–2006 Fellows Douglas N. Arnold Dennis A. Hejhal Fernando Porté-Agel Daniel L. Boley John R. Hiller Yousef Saad Graham V. Candler Thomas W. Jones L. E. Scriven Bernardo Cockburn Daniel D. Joseph Shashi Shekhar Christopher J. Cramer Yiannis N. Kaznessis J. Ilja Siepmann H. Ted Davis Thomas H. Kuehn Charles C. S. Song Philippe de Forcrand (adjunct) Vipin Kumar Fotis Sotiropoulos Jeffrey J. Derby David J. Lilja Kumar K. Tamma David H. Du John S. Lowengrub David D. Thomas David M. Ferguson Mitchell B. Luskin Donald G. Truhlar Efi Foufoula-Georgiou Krishnan Mahesh Oriol T. Valls Jiali Gao Kevin H. Mayo Randall H. Victora Steven L. Girshick Alon V. McCormick Renata M. Wentzcovitch William B. Gleason Douglas H. Ohlendorf George L. Wilcox Alexander Y. Grosberg Hans G. Othmer Paul R. Woodward J. Woods Halley Suhas V. Patankar David A. Yuen

Associate Fellows

John P. Abraham Jerome F. Hajjar Yuan-Ping Pang Roger E. A. Arndt Franz Halberg Ted Pedersen Leonard J. Banaszak Shaul Hanany David Y. H. Pui Victor H. Barocas Joachim V. Heberlein Shri Ramaswamy David A. Blank Stephen S. Hecht P. Paul Ruden Robert W. Carr Wei-Shou Hu Lanny D. Schmidt Jane H. Davidson Steven R. Kass Terrence W. Simon Jürgen F. Fohlmeister Paul Kiprof Masha Sosonkina Roger L. Fosdick Uwe R. Kortshagen Friedrich Srienc Sean C. Garrick Perry H. Leo Heinz G. Stefan Wayne L. Gladfelter Kenneth R. Leopold Henryk K. Stolarski Richard J. Goldstein David G. Levitt Vaughan R. Voller Anand Gopinath William Li Kylie J. Walters David J. W. Grant (deceased, 2005) Robert L. Lysak Dong Wang Satish C. Gupta Christopher W. Macosko Darrin M. York Bojan Guzina David C. Morse

18 2006 Annual Research Report of the Supercomputing Institute Researchers and Administration

National Advisory Board The National Advisory Board is made up of national The Board is shown in the picture below: experts in several areas of high-performance computing.

Left to right: Daniel Reed, University of North Carolina at Chapel Hill and President’s Information Technology Advisory Committee; Albert Wagner, Argonne National Laboratory, chair; David E. Keyes, Columbia University, Brookhaven National Laboratory, and Lawrence Livermore National Laboratory; Robert Jernigan, Iowa State University

Administrative Staff Andrew Odlyzko Interim Director William Hellriegel Assistant to the Director Jane Zirbes Research Programs Administrator Tracey Bartlett Executive Office and Administrative Specialist Annice Larkin Executive Office and Administrative Specialist Debbie Schutta Executive Office and Administrative Specialist Ann Johns DTC Assistant Director for Human Resources Brian Carlton DTC/MSI Senior Accountant Shaun Kershner DTC/MSI Accountant Stephanie Huber DTC/MSI Principal Accounts Assistant Marni Anderson-Brown DTC/MSI Principal Office and Administrative Specialist and Receptionist

2006 Annual Research Report of the Supercomputing Institute 19 Researchers and Administration

Technical Support Staff User Support Birali Runesha Manager, User Support; Scientific Computation Consultant Wen Dong Web Interface Programmer Seema Jaisinghani Scientific Development and Visualization Laboratory Manager; Scientific Visualization Consultant Benjamin Lynch Basic Sciences Computing Laboratory Manager; Computational Chemistry Consultant Yuk Sham Medicinal Chemistry Visualization-Workstation Laboratory Manager; Digital Technology Computational Biology Laboratory Manager; Computational Biology/Biochemistry Consultant Zheng Jin Tu Computational Genetics Laboratory Manager; Computational Biology Consultant Haoyu Yu Data Mining Consultant Wayne Xu Computational Genomics Consultant Shuxia Zhang Scientific Computation Consultant

20 2006 Annual Research Report of the Supercomputing Institute Researchers and Administration

Technical Support Staff (continued) Large Systems Group Kirk Deen Large Systems Group Manager and IBM Power4 Systems Administrator John Griffin-Wiesner Linux Cluster/Unix Systems Administrator Gabe Turner Unix Systems Administrator

Unix Group Bridget Kromhout Unix Group Manager; Unix Systems Administrator Yectli Huerta Unix Systems Administrator Mark Nelson Unix Systems Administrator John Vestrum Unix Systems Administrator Leia Thor Accounts Creation

Windows/Macintosh Group Richard Flesvig Windows/Macintosh Group Manager; Windows/Mac Systems Administrator

Networking Group Samantha Thomas Network Group Manager; Network Administrator Carlton Hanna Network Assistant

2006 Annual Research Report of the Supercomputing Institute 21 Researchers and Administration

Committee and Panel Members Yusuf J. Abul-Hajj, Medicinal Chemistry Elizabeth A. Amin, Chemistry Victor H. Barocas, Biomedical Engineering and Scientific Computation Graham V. Candler, Aerospace Engineering and Mechanics and Scientific Computation John V. Carlis, Computer Science and Engineering Baoquan Chen, Computer Science and Engineering Christopher J. Cramer, Chemistry and Scientific Computation Jeffrey J. Derby, Chemical Engineering and Materials Science and Scientific Computation David H. Du, Computer Science and Engineering Scott C. Fahrenkrug, Animal Science Jiali Gao, Chemistry and Scientific Computation Sean C. Garrick, Mechanical Engineering William B. Gleason, Laboratory Medicine and Pathology David J. W. Grant, Pharmaceutics Timothy J. Griffin, Biochemistry, Molecular Biology, and Biophysics Alexander Y. Grosberg, Physics and Astronomy and Scientific Computation Satish C. Gupta, Soil, Water, and Climate Ashley T. Haase, Microbiology J. Woods Halley, Physics Wei-Shou Hu, Chemical Engineering and Materials Science Ashley James, Aerospace Engineering and Mechanics Thomas W. Jones, Astronomy and Scientific Computation Vivek Kapur, Microbiology Fumiaki Katagiri, Plant Biology Romas Kazlauskas, Biochemistry, Molecular Biology, and Biophysics Yiannis Kaznessis, Chemical Engineering and Materials Science Arkady Khodursky, Biochemistry, Molecular Biology, and Biophysics Vipin Kumar, Computer Science and Engineering and Scientific Computation Tongbin Li, Neuroscience David J. Lilja, Electrical and Computer Engineering and Scientific Computation David H. Live, Biochemistry, Molecular Biology, and Biophysics Mitchell B. Luskin, Mathematics and Scientific Computation Krishnan Mahesh, Aerospace Engineering and Mechanics Keven H. Mayo, Biochemistry, Molecular Biology, and Biophysics Alon V. McCormick, Chemical Engineering and Materials Science Gary W. Meyer, Computer Science and Engineering Mohammed F. Mokbel, Computer Science and Engineering Gary J. Muehlbauer, Agronomy and Plant Genetics Gary L. Nelsestuen, Biochemistry, Molecular Biology, and Biophysics Robert Numrich, Supercomputing Institute Douglas H. Ohlendorf, Biochemistry, Molecular Biology, and Biophysics Michael J. Olesen, Digital Technology Center Hans G. Othmer, Mathematics and Scientific Computation Ronald L. Phillips, Agronomy and Plant Genetics Ernest F. Retzel, Center for Computational Genomics and Bioinformatics P. Paul Ruden, Electrical and Computer Engineering

22 2006 Annual Research Report of the Supercomputing Institute Researchers and Administration

Committee and Panel Members (continued) Yousef Saad, Computer Science and Engineering and Scientific Computation Terrence W. Simon, Mechanical Engineering J. Ilja Siepmann, Chemistry and Scientific Computation Nathan M. Springer, Plant Biology Friedrich Srienc, Bioprocess Technology Institute and Chemical Engineering and Materials Science Jaideep Srivastava, Computer Science and Engineering and Scientific Computation Heinz G. Stefan, Civil Engineering David D. Thomas, Biochemistry, Molecular Biology, and Biophysics and Scientific Computation Donald G. Truhlar, Chemistry, Chemical Physics, Nanoparticle Science and Engineering, and Scientific Computation Oriol T. Valls, Physics and Astronomy Kenneth D. Vernick, Microbiology Carston R. Wagner, Medicinal Chemistry, chair Kylie J. Walters, Biochemistry, Molecular Biology, and Biophysics Dong Wang, Soil, Water, and Climate Renata M. Wentzcovitch, Chemical Engineering and Materials Science George L. Wilcox, Neuroscience and Scientific Computation Carrie M. Wilmot, Biochemistry, Molecular Biology and Biophysics Paul R. Woodward, Astronomy and Scientific Computation David A. Yuen, Geology and Geophysics and Scientific Computation

2006 Annual Research Report of the Supercomputing Institute 23 Researchers and Administration

External Support

Principal Investigator Source of Funding

Roger E. A. Arndt Defense Advanced Research Projects Agency Office of Naval Research William A. Arnold National Science Foundation Victor H. Barocas National Institutes of Health National Institutes of Health–National Heart, Lung, and Blood Institute National Institutes of Health–National Institute of Biomedical Imaging and Bioengineering National Science Foundation Subhash C. Basak Air Force Office of Scientific Research Department of Agriculture Timothy W. Behrens National Institutes of Health Alvin J. Beitz National Institutes of Health Judith Berman National Institutes of Health Rex N. Bernardo Department of Agriculture David Bernlohr National Science Foundation National Institutes of Health Anja-Katrin Bielinsky American Chemical Society Peter B. Bitterman National Institutes of Health David A. Blank National Science Foundation Mark W. Bolander National Institutes of Health Graham V. Candler Air Force Office of Scientific Research National Aeronautics and Space Administration Sandia National Labs James R. Chelikowsky National Science Foundation Department of Energy Bernardo Cockburn National Science Foundation Donald P. Connelly Minnesota Partnership for Biotechnology and Medical Genomics Christopher J. Cramer Department of Defense National Science Foundation Paul A. Crowell National Science Foundation Jane H. Davidson Department of Energy Department of Energy–National Renewable Energy Laboratory National Science Foundation Philippe de Forcrand Swiss National Funds

24 2006 Annual Research Report of the Supercomputing Institute Researchers and Administration

External Support (continued)

Principal Investigator Source of Funding

Jeffrey J. Derby National Aeronautics and Space Administration National Science Foundation National Science Foundation–Materials Research Science and Engineering Centers Mark D. Distefano National Institutes of Health Traian Dumitrica National Science Foundation National Science Foundation–Materials Research Science and Engineering Centers Gary M. Dunny National Institutes of Health Lynda B. M. Ellis National Institutes of Health Arthur G. Erdman NovaTek Scott C. Fahrenkrug Department of Agriculture David P. Fan National Institutes of Health S. H. Fatemi Jonty Foundation Kunin Foundation National Institutes of Health Stanley Medical Research Institute David M. Ferguson National Institutes of Health Jürgen F. Fohlmeister National Institutes of Health Roger L. Fosdick National Science Foundation Efi Foufoula National Aeronautics and Space Administration National Science Foundation Catherine W. French Department of Transportation James R. Fricton National Institutes of Health–National Institute for Dental and Cranofacial Research J. Steven Gantt National Science Foundation Jiali Gao Army Research Laboratories National Institutes of Health Sean C. Garrick, Army High Performance Computing Research Center Army Research Office National Science Foundation Susan I. Gibson Consortium for Plant Biotechnology Research Steven L. Girshick Army Research Office CFD Research Corporation Department of Energy LAM Foundation National Science Foundation Wayne L. Gladfelter National Science Foundation

2006 Annual Research Report of the Supercomputing Institute 25 Researchers and Administration

External Support (continued)

Principal Investigator Source of Funding

Jane Glazebrook National Science Foundation Richard J. Goldstein Advanced GasTurbine System Research Anand Gopinath Air Force Research Laboratory National Institutes of Health Jon Gottesman National Institutes of Health–National Eye Institute David J. W. Grant Allergan/Amgen/Bristol-Myers Squibb Boehringer Ingelheim Cares Foundation GlaxoSmithKline Inc. National Science Foundation Pfizer Timothy J. Griffin National Institutes of Health Bojan Guzina National Science Foundation Ashley T. Haase National Institutes of Health National Institutes of Health–National Institute of Allergy and Infectious Diseases Franz Halberg Earl Bakken Fund National Institutes of Health J. Woods Halley 3M/Department of Energy Department of Energy Department of Energy–Argonne National Laboratory National Science Foundation Shaul Hanany National Aeronautics and Space Administration Ramesh Harjani Semiconductor Research Corporation Robert P. Hebbel National Institutes of Health Joachim V. Heberlein Hypotherm National Science Foundation Stephen S. Hecht National Institutes of Health Eric A. Hendrickson National Institutes of Health Pierre-Gilles Henry National Institutes of Health John R. Hiller Department of Energy Charles L. Howe National Institutes of Health National Multiple Sclerosis Society Elizabeth G. Ingulli American Society of Nephrology Viking Children’s Fund Heiko O. Jacobs National Science Foundation Ashley James National Science Foundation Sharon A. Jansa National Science Foundation

26 2006 Annual Research Report of the Supercomputing Institute Researchers and Administration

External Support (continued)

Principal Investigator Source of Funding

Marc Jenkins National Institutes of Health Paul E. Johnson National Institutes of Health–National Institute of Diabetes and Digestive and Kidney Diseases Rodney L. Johnson National Institutes of Health Thomas W. Jones National Aeronautics and Space Administration National Science Foundation Daniel D. Joseph National Science Foundation Mathur S. Kannan National Institutes of Health George Karypis Army High Performance Computing Research Center National Institutes of Health National Science Foundation National Science Foundation/National Institutes of Health Steven R. Kass American Chemical Society–Petroleum Research Foundation National Science Foundation Fumiaki Katagiri Department of Agriculture National Science Foundation Romas Kazlauskas National Sciences and Engineering Research Council of Canada Pfizer Yiannis N. Kaznessis 3M American Chemical Society–Petroleum Research Foundation Army High Performance Computing Research Center National Institutes of Health National Science Foundation John H. Kersey Children’s Oncology Group National Institutes of Health–National Cancer Institute Arkady Khodursky National Institutes of Health Richard A. King National Institutes of Health H. Corby Kistler Department of Agriculture Kenneth S. Koeneman Department of Defense Uwe R. Kortshagen Department of Energy InnovaLight, Inc. National Science Foundation Daniel M. Kroll National Science Foundation

2006 Annual Research Report of the Supercomputing Institute 27 Researchers and Administration

External Support (continued)

Principal Investigator Source of Funding

Satish Kumar American Chemical Society–Petroleum Research Foundation Vipin Kumar Advanced Research and Development Activity National Aeronautics and Space Administration National Science Foundation Keith T. Kuwata American Chemical Society–Petroleum Research Foundation Scott M. Lanyon National Science Foundation David A. Largaespada Leukemia and Lymphoma Society of America Perry H. Leo Department of Energy Doreen G. Leopold Research Corporation Kenneth R. Leopold American Chemical Society–Petroleum Research Foundation National Science Foundation Jack L. Lewis National Institutes of Health Na Li Minnesota Medical Foundation David J. Lilja Intel Semiconductor Research Corporation Jizhen Lin National Institutes of Health–National Cancer Institute National Institutes of Health–National Institute on Deafness and Other Communication Disorders John D. Lipscomb National Institutes of Health David Live National Institutes of Health Mitchell B. Luskin Department of Energy National Science Foundation Robert L. Lysak National Aeronautics and Space Administration National Science Foundation Chris W. Macosko 3M National Science Foundation National Science Foundation–Materials Research Science and Engineering Centers Krishnan Mahesh Air Force Office of Scientific Research Department of Energy National Science Foundation Office of Naval Research Kent R. Mann National Science Foundation Susan C. Mantell National Science Foundation Department of Energy

28 2006 Annual Research Report of the Supercomputing Institute Researchers and Administration

External Support (continued)

Principal Investigator Source of Funding

Patrick W. Mantyh Department of Veterans Affairs Michael Mauer National Institutes of Health–National Institute of Diabetes and Digestive and Kidney Diseases Kevin H. Mayo National Institutes of Health–National Cancer Institute National Institutes of Health–National Institute of Allergy and Infectious Diseases Richard B. McClurg American Chemical Society Alon V. McCormick Army Research Office Industrial Partnership for Research in Interfacial and Materials Engineering David J. McLaughlin National Science Foundation Peter H. McMurry National Science Foundation Department of Energy Kristopher McNeill National Science Foundation Matthew F. Mescher National Institutes of Health James R. Mickelson American Kennel Club, Canine Health Foundation American Quarter Horse Association Department of Agriculture Morris Animal Foundation National Institutes of Health Jeffrey S. Miller National Institutes of Health Robert F. Miller National Institutes of Health–National Eye Institute Ned Mohan Office of Naval Research David C. Morse American Chemical Society–Petroleum Research Foundation National Science Foundation–Materials Research Science and Engineering Centers Kathy Moser National Institutes of Health Gary J. Muehlbauer Department of Agriculture Michael P. Murtaugh Department of Agriculture National Pork Board Karin M. Musier-Forsyth National Institutes of Health Samuel L. Myers, Jr. Department of Housing and Urban Development Deborah K. Nykanen National Aeronautics and Space Administration National Oceanic and Atmospheric Administration Douglas H. Ohlendorf National Institutes of Health Harry T. Orr National Institutes of Health

2006 Annual Research Report of the Supercomputing Institute 29 Researchers and Administration

External Support (continued)

Principal Investigator Source of Funding

Hans G. Othmer National Institutes of Health National Science Foundation Yuan-Ping Pang Defense Advanced Research Projects Agency Department of Veterans Affairs National Institutes of Health National Institutes of Health–National Institute of Allergy and Infectious Diseases James S. Pankow National Institutes of Health Duanqing Pei National Institutes of Health Erik J. Peterson Beckman Foundation Juvenile Diabetes Research Foundation Minnesota Medical Foundation National Science Foundation Ronald L. Phillips National Institutes of Health–National Institute of Allergy and Infectious Diseases Fernando Porté-Agel National Aeronautics and Space Administration National Science Foundation Philip S. Portoghese National Institutes of Health–National Institute on Drug Abuse National Science Foundation A. David Redish National Institutes of Health–National Institute of Mental Health Jean F. Regal Department of Defense Fernando L. Reitich Air Force Office of Scientific Research Army High Performance Computing Research Center National Science Foundation Jeffrey T. Roberts National Science Foundation Ann E. Rougvie National Institutes of Health National Science Foundation Jaijeet Roychowdhury Defense Advanced Research Projects Agency National Science Foundation Sandia National Labs Semiconductor Research Corporation P. Paul Ruden National Science Foundation Yousef Saad Department of Energy National Science Foundation

30 2006 Annual Research Report of the Supercomputing Institute Researchers and Administration

External Support (continued)

Principal Investigator Source of Funding

Michael J. Sadowsky Consortium for Plant Biotech Research Department of Agriculture Department of Agriculture/National Science Foundation National Institutes of Health–National Institute of Environmental Health Sciences Sea Grant Syngenta Crop Protection Deborah A. Samac National Science Foundation Fadil Santosa National Science Foundation Sachin S. Sapatnekar National Science Foundation Guillermo R. Sapiro National Geospatial-Intelligence Agency Office of Naval Research Patrick M. Schlievert National Institutes of Health Lanny D. Schmidt Department of Defense Department of Energy National Science Foundation Arturo Schultz Minnesota Department of Transportation/University of Minnesota Center for Transportation Studies L. E. Scriven BASF Department of Energy/Rohm and Haas Industrial Partnership for Research in Interfacial and Materials Engineering National Science Foundation National Science Foundation–International Opportunities for Scientists and Engineers Xerox Foundation Shashi Shekhar Army High Performance Computing Research Center Ronald A. Siegel National Institutes of Health J. Ilja Siepmann Department of Energy Merck Research Co. National Science Foundation Pfizer Rohm and Haas Terrence W. Simon Department of Energy National Aeronautics and Space Administration Sunpower Inc. Steven M. Sine National Institutes of Health Charles C. S. Song National Science Foundation Office of Naval Research

2006 Annual Research Report of the Supercomputing Institute 31 Researchers and Administration

External Support (continued)

Principal Investigator Source of Funding

Masha Sosonkina Department of Energy National Science Foundation Peter Southern National Institutes of Health Marian T. Stankovich National Institutes of Health Patrick J. Starr Ricardo, Inc. Paul J. Strykowski National Science Foundation Office of Naval Research Xcel Patricia E. Tam National Institutes of Health Kumar K. Tamma Army Research Office David D. Thomas National Institutes of Health Howard C. Towle National Institutes of Health Tim Tracy National Institutes of Health Natalia Tretyakova National Institutes of Health Donald G. Truhlar Department of Defense Department of Energy Minnesota Partnership for Biotechnology and Medical Genomics National Institutes of Health National Institutes of Health/National Science Foundation National Science Foundation Office of Naval Research Michael Tsapatsis National Science Foundation Oriol T. Valls National Science Foundation Anthony Varghese National Institutes of Health Gianluigi Veglia National Institutes of Health Randall H. Victora ISIC National Science Foundation National Science Foundation–Materials Research Science and Engineering Centers Seagate Western Digital Robert Vince Department of Defense Carston R. Wagner National Institutes of Health Kylie J. Walters National Institutes of Health Dong Wang Department of Agriculture George D. Weiblen Department of Agriculture

32 2006 Annual Research Report of the Supercomputing Institute Researchers and Administration

External Support (continued)

Principal Investigator Source of Funding

Douglas Weiss Department of Agriculture Jon B. Weissman National Science Foundation Renata M. Wentzcovitch National Science Foundation George L. Wilcox National Science Foundation Carrie M. Wilmot Minnesota Medical Foundation National Institutes of Health Darrin M. York Army Research Laboratories National Institutes of Health Nevin D. Young National Science Foundation David A. Yuen National Science Foundation Xiaoyang Zhu National Science Foundation

2006 Annual Research Report of the Supercomputing Institute 33 Events

Sponsored Symposia (continued)

Virtual Laboratory for Earth and Planetary Materials Workshop

The Virtual Laboratory for Earth and Planetary Materials David Kohlstedt, University of Minnesota, (VLab) held its first workshop on July 20–23, 2005 at Minneapolis, Minnesota the Supercomputing Institute. The workshop offered an Martin Kunz, University of California, Berkeley, opportunity for scientists involved in research related to California planetary materials and planetary processes to exchange Carolina Lithgow-Berteloni, University of Michigan, information and ideas. The spectrum of areas of expertise Ann Arbor, Michigan covered was very broad. Theoretical chemists, materials Caetano Miranda, Abdus Salam International Centre physicists, and information technology scientists came for Theoretical Physics, Trieste, Italy together with Earth and planetary scientists to define Richard O’Connell, Harvard University, Cambridge, novel key problems, identify technologies, and outline Massachusetts strategies to advance planetary materials science. Shrideep Pellickara, Indiana University, Further information about the workshop, including Bloomington, Indiana abstracts of the presentations and posters, can be found Marlon Pierce, Indiana University, Bloomington, at the VLab Web site: Indiana www.vlab.msi.umn.edu/events/workshops.shtml Tracy Rushmer, University of Vermont, Burlington, Vermont Speakers Sandro Scandolo, Abdus Salam International Centre Philip Allen, State University of New York, Stony for Theoretical Physics, Trieste, Italy Brook, New York Dan Shim, Massachusetts Institute of Technology, Jay Bass, University of Illinois at Urbana- Cambridge, Massachusetts Champaign, Illinois Ilja Siepmann, University of Minnesota, Razvan Caracas, Carnegie Institution of Washington, Minneapolis, Minnesota Washington, DC Slava Solomatov, Washington University in St. Louis, Stefano Cozzini, International School for Advanced St. Louis, Missouri Studies (SISSA), Trieste, Italy Frank Spera, University of California, Santa Barbara, Erin Dahlke, University of Minnesota, Minneapolis, California Minnesota Lars Stixrude, University of Michigan, Ann Arbor, Stefano de Gironcoli, International School for Michigan Advanced Studies (SISSA), Trieste, Italy Paul Tackley, University of California, Los Angeles, Adam Dziewonski, Harvard University, Cambridge, California Massachusetts Taku Tsuchiya, Ehime University, Matsuyama, Japan Gordon Erlebacher, Florida State University, Koichiro Umemoto, University of Minnesota, Tallahassee, Florida Minneapolis, Minnesota Adil Hasan, CCLRC E-Science Center, Rutherford Renata Wentzcovitch, University of Minnesota, Laboratory, United Kingdom Minneapolis, Minnesota John Hernlund, University of California, Los Dave Yuen, University of Minnesota, Minneapolis, Angeles, California Minnesota Marc Hirshmann, University of Minnesota, Minneapolis, Minnesota Bijaya Karki, Louisiana State University, Baton Rouge, Louisiana Amir Khan, University of Copenhagen, Denmark

2006 Annual Research Report of the Supercomputing Institute 35 Events

Outreach Programs

Environmental Science Career Days

The Supercomputing Institute participated in the Bell Museum of Natural History’s Environmental Science Career Days on February 26, 2005 and March 4, 2006. The events are intended to bring University research to the public and encouraging elementary and middle- school students to pursue science careers. University researchers who work in environmental sciences and natural resources talked about their experiences, described their trials and successes, and demonstrated hands-on examples. The Institute participated by showing several visualization projects to attract the students’ interest and to encourage curiosity about the role of supercomputing in environmental studies.

36 2006 Annual Research Report of the Supercomputing Institute Ongoing and Recently Completed Research Projects

January 1, 2005–March 15, 2006 University of Minnesota–Duluth Campus

College of Science and Engineering

Department of Chemical Engineering Michael A. Rother ...... 39

Department of Chemistry and Biochemistry Leng Chee Chang ...... 39 Paul Kiprof ...... 40 Viktor N. Nemykin ...... 40 Paul D. Siders ...... 41

Department of Computer Science Ted Pedersen ...... 41 Masha Sosonkina ...... 42

Department of Physics John R. Hiller ...... 42

Natural Resources Research Institute Subhash C. Basak and Brian D. Gute ...... 43 Arun Goyal ...... 43 Medical School

Department of Anatomy, Microbiology, and Pathology Lucia P. Barker ...... 44

Department of Biochemistry and Molecular Biology Lester R. Drewes ...... 44 Jean F. Regal, Ronald R. Regal, and Mark S. Rutherford ...... 45

38 2006 Annual Research Report of the Supercomputing Institute UM Duluth–Department of Chemical Engineering

Michael A. Rother, Principal Investigator Surfactant Effects on Viscous Interactions of Drops

urfactants (“surface-active agents,” e.g., soap) reside includes studying interactions of two spherical drops in at the interface between two liquids, or a liquid and buoyancy with arbitrary surfactant surface coverage and Sa gas, and modify the interfacial tension between two spherical drops in thermocapillary motion with near- the phases. The presence of surfactant affects the interac- ly uniform coverage, as well as continuing studies of tions between drops in an immiscible medium, including deformable drops. The primary objective is to develop a whether or not the drops coalesce. These interactions are fundamental understanding of the role of surfactants on important in emulsion stability, sedimentation and dilute dispersions of spherical and deformable drops in a creaming, polymer blending, rheology, liquid-liquid variety of flows. extraction, and geophysical flows. Thus, understanding how surfactants work is important to many industries, including food, pesticides, paints, ore flotation, and detergents. This project includes a study of surfactant effects on buoyancy-driven interactions of deformable drops and preliminary research on contaminated deformable drops interacting in thermocapillary motion. New work

UM Duluth–Department of Chemistry and Biochemistry

Leng Chee Chang, Principal Investigator Evaluation of Natural Products as Protein Kinase C Inhibitors

ature has produced many effective anticancer cal active compounds. The researchers are using the agents. Examples are microbial-derived drugs Medicinal Chemistry/Supercomputing Institute Nsuch as bleomycin and mitomycin C. The initial Visualization-Workstation Laboratory for this work. focus of this research is to identify noncytotoxic potent protein kinase inhibitors of eukaryotic with novel structures that may be useful in the treatment of human disease. The researchers are screening a variety of natural product extracts for inhibition of protein kinase using the Streptomyces 85E. There is evidence that a compound that inhibits aerial hyphae formation in S. 85E will also inhibit eukaryotic protein kinases. Research Group The specific aims of this research are: to evaluate the Benjamin Lien, Graduate Student Researcher extracts as protein kinase inhibitors; to isolate and char- Nicholas Vidor, Graduate Student Researcher acterize the novel structures of bioactive compounds; and Wei Xiang, Research Associate to perform several two-dimensional nuclear magnetic resonance experiments for structure elucidation of biologi-

2006 Annual Research Report of the Supercomputing Institute 39 UM Duluth–Department of Chemistry and Biochemistry

Paul Kiprof, Associate Fellow High-Valent Transition Metal Arene Complexes and Carbonium Ions

his research project studies high-valent transition these complexes is necessary and is performed at high metal arene complexes and the stability of levels of theory accounting for the effect of substituents. Trearrangement of carbocations. High-valent tran- The second focus area concerns carbocations, which sition metal arene complexes are rare and generally unsta- are stabilized by oxygen atoms. This leads to unusual ble compared with their low-valent counterparts. A reactions that have not been studied systematically. The detailed study of the factors governing the stability of researchers are exploring the effect of the heteroatoms at high levels of theory and are studying the reactions that these species undergo. Research Group Beau Barker, Graduate Student Researcher Melissa Frank, Graduate Student Researcher Dimitry Litvinov, Graduate Student Researcher Michael McGinn, Undergraduate Student Researcher Spencer Pruitt, Undergraduate Student Researcher Nicole M. Settergren, Undergraduate Student Researcher

Victor N. Nemykin, Principal Investigator Theoretical Modeling of the Ground- and Excited-State Properties in Polynuclear and Mixed-Valence Porphyrin, Tetraazaporphyrins, and Phthalocyanines his project involves using the software program GAUSSIAN03 to calculate the geometries, electron- Tic ground states, and spectroscopic properties of different poly(ferrocenyl)-containing and other polynuclear macrocycles. In addition, the researcher is predicting the electronic absorption and circular dichroism spectra of these metallo-complexes. Finally, he is using density functional theory methods to investigate multi-electron oxidation processes, formation of the mixed-valence states, and electron-migration properties of these compounds.

40 2006 Annual Research Report of the Supercomputing Institute UM Duluth–Department of Chemistry and Biochemistry

Paul D. Siders, Principal Investigator Simulation of the Phase Diagram of Solid Carbon Dioxide

his research concerns the properties and phase boundaries of solid carbon dioxide with density Research Group functional theory. The researchers are generating Jason Dorweiler, Undergraduate Student Researcher T Hillary Waterhouse, Undergraduate Student pseudopotentials and testing them for use in the SIESTA Researcher and ABINIT program suites. The model test systems for this are dimers and small clusters. The goal of the research is to calculate bulk and molecular properties and coexistence lines of solid carbon dioxide from zero pressure to 50 GPa, at temperatures up to 2,000 K.

UM Duluth–Department of Computer Science

Ted Pedersen, Associate Fellow Word Sense Disambiguation in High-Dimensional Feature Spaces

ost words in natural language have multiple possible meanings. This simple fact causes no Research Group Mend of difficulties for computer systems that Mahesh Joshi, Graduate Student Researcher seek to understand human language. The goal of this Anagha Kulkarni, Graduate Student Researcher project is to develop computational methods that auto- Amruta Purandare, Graduate Student Researcher matically determine which meaning of a word is intend- Bridget A. Thomson McInnes, Graduate Student ed in a particular context, and easily adapt to the varia- Researcher tions in word meaning that accompany changes in the subject matter and intended audience of a text. Word meanings are central to language understanding, and success in this research will improve the ability of computer systems to perform translation, retrieve information from the Web, and summarize documents.

2006 Annual Research Report of the Supercomputing Institute 41 UM Duluth–Department of Computer Science

Masha Sosonkina, Associate Fellow Optimizations of a Parallel Algebraic Recursive Multilevel Solver

arallel communication overhead may substantially These researchers are using a sample distributed appli- affect the overall performance of a scientific dis- cation, parallel Algebraic Recursive Multilever Solver Ptributed application. For a given parallel algorithm, (pARMS), and are studying its most communication- one may attempt to analytically model and predict com- intensive tasks. In particular, they are considering several munication overhead. Fine-tuning and detailed experi- message-passing implementations of the distributed mental study is also needed, however, to account for such sparse matrix dense vector multiplication used in issues as communication library implementation and par- pARMS for distributed preconditioning operations and allel architecture performance. iterative acceleration. They are also investigating how pARMS performance changes depending on the choice of mapping to the nodes in a cluster. Research Group Suchitra Goopy, Graduate Student Researcher Paul Gordon, Graduate Student Researcher Sam Storie, Graduate Student Researcher Meng-Shiou Wu, Graduate Student Researcher

UM Duluth–Department of Physics

John R. Hiller, Fellow Nonperturbative Analysis of Field Theories Quantized on the Light Cone

he interactions between fundamental particles Villars regularization, which requires the introduction of can be described with quantum field theories, unphysical massive particles, and supersymmetry. This Tand the use of light-cone coordinates can be researcher has applied these methods to various field the- advantageous in determining the properties of the bound ories, in particular Yukawa theory, quantum electrody- states that these particles can form. The resulting coupled namics (QED), and super Yang-Mills (SYM) theory, and system of integral equations for the bound-state wave is continuing to explore their use with the ultimate goal functions must be solved numerically. These equations, of applying them to quantum chromodynamics (QCD), however, contain infinities that must be removed in order the theory of the strong interactions that determine the to properly define the given theory. This project consid- properties of mesons and baryons. Recent work has been ers two methods for the removal of such infinities: Pauli- in the dressed-fermion sectors of Yukawa theory and QED, where the problem has been solved for two and one-boson truncations, respectively, and in the high-reso- Collaborator lution calculations of a stress-energy correlator in two- Sophia Tchabycheva, Department of Physics, Southern dimensional SYM theory that provide direct evidence for Methodist University, Dallas, Texas the Maldacena conjecture of equivalence between SYM theory and string theory.

42 2006 Annual Research Report of the Supercomputing Institute UM Duluth–Natural Resources Research Institute

Subhash C. Basak, Principal Investigator Brian D. Gute, Principal Investigator A Comparative Study of Semi-Empirical and Ab Initio Quantum Chemical Calculations in Predicting Property/Bioactivity/Toxicity of Chemicals he primary goal of this research is to compare quantum chemical descriptors calculated by vari- Tous levels of ab initio theory in the hierarchical quantitative structure-activity relationship (HiQSAR) studies of different classes of chemicals. The researchers examine the utility of these quantum chemical descriptors in predicting physicochemical and biologically relevant properties of chemicals. The group has performed extensive quantum chemical calculations on a set of non- proprietary mosquito repellants. They have used structures optimized by semi-empirical AM1 to density func- Research Group tional theory to characterize the biophores by a novel Denise Mills, Staff hierarchical molecular overlay analysis. This provides a Przemyslaw Miszta, Research Associate better understanding of the structural motif responsible Ramanathan Natarajan, Staff for repellent activity. Nowak Wiesiek, Research Associate

Arun Goyal, Principal Investigator Development of High-Value Protein Production in Hybrid Poplar

afeners are used to protect crops against herbicide expression. Many of the genes that were upregulated by damage by enhancing herbicide metabolism in the safeners were not induced by the three abiotic stresses. Splant. The identification and analysis of gene The researchers used cDNA microarray chips to identify expression patterns by safener treatment may lead to a genes that may be used for identifying genes and unique better understanding of molecular events involved in chemical-inducible promoters. safener action. These researchers used a carrier deoxyribonucleic acid (cDNA) microarray composed of fluxo- genim-treated subtractive cDNA clones to identify expression patterns of genes using different safeners and three abiotic stresses. They used three different safeners— fluxofenim, oxabetrinil, and benoxacor, all of which detoxify chloroacetanilide herbicides—and water, chill- Research Group and Collaborators ing, and wind stresses to evaluate differences in the gene Vivek Kapur, Faculty Collaborator expression pattern. The comparison of expression pat- Neil D. Nelson, Faculty Collaborator terns between different safener chemicals revealed that A. S. Rishi, Research Associate structurally similar molecules show almost identical gene

2006 Annual Research Report of the Supercomputing Institute 43 UM Duluth–Department of Anatomy, Microbiology, and Pathology

Lucia P. Barker, Principal Investigator Molecular Characterization of Mycobacterium marinum Biofilms

he mycobacterial species Mycobacterium marinum inum biofilms grown in flow-cells for use in a differential is a marine pathogen that infects poikilothermic fluorescence induction (DFI) system. In a complimenta- Tanimals such as fish and frogs and will also infect ry approach to the DFI studies, the researchers isolate humans. M. marinum can form biofilms both in the lab- proteins from harvested M. marinum biofilms and the oratory and in the environment, but little is known planktonic (free-floating) counterparts within the same about the molecular factors responsible for this biofilm culture and subject these proteins to two-dimensional gel formation. These researchers use a flow-cell system for electrophoresis. The researchers are using Supercom- the study of M. marinum biofilm formation in situ. They puting Institute laboratories to identify peptide sequences quantify biofilm formation and observe deposition of from mass spectrometry on these proteins. These studies organisms upon a plastic matrix using both standard and will lead to an understanding of the mechanisms by fluorescence microscopy. Further, they harvest M. mar- which mycobacteria form biofilms in nature and on artificial surfaces, and a more specific understanding of how biofilms can contribute to the pathogenesis of these Research Group organisms. Ganna (Ann) Polshyna, Staff

UM Duluth–Department of Biochemistry and Molecular Biology

Lester R. Drewes, Principal Investigator Microarray Analysis of Blood-Brain Transport and Metabolism

ketogenic diet is a high-fat, low-carbohydrate diet novel treatments of epilepsy. These researchers combine that has been long used therapeutically to control oligonucleotide microarray expression analysis with Aepileptic seizures, but the protective mechanism is robust statistical analysis in order to define the molecular not known. The purpose of this study is to investigate response of the brain to the efficacious anti-seizure thera- the molecular basis for ketogenic diet-induced resistance py. They examine differences in gene expression profiles to seizures at the gene expression level with the possibili- in the cerebral cortex of rats fed either a ketogenic or ty of revealing important pharmacological targets for control diet. The identification of genes differentially expressed as a consequence of the ketogenic diet may provide insights into the biochemical adaptation in the brain that occurs with this anti-convulsant therapy and Research Group and Collaborator may reveal important pharmacological targets for novel Bradley E. Enerson, Section of Cardiovascular Medicine, Yale University, New Haven, Connecticut treatments of epilepsy. Corwin Nelson, Undergraduate Student Researcher Mary Sneve, Staff Justin Spanier, Graduate Student Researcher

44 2006 Annual Research Report of the Supercomputing Institute UM Duluth–Department of Biochemistry and Molecular Biology

Jean F. Regal, Principal Investigator Ronald R. Regal, Co-Principal Investigator Mark S. Rutherford, Co-Principal Investigator Differential Allergen Sensitivity in Asthma of Young and Adult Mammals he objective of this research is to determine if young and adult animals differ in their sensitivity Tto allergens, both in the induction phase of asthma as well as in elicitation of the asthma symptoms. Besides examining pulmonary function and inflamma- tion in the lung, this project examines gene expression in the lungs of both young and adult mammals to determine if differences can be identified in the mechanism of asthma depending on age and gender. Molecular differences discovered in different asthma phenotypes may Research Group Mingqian Duan, Research Associate provide information regarding appropriate therapy for Gail Flickinger, Research Associate the disease depending on the age and gender of the indi- Amy Greene, Research Associate vidual. The researchers are using the resources of the Julie Hendrickson, Research Associate Computational Genetics Laboratory to assist in the Jessica Meehan, Research Associate analysis of the gene expression data. Peggy Mohrman, Research Associate

2006 Annual Research Report of the Supercomputing Institute 45 University of Minnesota–Hormel Institute

The Hormel Institute Zigang Dong ...... 47

46 2006 Annual Research Report of the Supercomputing Institute UM–Hormel Institute

Zigang Dong, Principal Investigator Signal Transduction in Cancer Development

hese researchers are using Supercomputing Institute resources perform automatic docking Research Group and scoring of resveratrol analogues into the Svetlana Ermakova, Research Associate T Sergey Fedorov, Research Associate binding site COX-2 in order to discover promising can- Zhiwei He, Research Associate didates for in vitro and in vivo studies. They are also Ming Li, Research Associate comparing the efficiency of different approaches for Evgeny A. Rogozin, Research Associate automatic docking. Olga Rogozina, Research Associate

2006 Annual Research Report of the Supercomputing Institute 47 University of Minnesota–Twin Cities Campus

Academic Health Center Cancer Center Sharon E. Murphy ...... 60 Jennifer J. Westendorf ...... 60 Center for Computational Genomics and Bioinformatics Ernest F. Retzel ...... 61 Center for Drug Design Courtney Aldrich ...... 61 Robert Vince ...... 62 Stem Cell Institute Catherine M. Verfaillie ...... 62 College of Agricultural, Food, and Environmental Sciences Department of Agronomy and Plant Genetics James A. Anderson ...... 63 Rex N. Bernardo ...... 63 David F. Garvin ...... 64 Gary J. Muehlbauer ...... 64 Ronald L. Phillips and Howard W. Rines ...... 65 Kevin P. Smith ...... 65 David A. Somers ...... 66 Department of Animal Science Scott C. Fahrenkrug ...... 66 Department of Entomology Ann M. Fallon ...... 67 Department of Horticultural Science Christian A. Thill ...... 67

48 2006 Annual Research Report of the Supercomputing Institute University of Minnesota–Twin Cities Campus

Department of Plant Pathology James M. Bradeen ...... 68 H. Corby Kistler ...... 68 Deborah A. Samac ...... 69 Brian J. Steffenson ...... 69 Les J. Szabo ...... 70 Nevin D. Young ...... 70 Department of Soil, Water, and Climate Michael J. Sadowsky ...... 71 Dong Wang ...... 71 College of Agricultural, Food, and Environmental Sciences and College of Human Ecology Department of Food Science and Nutrition Gary A. Reineccius ...... 72 College of Agricultural, Food, and Environmental Sciences and Institute of Technology Department of Biosystems and Agricultural Engineering John L. Nieber ...... 72 College of Biological Sciences

BioTechnology Institute Friedrich Srienc ...... 73 Marc G. von Keitz ...... 73 Department of Ecology, Evolution, and Behavior Sharon A. Jansa ...... 74 Scott M. Lanyon ...... 74 Georgiana May ...... 75 Joseph P. McFadden ...... 75 Anne E. Pusey ...... 76 Shinya Sugita ...... 76

2006 Annual Research Report of the Supercomputing Institute 49 University of Minnesota–Twin Cities Campus

Department of Plant Biology J. Stephen Gantt ...... 77 Susan I. Gibson ...... 77 Jane Glazebrook ...... 78 Fumiaki Katagiri ...... 78 Paul A. Lefebvre and Carolyn D. Silflow ...... 79 M. David Marks ...... 79 David J. McLaughlin ...... 80 Nathan M. Springer ...... 80 Peter L. Tiffin ...... 81 Kathryn A. VandenBosch ...... 81 George D. Weiblen ...... 82 College of Biological Sciences and Medical School Department of Biochemistry, Molecular Biology and Biophysics Ian M. Armitage and Bruce L. Martin ...... 82 Leonard J. Banaszak ...... 83 David A. Bernlohr ...... 83 Anja-Katrin Bielinsky ...... 84 Bianca M. Conti-Fine ...... 84 Timothy J. Griffin ...... 85 Eric A. Hendrickson ...... 85 Alan B. Hooper ...... 86 Christine B. Karim ...... 86 Romas Kazlauskas ...... 87 Arkady Khodursky ...... 87 John D. Lipscomb ...... 88 David H. Live ...... 88 Hiroshi Matsuo ...... 89 Kevin H. Mayo ...... 89 Gary L. Nelsestuen ...... 90 Douglas H. Ohlendorf ...... 90 Claudia Schmidt-Dannert ...... 91 David D. Thomas ...... 92 Howard C. Towle ...... 93 Lawrence P. Wackett ...... 93 Kylie J. Walters ...... 94 Carrie M. Wilmot ...... 94

50 2006 Annual Research Report of the Supercomputing Institute University of Minnesota–Twin Cities Campus

Department of Genetics, Cell Biology, and Development Judith G. Berman ...... 95 Duncan J. Clarke ...... 95 Kathleen F. Conklin ...... 96 Sean D. Conner ...... 96 Stephen C. Ekker ...... 97 David P. Fan ...... 97 Thomas S. Hays ...... 98 David A. Largaespada ...... 98 Michael B. O’Connor ...... 99 Laura P. W. Ranum ...... 99 Ann E. Rougvie ...... 100 Brian G. Van Ness ...... 100 College of Education and Human Development Institute of Child Development Byron R. Egeland ...... 101 College of Liberal Arts Department of Economics Zvi Eckstein ...... 101 Andrea Moro ...... 102 Department of Geography Eric S. Sheppard ...... 102 Department of Sociology John Robert Warren ...... 103 College of Natural Resources Department of Bio-based Products Shri Ramaswamy ...... 103 Simo Sarkanen ...... 104 College of Pharmacy William F. Elmquist ...... 104 Daniel M. Kroll ...... 105

2006 Annual Research Report of the Supercomputing Institute 51 University of Minnesota–Twin Cities Campus

Department of Experimental and Clinical Pharmacology Marnie L. Peterson ...... 105 John St. Peter ...... 106 Robert J. Straka ...... 106 Tim Tracy ...... 107 Department of Medicinal Chemistry S. Mbua Ngale Efange ...... 107 David M. Ferguson ...... 108 Rodney L. Johnson ...... 108 Ramaiah Muthyala ...... 109 Philip S. Portoghese ...... 109 Shana J. Sturla ...... 110 Natalia Tretyakova and Darrin M. York ...... 110 Carston R. Wagner and Donald G. Truhlar ...... 111 Chengguo Xing ...... 111 Department of Pharmaceutics David J. W. Grant ...... 112 Ronald A. Siegel ...... 112 Raj Suryanarayanan ...... 113 College of Veterinary Medicine Department of Veterinary and Biomedical Sciences Mitchell S. Abrahamsen ...... 113 Alvin J. Beitz ...... 114 Yinduo Ji ...... 114 Mathur S. Kannan ...... 115 James R. Mickelson ...... 115 Michael P. Murtaugh ...... 116 Pamela J. Skinner ...... 116 Bruce K. Walcheck ...... 117 Douglas J. Weiss ...... 117 Department of Veterinary Population Medicine Srinand Sreevatsan ...... 118 Curtis L. Carlson School of Management Department of Human Resources and Industrial Relations Brian P. McCall ...... 118 Department of Information and Decision Sciences Paul E. Johnson ...... 119 Department of Operations and Management Science William Li and Christopher J. Nachtsheim ...... 119

52 2006 Annual Research Report of the Supercomputing Institute University of Minnesota–Twin Cities Campus

Hubert H. Humphrey Institute of Public Affairs Samuel L. Myers, Jr...... 120 Institute of Technology Department of Aerospace Engineering and Mechanics Graham V. Candler ...... 121 Ryan S. Elliott ...... 121 Roger L. Fosdick ...... 122 Ashley James ...... 122 Daniel D. Joseph ...... 123 Perry H. Leo ...... 124 Krishnan Mahesh ...... 125 Department of Astronomy Thomas W. Jones ...... 125 Department of Biomedical Engineering Victor H. Barocas ...... 126 Bin He ...... 127 David J. Odde ...... 127 Jonathan N. Sachs ...... 128 J. Thomas Vaughan ...... 128 Department of Chemical Engineering and Materials Science Robert W. Carr ...... 129 James R. Chelikowsky and Yousef Saad ...... 130 H. Ted Davis ...... 131 Jeffrey J. Derby ...... 131 C. Daniel Frisbie ...... 132 Wei-Shou Hu ...... 133 Yiannis N. Kaznessis ...... 134 Satish Kumar ...... 134 Chris W. Macosko ...... 135 Jennifer A. Maynard ...... 135 Richard B. McClurg ...... 136 Alon V. McCormick ...... 136 David C. Morse ...... 137 David J. Norris ...... 137 Lanny D. Schmidt ...... 138 L. E. Scriven ...... 138 L. E. Scriven and H. Ted Davis ...... 139 Michael Tsapatsis ...... 140 Renata M. Wentzcovitch ...... 141

2006 Annual Research Report of the Supercomputing Institute 53 University of Minnesota–Twin Cities Campus

Department of Chemistry and Chemical Physics Program Elizabeth A. Amin ...... 142 George Barany ...... 142 David A. Blank ...... 143 Christopher J. Cramer ...... 144 Mark D. Distefano ...... 145 Jiali Gao ...... 146 Jiali Gao and Jeffrey T. Roberts ...... 147 Wayne L. Gladfelter ...... 147 Marc A. Hillmyer ...... 148 Thomas R. Hoye ...... 148 Steven R. Kass ...... 149 Doreen G. Leopold ...... 149 Kenneth R. Leopold ...... 150 Kent R. Mann ...... 150 Kristopher McNeill ...... 151 Karin M. Musier-Forsyth ...... 151 R. Lee Penn ...... 152 J. Ilja Siepmann ...... 153 Marian T. Stankovich and Jiali Gao ...... 154 Andreas Stein ...... 154 T. Andrew Taton ...... 155 Donald G. Truhlar ...... 156 Gianluigi Veglia ...... 157 Darrin M. York ...... 157 Xiaoyang Zhu ...... 158 Department of Civil Engineering William A. Arnold ...... 158 Steven L. Crouch and Sofia G. Mogilevskaya ...... 159 Bojan Guzina ...... 159 Jerome F. Hajjar ...... 160 Raymond M. Hozalski ...... 160 Mihai Marasteanu ...... 161 Taichiro Okazaki ...... 161 Arturo Schultz and Catherine W. French ...... 162 Michael J. Semmens ...... 162 Carol K. Shield and Catherine W. French ...... 163 Vaughan R. Voller ...... 163 St. Anthony Falls Laboratory Roger E. A. Arndt ...... 164 Efi Foufoula ...... 164 Miki Hondzo and John S. Gulliver ...... 165 Fernando Porté-Agel ...... 165 Charles C. S. Song ...... 166 Heinz G. Stefan ...... 166

54 2006 Annual Research Report of the Supercomputing Institute University of Minnesota–Twin Cities Campus

Department of Computer Science and Engineering Daniel L. Boley ...... 167 David H. Du ...... 167 Tian He ...... 168 George Karypis ...... 168 Vipin Kumar ...... 169 Yousef Saad ...... 169 Shashi Shekhar ...... 170 Jon B. Weissman ...... 171 Pen-Chung Yew ...... 171 Zhi-Li Zhang ...... 172 Department of Electrical and Computer Engineering Rhonda Franklin Drayton ...... 173 Anand Gopinath ...... 173 Ramesh Harjani ...... 174 Heiko O. Jacobs ...... 174 Mostafa Kaveh ...... 175 David J. Lilja ...... 175 Ned Mohan ...... 176 Jaijeet Roychowdhury ...... 176 P. Paul Ruden ...... 177 Sachin S. Sapatnekar ...... 177 Guillermo R. Sapiro ...... 178 Randall H. Victora ...... 178 Department of Geology and Geophysics David A. Yuen ...... 179 Department of Mechanical Engineering Jane H. Davidson ...... 180 Traian Dumitrica ...... 180 Arthur G. Erdman ...... 181 Sean C. Garrick ...... 181 Steven L. Girshick ...... 182 Richard J. Goldstein ...... 182 Joachim V. Heberlein and Emil Pfender ...... 183 Uwe R. Kortshagen ...... 183 Perry Y. Li ...... 184 Susan C. Mantell and Jane H. Davidson ...... 184 Virgil A. Marple ...... 185 Peter H. McMurry ...... 185 David Y. H. Pui ...... 186 Terrence W. Simon ...... 187 Patrick J. Starr ...... 188 Paul J. Strykowski and Terrence W. Simon ...... 188 Kumar K. Tamma ...... 189

2006 Annual Research Report of the Supercomputing Institute 55 University of Minnesota–Twin Cities Campus

Department of Physics Paul A. Crowell ...... 190 Eric D. Ganz ...... 190 Alexander Y. Grosberg ...... 191 J. Woods Halley ...... 192 Shaul Hanany ...... 193 Norton M. Hintz ...... 193 Robert L. Lysak ...... 194 Oriol T. Valls ...... 194 Theoretical Physics Institute Philippe de Forcrand ...... 195 School of Mathematics Bernardo Cockburn ...... 195 Dennis A. Hejhal ...... 196 Mitchell B. Luskin and Richard D. James ...... 196 Wei-Ming Ni ...... 197 Andrew Odlyzko ...... 197 Hans G. Othmer ...... 198 Fernando L. Reitich ...... 198 Fadil Santosa ...... 199 Institute For Mathematics and Its Applications Arnd Scheel ...... 199 Medical School Department of Dermatology Mimi Cho and Marna E. Ericson ...... 200 Department of Laboratory Medicine and Pathology Donald P. Connelly ...... 200 Lynda B. M. Ellis ...... 201 Michael A. Farrar ...... 201 William B. Gleason ...... 202 Myron D. Gross ...... 202 Franz Halberg and Germaine G. Cornélissen ...... 203 Stephen S. Hecht ...... 203 John H. Kersey ...... 204 Matthew F. Mescher ...... 204 Harry T. Orr ...... 205 Sherif Tawfic ...... 205 Michael Tsai ...... 206

56 2006 Annual Research Report of the Supercomputing Institute University of Minnesota–Twin Cities Campus

Department of Medicine Timothy W. Behrens ...... 207 Peter B. Bitterman ...... 207 Jeffrey J. Connaire and Mark E. Rosenberg ...... 208 William C. Duane ...... 208 Patrick M. Gaffney ...... 209 Kalpna Gupta ...... 209 Jennifer L. Hall ...... 210 Robert P. Hebbel ...... 210 Ajay Israni ...... 211 Sagarika Kanjilal and Vivek Kapur ...... 211 Richard A. King and Marshall I. Hertz ...... 212 Cary N. Mariash ...... 212 Anna M. Masellis ...... 213 Jeffrey S. Miller ...... 213 Kathy L. Moser ...... 214 Erik J. Peterson ...... 214 Keith M. Skubitz ...... 215 Clifford J. Steer and Betsy J. Kren ...... 215 Patricia E. Tam ...... 216 Anthony Varghese ...... 216 Department of Microbiology Paul R. Bohjanen ...... 217 P. Patrick Cleary ...... 217 Dana Davis ...... 218 Gary M. Dunny ...... 218 Ashley T. Haase ...... 219 Marc K. Jenkins ...... 219 Russell C. Johnson ...... 220 Vivek Kapur ...... 221 Patrick M. Schlievert and Marnie L. Peterson ...... 222 Peter Southern ...... 222 Kenneth D. Vernick ...... 223 Department of Neurology Christopher M. Gomez ...... 223 William R. Kennedy ...... 224

2006 Annual Research Report of the Supercomputing Institute 57 University of Minnesota–Twin Cities Campus

Department of Neuroscience Bagrat Amirikian ...... 224 W. Dale Branton ...... 225 Jon Gottesman and Robert F. Miller ...... 225 Alexander E. Kalyuzhny ...... 226 Naoko Koyano and Steven C. McLoon ...... 226 Tongbin Li ...... 227 Teresa A. Nick ...... 227 A. David Redish ...... 228 Martin W. Wessendorf ...... 228 George L. Wilcox ...... 229 Department of Neurosurgery Stephen J. Haines ...... 229 Department of Orthopaedic Surgery Jack L. Lewis and Narendra K. Simha ...... 230 Department of Otolaryngology John H. Anderson ...... 230 Steven K. Juhn ...... 231 Jizhen Lin ...... 231 Department of Pediatrics Bruce R. Blazar and Angela Panoskaltsis-Mortari ...... 232 Elizabeth G. Ingulli ...... 232 Michael Mauer and Youngki Kim ...... 233 Alfred F. Michael and Clifford E. Kashtan ...... 233 Julie A. Ross ...... 234 Scott B. Selleck ...... 234 Xiangzheng Zhou ...... 235 Department of Pharmacology Duanqing Pei ...... 235 Li-Na Wei ...... 236 W. Gibson Wood ...... 236 Department of Physical Medicine and Rehabilitation Paula M. Ludewig ...... 237 Robert P. Patterson ...... 237 Department of Physiology Jürgen F. Fohlmeister ...... 238 Doris A. Taylor ...... 238 Department of Psychiatry S. H. Fatemi ...... 239

58 2006 Annual Research Report of the Supercomputing Institute University of Minnesota–Twin Cities Campus

Department of Radiology Mark J. Conroy ...... 239 Noam Harel and Patrick J. Bolan ...... 240 Pierre-Gilles Henry ...... 240 Department of Surgery Peter S. Dahlberg ...... 241 Lester F. Harris and Leonard S. Schutz ...... 241 Bernhard J. Hering ...... 242 Paul A. Iaizzo ...... 242 David E. R. Sutherland ...... 243 Department of Therapeutic Radiology Daniel A. Vallera ...... 243 Department of Urologic Surgery Kenneth S. Koeneman ...... 244 Carl S. Smith ...... 244 Robert M. Sweet ...... 245 Gerald W. Timm ...... 245 School of Dentistry Department of Developmental and Surgical Sciences Massimo Costalonga ...... 246 Department of Diagnostic and Biological Sciences Dwight L. Anderson ...... 246 James R. Fricton and Sandra L. Myers ...... 247 Raj Gopalakrishnan and Anna Petryk ...... 247 Mark C. Herzberg ...... 248 Ching-Chang Ko ...... 248 Patrick W. Mantyh ...... 249 Joel D. Rudney ...... 249 School of Public Health Division of Biostatistics Patricia M. Grambsch and James D. Neaton ...... 250 Na Li ...... 250 Wei Pan ...... 251 Division of Environmental Health Sciences Lisa A. Peterson ...... 251 Peter C. Raynor ...... 252 Division of Epidemiology and Community Health James S. Pankow and Michael B. Miller ...... 252

2006 Annual Research Report of the Supercomputing Institute 59 UM TC–Cancer Center

Sharon E. Murphy, Principal Investigator Nicotine, Nitrosamines, and P450 2A Enzymes

he tobacco-specific, nicotine-derived nitrosamine significant differences in both the rate and specificity of NNK is a potent lung carcinogen in rodents and NNK metabolism. The metabolism of nicotine, the Ta likely causative agent for lung cancer in smok- addictive component of tobacco, which is structurally ers. To exert its carcinogenic potential, NNK must be similar to NNK, is also catalyzed by P450 2A enzymes. metabolically activated. Activation is catalyzed by Recently, P450 2A6 was crystallized and the coordinates cytochrom P450 enzymes (P450s). P450s from the 2A made available to these researchers. They are using family are among the best catalysts of NNK activation. A molecular modeling to investigate the potential interac- small number of amino acid changes, however, result in tions between specific amino acids in the active site of the human P450 2A enzymes and nicotine and NNK. This work will help to interpret the effect of amino acid Research Group substitutions and naturally occurring polymorphisms on Kari Dicke, Graduate Student Researcher the selectivity of NNK and nicotine metabolism by P450 Linda von Weymarn, Research Associate 2A enzymes. Jeannette Zinggeler, Graduate Student Researcher

Jennifer J. Westendorf, Principal Investigator LEF1 Regulation of Gene Expression

EF1 is a transcription factor that regulates gene These results may increase understanding of bone forma- expression during development and carcinogenesis. tion and may lead to new therapeutic targets for osteo- LThese researchers studied LEF1’s role in bone for- porosis. mation. They created stable osteoblast cell lines that express less LEF1 than normal. These cell lines form bone at a faster rate than normal cells. The researchers used microarray analysis to identify the molecular events that accelerate bone formation in LEF1-suppressed cells.

Research Group Suzanne Grindle, Research Associate Rachel Kahler, Research Associate

60 2006 Annual Research Report of the Supercomputing Institute UM TC–Center for Computational Genomics and Bioinformatics

Ernest F. Retzel, Principal Investigator Genome Sequence Analysis

his project involves the analysis of plant genomes, both those that have been completed and those Research Group Tthat are in progress. One of the group’s primary John A. Crow, Staff tools is the ENSEMBL pipeline, a genome-analysis envi- Chris Dwan, Staff ronment that requires considerable computational power Michael Heuer, Staff for processing. The researchers have adapted these tools Mike Karo, Staff for the Supercomputing Institute’s LINUX Cluster. The Timothy Kunau, Graduate Student Researcher results of this project are then published on the World Anne Lamblin, Research Associate Wide Web. Robert Milius, Research Associate Jay Vasewani, Staff

UM TC–Center for Drug Design

Courtney Aldrich, Principal Investigator Design of Inhibitors of Siderophore Biosynthesis

uberculosis (TB) is the world’s leading cause of virulence-confering siderophore mycobactin. The infectious disease mortality by a bacterial researchers are using the Medicinal Chemistry/ Tpathogen, with approximately two million deaths Supercomputing Institute Visualization-Workstation per year. Mycobacterium tuberculosis, the causative agent Laboratory for this project. of TB, is notoriously slow-growing, requiring prolonged antibiotic treatment. This project focuses on discovery of Research Group siderophore biosynthesis inhibitors as agents against M. Eric Bennett, Research Associate tuberculosis. Specifically, this approach is directed towards Chunhua Qiao, Research Associate the inhibition of MbtA, a stand-alone adenylation Ravindranadh Somu, Research Associate enzyme that catalyzes the first biosynthetic step of the

2006 Annual Research Report of the Supercomputing Institute 61 UM TC–Center for Drug Design

Robert Vince, Principal Investigator Design of Anti-HIV Drugs

hese researchers use Supercomputing Institute odeficiency virus) genome. These molecular modeling laboratories and the Netfinity cluster to model studies help the researchers to decide which molecules to Tcandidate drug molecules into the active sites of synthesize for testing. Additionally, this group provides multiple enzymes encoded by the HIV (human immun- computational support to other Center for Drug Design research projects.

Research Group Eric Bennett, Research Associate Srikanth Kolluru, Research Associate Xingnan Li, Graduate Student Researcher Ding Lu, Graduate Student Researcher Swati More, Graduate Student Researcher Abbas Raza, Research Associate Ye Tang, Graduate Student Researcher Zhengqiang Wang, Research Associate

UM TC–Stem Cell Institute

Catherine M. Verfaillie, Principal Investigator Gene Expression Studies

he objective of this project is to study stem cell behavior, including proliferation, differentiation, Research Group Tand possibly “de-differentiation” to further our Shannon M. Buckley, Graduate Student Researcher understanding of the potential of stem cells to improve Craig Eckfeldt, Graduate Student Researcher human and animal health. This involves basic research Suzanne Grindle, Research Associate into genetics and genomics, developmental biology, cell Ben Kidder, Graduate Student Researcher biology, and the physiology of stem cells and their differ- Todd Lenvik, Research Associate entiated progeny. The researchers have initiated studies to Eric Mendenhall, Graduate Student Researcher Beatriz Pelacho, Research Associate identify the expression gene profile of umbilical cord Huilin Qi, Research Associate blood stem and progenitor cells. They hypothesize that Zubaid Rafique, Graduate Student Researcher specific transcription factors, signaling molecules, cell Stephanie Salesse, Research Associate membrane receptors, and secreted factors will play Robert Schwartz, Graduate Student Researcher important roles in regulating proliferation versus differ- Fernando Ulloa, Graduate Student Researcher entiation decisions. The researchers are using the Michael Weinreich, Graduate Student Researcher Computational Genetics Laboratory for their gene expression experiments.

62 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Agronomy and Plant Genetics

James A. Anderson, Principal Investigator Haplotype Polymorphism in Polypoid Wheats and Their Diploid Ancestors

hese researchers are interested in breeding wheat lines, sequence the amplicons, and assess haplo- improved varieties of wheat. They are using the type polymorphism. The final step will be to integrate TBasic Sciences Computing Laboratory, the these new SNPs into wheat genetic maps. Scientific Development and Visualization Laboratory, To date, SNPs have been uncovered from 40 loci in and the Computational Genetics Laboratory to investi- chromosome 3A, 43 loci in chromosome 3B, and 57 loci gate single nucleotide polymorphism (SNP). They select in chromosome 3D, using the genome-specific primers expressed sequence tag (EST) unigenes detecting single designed for the project. This work is part of a greater or at most two genes per wheat genome from the data- collaboration among several laboratories; the polymor- base of mapped ESTs and other EST databases, and are phisms and their primers can be accessed at: designing conserved polymerase chain reaction primers rye.pw.usda.gov/snpworld/Search. for the development of sequence tagged sites (STSs) spanning one or more introns in chromosome group 3. Research Group They use STS polymorphisms among the three wheat Emily Conley, Staff diploid ancestors to develop A-, B-, and D genome-spe- Sixin Liu, Research Associate cific primers, and then amplify STSs from the wheat A, Susan Reynolds, Staff B, and D genomes in a sample of wild emmer and bread Dindo Tabanao, Graduate Student Researcher

Rex N. Bernardo, Principal Investigator In Silico Gene Mapping From Phenotypic Pedigree and Genomic Data in Plant Breeding lant breeding programs in major crop species have methods for finding genes from existing data, thereby accumulated massive amounts of performance data allowing a greater leverage of current investments in cul- Pfor different traits of economic importance. To tivar development and in plant genome research. date, however, the data routinely generated in plant- breeding programs have been underutilized in gene mapping. The goal of this project is to develop methods for mapping genes from phenotypic data that are routinely generated in a plant-breeding program, from pedigree records that are kept in the course of a breeding program, and from genomic sequence data that are, or will be, generated from genomic screens of breeding germplasm. The researchers are using computer modeling Research Group to evaluate the usefulness of in silico mapping via mixed- Martin Arbelbide, Graduate Student Researcher model analysis in the context of a breeding program for Jianming Yu, Research Associate soybean, a self-pollinated crop, and maize, a cross-pollinated crop. This project aims to develop computational

2006 Annual Research Report of the Supercomputing Institute 63 UM TC–Department of Agronomy and Plant Genetics

David F. Garvin, Principal Investigator Genetic and Genomic Approaches to Improve Disease Resistance and Nutrient Value in Wheat he Garvin laboratory is pursuing research to identify changes in gene expression that accom- Tpany pathogen infection of wheat. They use Affymetrix GeneChips to identify changes in gene expression between resistant and susceptible wheat lines after exposure to the causal agent of leaf rust, and to track the expression of genes of interest over time. The goal of the project is to identify genes that are involved in durable adult plant resistance to leaf rust, and to contrast patterns of gene expression associated with durable resistance observed in wheat lines that harbor typical race-specific resistance genes.

Gary J. Muehlbauer, Principal Investigator Gene Expression Analysis in Barley and Wheat

his group uses resources at the Computational barley and wheat. These researchers are comparing gene Genetics Laboratory to study aspects of the bar- expression profiles in barley, wheat, and F. graminearum Tley and wheat genomes. One area of interest is in uninfected and F. graminearum-challenged barley and the gene expression profiles during the infection of barley wheat. and wheat with the fungal pathogen Fusarium gramin- The Muehlbauer group is also interested in gene earum. F. graminearum infection of barley and wheat expression profiles during vegetative branching. They are flowers causes Fusarium head blight, a major disease in examining and comparing the gene expression profiles in four low branching barley mutants with wild-type branching plants. Research Group and Collaborator A final research area involves using gene expression Hatice Bilgic, Research Associate data to physically map genes to barley chromosomes. Jayanand Boddu, Research Associate Using a combination of microarray technology and spe- Seungho Cho, Research Associate cialized cytogenetic stocks, they have developed an Haiyan Jia, Graduate Student Researcher approach to map thousands of genes to chromosomes. Song Joong Yun, Chonbuk National University, Jeonju, South Korea

64 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Agronomy and Plant Genetics

Ronald L. Phillips, Principal Investigator Howard W. Rines, Co-Principal Investigator Chromosomal Distribution of Maize Repetitive Sequences

he focus of this project is to evaluate the maize RH and OMA lines. The researchers are using the genome and its content. Oat-maize addition Computational Genetics Laboratory and the Digital T(OMA) lines have been developed that are a set Technology Computational Biology Laboratory for this of alien introgression lines of oat that contain a single project. maize chromosome. From these lines, radiation hybrids (RH) are being developed. The RH lines make it possible to map sequences in the maize genome without requiring Research Group polymorphisms. Two characteristics of the maize genome Howard Chen, Undergraduate Student Researcher Jen Jacobs, Graduate Student Researcher are that the genic portion is highly duplicated, and that a Alexander Kahler, Graduate Student Researcher majority of the sequences are repetitive. This group is Penny Kianian, Graduate Student Researcher analyzing the data from a genomic microarray trial that Wade Odland, Graduate Student Researcher surveyed the difference in major repetitive sequences Ron Okagaki, Research Associate abundance between the maize chromosomes. They are Evan Ribnick, Undergraduate Student Researcher also developing ways to analyze the marker data from

Kevin P. Smith, Principal Investigator Genetic Mapping of Valuable Traits in Barley

hese researchers are investigating the genetics of of interest for these researchers is the use of mixed mod- numerous traits in barley. Much of this work els to detect marker-trait associations using breeding Tinvolves construction of genetic linkage maps germplasm. with molecular markers using experimental mapping populations. The group is also developing new genetic markers for mapping. Polymerase chain reaction primers Research Group for simple sequence repeat markers are designed from Stephen Baluch, Graduate Student Researcher deoxyribonucleic acid sequence information from barley Karen Beaubien, Staff expressed sequence tag libraries. These new markers are Federico Condon, Research Associate designed to fill in gaps and improve overall coverage of Charlie Gustus, Staff the barley genetic map. Current quantitative trait locus Lexingtons Nduulu, Research Associate mapping studies focus on disease resistance genes, genes Ahmad Sallam, Graduate Student Researcher that contribute to yield and agronomic performance, and Song Joong Yun, Research Associate genes that are involved in malting quality. Another area

2006 Annual Research Report of the Supercomputing Institute 65 UM TC–Department of Agronomy and Plant Genetics

David A. Somers, Principal Investigator Investigating Transgene Locus Structure

his project uses a bioinformatics approach to thaliana to determine its DNA binding and cleavage investigate the role of topoisomerase II in creat- properties, and have determined cleavage consensus Ting doubled stranded breaks in deoxyribonucleic sequences. They are now in the process of mining and acid (DNA) during integration of delivered DNA into mapping the Arabidopsis genome for these sites and to the genome of the plant Arabidopsis thaliana. The determine the association of the sites with transferred researchers have characterized topoisomerase II from A. DNA (T-DNA) integration sites reported in genome- wide databases. Determining this association will allow Research Group investigation of mechanism(s) of T-DNA integration in Irina Makarevitch, Graduate Student Researcher plant genomes and transgene locus formation.

UM TC–Department of Animal Science

Scott C. Fahrenkrug, Principal Investigator Vertebrate Comparative and Functional Genomics for Medicinal and Agricultural Research he Fahrenkrug group is developing a database to species and will allow for the identification of regions of facilitate the integration of physical and genetic conserve synteny. This conserved synteny, as well as phe- Tdata from human, mouse, zebrafish, and livestock notypic and gene-expression data, has been used to func- genomes. This database will allow for collection, storage, tionally annotate vertebrate genes. and analysis of genetic and sequence data from these The researchers are also interested in gene expression profiling studies of livestock animals. They have studied gene expression in isolated and cultured porcine islets for indicators of islet function, immunogenicity and quality. Research Group and Collaborators They are also working on an expression profiling study John Carlis, Faculty Collaborator Holstein cattle liver and mammary tissues to examine the Daniel A. Carlson, Graduate Student Researcher Karl J. Clark, Research Associate effects of the selection for milk production. They do this Lynda B. M. Ellis, Faculty Collaborator by comparing tissues from the University of Minnesota Sean Goggins, Graduate Student Researcher static control (from 1964) and contemporary selected Bhupinder Juneja, Graduate Student Researcher lines of Holsteins during the pariparturient period. The Eric Klee, Graduate Student Researcher database and gene expression studies will assist in under- Michael Pickart, Research Associate standing the function of genes in processes of medical Kevin Roberg-Perez, Research Associate and agricultural importance. Min Wang, Research Associate Hehuang Xie, Research Associate Yongqing Zhang, Graduate Student Researcher

66 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Entomology

Ann M. Fallon, Principal Investigator Molecular Biology of the Mosquito

hese researchers are exploring gene regulation and expression in mosquitoes. They are using Research Group Tresources available at the Computational Genetics Anne Gerenday, Staff Laboratory to perform their sequence analyses. Karen Moline-Shih, Graduate Student Researcher Yongjiao Zhai, Graduate Student Researcher

UM TC–Department of Horticultural Science

Christian A. Thill, Principal Investigator Potato Breeding and Genetics

his group’s research includes breeding, genetics, cytogenetics, and the utilization of wild Tgermplasm in potato cultivar development and enhancement. The group’s emphasis includes both basic and applied research and includes developing efficient Research Group breeding techniques to incorporate traits from wild Sonia Bolvaran, Graduate Student Researcher Ioana Dinu, Graduate Student Researcher germplasm to cultivated potato and developing breeding Dave Esplin, Graduate Student Researcher materials and cultivars with high yield, yield stability, Angel Lara-Chavez, Graduate Student Researcher pest resistance, and quality. The researchers used Dimitre Mollov, Graduate Student Researcher resources at several of the Supercomputing Institute laboratories for this project.

2006 Annual Research Report of the Supercomputing Institute 67 UM TC–Department of Plant Pathology

James M. Bradeen, Principal Investigator Expanded Genomics Resources for Disease-Resistant Potato Species

enetic control of potato diseases can reduce maps for the late-blight-resistant Solanum bulbocastanum. grower and environmental costs. Wild potato They are evaluating an in vitro analog of meiosis and Gspecies are promising resistance-gene sources. amplified fragment length polymorphism markers previ- Complementing their phenotype and molecular analyses, ously mapped in cultivated potato for the construction of these researchers are constructing linkage and physical a medium-density linkage map. They are also developing genome-wide physical maps for putative disease-resistance genes. The linkage and physical maps will allow Research Group rapid isolation of important disease-resistance genes and Riccardo Aversano, Research Associate make emerging potato and tomato genomics tools acces- Steven McKay, Graduate Student Researcher sible for important Solanum species. This project pro- Ben Millett, Graduate Student Researcher vides preliminary data for expanded future efforts to Dimitre Mollov, Staff develop comparative linkage maps and genome-wide Edmund Quirin, Graduate Student Researcher physical maps for disease-resistance genes for species Maria Sanchez, Graduate Student Researcher throughout the genus. Ryan Syverson, Research Associate Adriana Telias, Graduate Student Researcher

H. Corby Kistler, Principal Investigator Functional Genomics of Fusarium graminearum

usarium head blight or scab caused by Fusarium ease. This group’s goals are to identify and characterize graminearum is a destructive disease on wheat and genes important for plant infection and colonization, sec- Fbarley. Infested cereals are reduced in yield and ondary metabolism, and sexual development of F. contaminated with harmful mycotoxins. In the past graminearum using microarray analyses and targeted decade, the disease has resulted in billions of dollars of mutation of selected genes. economic loss to U.S. agriculture. Better understanding Objectives of this research include: to utilize the avail- of F. graminearum pathogenesis and differentiation is able sequence information to develop a whole genome critical because effective fungicides and highly resistant microarray of F. graminearum; to analyze gene expression plant varieties are not available for controlling the dis- profiles of F. graminearum in different infection and colonization stages, in mutants defective in plant infection or toxin production, and in different developmental stages; Research Group and to experimentally determine the biological functions Liane Gale, Research Associate of selected candidate genes identified in microarray Samuel Gale, Staff experiments. Overall, this research will develop and uti- Rubella Goswami, Graduate Student Researcher Karen Hilburn, Staff lize functional genomic resources and/or approaches to Matias Pasquali, Research Associate identify genes important for F. graminearum pathogenici- Kye-Yong Seong, Research Associate ty, development, and secondary metabolism.

68 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Plant Pathology

Deborah A. Samac, Principal Investigator Transcriptome Analysis of Biotic and Abiotic Stress in the Model Legume Medicago truncatula he annual medic, Medicago truncatula (barrel their function and contribution to resistance. The long- medic) is the focus of functional and comparative range goal of the project is to transfer resistance in the Tgenomic studies in a number of laboratories model system to crop legumes. worldwide. The Samac laboratory is developing tools for using M. truncatula to better understand the responses of Research Group crop legumes like alfalfa to stress for pathogens and toxic Divya Chandran, Graduate Student Researcher concentration of aluminum in soil. The group uses Dawn Foster-Hartnett, Research Associate microarrays to compare gene expression in accessions Silvia Penuela, Research Associate with contrasting resistance or susceptibility to biotic and Judy Schnurr, Research Associate abiotic stress. They evaluate select genes to determine Mesfin Tesfaye, Research Associate

Brian J. Steffenson, Principal Investigator Molecular Mapping of Disease Resistance Genes in Wild Cereal Progenitors

ild barley and wheat have not been fully tributing to important phenotypes in wild and cultivated exploited in breeding programs. The long- cereals. The data can be used to hasten the development Wterm goals of this group’s research are to of adapted cereal cultivars with enhanced disease resist- develop, through comparative genomic analysis, efficient ance, which will help alleviate food shortages worldwide. methods for exploiting allelic diversity in wild cereal progenitors for cultivated cereal improvement. They pheno- typed large core collections of wild cereal progenitors for resistance to six important diseases at both the seedling and adult plant stages. They also genotyped this same germplasm with molecular markers that span the genomes. These data were analyzed to measure genetic Research Group diversity, facilitate comparative genomic assessments of Ben Alsop, Graduate Student Researcher wild and cultivated cereals, select genetically unique Claudia Castell, Research Associate accession with broad-based resistance for use in the Pablo Olivera, Graduate Student Researcher national breeding programs, and test the feasibility of Joy Roy, Research Associate association mapping for identifying genomic regions con-

2006 Annual Research Report of the Supercomputing Institute 69 UM TC–Department of Plant Pathology

Les J. Szabo, Principal Investigator Wheat Stem Rust Fungus Genome Sequencing

he major objectives of this project are: to produce tate the assembled genome sequence; and to make these an assembled genome sequence of Puccinia data publicly available. These researchers are using the Tgraminis, the fungus that causes stem rust in Basic Sciences Computing Laboratory for this project. wheat; to develop expressed sequence tags from complementary deoxyribonucleic acid (cDNA) libraries representing different stages of fungal development; to develop restriction fingerprint map of fosmid clones; to anno-

Research Group Shaobin Zhong, Research Associate Jerry L. Johnson, Staff Doug Brown, Staff

Nevin D. Young, Principal Investigator Sequencing the Gene Space of the Model Legume Medicago truncatula

he Young laboratory leads an international consortium of laboratories that is currently sequenc- Research Group and Collaborator ing the euchromatin of the model legume, Steven Cannon, Research Associate T Ameline Carine, Research Associate Medicago truncatula. A combination of cytogenetic and Benjamin S. Chacko, Staff large-scale sequence data demonstrates that the M. trun- Daniel Feldman, Undergraduate Student Researcher catula genome is organized into distinct gene-rich Michael Kantar, Undergraduate Student Researcher euchromatin separate from repeat-rich pericentromeric Nyaling Moorosi, Undergraduate Student Researcher heterochromatin. Thus, the M. truncatula gene-space can Joann Mudge, Research Associate be sequenced in a highly efficient manner using a com- Michael O’Toole, Undergraduate Student Researcher prehensive “Bacterial Artificial Chromosome (BAC)-by- Diana Rommelfanger, Undergraduate Student BAC” strategy. This map-based approach to sequencing Researcher M. truncatula will be leveraged through structural Elizabeth Shoop, Visiting Faculty Collaborator genomic comparisons with Arabidopsis and crop legumes. Jayprakash Vasdewani, Staff Bing-Bing Wang, Research Associate As part of the laboratory’s work in genome sequencing, Min Wang, Research Associate they are also developing software tools to compare and Shelley Wang, Research Associate visualize evolutionary histories of complex genomes.

70 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Soil, Water, and Climate

Michael J. Sadowsky, Principal Investigator Complete Genomic Sequencing of Arthrobacter aurescens TC1

hese researchers are sequencing and annotating the genome of the bacterium Arthrobacter Research Group Taurescens TC1. They are also doing a functional Kevin Drees, Research Associate analysis of environmentally regulated genes in Matthew Hamilton, Graduate Student Researcher Bradyrhizobium japonicum using microarrays. They are Nir Shapir, Research Associate using the resources at Computational Genetics Laboratory for this research.

Dong Wang, Associate Fellow Modeling Two-Dimensional Fumigant Gas Transport in Subsurface Soils and Volatilization Into the Atmosphere he dynamics of pesticide volatilization is strongly These researchers have developed a simulation model controlled by the subsurface transport and ambi- and have recently incorporated into it a stochastic Tent environmental conditions, which may be parameter generator using Monte Carlo simulations. The described with process-based transport models. next step is to expedite the run times by adopting more Application of simulation models can provide accurate computationally efficient numerical schemes. characterizations of fate and transport of volatile organic chemicals such as 1,3-dichloropropene and chloropicrin and their concentration dynamics that may be used as an Research Group index for pest control efficacy. Many parameters are often Karli J. Anderson, Supercomputing Institute required for these types of mathematical models that Undergraduate Intern translate to the initial and boundary conditions. Mark Green, Graduate Student Researcher Selection of a combination of sets of parameters opti- Jianming He, Research Associate mized for better distribution uniformity and the least Charles Hyatt, Graduate Student Researcher volatilization loss has a practical value for field applica- Jindong Wu, Graduate Student Researcher tion by pesticide specialists and farm managers.

2006 Annual Research Report of the Supercomputing Institute 71 UM TC–Department of Food Science and Nutrition

Gary A. Reineccius, Principal Investigator Investigation of Cyclodextrin-Flavor Interactions

yclodextrins have been shown to deliver labile fla- This study aims to determine a means of predicting vor compounds in dry food applications; howev- cyclodextrins interaction with flavor compounds. The er, complete flavor formulations cannot be deliv- researchers have used the molecular-simulation program C NSIGHT ered because of both cost and binding specificity. I II to develop a method to determine binding Therefore, cyclodextrins should only be used to deliver energies of cyclodextrin-flavor complexes. They are con- the unstable portions of a flavoring. This requires an tinuing to use this program to model interactions. understanding of what components cyclodextrins will bind and protect.

Research Group Stephen Brose, Graduate Student Researcher

UM TC–Department of Biosystems and Agricultural Engineering

John L. Nieber, Principal Investigator Simulation of Free Surface Flows in Open Channels

his project uses computational fluid dynamics the channel boundary and deposition of transported sed- models to simulate subcritical flows in natural iment. They began the project by simulating flows in Tstream channels. The purpose is to evaluate the prismatic channels composed of cross-sectional geometric details of the shear stresses that develop along channel elements such as rectangles or trapezoids. After success- boundaries, leading to the erosion of channel bottom or fully completing the first test, they plan to use cross-sec- side walls, and also the development of areas in the flow tion data collected from a stream in Minnesota. where transported sediment is deposited. Eventually, the researchers plan to couple the mechanics of erosion of

Research Group and Collaborators Dario Canelon, Visiting Faculty Collaborator Tom Miller, Emmons and Olivier Resources, Inc., Minnehaha Creek Watershed District, Oakdale, Minnesota Brennon Schaefer, Graduate Student Researcher

72 2006 Annual Research Report of the Supercomputing Institute UM TC–BioTechnology Institute

Friedrich Srienc, Associate Fellow Elementary Mode Analysis for Biochemical Networks

volution has supplied biological organisms with a coli to investigate how the gene regulation of genetic highly coupled network of thousands of enzyme- mutants is phenotypically expressed. Ecatalyzed reactions. Scientific advances in recent decades, like polymerase chain reaction, have provided means for altering the topography of these reaction networks. Analysis of native and recombinant networks has been simplified by a number of theoretical tools. One Research Group such method is elementary mode analysis. An elementary Ross Carlson, Graduate Student Researcher mode is the simplest balanced combination of substrates, Alan Gilbert, Graduate Student Researcher products, and reactions that enforces a steady-state Johnathan Gorke, Graduate Student Researcher James Kacmar, Graduate Student Researcher restriction on internal metabolites. Greg W. Sitton, Graduate Student Researcher These researchers are using elementary mode analysis Cong T. Trinh, Graduate Student Researcher to identify all genetically independent flux distributions Natarajan Vijayasankaran, Graduate Student for the production of biomass and other metabolites in Researcher Escherichia coli. They are also developing a database to Aaron Wlaschin, Graduate Student Researcher bridge the gap between fluxonomics and genomics of E.

Marc G. von Keitz, Principal Investigator Data Management for High-Throughput Screening Facility

he University of Minnesota’s High-Throughput Screening (HTS) Facility is a campus-wide Tresource managed by the BioTechnology Institute. One of the primary services of the facility is to screen small molecule libraries against a wide array of protein- and cell-based assays. The HTS facility is running their data-management software program on the ORACLE database servers managed by the Supercom- puting Institute. Researchers from several departments at Research Group the University are using HST Facility’s small molecule Nick Hahn, Staff screening capability.

2006 Annual Research Report of the Supercomputing Institute 73 UM TC–Department of Ecology, Evolution, and Behavior

Sharon A. Jansa, Principal Investigator Molecular Phylogenetic Studies of Mammals

his research focuses on reconstructing the evolu- Muroid rodents are the most speciose group of mam- tionary history for two groups of mammals: mals, but their evolutionary history remains poorly Tdidelphid marsupials and muroid rodents. understood. This research focuses on using slowly evolv- Didelphid marsupials are a small radiation of approxi- ing nuclear gene sequences to reconstruct phylogenetic mately 20 genera endemic to South America. The project relationship among rodent genera, concentrating on investigates the phylogenetic relationships among these Madagascar and the Philippines. Each of these regions genera using deoxyribonucleic acid sequences from five has an endemic rodent fauna, but it is not understood nuclear-encoded genes. The resulting data will not only how rodents got to the islands or how they speciated illuminate the evolutionary history of this small radia- once they arrived. tion, but will provide the basis for investigating patterns These researchers are using the Computational of molecular evolution among mammals. Genetics Laboratory for these phylogenetic studies.

Research Group Karl Gruber, Graduate Student Researcher

Scott M. Lanyon, Principal Investigator Phylogeny and Evolution of the Passerine Birds

he avian order Passeriformes is one of the largest data from approximately 750 species of birds. They used terrestrial vertebrate radiations. Testing alternative the Computational Genetics Laboratory to employ a Texplanations for this remarkable radiation variety of optimality criteria in exploring the evolution- depends critically on analysis of morphological, molecu- ary relationship among these species. They also explored lar, behavioral, and ecological variation in conjunction a variety of graphical projections of the resultant evolu- with a thorough understanding of evolutionary relation- tionary trees, including hyperbolic techniques. ships within the group. This project focused on interpreting phenotypic variation among species of passerines in the context of phylogenies derived from molecular data. The researchers collected deoxyribonucleic acid sequence

Research Group F. Keith Barker, Research Associate Muir D. Eaton, Graduate Student Researcher

74 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Ecology, Evolution, and Behavior

Georgiana May, Principal Investigator Evolutionary Genetic Analyses of Host/Microbe Interactions

hese researchers used a number of evolutionary, genetic, and genomic computer analyses and Ttools to investigate the evolution of host/microbe interactions. Some analyses test statistical significance by Research Group and Collaborator permutation of an empirically derived dataset, and thus Jonathan Arnold, Department of Genetics, University require computational resources beyond that of a desktop of Georgia, Athens, Georgia computer. The researchers are using resources at the Andrew Baumgarten, Graduate Student Researcher Computational Genetics Laboratory for their projects, Ethy Cannon, Graduate Student Researcher which include large datasets for resistance gene families Brett Couch, Research Associate in plants and deoxyribonucleic acid sequence-based pop- Anja Forsche, Research Associate Keun-Sub Lee, Graduate Student Researcher ulation genetic data for fungal pathogens. Andrew Munkacsi, Graduate Student Researcher Jean Pan, Research Associate David Schladt, Graduate Student Researcher Russel Spangler, Research Associate Peter Voth, Graduate Student Researcher

Joseph P. McFadden, Principal Investigator Modeling Effects of Land Cover Heterogeneity on Regional Climate and Hydrology in the Arctic his project uses a version of the regional atmos- tor of four or five, increase the time period being simu- pheric models RAMS that was developed for sea- lated, and implement ensemble or factorial model experi- Tsonal to interannual simulations (ClimRAMS) to ments. Although this project focuses on an arctic study the effects of land cover heterogeneity on the cli- domain, the modeling approaches will be valuable for mate and hydrology of arctic Alaska. The model repre- other regions that have a high degree of landcover het- sents the effects of vegetation, seasonal permafrost evolu- erogeneity. tion, snow accumulation, snowmelt, and the resulting changes in surface moisture and energy exchange. This researcher is developing a coupled modeling system that will incorporate a snow-transport model (Snow-Tran-3D) and a new, community land surface model (CLM). Simulations can now be performed for 12- to 13- month periods using three 2-way-interactive, nested model grids. The model grids have horizontal resolutions of 60, 20, and 5 kilometers. The next phase of the research is to increase the horizontal resolution by a fac-

2006 Annual Research Report of the Supercomputing Institute 75 UM TC–Department of Ecology, Evolution, and Behavior

Anne E. Pusey, Principal Investigator Creation of a Visual Database of Chimpanzee Behavior

he study of the chimpanzees of Gombe National in color. Since 1993, over 600 hours of video have been Park, Tanzania, has been continuous since 1960. shot during daily follows of the chimpanzees through the TOver this period, 35mm photographs have been forest. The purpose of this project is to enter all this visu- taken of the chimpanzees, both in black and white and al material into a database. The material will be stored at several different resolutions so that it can be used both for high-quality illustrations and as Web images. The database will be constructed so that the material can be Research Group and Collaborator Mete Celik, Graduate Student Researcher indexed in progressively more detail. The long-term aim Wendy MacCannell, Graduate Student Researcher is to make the database searchable on the Web to quali- Sandeep Mane, Graduate Student Researcher fied users for research and education. The project uses Carson Murray, Graduate Student Researcher the Scientific Development and Visualization Lilian Pintea, Graduate Student Researcher Laboratory. April Rog, Undergraduate Student Researcher Mark Sanders, Research Associate Joann Schumacher-Stankey, Staff Shashi Shekhar, Faculty Collaborator Emily Wroblewski, Graduate Student Researcher Jin Soung Yoo, Graduate Student Researcher

Shinya Sugita, Principal Investigator Theory and Application of Quantitative Reconstruction of Vegetation in the Past

aleoecology has provided vital information on the been used to evaluate the effects of these factors on fossil past patterns of environmental changes from local pollen assemblages in relatively simply landscapes. Pto continental and global scales. Knowledge about This project’s aims were: to further improve and test changing climate and vegetation has been important not the group’s models in more complex and realistic land- only for academic interests but also for global climate scapes; to develop models and methods for quantitative research and policy in view of the human-induced global reconstruction of vegetation using currently available warming. For a better understanding of changing climate pollen-dispersal models; and to develop a general guide- and vegetation, researchers need improved models and line for applications of the models in empirical paleoeco- empirical methods that can be used for quantitative logical studies. reconstruction of vegetation and landscapes using fossils. Many factors, including heterogeneity of vegetation, species composition, size of study sites, wind conditions, and dispersal characteristics of fossil materials, all interact with each other and produce complex relationships between fossil assemblages and surrounding vegetation. Models developed by this researcher and others have

76 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Plant Biology

J. Stephen Gantt, Principal Investigator Gene Function in Legumes

egumes comprise the third largest family of flower- The group created a database that will allow them to ing plants and are an important food source for track, organize, and publicize their data. The goal was to Lhumans and animals. They also form symbiotic easily input multiple forms of data that can be used by associations with rhizobial bacteria that can lead to fixa- bench scientists and analyzed by researchers around the tion of atmospheric nitrogen, providing the major source world. of biologically available nitrogen. Little is known, however, about the legume genes that are involved in bacterial and fungal symbioses, nitrogen fixation, pathogen defense, or environmental interactions. These researchers used ribonucleic acid interference to silence specific genes in transgenic roots that were then examined for altered Research Group symbiotic relationships, nitrogen fixation, and develop- Sajeet Haridas, Graduate Student Researcher ment. Results indicated that the system works well and Sergey Ivashuta, Research Associate can be used to infer gene function.

Susan I. Gibson, Principal Investigator Identification of Sugar-Regulated Genes From the Model Plant Arabidopsis thaliana

he levels of soluble sugars, such as glucose and senger ribonucleic acid level. The group is using the sucrose, are known or postulated to help regulate Computational Genetics Laboratory to analyze this data Tdiverse aspects of plant development, metabo- to determine which genes are expressed at significantly lism, and physiology. Although the role of sugar levels in different levels in response to feeding different sugars. some plant processes has been well documented, whether sugar levels help regulate many other processes remains unknown. In addition, very little is known about the Research Group molecular mechanisms by which plants sense and Tim Heisel, Graduate Student Researcher respond to sugar levels. To help address these questions, Yadong Huang, Graduate Student Researcher these researchers are using Affymetrix GeneChips con- Chun-Yao Li, Research Associate taining information from ~24,000 Arabidopsis genes to Shu Wei, Research Associate identify those plant genes that are regulated by sucrose, glucose, mannose and/or sorbitol at the steady-state mes-

2006 Annual Research Report of the Supercomputing Institute 77 UM TC–Department of Plant Biology

Jane Glazebrook, Principal Investigator Functional Genomics Analysis of Plant Defense Responses

hese researchers are designing polymerase chain reaction-based polymorphic markers for genetic Tmapping of disease-resistance loci. In addition, they are analyzing microarray data from plants infected with a bacterial pathogen. They are using software packages available through the Supercomputing Institute for this project.

Research Group Raka Mitra, Research Associate Lin Wang, Graduate Student Researcher

Fumiaki Katagiri, Principal Investigator Elucidation of Plant Disease-Resistance Mechanisms

his group is studying how plants defend them- attack. The researchers are focusing on resistance gene- selves from pathogens. One important form of mediated disease resistance, which is usually strong and Tdefense is inducible defense, i.e., the defense highly specific. Using Arabidopsis as a plant host and mechanisms are turned on upon recognition of pathogen Pseudomonas syringae as its pathogen, the researchers investigate how plants recognize molecular signals of pathogen attack and how plants coordinate defense Research Group responses upon recognition. The project uses molecular Joseph Foley, Undergraduate Student Researcher biology, biochemistry, genetics, reverse genetics, Charles Hernick, Staff genomics, expression profiling, proteomics, structural Anand Janakiraman, Graduate Student Researcher biology, and computational biology to gain insights into Lisa Lenarz-Wyatt, Staff these topics. Understanding plants’ natural defense Yiping Qi, Graduate Student Researcher mechanisms will lead to plant disease control methods Masanao Sato, Research Associate that are safer to humans and to the environment. Kenichi Tsuda, Research Associate Remco van Poecke, Research Associate Lin Wang, Graduate Student Researcher

78 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Plant Biology

Paul A. Lefebvre, Principal Investigator Carolyn D. Silflow, Co-Principal Investigator Identification of Genes Required for Flagellar Function and Assembly in the Unicellular Green Alga Chlamydomonas reinhardtii hlamydomonas is the premier model system for tending the flagella are regulated by studying mutants the dissection of the molecular mechanisms regu- with defective control of flagellar number. The C lating the assembly and function of the cilia and researchers are using Supercomputer Institute laboratories flagella of eukaryotes. Now that the sequence of the for analyzing the predicted proteins from cloned genes, genome has been obtained and the molecular map of the for analyzing the genes in the context of the whole genome has been completed, these researchers are seeking genome, and for comparing the predicted protein to elucidate the mechanisms that control the assembly sequences from Chlamydomonas with homologous pro- and functioning of cilia and flagella. To this end, they are teins from other eukaryotic organisms. applying a newly developed insertional mutagenesis approach, which, in combination with thermal asymmetric interlaced polymerase chain reaction procedures, Research Group allows them to rapidly clone genes mutated by the inser- Nancy Haas, Staff tion of a selectable marker gene by transformation. Matt Laudon, Staff Initially they are focusing their efforts on two classes of Matthew Lavoie, Staff genes. First, they are seeking to understand the control of Brian Piasecki, Graduate Student Researcher flagellar assembly by cloning and characterizing all genes Xiaodong Sun, Graduate Student Researcher involved in the regulation of flagellar length. Second, Lai-Wa Tam, Research Associate they are seeking to understand how the basal bodies sub-

M. David Marks, Principal Investigator Use of a Contradictory Glabra3 Mutant to Study Arabidopsis Trichome Development

hese researchers are using trichome development in Arabidopsis to address basic biological ques- Ttions concerning control of cell fate, pattern formation, and cell differentiation. The trichomes provide a barrier that helps protect many plants from insects, drought, or excess sunlight. Many of the cellular processes that control trichome cell fate and differentiation are found in all eukaryotic cells. Thus, the analysis of trichomes may lead to a better understanding of cellular differentiation of all eukaryotic cells, both plant and ani- Research Group mal. The researchers are using the Computational Edward K. Gilding, Graduate Student Researcher Genetics Laboratory for this project.

2006 Annual Research Report of the Supercomputing Institute 79 UM TC–Department of Plant Biology

David J. McLaughlin, Principal Investigator Assembling the Fungal Tree of Life

his group is engaged in a collaborative project, diverse phylogenetic analyses of these data, including Assembling the Fungal Tree of Life (AFTOL), to analyses that incorporate evidence from subcellular char- Tcontribute toward a comprehensive phylogenetic acters. This project is based in five laboratories at four hypothesis of the fungi. AFTOL is developing broad universities. The McLaughlin group is studying subcellu- datasets of molecular and subcellular characters, which lar characters across all the fungi as well as phylogeny of will be accessible via the World Wide Web in continu- selected species in four families. They use resources at the ously updated databases. The project will sample seven Basic Sciences Computing Laboratory and the molecular regions in approximately 1,500 species in all Computational Genetics Laboratory for phylogenetic major groups of fungi. The researchers will perform analyses of molecular and subcellar data.

Research Group Gail Celio, Research Associate Bryn Dentinger, Graduate Student Researcher Mahajabeem Padamsee, Graduate Student Researcher

Nathan M. Springer, Principal Investigator Genome Structure and Allele-Specific Gene Expression Patterns in Maize

hese researchers use oligonucleotide microarrays these data. Current work involves combining this analysis to study the maize genome. Their primary inter- with the group’s allele-specific expression assays to dissect Tests are studying comparative genome organiza- quantitative and qualitative genetic variation. tion in related maize lines and studying the expression levels of two alleles in hybrid individuals. Towards this goal, they have designed and utilized custom oligonucleotide microarrays. The researchers are using Computational Genetics Laboratory resources to analyze

Research Group William Haun, Graduate Student Researcher Soma Narasimhulu, Research Associate Andrew Shaffer, Undergraduate Student Researcher Robert Stupar, Research Associate Roseanne M. Wolf, Undergraduate Student Researcher

80 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Plant Biology

Peter L. Tiffin, Principal Investigator Effect Natural Selection Has Had in Driving the Inter-Specific Divergence of Plant Defense Proteins athogens and herbivores can cause extensive dam- mine: whether the selective histories of defense genes dif- age to the plant they attack and have been shown fer among geographically distinct populations; if there Pto be important agents of natural selection. How are consistent inter-genetic patterns in the rates at which this selection affects intra-specific diversity and inter-spe- genes evolve; and if selection has driven the divergence of cific divergence of plant defense genes is, however, not duplicated defense genes. well understood. These researchers use deoxyribonucleic acid (DNA) sequence analyses in order to characterize how selection has affected plant defense genes. By analyz- Research Group ing sequences from geographically isolated populations of David Moeller, Research Associate one wild relative of maize, two closely related teosinte species, and several grass genera, they attempted to deter-

Kathryn A. VandenBosch, Principal Investigator Analysis of Gene Expression in Medicago truncatula

his project investigates the genome function of a malization and analysis of significance, which produces model legume, Medicago truncatula, with an lists of genes with statistically reproducible behavior in Temphasis on interactions with microbes and uti- the experiment. The last step in data analysis included lization of nutrients. The researchers are using deoxyri- gene clustering, principal component analysis, and other bonucleic acid (DNA) microarrays as one of the approaches. approaches to study reproductive and vegetative development in this plant and its response to pathogenic and symbiotic microbes and different nutrient conditions. For their microarray experiments, the researchers have constructed two types of carrier DNA chips, representing about 1,000 or 6,000 unique genes. They have also Research Group begun to use oligonucleotide (70mer) arrays constructed Kavitha Kuppusamy, Graduate Student Researcher to represent 16,000 unique genes from Medicago. Dasharath Lohar, Research Associate Existing microarray technologies require implementation Vladimir Portyanko, Research Associate of statistical methods in experimental designs as well as Natasha Sharopova, Research Associate in interpretation of results. The researchers perform nor-

2006 Annual Research Report of the Supercomputing Institute 81 UM TC–Department of Plant Biology

George D. Weiblen, Principal Investigator Low-Copy Nuclear Genes for Species-Level Phylogenetics in Moraceae

he Moraceae family comprises 37 genera and The researchers use deoxyribonucleic acid (DNA) approximately 1,100 primarily tropical and sub- sequence data from nuclear and ribosomal gene regions Ttropical species. In the past year, these researchers as well as data from morphology to perform phylogenetic have reconstructed a family-level phylogeny using two reconstructions of all species within the tribe. Using this genes and have explored the biogeographical history of phylogeny, the group conducts focused studies of charac- Moraceae. The group has now begun studies focused at ter evolution, biogeography, and pollination biology. the species level within Moraceae. A second study explores the evolutionary history and One study focuses on the tribe Castilleae, which com- co-cladogenesis in a highly species-rich fig community in prises 11 genera and 59 species distributed pantropically. Papua, New Guinea. The group is examining the associations of figs, fig wasp pollinators (Ceratosolen spp.), and fig wasp parasitoids. The results of this study will be Research Group compared to previous studies on the fig-fig wasp com- Wendy Clement, Graduate Student Researcher munity. This is also the first detailed investigation of the Nina Ronsted, Research Associate associations among Ceratosolen pollinators and para- Summer Silvieus, Graduate Student Researcher sitoids. Nyree Zerega, Research Associate

UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Ian M. Armitage, Principal Investigator Bruce L. Martin, Co-Principal Investigator Structure/Function Studies of Biomolecules Involved in Alzheimer’s Disease, Cellular Metal Homeostasis, and Immune Suppression mong other methods, these researchers are using structure and metal exchange properties of proteins multi-nuclear/dimensional magnetic resonance involved in the maintenance of metal homeostasis in A(NMR) methods to forge new inroads into the vivo; structural/functional studies of select molecules associated with the pathogenesis of Alzheimer’s disease. Past solution structural studies by NMR have provided Research Group and Collaborators and angstrom level description of the immunosuppressive Robert Alver, Staff drug, cyclosporine A, bound to its cytosolic receptor pro- Issam El Ghazi, Research Associate tein, cyclophilin. Grant J. Giesler, Jr., Faculty Collaborator The researchers use the Basic Sciences Computing John D. Hoekman, Staff Laboratory and the Medicinal Chemistry/Supercom- David Lahti, Research Associate puting Institute Visualization-Workstation Laboratory to Laurel Sillerud, Department of Biochemistry and Molecular Biology, University of New Mexico, process the multidimensional NMR datasets, to calculate Albuquerque, New Mexico the three-dimensional structures of the biomolecules, and Abigail M. Tokheim, Staff to visualize those calculated structures. Qian Wang, Graduate Student Researcher

82 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Leonard J. Banaszak, Associate Fellow Structure/Function Studies of Biological Macromolecules

hese researchers are performing studies to uncov- that eventually reside in a cellular organelle. Because er the nature of the interactions between lipid these are also biological macromolecules with thousands Tand proteins and to use structural studies to aid of atoms, the analyses of the x-ray data and refinement of in the understanding of lipoprotein assembly. To do this, the molecular coordinates involve computationally they are producing recombinant proteins including a intense methods. liver microsomal protein called “microsomal transfer protein” and fragments of the protein labeled “apoB.” Both Research Group and Collaborators are involved in the production of low-density lipopro- Ed Hoeffner, Staff tein. The researchers then carry out crystallization trials Wasantha Ranatunga, Staff and collect x-ray diffraction data. They use the facilities Kelly Strait, Graduate Student Researcher at the Basic Science Computing Laboratory to perform James R. Thompson, Mayo Proteomics Research the computationally intensive analyses of the x-ray data Center and Department of Physiology and and to construct the molecular model. Biophysics, Mayo Medical Foundation, Rochester, Another goal of the project is to gather x-ray diffrac- Minnesota Todd Weaver, Department of Chemistry, University of tion data and eventually the molecular structure of Wisconsin, La Crosse, Wisconsin translocatable proteins. These are nuclear coded proteins

David A. Bernlohr, Principal Investigator Role of Adipocytes in Mammalian Lipid Metabolism

hese researchers are primarily concerned with of this large, multigene family. The group is studying the lipid metabolism, specifically the mechanism(s) physiological roles of FABPs in health and disease. Tthat cells use to move water-insoluble lipids The researchers use a combination of protein chem- across membranes and within cells, a process called lipid istry, structural biology, metabolism, and gene expression trafficking. To do this, the researchers study both plasma techniques to test experimental hypotheses. membrane fatty acid transporters and cytoplasmic fatty acid binding proteins (FABPs). One project examines the mechanism of fatty acid Research Group transport across the plasma membrane and the molecular Paul Grimsrud, Graduate Student Researcher regulation of transporter gene expression by insulin and Angela Hall, Graduate Student Researcher lipids. The major goals are to determine the biochemical Ann Hertzel, Research Associate components of the transport system, the mechanism of Sandra Lobo, Research Associate Anne Smith, Staff fatty acid transfer across membranes, and its regulation at Lisa Ann Smith, Staff the protein and gene level. Brian Thompson, Graduate Student Researcher A second project examines the structure/function rela- Brian Wiczer, Graduate Student Researcher tionships of FABPs and their genes, focusing on the Bruce Witthuhn, Research Associate adipocyte (FABP4) and keratinocyte (FABP5) members

2006 Annual Research Report of the Supercomputing Institute 83 UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Anja-Katrin Bielinsky, Principal Investigator The Role of S Phase Checkpoint Kinases Mec1 and Rad53 in Regulating Replication Stress Hotspots in Budding Yeast o maintain genomic stability, eukaryotic cells collapse, leading to chromosome breakage. To study have evolved various mechanisms to ensure the replication fork dynamics in S phase checkpoint mutants, Torder and fidelity of cell cycle events. In budding these researchers have developed a replication origin array yeast, the S phase checkpoint kinases Mec1 and Rad53 that contains the ~430 potential replication origins in are required to prevent premature entry into mitosis, to budding yeast. In S phase checkpoint mutants, they inhibit late-firing replication origins, and to stabilize observed genome-wide activation of late-firing origins, as stalled replication forks when cells are exposed to replica- expected. Surprisingly, they also observed that regions tion stress. In the absence of a functional S phase check- surrounding specific early-firing origins were not replicat- point, origin firing is deregulated and replication forks ed efficiently in these mutants, likely due to immediate replication fork arrest, as indicated by the accumulation of small nascent deoxyribonucleic acid strands. Further Research Group analysis showed that these regions—replication stress Yung-Tsi Bolon, Graduate Student Researcher hotspots—are prone to chromosome breakage even in Sharbani Chattopadhyay, Graduate Student Researcher the absence of exogenous stress, similar to fragile sites in Miruthubashini Raveendranathan, Graduate Student Researcher the human genome. The group is currently investigating the mechanism of double strand break formation at replication stress hotspots.

Bianca M. Conti-Fine, Principal Investigator Modeling T Cell and B Cell Epitopes on Human Factor VIII

enetic absence of functional coagulation factor requires the intervention of fVIII-specific CD4+ T cells. VIII (fVIII) causes hemophilia A. Patients with These cells may also be involved in preventing and curb- Gsevere disease require therapeutic administration ing inhibitor synthesis, however. of human fVIII and may develop antibodies (Abs) that These researchers are trying to identify the functional block fVIII function. These Abs are called inhibitors and properties of the fVIII-specific CD4+ T cells in hemo- are a serious complication of hemophilia A, because they philia A patients who develop inhibitors and in those make treatment with fVIII inefficient and costly. Experi- who do not. This research will allow them to understand ments in animal models indicate that the presence of the immune mechanism that prevents an immune inhibitors will make attempts to develop gene therapy response to fVIII from progressing to a sustained anti- approaches to hemophilia A difficult. Inhibitor synthesis fVIII Ab response. This information will help elucidate the mechanisms of inhibitor development; it will also help researchers design safe and effective treatments to Research Group curb inhibitor synthesis in hemophilia A patients who Brenda M. Diethelm-Okita, Staff have already developed inhibitors and to prevent Soheila Gharagozlou, Research Associate inhibitor formation in patients at risk.

84 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Timothy J. Griffin, Principal Investigator Proteomic Analysis Using Mass Spectrometry

n the evolving era of genome biology, mass spectrom- Ongoing projects and collaborations in the Griffin etry has emerged as a leading tool by which to meas- laboratory include: Iure the various properties of the protein products • Biomarker discovery and molecular characterization expressed by the genome. The complexity of biological of oral cancer progression. systems, however, continually proves challenging to these • Characterization of oxidative stress induced protein existing methodologies, necessitating the development of damage and its implications in cellular function and novel tools to obtain the information required to gain a disease. comprehensive understanding of these systems. The • Investigation of the connection between stress and Griffin laboratory is interested in developing proteomics growth signaling in model organisms and cell lines. methods using mass spectrometry to investigate mechanisms of cellular regulation and protein function. These evolving, high-throughput methods also present many Research Group informatic challenges in capturing, analyzing and visual- Sri Bandhakavi, Research Associate izing the information in order to formulate hypotheses Mikel Roe, Graduate Student Researcher and enable new discoveries. Hongwei Xie, Research Associate

Eric A. Hendrickson, Principal Investigator A Human Somatic Cell Model for Dyskeratosis Congenita: DNA Repair, Telomeres, and Genetic Stability his researcher is involved in two projects using human somatic cells that is probably related to its ability Supercomputing Institute laboratories. The first to regulate telomere length and genomic stability. This Tproject aims to understand the function of project includes experiments that elucidate the genetic human KARP-1 (Ku86 autoantigen related protein-1) as and molecular role(s) of Ku86 and KARP-1 in deoxyri- it relates to its role as a candidate gene for dyskeratosis bonucleic acid (DNA) double-strand break (DSB) repair, congenita (DC), a rare inherited disorder. Cells derived telomere length regulation, and genomic stability in from DC patients have short telomeres, reduced expres- human cells. The ultimate goal of this research is to use sion levels of human telomeric ribonucleic acid, reduced Ku86 and KARP-1 mutant cell lines as tools to under- activity of telomerase, genomic instability, and prolifera- stand the molecular mechanisms of DNA DSB repair in tive disfunction. The ultimate goal of these studies is to humans. use human somatic cell lines altered in their expression of KARP-1 to understand the molecular mechanisms of telomere disfunction. The goal of the second project is directed towards a somatic cell genetic analysis of the Ku86:KARP-1 locus in human cells. Ku86:KARP-1 plays an essential role in

2006 Annual Research Report of the Supercomputing Institute 85 UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Alan B. Hooper, Principal Investigator Biochemistry of Ammonia Monooxygenase of Nitrosomonas

nergy for growth of the bacterium Nitrosomonas cytochrome c544 (cytc554), which oxidizes hydroxy- europaea comes only from the oxidation of ammo- lamine and directs pairs of electrons into a membrane Enia to hydroxylamine and hydroxylamine to nitrite electron transport chain. The researchers also investigated by a monooxygenase and dehydrogenase, respectively. the tetra heme cytochrome cM 552 (cytcm552), which These researchers made significant progress in purifying, they believe is a cytc544-ubiquinone reductase, and to characterizing and determining the structure of redox ammonia monooxygenase. They used x-ray crystallogra- enzymes in the periplasm, including a remarkable 36 phy, electron paramagnetic spectroscopy, mass spectrom- heme complex of hydroxylamine oxidoreductase and etry, use of proteoliposomes, active site labeling, and other techniques of protein chemistry and enzymology.

Research Group Brad Elmore, Research Associate Hyung J. Kim, Research Associate

Christine B. Karim, Principal Investigator Modeling of Phosphorlamban Including Spin Labels

hospholambam (PLB) is a small membrane peptide that inhibits the Ca-ATPase in the heart muscle. PThis researcher used chemical synthesis and electronic paramagnetic resonance to probe the structural dynamics of PLB in lipid bilayers. She then synthesized derivatives of monomeric PLB, each of which contained a single spin-labeled TOAC amino acid providing direct insight into the conformational dynamics of the peptide backbone. The researcher used modeling resources at the Basic Sciences Computing Laboratory to clarify the experimental data on PLB.

86 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Romas Kazlauskas, Principal Investigator Catalytic Plasticity in Enzymes

nzymes evolve into new enzymes by acquiring new catalytic abilities. These researchers are mimicking Research Group and Collaborators Ethis process in the laboratory to create new Peter Bernhardt, Department of Organic Chemistry, enzymes for organic synthesis. They are using the Basic Massachusetts Institute of Technology, Cambridge, Sciences Computing Laboratory and the Computational Massachusetts Genetics Laboratory to perform molecular modeling and Kurt Faber, Institute of Organic Chemistry, University visualizations. of Graz, Graz, Austria Recent activity by this group includes modeling the Ryota Fujii, Research Associate Yun Jiang, Graduate Student Researcher enantioselectivity of subtilisin and attempting to identify Amina Clarisse Lobban, Graduate Student Researcher the origin of the catalytic plasticity of subtilisin for chiral Krista Morley, Department of Chemistry, McGill sulfur compounds. University, Montreal, Quebec, Canada Paul Mugford, Department of Chemistry, McGill University, Montreal, Quebec, Canada Krzysztof Okrasa, Research Associate Chris Savile, Graduate Student Researcher

Arkady Khodursky, Principal Investigator Exploring and Modeling Transcription Activity of the Escherichia coli Genome

esearch in the Khodursky group focuses on metabolism in bacteria and develops methodology for understanding the physical basis for higher-order highly parallel linkage mapping in one and three dimen- Rchromosomal organization in bacteria and the sions. effects of this organization on the transcriptional and replication activity of the genome. The group has been developing genomic experimental, computational, and Research Group analytical tools to study regulation of transcription in Kyeong Jeong, Graduate Student Researcher model microbes. They have designed and developed Betsy Martinez-Vaz, Research Associate microarray resources for laboratory and pathogenic Ninad Pendse, Graduate Student Researcher strains of Escherichia coli and the yeast Saccharomyces Lakshmi Naarayanan Ramakrishnan, Graduate Student cerevisiae. Current work is concentrating on defining spa- Researcher tial components in genome-wide transcriptional patterns Dipen Sangurdekar, Graduate Student Researcher and on their application to the dimensionality reduction Kyeong Soo, Graduate Student Researcher problem. The Khodursky group also investigates tran- Yang Xie, Graduate Student Researcher scriptional controls of antibiotic resistance and energy Zhigang Zhang, Graduate Student Researcher

2006 Annual Research Report of the Supercomputing Institute 87 UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

John D. Lipscomb, Principal Investigator Structure and Mechanism of Oxygenase Enzymes

xygenase enzymes use molecular oxygen to oxi- Research Group dize a wide range of biological and man-made Brian Brazeau, Graduate Student Researcher Ocompounds with the incorporation of one or John Broadwater, Research Associate both atoms of oxygen from molecular oxygen in the Sarmistha Chakrabarty, Graduate Student Researcher products. These researchers are using the Basic Sciences Alex Galaitsis, Graduate Student Researcher Computing Laboratory to study the crystal structure of Mary Gessel, Graduate Student Researcher some of these enzymes and to plan mutagenesis studies. Stephanie Groce, Graduate Student Researcher The first project studies a series of dioxygenase Elena G. Kovaleva, Research Associate enzymes. These enzymes interact with aromatic com- Aimin Liu, Research Associate pounds, which causes enormous amounts of carbon to Yasmina Mekmouche, Research Associate Matthew Neibergall, Graduate Student Researcher reenter the carbon cycle and also allows manmade aro- Codrina Popescu, Research Associate matics, some of which are carcinogens, to be degraded. Melanie Rogers, Research Associate In the second project, the researchers are investigating Michael Valley, Graduate Student Researcher another type of oxygenase that is typified by methane Matt Wolfe, Graduate Student Researcher monoxygenase. This enzyme catalyzes the oxidation of Jingyan Zhang, Research Associate methane to methanol with the incorporation of one Hui Zheng, Research Associate atom of oxygen. Methane is generated in large quantities in the environment and is a potent greenhouse gas.

David H. Live, Principal Investigator Structure and Dynamics of Mucin Glycoproteins

hese researchers are working to determine the tide components that aid in understanding the confor- structural and dynamic properties of mucin mational features displayed by mucins. A noteworthy Tmotifs. These motifs, characterized by regions of aspect of the nuclear magnetic resonance experiments highly O-glycosylated protein, can be found in secreted was strong evidence for a well-defined organization even mucin glycoproteins, in mucin domains of integral mem- for a short mucin segment based on a glycosylated pen- brane cell-surface glycoproteins, and as components of tapeptide STTAV from the cell surface protein CD43. the glycoprotein complexes in connective tissue. They The comparatively rigid conformation is important in can function both as purely structural elements and in understanding the physical properties related to mucin molecular recognition by virtue of their ability to display solutions, and in their ability to display locally high con- a variety of carbohydrate epitopes on the same protein centrations of carbohydrate epitopes in enhancing inter- core. These researchers have reported on the structure of actions with receptors. The generality of these structural a mucin glycopeptide that has offered new insights into principles is being examined in studying segments of gly- the intramolecular interactions between sugar and pep- cosylated MUC proteins, displayed aberrantly on cancer cells, and considered as targets for directing anti-cancer Research Group therapy, and to the central rigid mucin domain of alpha- Andrew Borgert, Graduate Student Researcher dystroglycan which is important in organizing components of the neuromuscular junction.

88 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Hiroshi Matsuo, Principal Investigator Structural Studies of Human DEK Protein

he mammalian protein DEK was first identified ular mechanism by which this C-terminal domain func- in patients with a subtype of acute myelogenous tions in the development of diseases. They are using Tleukemia. This 43-kDa nuclear protein has since Supercomputing Institute resources to analyze the NMR been implicated in several cellular pathways and associat- data and to calculate three-dimensional structures of pro- ed with a number of human neoplastic, neurodegenera- teins. tive, and autoimmune diseases. Biochemical data suggest the presence of a C-terminal functional domain, as this Research Group region can partially reverse abnormal genetic instabilities Kuan-ming Chen, Graduate Student Researcher of cells from ataxia telangiectasia patients and appears to Matthew H. Devany, Graduate Student Researcher confer antigenesity to anti-DEK antibodies in juvenile Aya Kitamura, Research Associate rheumatoid arthritis. These researchers use nuclear mag- Yongjan Lu, Research Associate netic resonance (NMR) spectroscopy to reveal the molec-

Kevin H. Mayo, Fellow Protein-Protein and Peptide-Peptide Interactions

n an earlier study, these investigators focused on three tides, calculating binding energies for those dimers and proteins from the CXC-chemokine family. The group tetramers, and determining the per residue contributions Ishowed that these proteins exchange subunits and into binding energy. They will then perform computa- form heterodimers. They confirmed that heterodimers tional mutations for alanine and determine their effect are energetically stable. The residues that contribute to on the binding energy contributions from mutated heterodimerization or against it were determined from residues. calculations of binding energies and per residue contributions to binding energy. The researchers have now applied the same methodology to study several peptides that were designed based on Research Group studied chemokine sequences. These peptides form beta- Monica M. Arroyo, Graduate Student Researcher sheets in solution, and associate into dimers and Ruud Dings, Research Associate tetramers. Importantly, they exhibit anti-angiogenic Mark A. Klein, Graduate Student Researcher activity and therefore can potentially be used for cancer Nathan Lockwood, Graduate Student Researcher treatments. The group is collecting several trajectories for Irina Nesmelova, Research Associate each of the dimers and tetramers for three different pep-

2006 Annual Research Report of the Supercomputing Institute 89 UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Gary L. Nelsestuen, Principal Investigator Biomarker Study for Lung Transplant Chronic Rejection Using Bronchoalvelar Lavage Fluid hronic rejection (bronchiolitis obliterans syn- duct the research and have found that human neutral- drome, BOS) is the major cause of low survivor phile peptide and clara cell protein showed significantly Crate of lung transplant. So far, there is no method different expression levels in BOS and pre-BOS samples. for early prediction of the occurrence of chronic rejec- The different expression of matrix metalloproteinases-9 tion. These researchers are studying the proteme of bron- may give an insight into the mechanism of the disease. choalvelar lavage fluid to find a protein biomarker for diagnosis and early prediction of the disease. They are combining proteomics and bioinformatics tools to con-

Research Group Joshua T. Wilson-Grady, Staff Yan Zhang, Graduate Student Researcher

Douglas H. Ohlendorf, Fellow Structural Analysis of Macromolecules

he goal of these studies is to understand the Research Group structural basis of how macromolecules function. Mohammed Badasso, Research Associate TThe current focus is on two groups of proteins: C. Kent Brown, Graduate Student Researcher dixoygenases that use metal ions to cleave aromatic rings Jeffrey Digre, Staff and proteins from gram-positive pathogens. Examples of Cathleen A. Earhart, Research Associate dioxygenases are protocatechuate 3,4-dioxygenase Amanda Harrison, Undergraduate Student Researcher (PCD), homoprotocatechuate 2,3-dioxygenase (HPCD), Rebecca Hoeft, Graduate Student Researcher and 1,2-catechol dioxygenase (CTD). Examples of pro- Medora Huseby, Undergraduate Student Researcher teins from gram-positive pathogens are pyrogenic toxin Oana Lungu, Undergraduate Student Researcher Fikre Mengistu, Undergraduate Student Researcher superantigens, exfoliative toxins, streptococcal C5a pro- Gosu Ramachandriah, Research Associate tease, and aggregation substance and the pheromone Ke Shi, Research Associate response protein prgX from Enterococcus faecalis. Patrick Trogdon, Undergraduate Student Researcher The researchers are refining structures of substrate and inhibitor complexes of mutants of PCD, HPCD, and CTD, and are solving and refining the structures of several proteins from pathogens.

90 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Claudia Schmidt-Dannert, Principal Investigator Substrate-Docking Modeling of Linear Substrates in Polyketide Synthase Thioesterase Binding Packets ome of the most important antibiotics and other and these researchers are using these to dock various medicinally relevant compounds are known to be structures into their catalytic sites to obtain information Sbiosynthesized in bacteria by the actions of giant for future site-directed mutagenesis studies. The results catalytic protein complexes known as polyketide synthas- will also be used to support, explain, or refute experi- es (PKS). To better understand the mechanisms involved mentally determined hydrolysis and cyclization results in cyclization of natural and non-natural linear precur- using the same precursor molecules. sors in PK systems, this project focuses on modeling the docking of various substrates in the known binding Research Group pocket of the terminal enzyme domain known as the Christine Salomon, Research Associate thioesterase (TE). Crystal structures have been published for the 6-deoxyerythronolide and the pikromycin TEs

2006 Annual Research Report of the Supercomputing Institute 91 UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

David D. Thomas, Fellow Molecular Dynamics of Muscle Proteins

he goal of this research is to understand the membrane ion pumps and channels as they excite and molecular dynamics associated with force-gener- relax muscle. To test and refine structural models of con- Tating proteins during muscle contraction and formational transitions in muscle proteins, these researchers use site-directed spectroscopic probes to detect biologically relevant motions. This work is clearly Research Group and Collaborators dependent upon choosing appropriate labeling sites and Mike Autry, Research Associate accurately interpreting spectroscopic data. The Vincent Barnett, Faculty Collaborator researchers use molecular dynamics simulations of spin- Sarah Blakely, Graduate Student Researcher labeled proteins to accurately predict the shape of elec- Adam R. Burr, Supercomputing Institute tron paramagnetic resonance (EPR) spectra before they Undergraduate Intern do their experiments. They can thus design more effec- Michael J. Enz, Undergraduate Student Researcher tive labeling site for measuring distances and dynamics. Lennane Michel Espinoza-Fonseca, Graduate Student Direct simulation of EPR spectra enables the researchers Researcher Yao Fan, Graduate Student Researcher to interpret ambiguous data. By using molecular dynam- Nicole Flohr, Undergraduate Student Researcher ics simulations, they can model structural transitions that Edmund Howard, Graduate Student Researcher occur in response to events such as phosphorylation of Henry Jakubowski, Department of Chemistry, College muscle regulatory regions or in protein binding. of St. Benedict/St. John’s University, St. Joseph, Minnesota David J. E. Kast, Graduate Student Researcher Jennifer Klein, Graduate Student Researcher Alexey Konovalov, Research Associate Vicci Korman, Research Associate Eric Lantz, Undergraduate Student Researcher Jennifer Levine, Graduate Student Researcher Dawn Lowe, Faculty Collaborator Alan Lueke, Graduate Student Researcher John J. Matta, Research Associate Yuri Nesmelov, Research Associate Irina Nesmelova, Research Associate Valentin Novikov, Research Associate Nicolas Ortiz, Graduate Student Researcher Beverly G. Ostrowski, Research Associate Germana Paterlini, Certusoft, Minneapolis, Minnesota Ewa Prochniewicz-Nakayama, Research Associate Seth Robia, Research Associate Osha Roopnarine, Faculty Collaborator Wendy Smith, Research Associate Terry Steele, Graduate Student Researcher Jack T. Surek, Graduate Student Researcher Mohac Tekmen, Graduate Student Researcher Kurt Torgersen, Staff Nicolas Ward, Undergraduate Student Researcher Deb Winters, Research Associate Jamillah Zamoon, Graduate Student Researcher

92 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Howard C. Towle, Principal Investigator Nutritional and Hormonal Control of Hepatic Gene Expression

his project is aimed at understanding how the heterodimer partner Mlx when complexed with DNA. transcription factor ChREBP regulates hepatic These studies are aided by molecular modeling of struc- Tgenes in response to changes in glucose. This tures based on previous work on other family members. transcription factor has recently been identified as a key component in regulating the transcription of ligogenic enzyme genes in liver. Little is known regarding its domain of action, however; for example, what pathways does it affect positively or negatively? These researchers are using deoxyribonucleic acid (DNA) microarrays to assess the affect of inhibiting ChREBP in primary cul- Research Group tured hepatocytes. They are using resources of the Basic Lin Ma, Graduate Student Researcher Sciences Computing Laboratory and the Computational Brennon O’Callaghan, Staff Genetics Laboratory to perform their analyses. They also Nicolas Tsatsos, Graduate Student Researcher are trying to determine the structure of ChREBP and its

Lawrence P. Wackett, Principal Investigator Identification of Novel Metabolism and Biocatalysis

his project is focused on identifying novel metab- as a starting point for comparative genome analysis with olism and biocatalytic reactions through a combi- the sequenced genomes of a similar organism. Using this Tnation of computational and experimental tech- methodology, gene targets for the novel metabolism can niques. The Wackett laboratory has developed two be identified and cloned, and the clones tested for func- approaches to identifying novel biocatalysis. The first tionality and whether they are responsible for the novel involves experimentally identifying genes involved in metabolism. novel metabolism, then analyzing the sequence of these genes computationally, using such resources as genome analysis, phylogenetic analysis, and protein scheduling. These techniques allow for determining how widespread the gene is and what ancestral links the gene may share, and may give insights into the potential catalytic mecha- Research Group nisms or mechanism of action of the gene product. Jeff Osborne, Research Associate The second method is based upon mining informa- Dave Roe, Graduate Student Researcher tion from the available genomes. Experimental identifica- Jennifer Seffernick, Research Associate tion of an organism with a novel metabolism can be used

2006 Annual Research Report of the Supercomputing Institute 93 UM TC–Department of Biochemistry, Molecular Biology, and Biophysics

Kylie J. Walters, Associate Fellow Studying the Ubiquitin Proteasome Pathway by Nuclear Magnetic Resonance Spectroscopy hese researchers study how the ubiquitin-protea- hHR23a and S5a. To determine how ubiquitin and its some pathway targets protein substrates for chains are recognized in cells these researchers have Tdegradation. Central to this process are the ubiq- solved the structures of hHR23a and S5a alone as well as uitin recognition family of proteins, which include complexed with ubiquitin. Current studies focus on the mechanisms used by cells to determine the outcome of ubiquitylation and how ubiquitin recognition proteins Research Group collaborate towards this agenda. An additional project Roger Chen, Undergraduate Student Researcher focuses on how substrate proteins are identified in cells Xiang Chen, Research Associate and why this process sometimes goes awry. Matt DeLoia, Graduate Student Researcher Yang Kang, Graduate Student Researcher Casey Litchke, Undergraduate Student Researcher Fen Liu, Graduate Student Researcher Rebecca Vossler, Undergraduate Student Researcher Qinghua Wang, Research Associate Naixia Zhang, Research Associate

Carrie M. Wilmot, Principal Investigator X-ray Crystallographic Studies of Reaction Intermediates in Proteins Containing Organic or Metal Co-Factors his research focuses on the dynamics of molecular assembled into “movies of catalysis” at the molecular catalysis, particularly involving novel co-factors level. By understanding these reactions in such detail, Tand metal ions. The principal tool of the research better drugs can be designed, proteins can be rationally is macromolecular x-ray crystallography. The project engineered for biotechnological purposes, and chemists involves freeze trapping catalytic intermediates in the can design simpler industrial catalysts to control analo- crystal, both anaerobically and aerobically, leading to gous reactions. Specific topics of interest to this group “snapshots” along the reaction pathways. These can be include structural enzymology involving the co-factor tryptophan tryptophylquinone of methylamine dehydrogenase, dioxygen activation by the copper-containing Research Group amine oxidase from yeast, and enzymes involved in nitri- Sean Agger, Graduate Student Researcher fication by Nitrosomona europea. Teresa de la Mora, Graduate Student Researcher Ed Hoeffner, Staff Bryan Johnson, Graduate Student Researcher Arwen Pearson, Research Associate Kevin Watts, Graduate Student Researcher

94 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Genetics, Cell Biology, and Development

Judith G. Berman, Principal Investigator Microarray Analysis of Candida albicans

his group studies the human pathogenic fungus changing patterns, are also being compared in a set of 11 Candida albicans. They built and now use whole- yeast species that span the evolutionary distance between Tgenome microarrays in several different ways. these two yeasts. They use messenger ribonucleic acid (mRNA) to analyze the transcription profiles of mutant strains and of wild- Research Group and Collaborator type strains grown under different conditions. A current Anne Bantel, Undergraduate Student Researcher effort is to define the constellation of cell cycle-regulated Jessica Bell, Graduate Student Researcher genes in wild-type and mutant cells. They also analyze Eric Bensen, Research Associate the deoxyribonucleic acid (DNA) content of clinical and Kelly Bouchonville, Graduate Student Researcher laboratory strains that have undergone genome changes Michelle Carlson, Graduate Student Researcher using comparative genome hybridization (CGH). CGH Justin Fendos, Undergraduate Student Researcher has revealed a number of chromosome number changes Ken Finley, Graduate Student Researcher (aneuploidies) in laboratory strains that have undergone Anja Forche, Research Associate Cheryl Gale, Faculty Collaborator molecular manipulations. In addition, they are now Merima Helic, Undergraduate Student Researcher focusing on aneuploidies associated with the acquisition Preeti Joshi, Graduate Student Researcher of resistance to commonly used anti-fungal drugs. The Carrie Ketel, Research Associate group is also performing global transcription array analy- Mark McClellan, Staff sis, in collaboration with the group of Naama Barkai at Shona Mookerjee, Research Associate the Weizmann Institute of Science. This work has identi- Maryam Nejad, Staff fied differences in the sub-patterns of gene regulation Aaron Quick, Undergraduate Student Researcher between C. albicans and its distant relative, the model Anna Selmecki, Graduate Student Researcher yeast Saccharomyces cerevisiae. The global patterns identi- Helen Wang, Graduate Student Researcher fied, as well as DNA sequence motifs associated with the Nicole Waxmonsky, Graduate Student Researcher

Duncan J. Clarke, Principal Investigator Analysis of Yeast Cell Cycle Control

he goal of this group’s research is to understand yeast combined with more modern approaches that rely mechanisms that cause genome instability. In on access to databases such as genome sequence and pro- Thumans, genome instability contributes to the teome databases. incidence of birth defects and spontaneous abortion, and is a key factor in the etiology of cancer. More specifically, the group works on cell cycle checkpoint controls, sister chromatid cohesion, chromosome dynamics, and ubiquitin-dependent proteolysis. These related areas are critical for the maintenance of a stable genome. The researchers Research Group uses yeast as a model system to rapidly discover new con- Catherine Andrews, Research Associate cepts that can then be translated to the human system. Amit Vas, Research Associate They use genetic approaches traditionally used to study

2006 Annual Research Report of the Supercomputing Institute 95 UM TC–Department of Genetics, Cell Biology, and Development

Kathleen F. Conklin, Principal Investigator Identification and Characterization of a Novel Human Gene

hese researchers are working on a novel gene identified in humans called NOM1. They are Tstudying its homologs in other species and are trying to identify the cellular pathways and processes in which it participates. The researchers are using resources available at the Computational Genetics Laboratory and the Scientific Development and Visualization Laboratory for this work.

Research Group Christine Munster, Graduate Student Researcher Brian Ruis, Staff

Sean D. Conner, Principal Investigator The Role of Phosphorylation in Clathrin-Mediated Endocytosis

lathrin-mediated endocytosis is fundamental to a Phosphorylation plays a critical role in clathrin and diverse range of biological processes. For exam- AP2 function. Endocytosis is disrupted if AP2 and/or Cple, clathrin-coated vesicles mediate the clearance clathrin phosphorylation cycles are altered. While phos- of receptor-bound growth factors from the plasma mem- phorylation is clearly important, the mechanistic impact brane, are essential for nutrient uptake, and participate in on coat protein function is ill-defined. The goal of these the recycling of synaptic vesicles in neurons. Myriad pro- researchers is to define the role of phosphorylation in teins have been functionally implicated in this ubiquitous endocytosis by dissecting the functional consequence of internalization pathway; however, two oligomeric protein specific coat protein phosphorylation events and by complexes constitute the major coat proteins: clathrin understanding the mechanisms that regulate their respec- and AP2. tive kinases.

Research Group Davin Henderson, Research Associate Erika Sorensen, Graduate Student Researcher

96 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Genetics, Cell Biology, and Development

Stephen C. Ekker, Principal Investigator Microarray Analysis of Zebrafish Models

hese researchers use the zebrafish as a model vertebrate system. Using a technology developed at TThomas Jefferson University, they created microarrays with enhanced signal:noise hybridization signals. This significantly enhanced the value of the Research Group microarray comparisons. The bottleneck with these Eleanor Chen, Research Associate arrays was the downstream annotation, and the Suzanne Grindle, Research Associate researchers established an annotation pipeline. This proj- Mara Robu, Research Associate ect used resources at the Computational Genetics Laboratory.

David P. Fan, Principal Investigator Effects of Persuasive Information on Public Opinions and Behaviors

his project studies mathematical modeling and statistical analysis of the impact of persuasive Tinformation on public opinions and behaviors. The project compares different models for information impact traceable to various factors, such as biological infection and toxicology. The researcher is using resources at the Computational Genetics Laboratory.

2006 Annual Research Report of the Supercomputing Institute 97 UM TC–Department of Genetics, Cell Biology, and Development

Thomas S. Hays, Principal Investigator Structure and Function of Cytoplasmic Dynein

hese researchers are elucidating the function of the subunits and how each subunit contributes to the cytoplasmic dynein in cell and developmental specification of function. The group is trying to under- Tfunctions. The first goal is to dissect the subunit stand the molecular basis for the multiplicity of dynein structure using molecular genetic tools and analyze the function. cytological, developmental, and biochemical phenotypes Another goal of this research is to identify how the of mutations in dynein. They have cloned and isolated dynein acts in mitosis to ensure proper spindle assembly mutations in the heavy, intermediate, and light chain and chromosome movements. A final goal is to use subunits and are determining the functional domains of genetic modifier screens to elucidate dynein function and regulation in development by the identification of interacting components. The group is pursuing genetic inter- Research Group actions that may elucidate a role for dynein mediated Mingang Li, Graduate Student Researcher vesicular trafficking in signal transduction mechanisms Lingzhi Ma, Staff that are developmentally significant. Sarah Mische, Graduate Student Researcher Rukmini Reddy, Staff Madeline Serr, Staff

David A. Largaespada, Principal Investigator Microarray Analysis of Myeloid Leukemia

hese researchers are performing microarray analyses on acute myeloid leukemia (AML) samples Tfrom mice. AML samples with specific gene mutations are compared to controls without these mutations. In addition, the researchers are comparing parental AML samples with subclones derived by selection for resistance to chemotherapeutic drugs. The group is using the Computational Genetics Laboratory for this project.

Research Group Suzanne Grindle, Research Associate Diane Hasz, Research Associate Kelly Morgan, Undergraduate Student Researcher Kevin Roberg-Perez, Research Associate Michaela Long Tsai, Graduate Student Researcher

98 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Genetics, Cell Biology, and Development

Michael B. O’Connor, Principal Investigator Modeling of Aspects of Drosophila Development

hese researchers are involved in two research proj- The second project attempts to elucidate how the ects involving Drosophila. The first investigates Halloween-group gene shroud mediates response to the Tthe molecular basis for co-substrate dependence insect steroid hormone ecdysone during morphogenesis of Sog processing. BMP signaling is modulated in of the Drosophila embryo. This hormone regulates a wide Drosophila by Sog, a BMP antagonist that is proteolyti- variety of developmental events in insects. cally degraded by tolloids. Unlike its vertebrate counterpart, Chordin, Sog requires BMP ligands as obligatory co-substrates for its processing. This BMP-dependence allows Sog to elicit a short-range inhibitory effect as well as a long-range positive effect onto BMP signaling. Chordin only exhibits a short-range inhibitory effect. By comparing how the processing sites of Sog and Chordin Research Group fit into the catalytic pocket of the enzymes, the Robinette Aley, Staff researchers are beginning to understand the molecular Hajime Ono, Research Associate basis of the co-substrate requirements for Sog, a trend Mihaela Serpe, Research Associate evolutionarily conserved in insects.

Laura P. W. Ranum, Principal Investigator Genetic Mapping of a Novel Familial ALS Gene

n a simple autosomal dominant family, the goal of tion to understanding ALS, an equally important goal of linage analysis and a genome screen is to identify this project is to develop and validate the proposed hap- Iregions of the genome that are shared among affected lotype genome screening strategy as a novel method to individuals in the family. To enhance the power of the enhance the power of genetic mapping studies for other amyotrophic lateral sclerosis (ALS)-A family for informa- diseases. tive linkage analysis, these researchers have generated a panel of haploid cells lines for all available affected family members and other key individuals in the pedigree. This genome-wide panel of haploid cell lines generated over the past two and one-half years now allows the researchers to directly establish and compare haplotypes for entire chromosomes among affected individuals. The results of this method allow the researchers to directly Research Group identify regions that are shared by all affected family Joline Dalton, Staff members and are thus candidates regions for the ALS-A Katherine Dick, Graduate Student Researcher gene, as well as regions that are clearly excluded. In addi-

2006 Annual Research Report of the Supercomputing Institute 99 UM TC–Department of Genetics, Cell Biology, and Development

Ann E. Rougvie, Principal Investigator Understanding Cellular Timekeeping

ork in the Rougvie laboratory seeks to under- the transition from the larval to adult form. The stand how cells execute specific events at pre- approach is to identify mutations that cause this event to Wcise times during development. To under- occur at the wrong time during development, and then stand how a cellular timekeeper works, the researchers to study the genes defined by these mutations. These studied a developmentally simple organism, the nema- genes are referred to as “heterochronic” genes because tode Caenorhabditis elegans. Specifically, they dissected their mutation alters the relative timing and sequence of the timing mechanism that restricts the differentiation of many developmental events in the animal. hypodermal cells to a time late in the life of the worm, The long-term goal of this research is to determine how developmental timing mechanisms are integrated with the spatial and sexual cues required for proper Research Group development of a multi-cellular organism. Aric Daul, Research Associate Masamitsu Fukuyama, Research Associate Ming Li, Graduate Student Researcher Jason Tenneson, Graduate Student Researcher

Brian G. Van Ness, Principal Investigator Gene Expression Profiling of a Myeloma Cell Line; Single Nucleotide Polymorphism Genotyping hese researchers are involved in two projects both soluble factors and cell contacts in the bone marrow using the Computational Genetics Laboratory. In microenvironment. Tthe first, they are performing gene profiling of a The second project supports an Academic Health myeloma cell line, which has revealed similarities and Center single nucleotide polymorphism (SNP) genotyp- unique signatures among IL-6 response, N-ras-activating ing effort, coordinated through faculty in different mutations, and coculture with bone marrow stromal departments. They have constructed a common custom cells. The researchers have demonstrated gene expression SNP chip that represents validated genetic variations in patterns in myeloma cells that distinguish an intrinsic 45 cellular pathways and 53 functional cellular processes genetic transformation event and patterns derived from that will be associated with population risk and outcomes as described in each program of the participating faculty. Using a common platform and SNP chip will provide Research Group significant opportunities for developing common techni- Kristin Boylan, Research Associate cal and analytical approaches as well as data comparisons. Paula Croonquist, Graduate Student Researcher Christine Ramos, Staff

100 2006 Annual Research Report of the Supercomputing Institute UM TC–Institute of Child Development

Byron R. Egeland, Principal Investigator Minnesota Longitudinal Study of Parents and Children

hese researchers are conducting a longitudinal The group used the software application S-Plus at the study, which began in 1975, of high-risk children Scientific Development and Visualization Laboratory, Tand their families. The assessments, which were which allowed them to analyze the data by methods that detailed and comprehensive, began before the birth of are not available in ordinary statistical software packages. the first child and continued at regular intervals until the children reached age 26. Originally, the researchers were interested in predicting good and poor parenting and parent-child relationship outcomes in the high-risk sample with a particular interest in understanding the causes and consequences of child maltreatment. The current aims include determining the antecedents and developmental pathways leading to competence and maladapta- tion in childhood, adolescence, and young adulthood. This includes studying school drop-outs, drug and alco- Research Group Michael F. Lorber, Research Associate hol abuse, adolescent depression, conduct disorder, and other forms of psychopathology as well as resilience.

UM TC–Department of Economics

Zvi Eckstein, Principal Investigator Estimation of Discrete Stochastic Dynamic Programming Models of Economic Behavior hese researchers have been involved in two projects concerning with models of economic behav- Tior. The goal of the first project was to develop new methods to solve and estimate discrete stochastic dynamic programming (DS-DP) models, and to use these to study decision-making in areas such as human capital investment, occupational choice, and investment in health. The researchers investigated the use of simulation methods on three problems: a model of life cycle Research Group and Collaborator decisions of young women, a model of the childcare use Abby R. Barker, Graduate Student Researcher and return-to-work decision of working women after Suqin Ge, Graduate Student Researcher childbirth, and a model of the impact of education on Michael P. Keane, Department of Economics, Yale marriage market opportunities for women. University, New Haven, Connecticut A second research area, begun this year, concerns the Ahmed Khwaja, Graduate Student Researcher impact of compliance with the minimum wage law on Eric Olson, Graduate Student Researcher wages, unemployment, and labor mobility.

2006 Annual Research Report of the Supercomputing Institute 101 UM TC–Department of Economics

Andrea Moro, Principal Investigator Structural Estimation of Political Economy Models

his project investigated two political economy ent theoretical models of voter turnout in order to test questions that have a crucial impact on electoral which theory performs best against the data. Tdesign. In the first project, the researcher empiri- The second project applied structural methods to cally estimated what affects voter turnout. This question empirically discover the reasons why incumbents in the has received considerable theoretical attention, but there United States Congress are re-elected disproportionately have been difficulties in testing the implications of differ- often. This research can provide insight about the effects ent theories using a reduced-form framework. This of changes in electoral design such as the length of con- approach estimated structurally the parameters of differ- gressional terms or the introduction of term limits.

Research Group Wen-Chi Liao, Graduate Student Researcher

UM TC–Department of Geography

Eric S. Sheppard, Principal Investigator Regional Economic Dynamics Modeling Spatio-Temporal Complexity

hese researchers seek to analyze spatio-temporal nal conditions. Methods to categorize their general systems that are neither close to equilibrium nor behavior and to evaluate their empirical plausibility in Tcan be described simply in terms of their behav- the presence of limited data have only emerged in mathe- ior with respect to a particular fixed point. Such complex matics and economics in the last decade. The applicabili- non-linear system may be frequently far from equilibri- ty of these to the analysis of discrete spatio-temporal sys- um, may exhibit irreversible and path-dependent behav- tems has been little explored, however. ior, and may have dynamical trajectories that are highly The group is using Supercomputing Institute sensitive to small changes in parameter values and exter- resources for four projects: exploring the dynamics of a multi-regional economic simulation, characterizing the dynamics across parameter space; modeling the nonlinear Research Group and Collaborator dyanmics of Plummer-Goodwin multi-regional coupled Luke Bergmann, Graduate Student Researcher macroeconomic systems; developing a model to simulate Paul S. Plummer, School of Geographical Sciences, the out-of-equilibrium dynamics of an alternative theo- Bristol University, Bristol, England, United retical model of multi-regional economics in the political Kingdom economy tradition; and extending symbolic dynamics techniques to mutli-regional timeseries.

102 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Sociology

John Robert Warren, Principal Investigator An Investigation of the Cumulative Effects of Job Characteristics on Health

hese researchers examined whether health out- membership for each observation is identified, the comes in late life are associated with the trajecto- researchers will implement multivariate regressions to Try of physical and psychosocial job characteristics study the associations between health and trajectory job by using data from the Wisconsin Longitudinal Study. characteristics. They used optimal matching analysis and cluster analysis to classify over 8,300 individual trajectories of job characteristics, separately for physical and psychosocial char- Research Group acteristics, across 105 time spells. After trajectory group Reiping Huang, Graduate Student Researcher

UM TC–Department of Bio-based Products

Shri Ramaswamy, Associate Fellow Visualization and Characterization of Three-Dimensional Bulk Structure of Porous Materials his research attempts to visualize and characterize multi-phase diffusion through the pore and fiber spaces the three-dimensional bulk structure of porous in the media. In addition, this group has developed a Tmaterials including paper and board using non- model to simulate the physics of simultaneous perme- intrusive techniques. Recent work has explored the use of ation and absorption of liquid in porous media. The x-ray micro-computed tomography to visualize the struc- results indicate that, in additional to inherent absorption ture of porous materials. These images are filtered to characteristics of cellulose fibers, the rate of permeation improve their clarity using techniques such as “anisotrop- through the pore space has a strong influence on the ic diffusion” to sharpen the image as well as to obtain overall absorption by porous media. better characterizations of the structure, binarized, and then analyzed for pore structure characterization. Research Group and Collaborator Structural parameters of interest include pore size distri- Richard Cairncross, Department of Chemical bution, average pore diameter, porosity distribution and Engineering, Drexel University, Philadelphia, average porosity, tortuosity, available transfer surface area, Pennsylvania and fiber-fiber bonded area. Recent work in this area Yves Defrenne, Graduate Student Researcher includes three-dimensional characterization of the struc- Huajiang Huang, Research Associate ture using a “sphere growing” algorithm to accurately Goo Lee, Graduate Student Researcher characterize the three-dimensional nature of the pores. Amod Modak, Graduate Student Researcher Using the actual three-dimensional structure, the group Jesil Pujara, Graduate Student Researcher has also developed techniques, in cooperation with their Matt Ryan, Graduate Student Researcher Jiehai Zhang, Research Associate collaborators, to predict transport properties such as per- Vasili Zhdankin, Graduate Student Researcher meability, diffusivity etc. The anisotropic diffusivity char- Huigang Zuo, Graduate Student Researcher acteristics also include consideration of the simultaneous

2006 Annual Research Report of the Supercomputing Institute 103 UM TC–Department of Bio-based Products

Simo Sarkanen, Principal Investigator Macromolecular Lignin Replication

ignin, the second most abundant biopolymer after direct template polymerization mechanism governed by cellulose, contributes prominently to cell-wall noncovalent interactions between corresponding aromat- Larchitecture in all vascular plants and trees. The ic residues in the putative daughter and parent chains. configuration of macromolecular lignin chains is determined by the sequences of inter-unit linkages between the monomer residues. This project investigates the possibility that lignin primary structure is controlled by a

Research Group Yi-ru Chen, Research Associate

UM TC–College of Pharmacy

William F. Elmquist, Principal Investigator Improving the CNS Delivery of Anti-Retroviral Compounds

uman immunodeficiency virus (HIV-1) renders been hampered by the fact that nucleoside drugs do not the host susceptible to a variety of serious cen- penetrate the blood-brain barrier (BBB) well and newer Htral nervous system (CNS) diseases such as treatments, i.e., protease inhibitors, also have very limit- Acquired Immunodeficiency Disease (AIDS) dementia ed delivery to the brain. complex and HIV-1 encephalopathy. The use of highly One component of the BBB that limits delivery of active antiretroviral therapy (HAART), including pro- HAART into the CNS is the membrane-bound drug tease inhibitors, has been effective in slowing the spread efflux pumps, such as p-glycoprotein (P-gp) and mul- of the virus, but drug-resistant tissue reservoirs, such as tidrug resistance-associated proteins. It appears that both the brain, remain. Treatment of HIV-1 in the brain has nucleosides and protease inhibitors are substrates for efflux transporters. The long-term objective of this Research Group research is to develop therapeutic strategies to enhance Ying Chen, Graduate Student Researcher the targeted delivery of antiretroviral drugs to the CNS Nagdeep Giri, Graduate Student Researcher by using novel drug delivery systems, such as polymeric Li Li, Graduate Student Researcher carriers. The hypothesis is that novel drug delivery sys- Guoyu Pan, Research Associate tems will enhance the brain distribution and CNS target- Naveed Shaik, Graduate Student Researcher ing of HAART and therefore improve efficacy.

104 2006 Annual Research Report of the Supercomputing Institute UM TC–College of Pharmacy

Daniel M. Kroll, Principal Investigator Mesoscale Simulations of the Statics and Dynamics of Complex Fluids

article-based simulation techniques have recently transport in complex geometries, and the dynamics and emerged as an attractive alternative to more tradi- rheology of complex liquids, including polymer solu- Ptional methods for studying phenomena as diverse tions, binary and tertiary mixtures, and biological macro- as rarefied gas dynamics and the dynamics and rheology molecules in solution. of soft materials such as polymer solutions and melts, biological macromolecules, colloids, and amphiphilic mixtures and membranes. The unique problems associated with the modeling and analysis of these systems has lead to the development of new coarse-grained simulation techniques that mimic the behavior of atomistic systems on the length scales of interest. Research Group and Collaborator This group’s research involves the development and Thomas Ihle, Department of Physics, North Dakota implementation of advanced simulation techniques for State University, Fargo, North Dakota studying this class of problems. Specifically, the group is Ravi Nandigam, Graduate Student Researcher developing and applying a new particle-based simulation Erkan Tuzel, Graduate Student Researcher technique for studying rarefied gas dynamics, flow and

UM TC–Department of Experimental and Clinical Pharmacology

Marnie L. Peterson, Principal Investigator Characterization of the Global Response of Vaginal Epithelial Cells to Infection

hese researchers are exposing an immortalized vaginal epithelial cell line to various infectious Tagents, including Staphylococcus aureus and its Research Group Toxic shock toxin-1. Following exposures, they will Christina Fair, Graduate Student Researcher obtain and process the total ribonucleic acid for Matthew Schaefers, Staff hybridization to an Affymetrix human genome microar- Dana Simonson, Graduate Student Researcher ray chip. They are using software at the Computational Genetics Laboratory to analyze the data.

2006 Annual Research Report of the Supercomputing Institute 105 UM TC–Department of Experimental and Clinical Pharmacology

John St. Peter, Principal Investigator Gene Expression Profiling in an Animal Model of Obesity and Insulin Resistance After Exposure to Various Nuclear Receptor Agonists and Antagonists nsulin resistance is a major factor in the development mechanisms related to emerging therapies for insulin of type 2 diabetes and is commonly noted in those resistance. The findings will also provide data for com- Iwith obesity. Recent pharmacologic therapy has been parison with future pharmacologic agents and may guide developed that directly improves the insulin-resistant the design of future studies. state via stimulation of the peroxisome proliferator-activated receptor (PPAR) system. Currently, there are two PPAR agonists, pioglitazone and rosiglitazone, that are marketed for human use based upon their blood-glucose lowering effect. These drugs have additional significant effects on lipid profile, fibrinolysis, and markers of the inflammatory state, but their effects differ from each other and the mechanisms related to these differences and to other changes are unknown. This researcher is using gene expression profiling to investigate potential mechanisms underlying the effects of these drugs. The results may provide insight into

Robert J. Straka, Principal Investigator Discordance Between N-acetyltransferase 2 Phenotype and Genotype in Hmong Subjects olymorphisms of N-acetyltransferase 2 (NAT-2) concordance between genotype and phenotype in a acetylation have relevance to drug toxicities and Hmong population in Minnesota. Pefficacy with a differential susceptibility to select The researchers have confirmed the predominance of cancers. Evidence of a phenotypic predominance of slow the NAT-2 SA phenotype, but there appears to be a lack acetylation phenotype in an ethnically distinct popula- of correlation between genotype and phenotype for tion may therefore have clinical implications for the indi- NAT-2. The predominance of SA phenotype determined vidualization and optimization of drub use as well as by a metabolic probe would not have been predicted by clinical epidemiological relevance pertaining to cancer knowledge of genotype along, which raises questions risk in this population. The purpose of this study is to about dietary, environmental, or physiological influences determine the genetic basis of an apparent predominance on metabolic activity. of a slow acetylator (SA) phenotype and to assess the

Research Group R. Todd Burkhardt, Research Associate

106 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Experimental and Clinical Pharmacology

Tim Tracy, Principal Investigator Substrate/Inhibitor Binding Modes of Cytochromes P450

he hepatic human cytochromes P450 are affinity and activator drug pharmacophores, but it was involved in the oxidative metabolism of xenobi- not clear which distinct sites in the enzyme these models Totics such as drugs. For these enzymes, substrate describe. Recently, they have identified protein-ligand specificity is broad and often difficult to predict. Yet interactions that allow the degree of in vitro activation of understanding specificity is important in designing better substrate metabolism to be predicted in silico. The same drugs because P450s affect the rate of drug clearance. models have also shown potential in the screening of vir- Therefore, P450 metabolism helps determine drug tual compound libraries, which could be used to discover dosage. Also possible is the competition or non-mutually highly specific inhibitors and activators of P450s for clin- exclusive binding of more than one drug for the same ical use. P450 isoform, resulting in lower or higher than usual clearance, respectively. Research Group and Collaborator These researchers are employing computational mod- Vikas Kumar, Graduate Student Researcher els that will quickly screen drugs for their ability to acti- Charles Locuson, Research Associate vate the metabolism of another drug. They have previ- Hiroshi Matsuo, Faculty Collaborator ously developed Three-Dimensional Quantitative Lian Wei, Graduate Student Researcher Structure Activity Relationship models to describe drug

UM TC–Department of Medicinal Chemistry

S. Mbua Ngale Efange, Principal Investigator Development of Pharmacological Agents for Studying Central Cholinergic Function

cetylcholine released from central, sympathetic, focus was to develop pharmacological agents and radioli- and peripheral neurons is involved in a wide gands that are directed at the nAChR and VACht. In Arange of biological functions. Cholinergic dys- addition, the researcher was interested in the develop- function has been implicated in a number of pathologic ment of new medications for the treatment of cocaine states, including Alzheimer’s disease, olivopontocerebellar and other psychostimulant dependence. These investiga- atrophy, and Parkinson’s disease, among others. tions involved the design, synthesis, radiolabeling, and Conversely, modulation of cholinergic function has been biological evaluation of new molecular entities, thus pro- found to have beneficial effects in a number of patholo- viding exposure to a broad spectrum of drug develop- gies. Such modulation may be effected through one or ment activities. more of the following molecular targets: sodium-dependent high affinity choline transporter, choline acetyltransferase, muscarinic acetylcholine receptors, nicotinic acetylcholine receptors (nAChR), the vesicular acetylcholine transporter (VaChT), and acetylcholinesterase. Using the prototypical nAChR and VAChT ligand nicotine and besamicol, respectively, this project’s primary

2006 Annual Research Report of the Supercomputing Institute 107 UM TC–Department of Medicinal Chemistry

David M. Ferguson, Fellow Opiate Bivalent Ligands: Structure/Function Studies

his project investigates the function of opioid Research Group and Collaborators receptor dimerization in ligand binding, selectivi- Gwen Cheve, Department of Medicinal Chemistry, Tty, and signal transduction using structure-based University of Mississippi, University, Mississippi modeling techniques. The researchers are using John Goodell, Graduate Student Researcher Supercomputing Institute resources to build structural Erik Jorvig, Graduate Student Researcher models of both protein receptors and bivalent ligands. Brian Kane, Graduate Student Researcher They have also created theoretical models for bivalent Stephanie Kerimo, Staff opioid ligands using quantum chemical methods and Gary Lam, Graduate Student Researcher have used molecular dynamics simulations for further Chuck Locuson, Research Associate Thomas G. Metzger, Research Associate conformational analysis. The group has nearly completed Colleen Murray, Graduate Student Researcher their evaluation of receptor complexes using sequence M. Germana Paterlini, Certusoft, Inc., Minneapolis, analysis techniques. The next step will be building mod- Minnesota els and performing simulations; this will be computa- Gennady Poda, Research Associate tionally intensive and will include homology modeling, Mahadevan Seetharaman, Research Associate ligand docking, and molecular dynamics simulations of Bengt Svensson, Research Associate dimeric receptor ligand complexes.

Rodney L. Johnson, Principal Investigator

Design of Peptidomimetics of the Dopamine Receptor Modulator Pro-Leu-Cly-NH2 and of an Samc Peptide Fragment as Inhibitors of Apoptosis hese researchers are designing and synthesizing pled receptor model of the dopamine receptor to identify conformationally constrained peptidomimetics of the modulatory site on the receptor. The group has also designed and synthesized peptidomimetics of the Smac Tthe dopamine receptor Pro-Leu-Gly-NH2. The peptidomimetics are used to construct a pharmacophore fragment AVPI based on a model of AVPI bound to the model of the modulatory site. Peptidomimetic pho- BIR3 binding site of the apoptitic protein XIAP. The toaffinity labeling agents are made in order to label the researchers are using the Basic Sciences Computing modulatory binding site and to use the G protein-cou- Laboratory and the Medicinal Chemistry/Supercom- puting Institute Visualization-Workstation Laboratory for this project. Research Group Swapna Bhagwanth, Graduate Student Researcher Abigail Fisher, Graduate Student Researcher Cory Kending, Graduate Student Researcher Bhooma Raghavan, Graduate Student Researcher Ravindranadh Somu, Research Associate Ashish Vartak, Graduate Student Researcher

108 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Medicinal Chemistry

Ramaiah Muthyala, Principal Investigator Design of Novel Inhibitors for VanX Enzyme-Vancomycin

hese researchers are using a drug discovery strategy that involves molecular modeling and chemi- Research Group Tcal synthesis to generate inhibitors for a protein Eric Bennett, Research Associate called VanX, whose activity is essential for bacteria to Srikanth Kolluru, Research Associate resist the antibiotic Vancomycin on cell wall biosynthesis. Xingnan Li, Graduate Student Researcher The crystal structure of VanX has been disclosed recently. Ding Lu, Graduate Student Researcher The researchers are using software available at the Swati More, Graduate Student Researcher Abbas Raza, Research Associate Medicinal Chemistry/Supercomputing Institute Ye Tang, Graduate Student Researcher Visualization-Workstation Laboratory for this project. Zhengqiang Wang, Research Associate

Philip S. Portoghese, Principal Investigator Structure/Function Studies of Opioid Bilayer Ligands

his project supports a coordinated effort to inves- lent ligand is established by comparing binding and tigate opioid receptor dimers/oligomers through a function with specifically designed control compounds. Tmultidisciplinary approach involving molecular biology, pharmacology, medicinal chemistry, and molecular modeling. The broad long-range goal is to gain an understanding of possible difference in the functional Research Group roles of opioid receptor monomers and dimers/oligomers. Eyup Akgun, Research Associate These researchers are designing and synthesizing phar- David J. Daniels, Graduate Student Researcher macologic tools to identify the presence of opioid recep- Nicolette Fernandes, Research Associate Rashmi Gupta, Graduate Student Researcher tor dimers. The design approach involves the simultane- Mary Lunzer, Staff ous occupation of neighboring and recognition sites in a Michael D. Powers, Staff heterodimer by a single bivalent ligand that contains ago- Sarika Prabhu, Research Associate nist and antagonist pharmacophores. Optimization of Jie Yang, Research Associate binding and function are accomplished by varying the Ajay Yekkirala, Staff length of the spacer that connects the pharmacophores. Yan Zhang, Research Associate The bridging of opioid recognition sites by a single biva-

2006 Annual Research Report of the Supercomputing Institute 109 UM TC–Department of Medicinal Chemistry

Shana J. Sturla, Principal Investigator Molecular Recognition of Alkylated Bases in Double-Stranded DNA

ancer incidence is linked to environmental fac- ty is poorly characterized in many cases. Structural char- tors that can give rise to genomic alternations. acteristics of DNA adducts can strongly influence their CThese mutations are initiated by carcinogen- biological effects. Many of the bioanalytical techniques induced structural changes that reflect the critical and that are typically used to detect DNA adducts, however, fundamentally chemical first step in the complex process provide limited structural information regarding these of cancer development. Enzymatic metabolism of xenobi- important bioconjugates. For this reason, little is known otic compounds often produces chemically reactive enti- about the structural and biological significance of certain ties with the potential to modify deoxyribonucleic acid lesions. (DNA). Because of such compounds’ transient nature The goal of this research is to develop structure-based and the diversity in their modes of reactivity, genotoxici- molecular probes for the detection and study of DNA adducts and their influence on DNA structure and function. The researchers want to establish a relationship Research Group between adduct structure, effects on DNA replication, Jiachang Gong, Research Associate DNA repair, and biological endpoints. Understanding Thu Nguyen, Research Associate how certain chemicals initiate cancer will help researchers to establish diagnostic tools for carcinogen exposure.

Natalia Tretyakova, Principal Investigator Darrin M. York, Associate Fellow Structural Studies of DNA Cross-Links by Anti-Tumor Drugs and Bifunctional Carcinogens eoxyribonucleic acid (DNA)–DNA cross-linking growth. Paradoxically, DNA cross-linking is also a com- appears to be essential for the cytotoxic and mon mode of action of some potent carcinogens. Danticancer activity of many anti-tumor drugs, These researchers used molecular dynamics simula- including nitrogen mustards, nitrosoureas, and psoralens. tions to investigate the cause of the observed difference The presence of a single interstrand cross-link can pre- in the biological outcomes of DNA cross-linking by vent DNA replication and transcription, eventually bifunctional carcinogens and anti-tumor drugs. The resulting in cell death and the inhibition of tumor results will help in understanding the mechanisms of action of these agents and in developing anti-tumor agents with minimal side effects. Research Group Danae Dorr, Research Associate Rebecca Guza, Graduate Student Researcher Kristopher Murphy, Graduate Student Researcher Colleen Murray, Undergraduate Student Researcher Rachel Loeber, Graduate Student Researcher Mahadevan Seetharaman, Graduate Student Researcher

110 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Medicinal Chemistry

Carston R. Wagner, Principal Investigator Donald G. Truhlar, Fellow Computational Analysis of Chemically Induced Protein Dimerization

he control of protein-protein interactions is a point-mutants of DHFR have been constructed in the necessary requirement for cellular biological laboratory and used to validate the results of the simula- Tprocesses. Synthetic systems that emulate this tions. control, such as chemical inducers of protein dimeriza- Additionally, the researchers have extended their stud- tion (CIDs), have diverse potential as model systems, as ies of DHFR assembly to the construction of reversibly bioprobes, and as therapeutic tools. These researchers oligomerized nanostructures from engineering dimeric have developed a CID system based upon bivalent DHFR proteins and bix-MTX. methotrexate ligands (bis-MTX) that dimerize dihydrofolate reductase (DHFR), and are investigating the role Research Group of ligand conformation in governing dimerization, the Jonathan C. T. Carlson, Graduate Student Researcher effects of protein surface cooperativity, and the contribu- Tsui-Fen Chou, Graduate Student Researcher tion of individual residues to the dimer interface. The Cindy Choy, Graduate Student Researcher group has conducted extensive dynamics simulations of Terry Davis, Research Associate the chemically induced dimer, with periodic-boundary Dan Drontle, Graduate Student Researcher condition solvation and particle mesh Ewald treatment of Phalguni Ghosh, Research Associate electrostatic interactions. The dynamics data have been Chunkyung Park, Research Associate used to calculate protein interaction energies and 11 Matt Swenson, Research Associate Brian White, Graduate Student Researcher

Chengguo Xing, Principal Investigator Bcl-2 Selective Inhibitors: Development and Application to Cancer Treatment

rug resistance is a significant stumbling block in the fight against cancer. Small molecules that Dinhibit anti-apoptotic Bcl-2 proteins have the potential to overcome such drug resistance. Most of current small-molecule inhibitors non-selectively target multiple anti-apoptotic Bcl-2 proteins. This project focuses on developing Bcl-2 selective inhibitors by a combination of computer modeling, virtual screening, and organ- Research Group ic synthesis. Jignesh Doshi, Graduate Student Researcher These researchers are using the Medicinal Liangyou Wang, Research Associate Chemistry/Supercomputing Institute Visualization- Workstation Laboratory for this project.

2006 Annual Research Report of the Supercomputing Institute 111 UM TC–Department of Pharmaceutics

David J. W. Grant, Associate Fellow Molecular Modeling of Drug Crystals

he focus of this research was to develop and eval- and improve experimental results and inferences and to uate means of engineering the properties of drugs enhance the understanding of the physico-chemical Tand excipients in solid state to improve the per- interactions occurring in pharmaceutically important sys- formance and quality of pharmaceutical dosage forms. tems. The group worked on the following specific proj- The researchers studied the relationship between the ects: prediction of crystal structures from powder pat- chemical properties of solid drugs and their solid-state terns; calculations of lattice energy of crystals from their structures, both crystalline and amorphous. unit cells; calculations of interaction energy between vari- This group used molecular modeling to supplement ous solutes and solvents; calculations of solvation energy of solutes by solvents; polymorph prediction of molecular crystals; interactions between molecules in crystals; ab Research Group initio geometry optimization and energy calculations; Dabing Chen, Graduate Student Researcher and molecular dynamic calculations to understand nucle- Sharmistha Datta, Graduate Student Researcher ation and crystal growth. Yushi Feng, Graduate Student Researcher Yuchuan Gong, Research Associate Sachin Lohani, Graduate Student Researcher David J. W. Grant passed away on December 9, 2005. Enxian Lu, Graduate Student Researcher He was a long-time Supercomputing Institute Agam Sheth, Graduate Student Researcher researcher and committee member. The staff and Yuegang Zhang, Supercomputing Institute Research researchers of the Supercomputing Institute extend Scholar their deepest condolences to the Grant family.

Ronald A. Siegel, Principal Investigator Use of Hydrogels in Biomedical Devices

he Siegel group is working on two related proj- drug delivery system that allows certain hormones to be ects investigating the use of hydrogels in biomed- delivered in a rhythmic manner, mimicking endogenous Tical devices. The first project involves a hydrogel secretion patterns. A computational chemomechanical model is being developed, consisting of coupled ordinary and partial differential equations describing spatiotempo- Research Group and Collaborator ral hydrogel dynamics, and their mutual feedback with Amardeep Bhalla, Graduate Student Researcher enzymatic reactions occurring outside the gel. This Terry Davis, Research Associate model is being used to explore ways of controlling the Takehisa Hanawa, Visiting Researcher behavior of autonomously oscillating hormone release Hao Hou, Graduate Student Researcher systems. Sidhartha S. Jena, Research Associate In the second project, chemical modification of the Clinton Jones, Undergraduate Student Researcher hydrogel is used to tailor its chemomechanical response Jee-Eun Lee, Graduate Student Researcher properties. Equation of state calculations, in which Siddharthya Mujumdar, Research Associate Eric Nuxoll, Graduate Student Researcher numerical parameters corresponding to these chemical Jon Urban, Graduate Student Researcher modifications, are compared against experimental data.

112 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Pharmaceutics

Raj Suryanarayanan, Principal Investigator Material Science of Pharmaceutical Solids

large fraction of pharmaceutical products are transitions of excipients may be of relevance and impor- administered as solids. These researchers are tance. The goal is to ensure reproducible and predictable Ainterested in the material science of pharmaceuti- performance of solid dosage forms with minimum batch- cal solids with a specific emphasis on their physical char- to-batch variations. acterization. They are investigating the polymorphic forms, degree of crystallinity, and the nature and extent of interaction with water for drugs and excipients. The methods used include x-ray powder diffractometry and Research Group thermoanalytical, spectroscopic, and microscopic tech- Sisir Bhattacharya, Graduate Student Researcher niques. The researchers are specifically interested in mon- Xiangmin Liao, Research Associate itoring and quantifying phase transitions at various stages Cletus Nunes, Graduate Student Researcher of pharmaceutical processing. While the active ingredient Jaidev Tantry, Research Associate is of predominant concern, there are cases where phase

Department of Veterinary and Biomedical Sciences

Mitchell S. Abrahamsen, Principal Investigator Host Response to Cryptosporidium parvum Infection

ryptosporidium parvum is an obligate intracellular the researchers can identify the genes that are differential- protozoan parasite that is a major cause of gas- ly expressed in response to cryptosporidial infection. This C trointestinal disease. C. parvum primarily infects study will provide a comprehensive foundation for fur- epithelial cells of the gastrointestinal tract, resulting in ther analyses of the role of specific biochemical pathways acute watery and profuse diarrhea that, while self-limit- during C. parvum infection and in the progression of ing in healthy patients, can be persistent and ultimately cryptosporidiosis, which will be valuable in developing life-threatening in immunocompromised patients. treatments for this disease. This project uses microarray technology to elucidate the host epithelial response to C. parvum infection. The researchers characterize host gene expression in mock- Research Group and C. parvum-infected human and bovine epithelial cell Juan Abrahante, Research Associate lines as well as primary bovine intestinal epithelial cells Mingqi Deng, Research Associate by using both Affymetrix high-density oligonucleotide Cheryl Lancto, Staff array and custom-designed cDNA (carrier deoxyribonu- Jin Liu, Graduate Student Researcher cleic acid) microarrays. By comparing expression levels Shidong Ma, Graduate Student Researcher between mock- and C. parvum-infected epithelial cells,

2006 Annual Research Report of the Supercomputing Institute 113 Department of Veterinary and Biomedical Sciences

Alvin J. Beitz, Principal Investigator Gene Expression in Mouse Models of Cancer Pain and Multiple Sclerosis

hese researchers are using Affymetrix microarray technology to identify changes in gene expression Ttwo different mouse models for cancer pain and multiple sclerosis. They have used GeneData EXPRESSIONIST and GENESPRING software to perform statistical analysis on their microarray results and are performing more replicates of their data.

Research Group Mary Baddorf, Graduate Student Researcher Jessica Lynch, Graduate Student Researcher

Yinduo Ji, Principal Investigator Functional Genomics and Molecular Pathogenesis of Staphylococcus aureus

taphylococcus aureus is an important human and researchers employed a systematic and comprehensive animal pathogen, causing both superficial skin and evaluation of the requirement for each gene for both cell S life-threatening infections worldwide. The rapid growth and infection and has developed a regulated anti- emergence of multi-drug resistance among S. aureus is sense ribonucleic acid interference system in S. aureus to generating an enormous public health concern. selectively control gene expression during culture and This project’s goals were to understand the molecular infection. The objectives were to create a library for high- mechanisms of the pathogenesis and to identity the novel throughput screening of gene products that are required targets for delivering efficacious preventative and/or ther- for S. aureus pathogenesis and to define gene products apeutic agents against S. aureus infections. The that contribute to different S. aureus infections.

Research Group Xulong Liang, Research Associate Junsong Sun, Research Associate Li Zheng, Research Associate

114 2006 Annual Research Report of the Supercomputing Institute Department of Veterinary and Biomedical Sciences

Mathur S. Kannan, Principal Investigator Dynamic Calcium Regulation in Airway Smooth Muscle

he Kannan laboratory is interested in elucidating erature pertaining to the binding sites were also obtained. the transcriptional regulation of expression of In silico analysis of the 5’ UTR of human CD38 shows TCD38 in smooth muscle cells by inflammatory the presence of putative binding motifs for different tran- cytokines. In previous studies, they have demonstrated scription factors such as NF-κB, AP1, and NF-IL6. that inflammatory cytokines TNF-α, IFN-γ and IL-1β, Future studies will involve transfection of airway smooth muscle cells with a vector containing the either the full- and the TH2 cytokine IL-13 increase CD38 expression and this is associated with increased intracellular calcium length 5’ UTR or with deletions of the various binding mobilization during activation by agonists. The aug- motifs and a luciferase reporter to delineate the role of mented CD38 expression in the presence of TNF-α various transcription factors in the regulation of CD38 requires activation of the transcription factor NF-κB, expression. although NF-κB-independent mechanisms seem to exist. These researchers have cloned the 5’ UTR of the human CD38 gene from K562 cells. The GENEQUEST module of LASERGENE 6.0 was used to identify the potential transcription factor binding sites in the 5’UTR of CD38 Research Group gene. The 5’ UTR of CD38 gene (3240bp) was entered Joseph A. Jude, Graduate Student Researcher into GENEQUEST and analyzed for the potential tran- Bit Na Kang, Graduate Student Researcher scription factor binding sites. The interested binding sites K. G. Tirumurugaan, Research Associate were chosen and the precise summaries of published lit-

James R. Mickelson, Principal Investigator Genetic Linage Analysis of Heritable Neuromuscular Disorders in Domestic Animals

imple and complex heritable diseases are relatively in the equine genome mapping effort where a major goal common in companion animal species due to is to construct a comparative horse-human genome map. Sselected breeding schemes that use common The researchers are using the Computational Genetics founders and family lines to propagate highly desirable Laboratory and the Digital Technology Computational traits. These researchers are using genetic linkage analyses Biology Laboratory. to begin to identify the genetic loci responsible for a number of heritable disorders in dogs and horses. The researchers obtain genotypes for microsatellite deoxyribonucleic acid (DNA) markers located at evenly spaced intervals across the genome and analyze them for statistically significant linkages to the trait in large, often-complex pedigrees. By identifying DNA markers that co-seg- Research Group regate with the trait, the researchers can essentially map Patricia Dranchak, Graduate Student Researcher the gene for the trait to that region of a specific chromo- Ned Patterson, Graduate Student Researcher some represented by that marker where the gene can ulti- Michelle Wagner, Research Associate mately be identified. The researchers are also taking part

2006 Annual Research Report of the Supercomputing Institute 115 Department of Veterinary and Biomedical Sciences

Michael P. Murtaugh, Principal Investigator Porcine Peyer’s Patch Expressed Sequences Associated With Disease

he Murtaugh laboratory is creating and analyzing transcripts, then determined which library clones to use a carrier deoxyribonucleic acid (cDNA) microar- based on sequence analysis results. After they determined Tray chip using cDNA clones from their porcine which sequences to use, they reorganized the cDNA Peyer’s patch libraries. They sequenced 6,000 cDNA clones and grew them again. To determine how accurately they had performed the reorganization, they sequenced Research Group approximately 600 random cDNA clones and performed Cheryl Dvorak, Research Associate a pairwise analysis using BLAST. These cDNA clones were Colleen Finnegan, Research Associate then used to create the microarray chips. The researchers Linda Foster, Research Associate have used the microarray chips for several hybridization Martha Fuentes, Research Associate experiments. Josephine Gnanandarajah, Graduate Student Researcher Geoff G. Hirsch, Graduate Student Researcher Kendra Hyland, Graduate Student Researcher Craig Johnson, Research Associate Juan Li, Graduate Student Researcher Gongping Liu, Research Associate Chad Ramler, Graduate Student Researcher Brenda Saxton, Undergraduate Student Researcher

Pamela J. Skinner, Principal Investigator Genomic Studies of Transmissible Spongiform Encephalopathies

ransmissible spongiform encephalopathies (TSE) microarrays to identify alterations in gene expression that or prion diseases are fatal neurodegenerative dis- occur in mouse brain infected with different strains of Teases with no known cure. One focus of this lab- scrapie. oratory is to gain insights into prion disease pathogenesis in order to understand the molecular events that lead to the neurodegeneration, and to develop early diagnostic tools and new drug therapies. Current efforts by this group involve the use of carrier deoxyribonucleic acid

Research Group Rebecca Merica, Research Associate Greg Snyder, Research Associate

116 2006 Annual Research Report of the Supercomputing Institute Department of Veterinary and Biomedical Sciences

Bruce K. Walcheck, Principal Investigator Mutational Analyses of Cell Adhesion Proteins

he Walcheck laboratory is investigating the function and regulation of various leukocyte cell sur- Tface determinants, such as adhesion molecules involved in leukocyte extravasation from the blood into the tissue. Numerous copy deoxyribonucleic acid constructs are being generated in order to examine the struc- Research Group ture-function relationship of particular leukocyte mem- Amy Herrera, Staff brane proteins. The researchers are using software avail- Polly Mattila, Graduate Student Researcher able through Supercomputing Institute as support soft- Catherine St. Hill, Research Associate ware (designing polymeric chain reaction primers, restric- David Tierney, Research Associate tion mapping, protein analysis) for engineering mutations.

Douglas J. Weiss, Principal Investigator Bovine Macrophage Modulation by Mycobacterium avium Subspecies Paratuberculosis

ovine paratuberculosis is a major disease problem immune-regulatory cytokine IL10. in dairy cows worldwide. Although the agent of This project evaluates the macrophage antimycobacte- Bparatuberculosis, Mycobacterium avium subspecies rial function and MAPK cell signaling activation leading paratuberculosis (MAP), has long been identified, there is to the survival of MAP in bovine macrophages. still a significant lack of knowledge about the immune and cell signaling mechanism involved in the susceptibility of macrophages (target cells) to infection. A family of protein kinases, mitogen-activated protein kinases (MAPK), may play a key role in Mycobacterium paratuberculosis modulation of macrophage response. Further, these researchers suggest that the causative agent of paratuberculosis regulates the differential activation of MAPK to disrupt macrophage function, so it can survive Research Group and proliferate in these cells. In particular, the researchers Cleverson de Sousa, Graduate Student Researcher believe that the activation of MAPKp38 plays a key role Oral Evanson, Research Associate in this process by stimulating the expression of the

2006 Annual Research Report of the Supercomputing Institute 117 UM TC–Department of Veterinary Population Medicine

Srinand Sreevatsan, Principal Investigator Host Gene Expression Profiles of Micobacterium avium Subspecies Paratuberculosis

ohne’s disease, a chronic inflammatory disease caused their effect on host macrophage and dendritic cells and by infection with Mycobacterium avium subspecies that these differences play a major role in determining Jparatuberculosis (MAP), is one of the most prevalent the character of infection. They are studying the differen- and costly diseases of cattle and sheep worldwide. This tial gene expression by the host and MAP strains in a group’s long-term objective is to provide a comprehensive peripheral blood-monocyte-derived macrophage and understanding of bacterial population genetics and host- dendritic cell models. This research will improve animal pathogen interactions in MAP infections. They hypothe- health and prevent disease caused by MAP through a size that genetically distinct subtypes of MAP differ in program of fundamental research that will enable the development of superior diagnostic reagents, vaccines, and antimicrobial agents. Research Group Harish K. Janagama, Staff Xiaochun Zhu, Graduate Student Researcher

Department of Human Resources and Industrial Relations

Brian P. McCall, Principal Investigator Determinants of Educational Attainment in Florida

his project used unique administrative data from the Florida Department of Education to study Tstudent transitions from high school into college, and then to examine a host of college outcomes. Florida collects detailed information on student educational and life histories and they provided access to this data so that the researcher could construct a file that contains a longitudinal history for all students from the time they are in high school until they (potentially) graduate from college. This “event history file” contains demographic, academic, social, economic, financial, and institutional data that will be used to study many important education issues.

118 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Information and Decision Sciences

Paul E. Johnson, Principal Investigator Patient Adaptation Analysis Using Bootstrapped Estimates of DEA Efficiency Scores

his study models patient adaptation to the condi- well patients are adapted to their environment of chronic tions of a specific chronic disease, type 2 dia- disease care. Tbetes. The researchers employed data envelop- At physician level, DEA was used to model physician ment analysis (DEA) methodology to describe each efficiency using patients included in the first-level analy- patient’s adaptation relative to the adaptation of the most sis. The medical cost for each patient was used as the successful patients. DEA has been applied in health serv- input variable and patient satisfaction, patient self-effica- ice research, but its estimates of efficiency scores have cy, and percent change in patient glycosylated hemoglo- been shown to be biased upwards. By “bootstrapping” bin were used as output variables. DEA, these researchers can correct the biases and also make statistical inference from DEA estimates. The study was conducted at two levels, patient level and physician level. At patient level, self-care behaviors of selected type 2 diabetes patients were used as inputs to Collaborator the DEA method; patient satisfaction and percent change Xiang Ao, Harvard Business School, Harvard University, Cambridge, Massachusetts in patient glycosylated hemoglobin were outputs. Fitness was estimated by bootstrapping DEA to measure how

UM TC–Department of Operations and Management Science

William Li, Associate Fellow Christopher J. Nachtsheim, Co-Principal Investigator Model-Robust Designs, Construction of Mixed-Level Designs, and Model- Discriminating Designs hese researchers focus on the construction of mixed-level designs. Orthogonal designs are the Tmost commonly used experimental designs in practice. The choice of optimal designs depends on criterion and complete catalogs of the candidate orthogonal designs. These researchers used a newly developed efficient algorithm and a theory based on the indicator function to construct complete sets of orthogonal designs with economic run sizes. After completing the 18-run Collaborator designs, they constructed 27-run designs. They then Kenny Ye, Department of Epidemiology and explored optimal blocking plans for these mixed-level Population Health, Albert Einstein College of designs. Blocking is a commonly used technique to Medicine, Bronx, New York reduce unwanted variations in statistics.

2006 Annual Research Report of the Supercomputing Institute 119 UM TC–Hubert H. Humphrey Institute of Public Affairs

Samuel L. Myers, Jr., Principal Investigator The Deterrent Effect of Fair Lending Enforcement Efforts on Racial Disparities in Loan Denial Rates hese researchers are collecting unique information loan underwriting procedures and credit scoring adopted on public and private fair lending enforcement by lenders and/or government-sponsored enterprises. Tefforts keyed to local areas from 1994 to 2003. This data collection is supplemented by information They are merging this information with data from the from the U. S. Department of Housing and Urban Cleveland Federal Reserve Board and Home Mortgage Development (HUD) on local enforcement efforts at Disclosure Act, which includes information on loan each HUD office in the U. S. application records plus lender files. Models of loan denial rates are estimated separately by The original data collection for this project focuses on race to compute a measure of residual discrimination. media accounts of allegations of racial discrimination, These models are estimated with and without the collect- court filing, administrative actions, and adverse news ed information on enforcement efforts. The researchers’ accounts of such mortgage innovations as automated hypothesis is that enforcement efforts at the local level help to reduce measured discrimination in loan denials.

Research Group Bosu Seo, Graduate Student Researcher

120 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Aerospace Engineering and Mechanics

Graham V. Candler, Fellow Simulation of Reacting Flows

hese researchers are continuing their numerical simulations of high-temperature reacting flows. TThis work has several applications: supersonic Research Group and Collaborators flow control using laser energy deposition, generation of Mike Barnhardt, Graduate Student Researcher atmospheric-pressure air plasmas for materials processing Iain D. Boyd, Department of Aerospace Engineering, and flow control, the study of how the Navier-Stokes University of Michigan, Ann Arbor, Michigan equations fail in high-speed, low-density flows, the study Travis Drayna, Research Associate Marie-Claude Druguet, Research Associate of micro-scale aerodynamics, and the analysis of turbu- Mark Emerick, Graduate Student Researcher lent reacting flows. The researchers use a suite of compu- Ryan Gosse, Research Associate tational fluid dynamics (CFD) codes developed for paral- Ramnath Kandala, Graduate Student Researcher lel supercomputers. These codes use implicit time inte- Brian Mader, Graduate Student Researcher gration to reduce the computational cost, and have been Ivan Marusic, Faculty Collaborator optimized for the IBM and SGI supercomputers. The Ioannis Nompelis, Research Associate group also uses an efficient parallelized direct simulation David Peterson, Graduate Student Researcher Monte Carlo code for low-density flow simulations for Krish Sinha, Graduate Student Researcher comparison with the continuum CFD simulations. This Joseph Stecher, Graduate Student Researcher work is leading to an improved understanding of how Pramod Subbareddy, Graduate Student Researcher Tian Wan, Graduate Student Researcher chemical reactions and fluid motion interact in a variety of technologically relevant applications.

Ryan S. Elliott, Principal Investigator Bifurcation and Stability Techniques for the Investigation and Discovery of Active Materials he objectives of this project are to investigate new powerful group theoretic methods can reveal general con- atomistic models that accurately represent a nections between equilibrium solution branches that are Tmaterial’s configurational energy landscape and to completely independent of the particular atomic models advance the development of analytic and computational used to describe the material’s energy landscape. The tools for interrogating these landscapes. Accordingly, the researcher is also developing numerical methods that researcher uses advanced phenomenological atomic inter- exploit the material’s symmetry properties. These meth- action models to characterize non-central forces in terms ods will reduce the dimension and complexity of the of atomic-bond angles, coordination number, and local equations that govern the solution branches, eliminate symmetry properties. The effects of thermal atomic singularities near bifurcation points, and even generate, vibration will also be included in the crystal’s energy without further computation, entire sets of new solution landscape. A numerical bifurcation and stability interro- branches from a previously computed branch. gation of these energy landscapes proves to be a subtle and computationally intensive task. To improve the efficiency of these investigations, this researcher is developing analytical methods that exploit the known space group symmetry of the material’s crystal structure. These

2006 Annual Research Report of the Supercomputing Institute 121 UM TC–Department of Aerospace Engineering and Mechanics

Roger L. Fosdick, Associate Fellow Large Deformations in Nonlinear Elasticity, Coexistent Phases, and the Thermodynamics of Propagating Phase Boundaries hese researchers are using the Supercomputing existence and growth of zones of evolving microstructure Institute for a program with three components: is not only responsible for the failure of materials but it Tcoexistant phases, singularities and constraints in also plays an important part of the design of devices and elastostatics, and dynamic phase transitions. The goal of in many emerging applications. the first phase is to carry out a theoretical and computa- The second component involves the nonlinear theory tional investigation of coexistent phase structures in of elasticity, which is more appropriate for investigating solids when subject to external load or environmental coexistent phase phenomena and singular behavior in the temperature, electrical, or magnetic stimulation. The mechanics of materials than its linear counterpart. The emphasis is on the role of singularities in problems where solutions are not regular. Research Group and Collaborators For the third project component, the researchers theo- Adair Roberto Aguiar, Department of Structural rize that a thermomechanical model including capillarity, Engineering, University of Sao Paolo, Sao Paolo, viscosity, and thermal conductivity is the preferred frame- Brazil Eric Petersen, Graduate Student Researcher work for their investigations in phase transitions. In this Gianni Royer-Carfagni, Department of Civil- setting, they hope to prove that the limiting solutions, as Environmental Engineering and Architecture, the capillarity, viscosity, and thermal conductivity University of Parma, Parma, Italy approach zero, are the physically relevant ones.

Ashley James, Principal Investigator Numerical Simulations of Liquid-Fluid Interface Flows With Topological Transitions and Surfactant Effects his research project simulates interfacial fluid the dynamics of several problems. One is an investigation flow to gain an improved understanding of how of the coalescence of two drops, including van der Waals Ttopological transitions of liquid-fluid interfaces forces, with the goal of developing a physically based occur and of the effect of surfactant on the evolution of model of the topological transition. A second project physical systems. The researchers have developed an involves simulations of the break-up of a drop in an interfacial flow solver incorporating the dynamics of extensional flow, aimed at understanding the role of sur- interfacial surfactant. factant in pinch-off processes. Finally, the group is inves- The group is working on simulations to understand tigating the effect of surfactant on the pinch-off of a periodic liquid thread. The researchers are continuing to modify their code to Research Group improve its accuracy and extend its capabilities. One Xueli Jiang, Graduate Student Researcher improvement is a higher-order method to reconstruct the Richard Martin, Undergraduate Student Researcher interface. The method is being implemented on an Yang Bee Vue, Supercomputing Institute Undergraduate Intern unstructured, adaptive mesh and will include surfactant Xiaofang Yang, Graduate Student Researcher solubility. The researchers will also model contact line dynamics.

122 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Aerospace Engineering and Mechanics

Daniel D. Joseph, Fellow Direct Numerical Simulation and Modeling of Multiphase Flows

his research group is continuing their investiga- adding a pressure correction term which compensates for tion of the fundamental dynamics of three- the irrotational shear stress at the fluid-fluid interface. Tdimensional motions of solid particles in The strategy of VPF is applied in the analysis of stress- Newtonian and viscoelastic fluids. The researchers have induced cavitation for axisymmetric flow past a sphere developed two separate scalable and highly efficient par- and the modeling of linear shear instability of a liquid jet allel finite-element codes, the arbitrary Lagrangian- surrounded by a gas stream. Furthermore, VPF and Eulerian (ALE) particle mover and the disordered local VCVPF analyses are performed to model the decay rate movement (DLM) particle mover. The study has focused of oscillations and standing waves in spherical drops and on the migration of particles in three-dimensional pres- bubbles. VPF and VCVPF are valid tools to analyze two- sure-driven flows and the development of explicit formu- phase flow in cases where vortical layers are confined to las for the lift forces on the particles by correlating data small regions in the domain so the irrotational assump- from direct numerical simulation. The research group is tion is reasonable. also devoted to the task of applying the approaches of viscous potential flow (VPF) and viscous correction of viscous potential flow (VCVPF) to the study of different Research Group problems in two-phase fluid dynamics. The VPF Juan Carlos Padrino, Graduate Student Researcher approach assumes irrotational fluid motion considering Jing Wang, Graduate Student Researcher Haoping Yang, Graduate Student Researcher viscous stresses in the normal stress balance across fluid- fluid interfaces. The VCVPF approach stems from VPF,

2006 Annual Research Report of the Supercomputing Institute 123 UM TC–Department of Aerospace Engineering and Mechanics

Perry H. Leo, Associate Fellow Studies of Crystal Morphologies

hese researchers studied microstructure crystal models, with focus on including anisotropic surface ener- formed in crystalline alloys and crystal growth gies and interfacial kinetics. The second was to use the Tprocesses. There were two goals to this work. The simulations as a test-bed to study the possibility of using first was to investigate three-dimensional sharp interface time-dependent far-field fluxes to control the microstructure evolution.

Research Group and Collaborators Anthony Anderson, Undergraduate Student Researcher Joel Bell, Graduate Student Researcher Vittorio Cristini, Qing Nie, Department of Biomedical Engineering, University of California, Irvine, California Jacob J. Hageman, Graduate Student Researcher Russell Hooper, Graduate Student Researcher Herng-Jeng Jou, Questek, Evanston, Illinois Jun-Seok Kim, Graduate Student Researcher Trygve Kristiansen, Graduate Student Researcher Shuwang Li, Graduate Student Researcher Xiangrong Li, Graduate Student Researcher Xiaofan Li, Department of Applied Mathematics, Illinois Institute of Technology, Chicago, Illinois Ellen K. Longmire, Faculty Collaborator John S. Lowengrub, Department of Mathematics, University of California, Irvine, California Paul Macklin, Graduate Student Researcher Saswata Majumder, Graduate Student Researcher Qing Nie, Department of Mathematics, University of California, Irvine, California Michael Renardy, Department of Mathematics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia Justin Sjulson, Undergraduate Student Researcher Nicolas Vera, Graduate Student Researcher Antheunis Versluis, Faculty Collaborator Steve Wise, Department of Mathematics, University of California, Irvine, California Yubao Zhen, Graduate Student Researcher Xiaoming Zheng, Research Associate Hua Zhou, Research Associate

124 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Aerospace Engineering and Mechanics

Krishnan Mahesh, Fellow Large-Eddy Simulation of Turbulent Flow in Complex Geometries

hese researchers worked with large-eddy simula- simulating the effects of plasmas on turbulent flows; tion (LES) of turbulent flows in realistic engi- high-speed flows with chemical reaction; LES of com- Tneering geometries. They developed a non-dissi- pressible flows in complex geometries; and simulation of pative, numerical algorithm for turbulent flow on bubbles. unstructured grids. The use of unstructured grids allows arbitrarily complex geometries to be efficiently gridded. Research Group A novelty of the algorithm is that it discretely conserves Pradeep C. Babu, Graduate Student Researcher not only momentum, but also kinetic energy. This allows Jeffrey Doom, Graduate Student Researcher robustness without numerical dissipation. Such robust- Shankar Ghosh, Graduate Student Researcher ness is imperative to perform accurate simulations in Yucheng Hou, Graduate Student Researcher Hyunchul Jang, Graduate Student Researcher complex geometries at high Reynolds numbers. Michael Mattson, Undergraduate Student Researcher The group worked on several projects that utilized and Suman Muppidi, Graduate Student Researcher further developed this simulation capability. These Noma Park, Research Associate included: simulation of turbulent jets in cross-flow; scalar Rajes Sau, Graduate Student Researcher mixing in turbulent jets; development of an energy-con- Martin Vysohlid, Graduate Student Researcher serving formulation for turbulent compressible flows;

UM TC–Department of Astronomy

Thomas W. Jones, Fellow Numerical Studies of Particles and Fluids in Astrophysics

his group continued its unique and highly successful study of the acceleration and propagation Research Group and Collaborators Tof high-energy charged particles, also known as Allen Eastlund, Undergraduate Student Researcher cosmic rays (CRs), as well as application to some frontier Paul P. Edmon, Graduate Student Researcher astrophysical problems. Recent work has included large, Blayne A. Field, Supercomputing Institute multidimensional magnetohydrodynamical (MHD) sim- Undergraduate Intern ulations and associated development projects that incor- Eric J. Hallman, Center for Astrophysics and Space porate the group’s innovative treatments of particle trans- Astronomy, University of Colorado, Boulder, port plus other enhancements designed to improve com- Colorado putational performance, such as adaptive mesh refine- Hyesung Kang, Department of Earth Sciences, Pusan ment. Specific areas of research include the study of the National University, Pusan, Korea formation and evolution of clusters of galaxies, especially Sean O’Neill, Graduate Student Researcher involving interactions with “relativistic radio plasma” Dongsu Ryu, Department of Astronomy and Space injected by active galaxies, and supernova remnants, the Sciences, Chengnam National University, Daejeon, hot, chaotic bubbles formed inside galaxies when explod- Korea ing stars blast through the diffuse media that surround Konstantin V. Sapogin, Graduate Student Researcher them. Ian L. Tregillis, Los Alamos National Laboratory, Los Alamos, New Mexico Dan Weisz, Graduate Student Researcher

2006 Annual Research Report of the Supercomputing Institute 125 UM TC–Department of Biomedical Engineering

Victor H. Barocas, Associate Fellow Computational Biomechanics and Biotransport

he Barocas group is continuing its work on proj- ics of the aqueous humor (a passive Newtonian fluid) ects in computational biomechanics and trans- and the iris (an active elastic solid) in the anterior por- Tport. One project concerns the coupled mechan- tion of the eye. This study emphasizes dynamic behavior, improving upon previous studies that treated the eye as a steady-state system. In another project, the group uses a Research Group and Collaborator novel macroscopic-microscopic finite element approach Devesh Amatya, Graduate Student Researcher to the modeling of fibrillar tissues. This computationally Rouzbeh Amini, Graduate Student Researcher intensive approach offers the potential to provide much Ram Balachandran, Graduate Student Researcher more insight into the mechanical behavior of tissues and Philip W. Bransford, Supercomputing Institute tissue equivalents (formed by cells entrapped in a recon- Undergraduate Intern stituted biogel). The group has demonstrated the effec- Preethi Chandran, Graduate Student Researcher tiveness of their approach on a test problem using work- Afton Ellis, Undergraduate Student Researcher Mike Evans, Graduate Student Researcher stations, but to study real systems, they must use much Pramote Hockareon, Research Associate greater mesh refinement and three dimensions, and must Eric Huang, Graduate Student Researcher include transient behavior. A third project concerns the David Nordsletten, Undergraduate Student Researcher design of a tissue-engineering cardiovascular valve; the Hari Radhakrishnan, Research Associate researchers are embedding a shell model of the valve Shramik Sengupta, Graduate Student Researcher leaflet within a three-dimensional transient solution of Mithun Shenoi, Graduate Student Researcher the Navier-Stokes equations for the blood. David Shreiber, Department of Biomedical In a new project, the Barocas group is developing a Engineering, Rutgers University, Piscataway, New computer-aided strategic design platform for protein Jersey crystallization. Paul Sonda, Research Associate Matthew Stay, Research Associate Triantafyllos Stylianopoulos, Graduate Student Researcher Fred Wentorf, Graduate Student Researcher

126 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Biomedical Engineering

Bin He, Principal Investigator Computational Study of Electrical Source Estimation

hese researchers completed a project this year that the previous approaches with the spatial and temporal concerned computer simulation and model con- knowledge they acquired from their model in the previ- Tstruction studies using the information criterion ous project. They also developed and validated FE-based (ICS) method and finite element (FE) modeling. They CPI. have successfully shown that the ICS method can accurately solve source identification and source localization problems arising from the brain inverse problem using electroencephalographic (EEG) and magnetoencephalographic (MEG) signals. They also successfully created a FE model of a human head. To further their work, the researchers have developed the so-called spatio-temporal Research Group cortical potential imaging (CPI) method based on Xiaoxiao Bai, Research Associate dynamic inverse theories. Previous approaches to solve Ding Lei, Graduate Student Researcher the inverse problem involve frame-by-frame reconstruc- Yingchun Zhang, Research Associate tion and do not take advantage of the temporal dynamics of the underlying process. The group worked to improve

David J. Odde, Principal Investigator Computational Cell Motility

hese researchers are simulating various cytoskeletal and signaling processes involved in cell divi- Research Group Tsion and growth. For example, microtubules are Andrew Bicek, Graduate Student Researcher linear, self-assembled polymers than control intracellular Clarence Chan, Graduate Student Researcher organization and transport, and their assembly is a highly Jennifer Craig, Graduate Student Researcher regulated process. This group uses Monte Carlo simula- Melissa Gardner, Graduate Student Researcher tion to test various theories about how microtubules Keegan Haselkorn, Graduate Student Researcher assemble and how the assembly is controlled in the cell. Nathan Henderlite, Undergraduate Student Researcher They are also interested in how kinase/phosphatase and Jason Meyers, Graduate Student Researcher GEF/GAP systems control cell motility. Specifically, they Doninique Seetapun, Graduate Student Researcher are investigating the role of spatial gradients generated by David Wulfman, Graduate Student Researcher these reaction-diffusion systems.

2006 Annual Research Report of the Supercomputing Institute 127 UM TC–Department of Biomedical Engineering

Jonathan N. Sachs, Principal Investigator Chitosan Interactions With Lipid Bilayers

hitosan is a biocompatible polymer used in gene an entropic effect related to the dehydration of chitosan. delivery. This researcher is using all-atom molec- The answers will help define the most relevant physico- Cular dynamics (MD) simulations to elucidate chemical parameters in designing efficient polymer-based molecular factors governing the interaction between lipid non-viral gene delivery vesicles. bilayers and chitosan. Classical MD simulations will describe the local structural perturbations in the lipids as well as changes in global material properties induced by chitosan. A series of simulations of chitosan and lipid bilayers will test the roles of headgroup charge and size, and acyl chain fluidity and saturation in determining the factors governing chitosan/lipid bilayer interactions. The simulations use the NAMD simulation package, primarily the CHARMM potential. This project has is designed to answer two questions: which intermolecular forces drive chitosan binding; and if electrostatics dominate the interaction or is it primarily

J. Thomas Vaughan, Principal Investigator Simulation of Radio Frequency Coils in Magnetic Resonance Imaging

agnetic resonance imaging (MRI) is a powerful Simulation of RF coils is important in coil design, as noninvasive imaging technique that is used it provides scientists and engineering insights into param- Mprimarily in medical applications to produce eters and effects that are not measurable in real life. As high-quality images of the inside of the human body. coils appear in more applications, this simulation Radio frequency (RF) coils play a key role in imaging— becomes even more important. These researchers are the imager transmits RF energy to the coil to excite the using Supercomputing Institute resources to perform nuclei to a higher energy level, and receives the RF signal these simulations, which require a great deal of memory from the excited nuclei. and processing speed.

Research Group Can E. Akgun, Graduate Student Researcher John Strupp, Research Associate Jinfeng Tian, Graduate Student Researcher

128 2006 Annual Research Report of the Supercomputing Institute UM TC–Chemical Engineering and Materials Science

Robert W. Carr, Associate Fellow Atmospheric Chemistry of Halogen-Containing Organic Compounds

his researcher used Supercomputing Institute useful and chemically interesting information on these resources for computational chemistry research reactions. Calculation of vibrational frequencies, in con- Ton the atmospheric chemistry of halogenated oxy junction with the geometries and energies, permit esti- radicals. This included carrying out ab initio molecular mates of rate coefficients when molecular theories of orbital and density functional calculations on selected reaction rates are applied. Comparison of the estimated halo-alkoxy radicals that are intermediates in the oxida- and experimental (where available) rate coefficients per- tive degradation of halocarbon pollutants in the atmos- mit development of rate coefficient model that will be phere, and searching for transition states leading to useful over the range of temperatures and pressures in the atmosphere. known products of their reaction with O2, NO, and other atmospheric species of interest. Geometry optimization and total energy calculations yield molecular structures of intermediates and transition states, and permit the detailed mechanisms of their reactions to be dis- cerned. This information is extraordinarily difficult, labo- rious, and time-consuming to obtain experimentally, but computational chemistry provides a method to obtain

2006 Annual Research Report of the Supercomputing Institute 129 UM TC–Department of Chemical Engineering and Materials Science James R. Chelikowsky, Principal Investigator Yousef Saad, Fellow High-Performance Algorithms for Electronic Materials

hese researchers are continuing their investigators such as silicon, germanium, gallium arsenide, and tions on electronic materials. These materials zinc telluride. A major part of this research program is to Tinclude ceramics such as silica and semiconduc- develop and implement new and novel algorithms for examining the electronic and structural properties of complex systems. The researchers’ applications focus on Research Group and Collaborators systems with numerous atoms and many degrees of free- Manuel Maria Alemany, Research Associate dom, such as surfaces, liquids, glasses, large clusters and Lee B. Ballard, Supercomputing Institute quantum dots (including magnetically doped dots), and Undergraduate Intern complex solids. The researchers have also initiated a pro- Scott Beckman, Research Associate gram on nanowires and on molecular transport. Gustavo Dalpian, Research Associate Michael R. Frasca, Supercomputing Institute Undergraduate Intern Xiangyang Huang, Research Associate Juan Carlos Idrobo, Research Associate Manish Jain, Graduate Student Researcher Eunjung Ko, Graduate Student Researcher Lingzhu Kong, Graduate Student Researcher Leeor Kronik, Department of Materials and Interface, Weizmann Institute of Science, Rehovoth, Israel Hyun Wook Kwak, Graduate Student Researcher Shen Li, Graduate Student Researcher Marie Lopez del Puerto, Graduate Student Researcher Dmitriy Melnikov, Department of Electrical and Computer Engineering, University of Illinois, Urbana-Champaign, Illinois Serdar Ogüt, Department of Physics, University of Illinois, Chicago, Illinois Murilo Tiago, Supercomputing Institute Research Scholar M. Claudia Troparevsky, Condensed Matter Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee Igor Vasiliev, Department of Physics, New Mexico State University, Las Cruces, New Mexico Nicholas J. Voshell, Supercomputing Institute Undergraduate Intern Yunkai Zhou, Research Associate

130 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemical Engineering and Materials Science

H. Ted Davis, Fellow Network Modeling of Solute Spreading in Porous Media

hese researchers were interested in determining network problem. Because of the large system sizes the scaling properties of spreading inert and reac- involved in this project, this was a demanding computa- Ttive solutes in porous media by using recently tional problem requiring the use of Supercomputing developed methods for calculation of transport response Institute resources. on self-similar or hierarchical lattices for the understanding of chromatographic systems, soils, and groundwater and oil reservoirs. The project involved calculating equiv- alent transport responses on regular pore networks to validate the results on self-similar lattices. The researchers evaluated the effect of local diffusion as opposed to complete nodal mixing and the effect of spatially distributed properties, such as reaction rates or the pore size, among Collaborator others. Vladimir Alvarado, Mechanical Engineering, Pontificia The group used Laplace transform of the local trans- Catholic University of Rio de Janeiro, Rio de port equation at the pore-level, transfer-function algo- Janeiro, Brazil rithms and particle tracking to find the solution of the

Jeffrey J. Derby, Fellow Materials Processing Fundamentals

he Derby group develops, implements, and employs large-scale numerical modeling to Tunderstand processes that are used for the production of advanced solid-state materials, especially bulk, single crystals. Of special emphasis is the representation of three-dimensional and transient continuum transport (flows and heat and mass transport), phase-change phe- Research Group nomena, and process design for a number of melt and Cornelia Bengea, Undergraduate Student Researcher crystal growth systems. They are developing and employ- Bing Dai, Graduate Student Researcher ing a number of parallel finite-element models for these David Gasperino, Graduate Student Researcher purposes. Specific project include detailed Bridgman Mr. Yong-Il Kwon, Graduate Student Researcher Lisa Lun, Graduate Student Researcher crystal growth modeling, model-based control of crystal Mr. Paul Sonda, Research Associate growth processes, modeling the sintering of crystalline Andrew Yeckel, Research Associate ceramics, modeling the dynamics of solution crystal growth, and modeling microgravity crystal growth.

2006 Annual Research Report of the Supercomputing Institute 131 UM TC–Department of Chemical Engineering and Materials Science

C. Daniel Frisbie, Principal Investigator Theoretical Characterization of the Transport Properties of Organic Semiconductors

olecular organic semiconductors in general device design and performance improvement. and oligoacenes in particular are currently the The main goal of this project is to calculate the elec- Mobject of much interest because of their poten- tronic structure and some molecular properties, such as tial application in (opto)electronic devices, especially ionization potentials, electron affinities, and isomeriza- field-effect transistors. Understanding the charge trans- tion barriers, of novel organic semiconductors. The result port mechanisms in these materials is a key point for of these calculations, in combination with experimental data, will allow the development of an integrated picture of the important factors affecting the electronic and the Collaborator charge transport properties of organic semiconductors. Demetrio da Silva Filho, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia

132 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemical Engineering and Materials Science

Wei-Shou Hu, Associate Fellow Genomic Exploration on Chinese Hamster Ovary Cells; Regulation of Natural Products Biosynthesis in Streptomyces hese researchers are involved in two projects using the Supercomputing Institute laboratories. Research Group and Collaborators TIn the first, they are continuing their long-term Charles M. Cameron, Graduate Student Researcher project investigating Chinese hamster ovary cells and the Marlene Castro-Melchor, Graduate Student Researcher genetic traits that confer these cells’ many desirable phe- Salim Charaniya, Graduate Student Researcher notypic traits. The researchers have taken a comprehen- Marcela de Leon Gatti, Graduate Student Researcher sive approach by combining genomic and proteomic Ziomara Gerdtzen, Graduate Student Researcher Patrick Hossler, Graduate Student Researcher tools and physiological studies to identify and isolate rel- Karthik Jayapal, Graduate Student Researcher evant genes. They use microarray and proteomic analysis Anne Kantardjieff, Graduate Student Researcher to identify important genes and expression patterns and Jin-Hong Kim, Undergraduate Student Researcher to use these to genetically modify cells. The results and Jongchan Lee, Graduate Student Researcher tools obtained from these efforts represent a significant Wei Lian, Graduate Student Researcher step toward large-scale gene expression profiling for these Lo Siaw Ling, Biological Sciences Department, cells. National University of Singapore, Singapore In the second project, the Hu group is studying Sarika Mehra, Graduate Student Researcher Streptomyces, the largest producers of industrially impor- Peter Morrin Nissom, Bioprocessing Technology tant, naturally occurring secondary metabolites. Center, National University of Singapore, Singapore Rakesh Motani, Graduate Student Researcher Secondary metabolite biosynthesis in Streptomyces is con- Arleen Sanny, Bioprocessing Technology Center, trolled by a complex regulatory network consisting of a National University of Singapore, Singapore large number of pathway-specific and global regulators Gargi Seth, Graduate Student Researcher organized in a hierarchical tree. The goal of this project is Kher Shing Tan, Bioprocessing Technology Center, to identify the possible positions of important genes on National University of Singapore, Singapore the regulatory hierarchy of secondary metabolism. This Fernando Ulloa-Montoya, Research Associate would serve as a model for studying synthesis and regula- David Umulis, Graduate Student Researcher tion of a variety of industrially important natural prod- Katie Wlaschin, Graduate Student Researcher ucts produced by other related species. Joon Chong Yee, Graduate Student Researcher

2006 Annual Research Report of the Supercomputing Institute 133 UM TC–Department of Chemical Engineering and Materials Science

Yiannis N. Kaznessis, Fellow Computer Simulations of Antimicrobial Peptides and of Protein Folding Trajectories

hese researchers are involved in two projects peptide lipid interactions from a biophysical perspective. using Supercomputing Institute resources. In the They implement large-scale molecular dynamics simula- Tfirst, they use computer simulations to investigate tions of a large number of antimicrobial peptides with model lipid micelles that model bacterial and mammalian membranes. The trajectory data arising from Research Group these simulations is then systematically analyzed to devel- Aaron Ross Beaber, Undergraduate Student Researcher John Barrett, Graduate Student Researcher op structural bioinformatics tools in order to derive a Dan Bolintineanu, Graduate Student Researcher cognitive quantitative structure activity relationship with Nicha Chitphakdithai, Undergraduate Student predictive ability that will facilitate the rational design of Researcher peptide antimicrobials. Jairav Desai, Undergraduate Student Researcher The goal of the second project is to devise new ways Yuhua Duan, Supercomputing Institute Research to design simple biological organisms to perform increas- Scholar ingly complex functions and tasks. Such tasks include the Himanshu Khandelia, Graduate Student Researcher detection of extremely dilute concentrations of specific Allison Langham, Graduate Student Researcher proteins, the regulated production of therapeutic proteins Chadrika Mulakala, Research Associate via small molecule induction, and the more complex pro- Robert Olivo, Undergraduate Student Researcher Giordi Orreggio, Undergraduate Student Researcher cessing of multiple regulatory input signals to produce a Boojala Reddy, Research Associate specific, coordinated genetic response. The methodology Howard Salis, Graduate Student Researcher pursued combines computational design with experimen- Abdallah Sayyed-Ahmad, Research Associate tal validation. Vassilios Sotiropoulos, Graduate Student Researcher Jonathan Tomshine, Graduate Student Researcher Spyros Vicatos, Graduate Student Researcher

Satish Kumar, Principal Investigator Continuum and Nanoscale Simulations of Polymer Dynamics

hese researchers are concerned with simulating thin films and fine patterns. This work aims at clarifying various aspects of polymer dynamics at the the highly nonlinear elastohydrodynamic interaction Tnanometer and continuum scales. They are per- between the elastic stresses in the wall and the viscous forming finite-element simulations of fluid flow between stresses in the fluid. a flexible wall and a cavity. This is a model problem rele- An ongoing project involves the simulation of hydro- vant to gravure printing and coating, extensively used dynamic instabilities that arise in fluid flow past polymer but poorly understood processes for the fabrication of gels. This instability modifies the fluid flow and may find use as a means of enhancing mixing in microfluidic devices, improving mass transfer rates in membrane- Research Group based separations, and creating topographically patterned Vasileios Gkanis, Graduate Student Researcher polymer surfaces. The researchers developed a finite-ele- Scott Roberts, Graduate Student Researcher ment code to simulate this instability, and are currently Xiuyan Yin, Graduate Student Researcher exploring the effects of fluid rheology.

134 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemical Engineering and Materials Science

Chris W. Macosko, Associate Fellow Analysis and Properties of Co-Continuous Blends

o-continuous polymer blends consist of distinct terns form by nonlinear interaction among interfaces, phases. The microstructure is sponge-like where flow, and phase transitions. A study of these processes is Cone of the phases plays the role of the sponge inherently multidisciplinary and involves fluid dynamics, and other(s) its complement. While there have been pre- thermodynamics, material science, computational mathe- vious studies of such blends, most have been experimen- matics, and interactions with experiments. Large-scale tal and the physical processes leading to the development computation is applied to both modeling the morpholo- of co-continuous morphologies and their properties are gy development of co-continuous blends and to analysis still poorly understood. These researchers are working on of two- and especially three- dimensional experimental theoretical, numerical, and experimental studies that they images of the morphology. hope will provide a unique insight into characterizing these processes. Research Group Large-scale computation and computational mathe- David Ackerman, Graduate Student Researcher matics are now primary tools in studying physical Joel R. Bell, Graduate Student Researcher processes characterized by randomness and nonlinearity. Mike Dolgovskij, Graduate Student Researcher Co-continuous polymer blends are ideal examples of Benedict L. Hanrahan, Supercomputing Institute such processes in which complex, randomly oriented pat- Undergraduate Intern Carlos Rene Lopez Barron, Graduate Student Researcher

Jennifer A. Maynard, Principal Investigator Protein Engineering Tools for Crystallography

hese researchers are performing standard molecular replacement and refinement of x-ray crystallo- Research Group Tgraphic data in order to develop structural mod- Joseph M. Pieper, Undergraduate Student Researcher els of proteins. They are using resources at the Basic Katherine Volzing, Undergraduate Student Researcher Sciences Computing Laboratory for this project.

2006 Annual Research Report of the Supercomputing Institute 135 UM TC–Department of Chemical Engineering and Materials Science

Richard B. McClurg, Principal Investigator Molecular Crystal Global Phase Diagrams

hese researchers developed methods for construc- ters consistent with a molecular point group and crystal tion of molecular crystal global phase diagrams. space group symmetry by using the organic molecular TThe phase diagrams present the crystalline phase crystal structures contained in the Cambridge Structural as a function of the coefficients of a general intermolecu- Database available at the Basic Sciences Computing lar potential based on molecular symmetry-adapted basis Laboratory. The group developed a working code for functions. Using the mean-field approximation, the constructing the phase diagrams and tested the method researchers began in a high-temperature, disordered refer- for tetrahedral molecules. The phase diagrams offer a ence state, then sought spontaneous symmetry-breaking knowledge-based means to improve intermolecular phase transitions and phase structure information at potential formulation and provide a means of rational lower temperature. They then deduced potential parame- guidance for crystal engineering of homologous molecular species.

Research Group J. Brandon Keith, Graduate Student Researcher

Alon V. McCormick, Fellow Molecular-Scale Chemical Reaction Engineering of Materials Synthesis

hese researchers are using the Supercomputing through the formalism of unimolecular reaction rate the- Institute for three projects. The first involves ory and weak collision theory, taking into full account Tmodel cluster growth, which has been traditional- the energetics of cluster-monomer collision and the redis- ly described with classical nucleaution theory. This tribution that energy within the internal structure of the method approximates the net growth as monomer addi- newly formed cluster. tion and evaporation, which gives results that are at best In the second project, the researchers are modeling the several orders of magnitude different from experimental properties of a curing or drying coating using a network values. This project seeks to model cluster growth formulation. Elements are combined in novel ways to model real viscoelastic systems. The third project involves simulations of polymeriza- Research Group tion and copolymerization of multifunctional acrylates Soumendra Basu, Graduate Student Researcher and methacrylates. The researchers have developed meth- Dan O’Neal, Graduate Student Researcher ods for characterizing the properties of the population of Anand Prakash, Graduate Student Researcher species present and their distribution in space. The types Benjamin Richter, Graduate Student Researcher of structures show a promising resemblance to certain Yang Ye, Graduate Student Researcher experimental observations.

136 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemical Engineering and Materials Science

David C. Morse, Associate Fellow Computational Polymer Physics

his group’s work in computational polymer physics focuses on elucidating molecular origins Tof both equilibrium and dynamic behavior of polymer fluids. The project includes three focus areas. Research Group and Collaborator The first concerns statistical thermodynamics of self- David Ackerman, Graduate Student Researcher assembling structures of block copolymers, studied pri- Kwanho Chang, Graduate Student Researcher marily by self-consistent field theory. The second investi- Matteo Pasquali, Department of Chemical gates viscoelasticity of solutions and networks of semi- Engineering, Rice University, Houston, Texas flexible polymers, studied by Brownian dynamics simula- Shriram Ramanathan, Graduate Student Researcher tion. The third involves entanglement and slip along Amit Ranjan, Graduate Student Researcher interfaces between entangled polymer melts, studied by parallel molecular dynamics simulation.

David J. Norris, Principal Investigator Modification of Thermal Emission via Metallic Photonic Crystals

he goal of this project is to study metallic pho- ity) and thin thermal barriers for applications such as fuel tonic crystals and their ability to modify thermal cells. Fundamental research is necessary to clarify the Temission. Photonic crystals are nanostructured underlying phenomena. solids that are three-dimensionally patterned on an optical length scale. Recent research has indicated that this structure can alter the “glow” from a heated metallic photonic crystal. This may allow the elimination of unwanted heat from thermal emission sources, such as the tungsten filament in a conventional light bulb. As a light bulb is extremely inefficient due to emission of long wavelength light as heat, the ability to reduce this emis- Research Group sion could greatly increase efficiency. Furthermore, these Sang Eon Han, Graduate Student Researcher materials may also be useful for obtaining improved ther- mophotovoltaic devices (for converting heat into electric-

2006 Annual Research Report of the Supercomputing Institute 137 UM TC–Department of Chemical Engineering and Materials Science

Lanny D. Schmidt, Associate Fellow Two-Dimensional Short-Contact-Time Reactor and Catalytic Radiant Burner Modeling hort-contact-time reactors used for the partial oxi- ied for chemical manufacture for carbon monoxide dation of alkanes to make synthesis gas (syngas), (CO)-free hydrogen streams for fuel cells. This research Solefins, and oxygenates have been extensively stud- group is studying the partial oxidation of alkanes to syngas and subsequent shift of CO to CO2 to obtain pure hydrogen streams on noble metal catalysts in millisecond Research Group and Collaborators tubular reactors. A major focus is the partial oxidation of Anders Bitsch-Larsen, Graduate Student Researcher ethane to ethylene, as well as catalytic wall reactors that Paul Dauenhauer, Graduate Student Researcher couple exothermic reactions with endothermic reactions Nick Degenstein, Graduate Student Researcher in order to eliminate thermal boundary layers. All of Olaf Deutschmann, Heidelberg University, Heidelberg, these projects involve coupling reaction kinetics with Germany Bradon Dreyer, Graduate Student Researcher complex fluid dynamics to obtain models that describe Abhishek Jhalani, Graduate Student Researcher these processes. Corey LeClerc, Department of Chemical Engineering, McGill University, Montreal, Quebec, Canada Greg Panuccio, Graduate Student Researcher James Salge, Graduate Student Researcher Ramanathan Subramanian, Graduate Student Researcher Balram Suman, Graduate Student Researcher Karthik Venkataraman, Graduate Student Researcher Ed Wanat, Graduate Student Researcher Kenneth Williams, Graduate Student Researcher

L. E. Scriven, Fellow Slitting of Magnetic Tapes

any coated products are formed by first coat- This project’s goal is to investigate and understand the ing a wide (but thin) web or film and then slitting process so as to generate materials and process slitting, cutting, or punching the web to yield guidelines that optimize the edge quality of tapes formed M BAQUS a narrow tape or other shape much smaller than the orig- by slitting. The researchers are using several A inal. A general problem of the slitting process associated finite element models, including two-dimensional and with these coated products is maintaining or achieving a three-dimensional models with different cutting mecha- defect-free cut edge. Such edges are crucial for yielding nisms, a mode III fracture model to simulate the crack in products that maximize the useful surface areas of the slit the magnetic supported layer, and a plane-strain mode II component. “sliding” fracture model to study delamination. The project also includes testing of the different mechanical, fracture, and adhesive properties of the films Collaborator to be studied, with ABAQUS finite element models used Raul Andruet, Imation, Oakdale, Minnesota to complement the experimental work.

138 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemical Engineering and Materials Science

L. E. Scriven, Fellow H. Ted Davis, Fellow Physics of Fluids in Processing Technologies

hese researchers continued their investigations into computational aspects of continuum and Research Group and Collaborators Tnetwork theories of fluid physics and transport in Costas Aggelidis, Graduate Student Researcher thin layers, in films, and in porous media structures. The Costas Apostolou, Graduate Student Researcher research is part of coordinated research programs on the Soumendra Kumar Basu, Graduate Student Researcher fundamentals of liquid structure, flow, and transport in Marcio Carvalho, Department of Mechanical commercially important process technologies, such as Engineering, Pontificia Universidade Católica do Rio precision coating, drying and curing of liquid films, de Janeiro, Rio de Janeiro, Brazil injection molding, and multiphase contacting in packed Juan de Santos, Faculty Collaborator Erin Glaser, Graduate Student Researcher beds. The problems are typically multidimensional and Xiaobo Gong, Graduate Student Researcher often time-dependent, resulting in systems of coupled Makoto Komatsubara, Research Associate partial differential equations that are solved by Galerkin- Linli Meng, Graduate Student Researcher type methods with finite element techniques, Newton Jae Wook Nam, Graduate Student Researcher iteration, parametric continuation for mapping of the Yoshiaki Narukawa, Graduate Student Researcher solution space, and integration in time with differential- Daniel J. O’Neal, Graduate Student Researcher algebraic equations’ solvers. The stability of the steady- Michael Owens, Graduate Student Researcher state solutions, which leads to eigenanalysis, as well as Eungsik Park, Graduate Student Researcher their response to small sinusoidally forced disturbances, is Lyudmila A. Pekurovsky, Graduate Student Researcher also important. To obtain comprehensive results, the Harikrishnan Radhakrishnan, Graduate Student Researcher basic problem must be solved many times; this demands Vijay Rajamani, Graduate Student Researcher the speeds offered by the high-end workstations and mas- Kristianto Tjiptowidjojo, Graduate Student Researcher sive parallelization capabilities of the Supercomputing Minoru Torigoe, Mitsubishi Chemical Company, Institute. Yokohama, Japan Takeaki Tsuda, Research Associate Jill M. White, Graduate Student Researcher Anthony A. Widboom, Supercomputing Institute Undergraduate Intern Jianping Zeng, Graduate Student Researcher

2006 Annual Research Report of the Supercomputing Institute 139 UM TC–Department of Chemical Engineering and Materials Science

Michael Tsapatsis, Principal Investigator Simulations of Zeolite Nanoparticle Aging and Coalescence

hese researchers are using the Supercomputing and growth processes must be better understood in order Institute for two projects. Both of the projects to optimize synthesis conditions. In the first project, Tuse simulations to gain insight into the mecha- numerical simulations of the aging and coalescence nism that occurs during the aging and coalescence of process are performed. The simulated mechanism starts zeolite nanoparticles. The zeolite nanoparticle nucleation with all initial particles as fresh primary particles. These particles are permitted to age, going through numerous intermediate aging steps, and after some time they age to Research Group a point where they are crystalline. The model permits Jungkuy Choi, Graduate Student Researcher any of the intermediates to coalesce with crystals of any Sunho Choi, Graduate Student Researcher size to become larger crystals. The simulations provide Tracy M. Davis, Graduate Student Researcher predictions of the concentration of the intermediates, the Tim Drews, Research Associate degree of crystallinity of the particles, and the particle Shubhajit Ghosh, Research Associate Chuan He, Graduate Student Researcher size distribution as a function of time. Recently, the Hae Kwon Jeong, Graduate Student Researcher researchers have been able to predict the experimental George Karanikolos, Research Associate crystallinity as a function of time by adjusting the kinetic John Krohn, Graduate Student Researcher parameters in the model and the number of intermediate Sandeep Kumar, Graduate Student Researcher steps. Zhiping Lai, Research Associate In the second project, Monte Carlo (MC) simulations Alex Lee, Graduate Student Researcher are used to analyze Small-Angle X-ray Scattering (SAXS) Sudeep Maheshvari, Graduate Student Researcher experimental data. The MC simulations produce pair Harikrishnan Ramanan, Research Associate distance distribution functions and scattering curves that Rajiv Ranjan, Graduate Student Researcher can be compared to SAXS experiments. Comparing the Joshua Sheffel, Graduate Student Researcher Maybelle Woo, Graduate Student Researcher simulations and experiments provides insight into the size, shape, and particle size distribution of zeolite nanoparticles.

140 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemical Engineering and Materials Science

Renata M. Wentzcovitch, Fellow Simulation of Materials/Minerals at Extreme Conditions of Pressure and Temperature

hese researchers are involved in projects that study the properties of materials at extreme con- Research Group and Collaborators ditions of pressure and temperature, such as pres- T Philip B. Allen, Department of Physics and sures around 100 Mbar and temperatures greater than Astronomy, Stony Brook University, Stony Brook, 10,000 K. They investigate electronic (electrical, thermal, New York and magnetic), structural, elastic, and thermal properties Stefano Baroni, SISSA and DEMOCRITOS National of materials up to these pressure and temperature ranges. Simulation Center, Trieste, Italy The research addresses problems in geophysical and Cesar R. S. da Silva, Research Associate planetary science as well as problems relevant for elec- Pedro da Silveira, Staff tronic and magnetic materials. Recent projects include: Stefano de Gironcoli, SISSA and DEMOCRITOS studies of the nature of the earth’s lower mantle; studies National Simulation Center, Trieste, Italy of the properties of mantle materials; pressure induced Gordon Erlebacher, Florida State University, Tallahassee, Florida spin transitions in iron bearing minerals; investigations of Kei Hirose, Department of Earth and Planetary the properties of H20 ice at very low temperatures under Sciences, TIT, Japan low and high pressures; and studies of minerals at ultra- Bijaya B. Karki, Department of Computer Science and high pressures and temperatures, typical of the cores of Department of Geology, Lousiana State University, the solar giants and terrestrial extra-solar planets. Baton Rouge, Louisiana Amel Laref, Research Associate Chris Leighton, Faculty Collaborator Baosheng Li, Department of Geosciences, Stony Brook University, Stony Brook, New York Li Li, Department of Geosciences, Stony Brook University, Stony Brook, New York John Parise, Department of Geosciences and Department of Chemistry, Stony Brook University, Stony Brook, New York Marlon Pierce, Indiana University, Bloomington, Indiana Ryan Renquist, Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York Yousef Saad, Faculty Collaborator Jun Tsuchiya, Geodynamic Research Center, Ehime University, Japan Taku Tsuchiya, Geodynamic Research Center, Ehime University, Japan Koichiro Umemoto, Research Associate Don Weidner, Department of Geosciences, Stony Brook University, Stony Brook, New York Zhongqing Wu, Research Associate Yonggang Yu, Graduate Student Researcher Dave Yuen, Faculty Collaborator Dong-Bo Zhang, Graduate Student Researcher

2006 Annual Research Report of the Supercomputing Institute 141 UM TC–Department of Chemistry and Chemical Physics Program

Elizabeth A. Amin, Principal Investigator New Approaches to Zinc-Binding Metalloprotein Active Site Modeling and Inhibitor Design inc-binding proteins play critical pharmacological genesis as well as in the spread of degenerative diseases roles and have been identified as important drug such as osteo- and rheumatoid arthritis. Research in the Ztargets. Attempts to model zinc in a macromolec- Amin group focuses on the design and optimization of ular and/or nanoparticle environment, however, have targeted MMP inhibitors and the development of new, often resulted in unreliable energies and geometries, and more accurate parameters and functional forms for zinc insufficient force-field representations continue to metalloproteins. impede the drug-design process targeting important zinc- The group has recently designed and optimized several binding enzymes such as the matrix metalloproteinases in silico lead series of small-molecule, MMP-3, MMP-8, (MMPs). MMPs comprise a class of zinc-binding and MMP-13 inhibitors built on thalidomide and fatty- endopeptidases responsible for extracellular matrix pro- acid skeletons, many of which show high predicted bio- tein breakdown and are involved in tumor-related angio- logical activity. The project also investigates protein-protein interactions involved in tissue remodeling and extracellular matrix protein degradation to elucidate details of Research Group osteo- and rheumatoid arthritis-related joint breakdown. Kara B. Johnson, Supercomputing Institute Undergraduate Intern

George Barany, Principal Investigator Design and Characterization of Biomolecules From Protein Core Modules to Cyclic Peptide Nucleic Acid he engineering of stable folded and functional designed peptides consist of core elements from bovine biomolecules has recently attracted much research pancreatic trypsin inhibitor and/or B1 immuno-globulin Tattention. Within this field, the Barany group is binding domain linked by natural or designed sequences, particularly interested in the design, synthesis, and char- and they contain a strategically placed cross-link to limit acterization of protein core modules and cyclic peptic conformational space to more collapsed conformations. nucleic acid (PNA). In globular proteins, core motifs can The studies carried out by these researchers exemplify be identified and their elements can be combined in suit- new approaches and are leading to significant and gener- able peptides to construct native-like molecules. The alized insights that contribute to the protein-folding problem. Cyclic PNAs are promising candidates for generating Research Group nanotubular structures, which can be useful as new cata- Sharon Gazal, Research Associate lysts, wire conductors, or drug transport systems. The Mian Liu, Research Associate Barany group is designing cyclic PNAs by means of Larry Masterson, Graduate Student Researcher molecular modeling studies. Dan Mullen, Research Associate James Wollack, Graduate Student Researcher

142 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemistry and Chemical Physics Program

David A. Blank, Associate Fellow Simulations of Third-Order Electronically Resonant Spectroscopies

he Blank group has expanded their experimental new direction for the interpretation of four-wave mixed work on the molecular response to electronic spectroscopy of a reactive system. They are running sim- Texcitation to include a class of spectroscopies gen- ulations based on a slight modification of the standard erally known as resonant four-wave mixing. A general formalism to test the new model. formalism for numerically simulating these experiments has been worked out in the literature. These researchers have recently completed a FORTRAN 90 code based on this formalism to simulate their experimental results. These simulations will allow the group to extract the relevant physical parameters, which govern the interaction Research Group of a solute with the surrounding environment. They are Tim Lorbiecke, Graduate Student Researcher now simulating a model system that is non-reactive in Sarah Schmidtke, Graduate Student Researcher the excited state. Hannah Staack, Undergraduate Student Researcher In addition, these researchers are continuing to inves- David Underwood, Research Associate tigate systems that undergo chemical reaction in the Nathan Wells, Graduate Student Researcher excited electronic state, and have new results to suggest a

2006 Annual Research Report of the Supercomputing Institute 143 UM TC–Department of Chemistry and Chemical Physics Program

Christopher J. Cramer, Fellow Using Computational Chemistry to Investigate Phenomena of Biological and Environmental Interest he Cramer group uses supercomputing resources to stress the limit of present-day computational Tchemistry tools in order to examine large systems of relevance to one or more areas in chemistry. In gener - al, they focus on systems containing unpaired electrons (because the solution of their electronic structure is more Research Group and Collaborators (continued) complicated) or on systems containing multiple metal Pablo César Jaque Olmedo, Supercomputing Institute atoms or of a very large organic nature (because they are Research Scholar difficult to deal with without supercomputing resources). Casey Kelly, Graduate Student Researcher Furthermore, the group tries to include any condensed- Christopher Kinsinger, Graduate Student Researcher phase effects, such as solvation, into the calculations in Bethany Kormos, Graduate Student Researcher order to make them more relevant to experimental obser - Stepan Lenevich, Graduate Student Researcher vations. John Lewin, Graduate Student Researcher The researchers are working on several specific proj - Anne Lewis, Undergraduate Student Researcher Antoni Llobet, Department of Chemistry, University ects. They include: including condensed-phase effects in of Girona, Girona, Spain quantum chemical calculations; calculation of accurate Yousi Ma, Undergraduate Student Researcher multiplet splittings in open-shell systems; characteriza - Maria C. Nagan, Division of Science, Truman State tion of organometallic systems with respect to structure University, Kirksville, Missouri and reactivity; and modeling the reactive conversion of Eric Patterson, Division of Science, Truman State crystalline gallazanes to gallium nitride. University, Kirksville, Missouri James Phillips, Department of Chemistry, University of Wisconsin, Eau Claire, Wisconsin Research Group and Collaborators Cristina Pizzarini, Department of Chemistry, University of Bologna, Bologna, Italy Joshua W. Allen, Supercomputing Institute Joe Scanlon, Graduate Student Researcher Undergraduate Intern Mark Seierstad, Research Associate William Arnold, Faculty Collaborator Edward C. Sherer, Graduate Student Researcher John Bumpus, Department of Chemistry, University of George C. Shields, Department of Chemistry, Northern Iowa, Cedar Falls, Iowa Hamilton College, Clinton, New York Colin Cairns, Department of Chemistry, Drake Lee Solstad, Undergraduate Student Researcher University, Des Moines, Iowa Elizabeth Stone, Undergraduate Student Researcher Natalie Elmasry, Undergraduate Student Researcher Corey Stotts, Undergraduate Student Researcher Laura Gagliardi, Department of Physical Chemistry, Jason D. Thompson, Graduate Student Researcher University of Geneva, Geneva, Switzerland Prateek Verma, Undergraduate Student Researcher Ben Gherman, Research Associate name withheld, Graduate Student Researcher David Heppner, Undergraduate Student Researcher Paul Winget, Graduate Student Researcher Pathumwadee Intharathep, Graduate Student Nathaniel Woodrum, Graduate Student Researcher Researcher

144 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemistry and Chemical Physics Program

Mark D. Distefano, Principal Investigator Modeling the Best Inhibitor Substrates of the Protein GeranylGeranyl Transferase and Protein Farnesyl Transferase he Protein GeranylGeranyl Transferase (PGGTase) and Protein Farnesyl Transferase T(PFTase) are enzymes involved in post-transla- Research Group tional modification. The ability to block specifically Leila Albers, Graduate Student Researcher either of these enzymes with a synthetic inhibitor can Zach Bjork, Undergraduate Student Researcher lead to the elaboration of new drugs preventing cellular Amanda DeGraw, Graduate Student Researcher transformation. These researchers are using published Ben Duckworth, Graduate Student Researcher data of the crystal structure of these enzymes and their Olivier Henry, Research Associate John Hsieh, Graduate Student Researcher natural substrates to elaborate what could be the best Hao Kuang, Graduate Student Researcher analogous sites according to steric, electrostatic, and Dan Mullen, Research Associate hydrophobic interactions in the active site of the pro- Dongfeng Qi, Graduate Student Researcher teins. The researchers are using the computer-modeling Matt Rose, Graduate Student Researcher program INSIGHTII for this project. Amy Tann, Graduate Student Researcher Lynn Weyer, Graduate Student Researcher Ju-Hua Xu, Research Associate

2006 Annual Research Report of the Supercomputing Institute 145 UM TC–Department of Chemistry and Chemical Physics Program

Jiali Gao, Fellow Computer Simulation of Chemical and Biochemical Interactions

he Gao group continued their multi-faceted research concerning the dynamics and mecha- Tnism of enzyme reactions, the structure and interactions of proteins, the simulation of trajectories on protein dynamics, and solvent effects on chemical reactions and interactions in condensed phases. Their Research Group and Collaborators (continued) approach is based on statistical Monte Carlo and molecu- Pablo César Jaque Olmedo, Supercomputing Institute lar dynamics (MD) simulations, making use of combined Research Scholar quantum mechanical and molecular mechanical Huitian Jiang, Research Associate (QM/MM) potentials. Gary S. Kedziora, Research Associate The group is involved in several project areas. These Lakshmi Kesavan, Graduate Student Researcher include: the mechanism of enzymatic reactions; the Pinsker Yen-lin Lin, Graduate Student Researcher structure and interaction of proteins; the simulation of Shuhua Ma, Supercomputing Institute Research molecular transport through membrane channels; and Scholar solvent effects on chemical reactions in solutions. Dan T. Major, Research Associate Sergio Marti, Graduate Student Researcher Heather Meads, Undergraduate Student Researcher Yirong Mo, Department of Chemistry, Western Research Group and Collaborators Michigan University, Kalamazoo, Michigan Cristobal Alhambra, AstraZeneca Pharmaceuticals LP, Kwangho Nam, Graduate Student Researcher Wilmington, Delaware Sten O. Nilsson Lill, Research Associate Maria Bohorquez, Department of Chemistry, Drake Sara Nunez, Albert Einstein School of Medicine, University, Des Moines, Iowa Yeshiva University, New York, New York Kyoungrim Byun, Life Science Research Center, SK Jiayun Pang, Graduate Student Researcher Chemicals, Korea Alberto Perez, Graduate Student Researcher Alessandro Cembran, Research Associate Tina Poulsen, Leo Pharma, Valby, Denmark Jun Kyung Chung, Graduate Student Researcher Xavier Prat-Resina, Visiting Researcher Jorge M. Estevez, Graduate Student Researcher Jingzhi Pu, Graduate Student Researcher Yao Fan, Graduate Student Researcher Ramakumar Rajamani, Visiting Researcher Gareth Forde, Research Associate Kin-Yiu (Kiniu) Wong, Graduate Student Researcher Qiang Gao, Graduate Student Researcher Wangshen Xie, Graduate Student Researcher Mireia Garcia-Viloca, Institute of Biotechnology and Jiangwei Yao, Undergraduate Student Researcher Biomedicine, Bellaterra, Spain Yan Zhou, Graduate Student Researcher Christian Hensen, Graduate Student Researcher

146 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemistry and Chemical Physics Program

Jiali Gao, Fellow Jeffrey T. Roberts, Co-Principal Investigator Computational Chemistry at the Research Site for Educators in Chemistry at the University of Minnesota he Department of Chemistry at the University of Minnesota has received a National Science Research Group and Collaborators TFoundation grant to establish a Research Site for Maria Bohorquez, Department of Chemistry, Drake Educators in Chemistry (RSEC). The focus of this RSEC University, Des Moines, Iowa is interdisciplinary research in chemical biology, compu- Joseph M. Brom, Department of Chemistry, University tational chemistry, environmental chemistry, and materi- of St. Thomas, St. Paul, Minnesota als chemistry. Specific areas of research include: alkyl Colin Cairns, Department of Chemistry, Drake effect on reaction rates of hydrogen atoms with alcohols University, Des Moines, Iowa Professor Jason Halfen, Department of Chemistry, in gas and solution phases; alkoxy and alkylperoxy radi- University of Wisconsin, Eau Claire, Wisconsin cals formed in the atmosphere; complexes of substituted Keith T. Kuwata, Department of Chemistry, Macalester 1,8-naphthyrides; condensed phase effects on the struc- College, St. Paul, Minnesota ture and bonding of nitrile donor-acceptor complexes; Erin B. Petersen, Undergraduate Student Researcher mixed aggregates of lithium compounds; and electro- James A. Phillips, Department of Chemistry, chemiluminescence reactions of organic molecules in the University of Wisconsin, Eau Claire, Wisconsin solution phase. This work is being performed in collabo- Lawrence M. Pratt, Department of Chemistry, Fisk ration with researchers from Drake University, the University, Nashville, Tennessee University of St. Thomas, the University of Wisconsin– Clayton F. Spencer, Department of Chemistry, Illinois Eau Claire, Macalester College, Fisk University, and College, Jacksonville, Illinois Lukas K. Valin, Undergraduate Student Researcher Illinois College.

Wayne L. Gladfelter, Associate Fellow Mixed Fluid Dynamics and Chemical Reaction Modeling of a Combinatorial Low- Pressure Chemical Vapor Deposition Reactor his project models the behavior of a low-pressure date the chemistry involved in the formation of thin chemical vapor deposition (LPCVD) reactor that films from organometallic precursors under moderate Tis used for combinatorial LPCVD experiments. vacuum. The accuracy of the model is being confirmed The researchers used CFD-ACE+ to create a computational by direct comparison of theoretical deposition rate pro- model of the physical reactor and to create a three-step files to the physical deposition rate profiles in the surface chemical reaction mechanism using parameters LPCVD reactor. from literature and experimentation. The model includes: transport and chemical properties for the molecular species used in the model; gas-phase reaction chemistry, to increase the correlation of predicted to experimentally measured deposition rates; and kinetic parameters for the gas-phase reactions, which are taken directly from experimental work done in the Gladfelter Research Group laboratory. The group is exploring the difference between Tyler Moersch, Graduate Student Researcher gas-phase and surface reaction chemical models. Compu- Amber Runge, Undergraduate Student Researcher tational modeling of the LPCVD process will help eluci-

2006 Annual Research Report of the Supercomputing Institute 147 UM TC–Department of Chemistry and Chemical Physics Program

Marc A. Hillmyer, Principal Investigator Calculation of Block Copolymer Self-Assembly by Self-Consistent Mean-Field Theory

lock copolymers consist of chemically distinct SCMFT has recently been expanded to include the polymer chains tethered together by covalent breadth in the molecular weight distribution that is pres - Bbonds. Current understanding of block copolymer ent in all block copolymers; predictions at strong and self-assembly in melts and solutions has been a product weak degrees of incompatibility between blocks are not of the synergy between self-consistent mean-field theory in complete agreement with experiment. The researchers (SCMFT) calculations and experimental investigation. are using SCMFT and experiment to investigate the effects of the molecular weight distribution on the mor - phology, periodicity, and order-disorder transition of Research Group block copolymers in light of the disagreements between Pedro Arrechea, Graduate Student Researcher theory and experiment. Nathaniel Lynd, Graduate Student Researcher

Thomas R. Hoye, Principal Investigator Computation of Proton and Carbon Nuclear Magnetic Resonance Chemical Shifts

uclear magnetic resonance (NMR) spectroscopy absolute configurations of the molecule) of organic com - is the single most powerful spectroscopic tool pounds, including the important subset of natural (and Nfor determining the three-dimensional structure unnatural) products having useful biological activities. (i.e., stereostructure consisting of the relative and The precise stereostructure imparts the biological func - tion to such compounds. Thus, methods for determining their unambiguous stereostructure are of considerable Research Group and Collaborators value. The Hoye group has begun to develop new Ziyad Al-Rashid, Graduate Student Researcher Andrew Aspaas, Graduate Student Researcher methodologies that involve the comparison of computed Amanda L. Bialke, Graduate Student Researcher with experimental spectroscopic parameters. The two Mr. Brian Eklov, Graduate Student Researcher principal features at the very core of nearly all NMR Christopher Jeffrey, Graduate Student Researcher spectroscopic analyses are chemical shifts and coupling Junha Jeon, Graduate Student Researcher constants ( J). The researchers have had experience and Shengxiang Ji, Graduate Student Researcher success applying Js to interesting structural problems, Jim Kabrhel, Graduate Student Researcher and are now beginning to exploit chemical shifts. The Aaron May, Graduate Student Researcher new hypothesis is that comparison of computed chemical Dorian P. Nelson, Graduate Student Researcher shifts for each member of a family of possible stereoiso - Huzaifa Rangwala, Graduate Student Researcher mers with the experimental chemical shifts for a single Troy Ryba, Graduate Student Researcher Elena P. Sizova, Graduate Student Researcher stereoisomer for which the relative configuration is not Feng Shao, Graduate Student Researcher yet known, will allow the configuration of that com - Liansheng Su, Graduate Student Researcher pound to be deduced with confidence. Jizhou Wang, Graduate Student Researcher Jennifer Werness, Undergraduate Student Researcher name withheld, Graduate Student Researcher Peng Zhao, Graduate Student Researcher

148 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemistry and Chemical Physics Program

Steven R. Kass, Associate Fellow Understanding Organic Systems via Molecular Orbital Calculations

he Kass group is continuing to carry out ab initio molecular orbital and density functional calcula- Research Group and Collaborators Ttions on a variety of chemical systems. The Mark Engen, Department of Chemistry, Winona State researchers pay particular attention to zwitterions (critical University, Winona, Minnesota species in biological processes), reactive intermediates Alireza Fattahi, Research Associate (key intermediates in numerous chemical and industrial Lev Lis, Research Associate processes), and antiaromatic compounds (potential sub- Matthew Meyer, Graduate Student Researcher strates for the design of novel materials). These results aid Bill Moldestad, Jr., Undergraduate Student Researcher in the design and interpretation of experimental data. Caroline E. Newcombe, Supercomputing Institute Undergraduate Intern Lawrence M. Pratt, Department of Chemistry, Fisk University, Nashville, Tennessee ZhiXin Tian, Research Associate

Doreen G. Leopold, Principal Investigator Computational and Anion Photoelectron Spectroscopic Studies of Bare and Partially Ligated Metal Clusters hese researchers are performing density functional clarify the assignments of the observed isomers and elec- theory (DFT) studies on small metal-containing tronic states, while also providing insight into unob- Tmolecules, which they also study experimentally served properties. The researchers have recently been using anion photoelectron spectroscopy. These gas-phase studying the molecule CrCu and its anion CrCu-; they experimental studies focus primarily on bare or partially plan to expand their investigations to include other het- ligated neutral and negatively charged transition metal eronuclear diatomics, such as YCu. clusters containing up to about 10 metal atoms. The combination of experimental and computational studies helps elucidate the interpretation of the spectroscopic data, while also potentially providing useful benchmarks to aid in the further development by other researchers of accurate and efficient computational methods. Measurements provided by the photoelectron spectra Research Group include electron affinities, energy differences among Beau Barker, Graduate Student Researcher ground and low-energy electronic states, and vibrational Stephen Richard Miller, Graduate Student Researcher frequencies. DFT calculations of these properties can

2006 Annual Research Report of the Supercomputing Institute 149 UM TC–Department of Chemistry and Chemical Physics Program

Kenneth R. Leopold, Associate Fellow Computational Studies of Reactive Molecular Complexes

his group’s research involves carrying out quan- spectroscopic experiments by providing information tum chemical calculations on molecular complex- about bond energies and electronic structure that is not Tes containing reactive moieties. In part, these otherwise available from experiments. Thus, the combi- studies represent the group’s continuing efforts to eluci- nation of theory and experimental spectroscopy provides date the effects of near-neighbor interactions on chemical a particularly complete picture of the systems the group processes. A recurring theme in this work has also been studies, one that could not be obtainable from either the- the study of atmospherically active molecules. Supercom- ory or experiment alone. puting Institute resources enhance ongoing microwave Ongoing and future work involves the calculation of barriers to internal motion in molecular complexes and the study of systems containing an open-shell moiety. Research Group Carolyn Brauer, Graduate Student Researcher Matthew Craddock, Graduate Student Researcher Erik Grumstrup, Undergraduate Student Researcher Galen Sedo, Graduate Student Researcher

Kent R. Mann, Principal Investigator Prediction and Simulation of Variable-Temperature 1H NMR of Quinoid Oligothiophese hese researchers have prepared thiophene olio- perature 1H nuclear magnetic resonance (NMR) results gomers for use as semiconducting materials in have shown that in solution these molecules undergo Tboth n-type and ambipolar thin-film transistors. conformational isomerization at relatively low tempera- They are focusing on one group of oligothiophene mole- tures. cules with a quinoid structure. X-ray crystallographic The group is now performing high-level molecular studies of this family of molecules have shown that they orbital calculations for these quinoidal molecules. They adopt a trans conformation (with respect to the thio- are using the Cambridge database for structure correla- phene rings) in the solid state. Interestingly, variable-tem- tions and are using NMR software available at the Supercomputing Institute to predict the chemical shifts of various quinoidal isomers. They are also using the Research Group software package MATHEMATICA to set up and solve the Michael Burand, Graduate Student Researcher secular equations for the time-dependent NMR Jason Burney, Graduate Student Researcher Hamiltonian and then to extract the imaginary part of Brendan Gordon, Graduate Student Researcher the NMR lineshape function obtained so that they can Kari Mitchell, Graduate Student Researcher perform non-linear curve fitting of the experimental spectra.

150 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemistry and Chemical Physics Program

Kristopher McNeill, Principal Investigator Computational Studies in Environmental Chemistry

hese researchers have begun taking a computational chemistry approach to their research into Research Group Tchemical problems of environmental interest. Anne Boreen, Graduate Student Researcher They have used nuclear magnetic resonance software Scott Brown, Graduate Student Researcher available through the Supercomputing Institute and plan Jeffrey M. Buth, Graduate Student Researcher to undertake electronic structure calculations using semi- Eric Castro, Graduate Student Researcher empirical and ab initio methods. The group is currently Angela DeGreeff, Graduate Student Researcher working on two project areas, chlorocarbon pollution Betsy Edhlund, Graduate Student Researcher Derek Fox, Graduate Student Researcher and pharmaceutical pollutants in surface waters. Joseph Fritsch, Graduate Student Researcher Matthew Grandbois, Graduate Student Researcher Sarah Kliegman, Graduate Student Researcher Douglas Latch, Graduate Student Researcher Laura MacManus-Spencer, Graduate Student Researcher Ann McNally, Graduate Student Researcher Alicia Peterson, Graduate Student Researcher Kris Wammer, Research Associate Jeff Werner, Graduate Student Researcher

Karin M. Musier-Forsyth, Principal Investigator Homology Modeling of the Escherichia coli Proline tRNA Synthetase and Human ProX Protein hese researchers are working to develop a three- homolog of the insertion/editing domain of E. coli dimensional homology model of the Escherichia ProRS. They are performing computational studies using Tcoli proline transfer ribonucleic acid synthetase molecular docking and MD simulations to study the (ProRS). Using this new model, they plan to study inter- editing activity of this human protein. actions of insertion domain with the catalytic site residues in the presence of substrate, and to dock modified proline analogs onto the active site of the enzyme and perform molecular dynamics (MD) simulations to identify different side-chains of ProRS that are critical for substrate binding. These studies will allow the group to narrow the choices for their experimental work, targeted Research Group at designing E. coli ProRS active site mutants that will Sanchita Hati, Research Associate recognize and activate non-cognate, modified proline Mithun Mitra, Graduate Student Researcher residues. Mahadevan Seetharaman, Research Associate The group is has also created a three-dimensional My-Nuong Vo, Graduate Student Researcher model of a freestanding human protein, ProX, a

2006 Annual Research Report of the Supercomputing Institute 151 UM TC–Department of Chemistry and Chemical Physics Program

R. Lee Penn, Principal Investigator Investigations of Faults in Nanocrystalline Material

obalt oxyhydroxide is a nanocrystalline material material. Quantifying the extent of faulting present in a consisting of laminar sheets of edge-sharing material, however, relies heavily on powder x-ray diffraction (XRD) and transmission electron microscopy CCoO6 octahedra that are joined by hydrogen bonding. Crystallographics faults in this stacking (TEM) as means to directly examine the crystal struc- sequence generate new surface types, which can in turn ture. By simulating XRD and TEM results for crystals affect many characteristics of the resulting particles. The with known stacking arrangements and comparing these presence and extent of thes faults is believed to influence simulations to experimental results, it is hoped that accu- the electrical properties, the rate of surface reactions, and rate assessment of the stacking order will be possible the ratio of products produced by dissolution of the

Research Group Sandeep Kumar, Graduate Student Researcher Jason Myers, Graduate Student Researcher

152 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemistry and Chemical Physics Program

J. Ilja Siepmann, Fellow Molecular Simulations of Phase Equilibria and Development of Transferable Force Fields and Efficient Monte Carlo Algorithms he Siepmann group uses Monte Carlo simulations to investigate self-aggregation, phase behav- Research Group and Collaborators Tior, and partitioning in polar and non-polar bulk Kelly E. Anderson, Graduate Student Researcher fluids and in heterogeneous and interfacial systems. In Divesh Bhatt, Supercomputing Institute Research particular, their efforts are directed to investigating the Scholar retention processes in gas-liquid and reversed-phase liq- Bin Chen, Department of Chemistry, Louisiana State uid chromatography, the solvation mechanisms in super- University, Baton Rouge, Louisiana critical extraction systems, in gas-expanded liquids, and Erin Dahlke, Graduate Student Researcher in micellar surfactant solutions. The group is developing Dylan Drake-Wilhelm, Undergraduate Student Researcher the Transferable Potentials for Phase Equilibria (TraPPE) Becky L. Eggimann, Graduate Student Researcher force field and contributes to the development of effi- Chad Geppert, Graduate Student Researcher cient Monte Carlo algorithms for complex molecules. Junseok Lee, Graduate Student Researcher Further application areas are vapor-liquid and vapor-solid Katie A. Maerzke, Graduate Student Researcher nucleation phenomena, polymorphism of pharmaceutical Edward J. Maginn, Department of Chemical and solids, and element partitioning in the earth’s core. Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana Matthew J. McGrath, Graduate Student Researcher Jeffrey J. Potoff, Department of Chemical Engineering, Wayne State University, Detroit, Michigan Jake L. Rafferty, Graduate Student Researcher Neeraj Rai, Graduate Student Researcher Mark R. Schure, Theoretical Separation Science Laboratory, Rohm and Haas Company, Spring House, Pennsylvania John M. Stubbs, Department of Chemistry, Grinnell College, Grinnell, Iowa Li Sun, Graduate Student Researcher Collin D. Wick, Chemical Science Division, Pacific Northwest National Laboratory, Richland, Washington Ling Zhang, Graduate Student Researcher Xin (Sophia) Zhao, Graduate Student Researcher Nikolay D. Zhuravelev, Graduate Student Researcher

2006 Annual Research Report of the Supercomputing Institute 153 UM TC–Department of Chemistry and Chemical Physics Program

Marian T. Stankovich, Principal Investigator Jiali Gao, Fellow Investigations Into Acyl-CoA Dehydrogenase

cyl-CoA dehydrogenases (ACD) are a group of trajectories of these simulations and their analysis could flavoenzymes that are key players in the electron shed new light on our understanding how the local active Atransport chain related to the β-oxidation of fatty site environment as well as distantly situated residues reg- acids. They are of intense biomedical interest, as muta- ulates these redox quantities. tions are the known cause for several of the life-threaten- Another area of interest for these enzymes is the ing metabolic diseases. Exploring the role of these muta- intensely debated catalytic mechanism. The α,β-dehy- tions (sometime situated far away from the catalytic site) drogenation reaction of fatty acid acyl-CoA, catalyzed by on catalysis as well as redox equilibria is very challenging. these enzymes, is composed of two distinct steps—a pro- Enzyme active site plays the most significant role in ton abstraction and a hydride transfer. It is as yet unclear controlling electron transfer in redox enzymes. These whether the two steps are concerted or stepwise. The researchers are using explicit molecular dynamics free recently completed potential of mean force calculation energy simulation to model the redox changes in these for the medium chain ACD indicates that the mecha- enzymes. Structural variations obtained from dynamic nism is stepwise and shows that the two-step (proton abstraction and hydride transfer) have similar reaction barriers. This group is therefore interested in calculating Research Group the rate constant and kinetic isotope effect by including Sudeep Bhattacharyay, Research Associate quantum mechanical contributions for the medium chain enzyme.

Andreas Stein, Principal Investigator Understanding Interfacial Interactions of Synthetic Clay/Polymer Nanocomposites

omposites of polymers with small quantities of were designed for facile dispersion in specific polymers. inorganic nano-lamellar solids have great poten- Using these layered solids, they are preparing nanocom- Ctial to increase polymer modulus and to decrease posites with nonpolar and polar polymers with a particu- permeability, thermal expansion, and flammability while lar focus on producing polymer nanocomposites with maintaining low density and optical clarity. Natural clays enhanced structural and barrier properties. Current are a logical source of inorganic nano-lamellae, but research focuses on matching the compatibility between despite extensive research, the potential property the synthetic clays and polyesters or polyolefins by enhancements have not been achieved, especially with appropriate surface functionalization of the clay. The nonpolar polymers. researchers are using resources at the Basic Sciences These researchers have recently developed several new Computing Laboratory for this project. nano-lamellar solids with surface functional groups that

Research Group Fan Li, Graduate Student Researcher

154 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemistry and Chemical Physics Program

T. Andrew Taton, Principal Investigator Complementary Assembly of Hard and Soft Nanomaterials

hese researchers use mesoscale, molecular dynam- with the goal of designing nanomaterial components that ics simulations to investigate how nanostructured will self-assemble into particular arrangements and mor- Tsoft materials such as block copolymers and liq- phologies. uid crystalline polymers respond to the presence of inorganic nanostructures such as nanospheres and nanorods. They recently demonstrated that metal nanorods can seed anisotropic domains of both block and liquid crystalline polymers in which the direction of anisotropy is dictated by the orientation of the rod. Dynamic density functional theory simulations illustrate this process on the nanoscale, and show that control over polymer orientation is initiated at the disorder-to-order transition by surface wetting on the nanorod, followed by propagation Research Group of order into the bulk polymer. The group is continuing Castro Laicer, Graduate Student Researcher their work by applying this same methodology to other self-assembling polymer systems in bulk and solution,

2006 Annual Research Report of the Supercomputing Institute 155 UM TC–Department of Chemistry and Chemical Physics Program

Donald G. Truhlar, Fellow Computational Chemical and Biochemical Dynamics

he Truhlar group conducts research in the following areas: the structure, dynamics, and thermodynamics of few-body systems; the thermal and T Research Group and Collaborators (continued) photochemical reaction dynamics of organic, metal- Keith Kuwata, Department of Chemistry, Macalester organic, and enzymatic systems; combustion kinetics and College, St. Paul, Minnesota atomospheric kinetics; the structure of water clusters and John Le, Graduate Student Researcher solid water; hydrogen diffusion in solid oxides; the struc- Jill Leas, Undergraduate Student Researcher ture and reactivity of nanoparticles; electrochemistry; Zhenhua Li, Research Associate catalysis; photochemistry; new methods for electronic Hai Lin, Research Associate Benjamin Lynch, Supercomputing Institute Research Scholar structure calculations; and the influence of solvation on Vanessa Audette Lynch, Graduate Student Researcher structure and dynamics in water, organic liquids, envi- Steven L. Mielke, Department of Chemistry, Northwestern ronmental media, ionic liquids, and supercritical liquids. University, Evanston, Illinois This research utilizes quantum mechanical, quantum sta- Masato Nakamura, College of Science and Technology, Nihon University, Funabashi, Japan tistical, semiclassical, and classical mechanical methods. Shikha Nangia, Graduate Student Researcher The researchers use both serial and parallel computer Shivangi Nangia, Graduate Student Researcher codes designed to run on the supercomputers; most of Pablo César Jaque Olmedo, Supercomputing Institute these have been developed by this group, but they also Research Scholar use electronic structure and molecular modeling packages Michelle Orthmeyer, Undergraduate Student Researcher Piotr Paneth, Department of Chemistry, Technical University that they have specially modified for their work. of Lodz, Lodz, Poland Lawrence R. Pratt, Department of Chemistry, Fisk University, Nashville, Tennesse Thomas J. Preston, Supercomputing Institute Undergraduate Research Group and Collaborators Intern Joseph M. Brom, Research Associate Jingzhi Pu, Research Associate Luis M. Campos, Department of Chemistry and Bala Ramu Ramachandran, Department of chemistry, Biochemistry, University of California, Los Angeles, Louisiana Tech University, Ruston, Louisiana California Michal Rostkowski, Graduate Student Researcher Arindam Chakraborty, Graduate Student Researcher Jose Javier Ruiz Pernia, Institute of Molecular Science, Adam Chamberlin, Graduate Student Researcher Universitate de Valencia, Burjassot,Valencia, Spain Christopher J. Cramer, Faculty Collaborator María Luz Sánchez Mendoza, Department of Chemical Erin Dahlke, Graduate Student Researcher Physics, Universidad de Extremadura, Badajoz, Spain Agnieszka Dybala, Institute of Applied Radiation Chemistry, Nathan Schultz, Graduate Student Researcher Technical University of Lodz, Lodz, Poland Grazyna Staszewska, Institute of Physics, Nicholas Benjamin A. Ellingson, Graduate Student Researcher Copernicus University, Torun, Poland Antonio Fernandez-Ramos, Department of Chemistry, Przemek Staszewski, Medical School, Biomedical Sciences Universidade de Santiago de Campostela, Santiage de and Medical Informatics, Nicholas Copernicus University, Campostela, Spain Torun, Poland Nuria Gonzalez Garcia, Department of Chemistry, Clayton Spencer, Department of Chemistry, Illinois College, Universitat Autònoma de Barcelona, Barcelona, Spain Jacksonville, Illinois Ian R. Haken, Supercomputing Institute Undergraduate Daniel Theis, Graduate Student Researcher Intern Jason Thompson, Mayo Proteomics Research Center, Mayo Sonia Ilieva, Department of Chemistry, University of Sofia, Clinic College of Medicine, Rochester, Minnesota Sofia, Bulgaria Oksana Tishchenko, Research Associate Mark Iron, Research Associate Rosendo Valero, Supercomputing Institute Research Scholar Ahren Jasper, Supercomputing Institute Research Scholar Yuan Zhang, Research Associate Kara B. Johnson, Supercomputing Institute Undergraduate Yan Zhao, Graduate Student Researcher Intern Chaoyuan Zhu, Research Associate

156 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Chemistry and Chemical Physics Program

Gianluigi Veglia, Principal Investigator New Computational Methods for the Determination of Structure and Dynamics of Membrane-Protein Assembly From Nuclear Magnetic Resonance Data he goal of this project is to find ways to refine the and solid-state nuclear magnetic resonance spectroscopy; existing structures of free membrane proteins and and to develop new computational techniques to refine Ttheir assembly. The long-term goal is to develop a the structure of protein complexes between integral systematic computational approach to simultaneously membrane proteins and between soluble proteins and study the structure, dynamics, and complexes between membrane-bound proteins. membrane proteins and soluble proteins. The project has the following aims: to develop new Research Group computational approaches to refine the structures of Andrew Bierbaum, Undergraduate Student Researcher globular proteins using both structural and dynamics Nathan Traaseth, Graduate Student Researcher constraints; to implement new force fields with implicit Larry Masterson, Graduate Student Researcher solvent treatment for refining the structures of mem- Kim Ha, Graduate Student Researcher brane proteins using constraints deriving from solution Lei Shi, Graduate Student Researcher

Darrin M. York, Associate Fellow Multiscale Quantum Models for RNA Catalysis

his project involves concurrent development and application of theoretical methods to model the molecular mechanisms of ribonucleic acid (RNA) Research Group and Collaborators T George Giambasu, Graduate Student Researcher catalysis. The particular focus of the project is on five Timothy Giese, Graduate Student Researcher main areas that integrate method development and appli- Brent Gregersen, Graduate Student Researcher cation. These include: development of generalized solvent Francesca Guerra, Department of Chemistry, boundary and many-body force field methods for molec- University of Calabria, Arcavacata di Rende (CS), ular simulation; construction of a database of quantum Italy calculations for RNA catalysis; design of new semiempir- Xabier Lopez, Department of Chemistry, Euskal ical Hamiltonian models for phosphoryl transfer reac- Herriko Universitatea, San Sebastian, Spain tions; application of hybrid quantum mechanical/molec- Yun Liu, Graduate Student Researcher ular mechanical methods to phosphate hydrolysis reac- Evelyn Mayaan, Graduate Student Researcher tions in enzymes and ribosymes; and development and Adam Moser, Graduate Student Researcher application of linear-scaling methods for deoxyribonucle- Kwamgho Nam, Graduate Student Researcher Olalla Nieto Faza, Supercomputing Institute Research ic acid and RNA systems. Scholar The application focus of this project is currently on Kevin Range, Graduate Student Researcher the study of non-enzymatic hydrolysis and transphospho- Alvaro Sanchez-deAndres, Graduate Student Researcher rylation reactions in solution, and on three prototype Carlos Silva Lopez, Graduate Student Researcher ribozyme and enzyme systems, namely, the hammerhead, Ismael Tejero-Villagrasa, Department of Physical hairpin, and hepatitis delta virus ribozymes. The Chemistry, Universitat Autonoma de Barcelona, researchers hope to provide new insight into nucleic acid Barcelona, Spain structure and stability and shed light into the molecular Curtis Wray, Undergraduate Student Researcher mechanisms of RNA catalysis.

2006 Annual Research Report of the Supercomputing Institute 157 UM TC–Department of Chemistry and Chemical Physics Program

Xiaoyang Zhu, Principal Investigator Determination of Excited Electronic States at Metal/Molecule Interfaces Using Quantum Chemistry Computational Methods hese researchers are determining the excited elec- electronic structure for short-chain alkane thiols, such as tronic structure of a variety of molecules deposit- methyl thiol, absorbed on a Au(111) cluster. Through a Ted on metal surfaces. The goal of this research is collaboration with the group of Professor Truhlar, they to provide interpretation of experimentally measured are determining the appropriate computational method two-photon photoemission spectra obtained by this to model the system and subsequently match it to the group. The first focus is the determination of the excited experimental data.

Research Group Loren Kaake, Graduate Student Researcher Chad Lindstrom, Graduate Student Researcher Matthias Muntwiler, Research Associate

UM TC–Department of Civil Engineering

William A. Arnold, Principal Investigator A Computational Chemistry Study of the Reduction of Disinfection Byproducts

hen drinking water is disinfected by chlorina- Current work has focused on developing a relationship tion, a large number of small halogenated between one-electron reduction potential and group elec- Worganics, including trihalomethanes, tronegativity values to facilitate reduction potential value haloacetic acids, halonitromethanes, haloketones, and prediction without extensive calculations. haloacetonitriles, are produced. Many of these compounds are known or suspected carcinogens. This researcher is studying the chemical reduction reactions that may be important in the fate of these compounds. There is little available information about potential reaction products, and no parameters exist that could be used to develop predictive linear free energy relationships. The goal of this project is to conduct a computational chemistry study to investigate potential mechanisms and pathways of disinfectant byproduct transformation in aqueous solution.

158 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Civil Engineering

Steven L. Crouch, Principal Investigator Sofia G. Mogilevskaya, Co-Principal Investigator Analysis of Viscoelastic Planes, Elastic Solids, and Transient Heat Conduction

hese researchers are using Supercomputing which the boundary displacements and tractions are rep- Institute resources for three projects. In the first, resented by truncated series of surface spherical harmon- Tthey are investigating the problem of an infinite ics and are running it on the supercomputers. isotropic viscoelastic plane containing an arbitrary num- The third project is concerned with a transient heat ber of circular holes and elastic inclusions. They devel- conduction problem of an infinite two-dimensional oped a time stepping boundary integral approach, but medium with multiple circular cavities. These researchers this approach is weakened by the fact that it assumes a have developed a semi-analytical method of solution that constant viscoelastic Poisson ratio. To consider the time- is capable of accurately computing the temperature and dependent viscoelastic Poisson ratio, they have developed heat flux at any point and any time, without the need to a new approach that is based on a temporal integral consider a series of discrete time steps. They are testing equation and are testing this new approach using ANSYS. their approach by a comparison of their results with the The second project investigates the problem of an infi- numerical results obtained with ANSYS. nite elastic solid containing an arbitrary number of randomly distributed spherical cavities and inclusions. The researchers have developed an efficient and accurate algo- Research Group rithm based on a spectral method is implemented in Elizaveta Gordeliy, Graduate Student Researcher Yun Huang, Graduate Student Researcher Hamid Sadraie, Graduate Student Researcher

Bojan Guzina, Associate Fellow Fast Solutions for Elastic-Wave Imaging of Solid Bodies

he aim of this research project is the development medical diagnosis. Specific techniques used include the of an advanced analytical and computational linear sampling method and the concept of topological Tframework for the rapid, three-dimensional imag- sensitivity. ing of subterranean obstacles using elastic (i.e., seismic) waves. It is an inverse scattering problem focused on resolving the location and shape of underground inclu- Research Group and Collaborator sions from non-invasive measurements performed on the Yuejian Cao, Graduate Student Researcher group surface. The researchers are using the supercom- Alejandro Martinez Castro, Graduate Student puters to develop an efficient numerical technique for Researcher the inverse scattering problem that would account for the Ivan Chikichev, Graduate Student Researcher full three-dimensional nature of the induced wave propa- Andrew Madyarov, Graduate Student Researcher gation. In addition, they are systematically and rigorously Sylvain Nintcheu, Computer Science and Mathematics tackling the associated forward scattering problem. An Division, Oak Ridge National Laboratory, Oak imaging approach for the rapid identification of subsur- Ridge, Tennessee face obstacles using be especially useful in defense appli- Kairat Tuleubekov, Graduate Student Researcher cations, oil prospecting, construction in urban areas, and

2006 Annual Research Report of the Supercomputing Institute 159 UM TC–Department of Civil Engineering

Jerome F. Hajjar, Associate Fellow Computer Studies of Structures

hese researchers have been involved in two proj- The goal is to develop parametric equations that could ects involving computer modeling of structures predict the fatigue strength for any socket connection Twith the goal of improving their resistance to geometry. fatigue. The first deals with the kind of tube/plate con- The objective of the second project, completed this nections used on sign, signal, and highmast lighting year, was to develop a reliability-based performance-based structures, which often fail because of wind-induced design methodology for earthquake engineering of com- vibration and fatigue. The researchers are conducting a posite steel/concrete building structures consisting of rec- finite element parametric study on the behavior of these tangular concrete-filled steel tube columns and steel gird- connections, called socket connections, by varying the ers. The study involved comprehensive demand evalua- tube slenderness, ring thickness, number and diameter of tion of a series of multi-story two-dimensional and three- anchors, and whether the tube is round or polygonal. dimensional composite frame structures.

Research Group Cenk Tort, Graduate Student Researcher

Raymond M. Hozalski, Principal Investigator Modeling Perchloroethylene Degradation in Anaerobic Aquifers

hese researchers have developed a finite-differ- stimulate growth of H2-utilizing dechlorinating bacteria. ences computer model to simulate per- One potential obstacle is that H2-utilizing dechlorina- Tchloroethene (PCE) dechlorination in an anaero- tors must compete with other H2-utilizing microbial bic aquifer using a membrane-curtain permeable-barrier populations. Initial modeling work assumed that H2-uti- approach. One implementation of this approach might lizing methanogens would be the primary competing be to install woven gas-permeable hollow-fiber mem- population. Soil column studies, however, have indicated that the competing population may actually be H -utiliz- brane fabric within a trench and supply H2 gas to the 2 membranes, from which it would be transferred directly ing homoacetogens. The researchers modified their to the groundwater without causing bubbles. This would model to incorporate H2 utilization by homoacetogens and ran simulations to test whether H2-derived acetate can serve as a significant electron donor source for down- gradient dechlorinator populations. Collaborator Lee Clapp, Department of Environmental Engineering, Texas A&M University, Kingsville, Texas

160 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Civil Engineering

Mihai Marasteanu, Principal Investigator Low-Temperature Cracking of Asphalt Concrete Pavements

ood fracture properties are an essential require- to predict the crack propagation in the asphalt mixture ment for asphalt pavements built in the northern samples. Additionally, they performed computational Gpart of the United States and in Canada, for analysis of experimental data of asphalt specimen testing which the prevailing failure mode is cracking due to low- including analysis, computer simulation, and new imag- temperature shrinkage stresses. Current specifications ing of data performance. address this issue through the use of strength and creep tests performed on un-notched samples. An increasing number of researchers have realized the limitations associated with predicting true fracture properties based on tests of these samples. As a consequence, a number of studies have started to investigate the application of the more complex fracture mechanics concepts to the behavior of bituminous materials. These researchers investigat- Research Group and Collaborator ed the use of the semicircular bend test to determine the Xue Li, Graduate Student Researcher low temperature fracture properties of asphalt mixtures. They developed a finite element program using ABAQUS

Taichiro Okazaki, Principal Investigator Finite Element Simulation of Seismic Steel Building Structures

he objective of this project is to analyze the seis- lytical results are then calibrated against test data. The mic performance of steel building structures. researchers are studying a variety of design issues using TBuilding structures are designed to resist seismic parametric studies. forces by undergoing inelastic deformation in a ductile fashion. The inelastic deformations concentrate near the connections of structural members. In steel structures, the high stresses and strains generated near these region, as well as changes in geometry and material properties, make the connections particularly vulnerable to fracture. Such connections include the beam-to-column connections and column base connections. These researchers are using finite element analysis to investigate the correlation between the configuration of the structure and the likelihood of fracture at the connections. They combine ana- Research Group lytical information with fracture mechanics concepts to Bulent Mercan, Graduate Student Researcher predict fracture-induced failure of connections. The ana-

2006 Annual Research Report of the Supercomputing Institute 161 UM TC–Department of Civil Engineering

Arturo Schultz, Principal Investigator Catherine W. French, Co-Principal Investigator Stability of Prestressed Concrete Through-Girder Pedestrian Bridges Under Lateral Impact restressed concrete through-girder pedestrian specifications promoted by the American Association of bridges, in which two prestressed bridge girders State Highway and Transportation Officials. The Psupport a deck on the bottom flanges, are easy to researchers are investigating the ductility and strength construct, economical, and durable. These researchers are characteristics of prestressed concrete bridge girders ana- investigating two safety issues regarding these bridges. lytically and have proposed modifications to correct for The first is the ductility of the prestressed concrete gird- errors. ers. These girders are long-span members and require a The second issue is the strength and stability of these large amount of prestressing steel to prevent sagging of bridges when subjected to vehicle impact. The the bridge under its own weight. As a result, the girders researchers are investigating strength and stiffness charac- do not meet current ductility requirements in the design teristics of connections among different parts of the bridge both numerically and experimentally. In parallel, they are working on new details, including alternate deck and railing systems and/or alternate connection schemes, Research Group to improve stability of the bridge. Eray Baran, Graduate Student Researcher

Michael J. Semmens, Principal Investigator Behavior of Aerated Membrane-Supported Biofilms in Crossflow

his project extends an existing FEMLAB model treatment. The researchers have completed work on a that has been developed to examine the growth single bacterial species and are continuing their research Tof biofilm on parallel hollow fiber membranes. with multiple species of bacteria that function synergysti- The membranes are aerated and supply the biofilm with cally in a single biofilm. oxygen. Wastewater flows between the membranes and a biofilm grows on the membranes. This biofilm grows together since the membranes are spaced closely to each other. The result is a continuous biofilm that can provide a high level of treatment in a very short detention time. This system has great practical application in wastewater

Research Group Ali Reza Admadi Motlagh, Graduate Student Researcher

162 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Civil Engineering

Carol K. Shield, Principal Investigator Catherine W. French, Co-Principal Investigator Application of Precast Decks and Other Elements to Bridge Structures

he Minnesota Department of Transportation Once the analysis is complete, the researchers can use the (MnDOT) has developed a new design for a results along with data from the bridge and laboratory Tbridge system that utilizes precast concrete ele- experiments to determine if this bridge performs satisfac- ments and has a partially precast deck system. During torily or if there are changes that must be made to the the design process, attention was given to certain features design. of the design in order to lower the chances for development of reflective cracking in the cast-in-place concrete. Together with MnDOT, these researchers have developed an instrumentation plan for the bridge along with plans Research Group for some laboratory experiments that will allow them to Charles Bell, Graduate Student Researcher detect whether or not these cracks have developed or will Yuying Hu, Graduate Student Researcher develop. They have decided to also use finite element Matthew J. Smith, Graduate Student Researcher modeling to check some of the design assumptions and to see if there are other issues that have been overlooked.

Vaughan R. Voller, Associate Fellow Fixed Grid Method for Simulating Dendritic Crystal Growth

n the mid-1980s, K. H. Tacke created an enthalpy method directed at solving the formation of a den- Idritic crystal in an undercooled melt. This approach required the application of a number of growth rules and, due to the limited computer resources of that time, could only be operated on relatively coarse grids. The object of this project was to revisit the Tacke solution. This involved modification of the approach: streamlining of the growth rules and application on finer grids. The results indicate that this is a cost-effective alternative to phase-field and level set calculations. The researcher used Supercomputing Institute resources in order to operate the model on two-dimensional and three-dimensional fine grids.

2006 Annual Research Report of the Supercomputing Institute 163 UM TC–Saint Anthony Falls Laboratory

Roger E. A. Arndt, Associate Fellow Partially and Fully Cavitating Flows

avitation is an important consideration in a vari- and turbines is increased and hydrofoil ships are designed ety of important engineering applications involv- for higher speeds, it becomes necessary to design lifting Cing liquid flow. As the performance of pumps surfaces that can operate effectively in the cavitating mode. The Arndt group’s research indicates that sheet/cloud cavitation is a highly complex and very Research Group and Collaborators important subset of the overall problem. Their earlier Lucas Gomez Fontecha, Graduate Student Researcher work has investigated the highly periodic formation of Damien T. Kawakami, Graduate Student Researcher cloud cavitation that leads to a highly structured wake Morten Kjeldsen, Norwegian University of Science and consisting of vortical clouds of bubbles. This phenome- Technology, Trondheim, Norway non leads to unsteady lift that cannot be accurately pre- James E. Kopriva, Graduate Student Researcher dicted at this stage. The group has now extended their Qiao Qin, White Hydraulics, Inc., Hopkinsville, numerical research to include fully cavitating and venti- Kentucky lated flows. Their aim is to develop the computational Hong Wang, Graduate Student Researcher tools to study a variety of cavitation problems. They are Martin Wosnik, Research Associate supplementing their computational efforts with detailed experimental work in a high-speed water tunnel.

Efi Foufoula, Fellow Wavelet-Based Multifractal Analysis of Rainfall, Atmospheric Turbulence, and Landscape everal geophysical signals, including precipitation in topography, among others, have been found to exhibit space and time, turbulent velocity fluctuations in statistical scale invariance. Analysis of these signals has Sthe atmospheric boundary layer, and landform been influenced by methods used in turbulence such as multifractal formalism. This formalism relates the scale- dependence of the statistical moments of turbulent veloc- Research Group ity fluctuations to the intermittent and multifractal Sukanta Basu, Graduate Student Researcher nature of the points at which abrupt local increases of Boyko Dodov, Research Associate velocities exist. Recently, wavelet-based multifractal Chandana Gangodagamage, Graduate Student analysis methodologies, which offer important advan- Researcher Rohit Gupta, Graduate Student Researcher tages compared to the traditional multifractal formalism, Daniel Harris, Research Associate have been explored for turbulence but have not yet been Bruno Lashermes, Graduate Student Researcher explored for the multifractal analysis of geophysical sig- Deborah Nykanen, Graduate Student Researcher nals. The goal of this research project is to re-examine Carl G. Peterson, Supercomputing Institute the scaling structure of rainfall, atmospheric turbulence, Undergraduate Intern and landscape features using wavelet-based methodolo- Roshan Shrestha, Supercomputing Institute Research gies and in particular the Wavelet Transform Modulus Scholar Maxima (WTMM) partition function method, and the Jamie Smedsmo, Graduate Student Researcher magnitude cumulant analysis method. Nikos Theodoratos, Graduate Student Researcher Lisa Tilman, Graduate Student Researcher Venugopal Vuruputur, Research Associate

164 2006 Annual Research Report of the Supercomputing Institute UM TC–Saint Anthony Falls Laboratory

Miki Hondzo, Principal Investigator John S. Gulliver, Co-Principal Investigator Computer Modeling of Bubbly Two-Phase Flows in Aquatic Environments

ubble plume models are applied to study de-strati- These researchers developed a two-fluid model that fication of lake water, aeration of reservoirs, waste- has flexibility in the definition of the multiphase and vis- Bwater treatment, and gas injection into liquid met- cous models, an easily understood definition of boundary als. Several existing models exemplify numerical model- conditions, a simple definition of spatial dimensionality ing as problem-specific art, solve a mixture momentum and time dependency, an efficient numerical solution, equation, and have limitations in the availability of docu- clear documentation, and user-friendly pre- and post- mentation, definition of boundary conditions, and post processing capabilities. It predicts water and air phase and pre-processing capabilities. The transfer of problem- velocities, water turbulent kinetic energy, and air volume specific models to a client or to a multidisciplinary fraction with accuracy similar to that of existing prob- research and development team is a difficult process. lem-specific models. This study addressed the questions: a) can one use a commercial code as a basis to develop a user-friendly, Collaborator efficient model that simulates two-phase flow in bubble Hector Bravo, Department of Civil Engineering, plumes? and b) what are the capabilities and limitations University of Wisconsin, Milwaukee, Wisconsin of such a model?

Fernando Porté-Agel, Fellow Large-Eddy Simulation of the Atmospheric Boundary Layer

esearchers use large-eddy simulation (LES) to resolution and speed of the simulations through the use study the turbulent transport of heat, momen- of parallel computing resources. Rtum, water vapor, and pollutants in the atmospheric boundary layer. LES is the state-of-the-art numerical technique to calculate the unsteady three-dimensional Research Group and Collaborators transport in turbulent flows. Until now, LES has not Sukanta Basu, Graduate Student Researcher been sufficiently faithful to the physics of the atmospher- Nenad Bjelogrlic, Graduate Student Researcher ic boundary layer, the main weakness being associated Matthew Carper, Graduate Student Researcher Kumar Chittabathini, School of Geosciences, University of with the limited ability to account for the dynamics that Edinburgh, Edinburgh, Scotland, United Kingdom are not explicitly resolved in the simulations. The main Aaron Fagerness, Graduate Student Researcher goal of this research is to address those limitations in Manuel Garcia-Munoz, Undergraduate Student Researcher order to make LES a more reliable tool to study land- Jan Kleissl, Department of Geography and Environmental Engineering, Johns Hopkins University, Baltimore, atmosphere exchange processes. In particular, the objec- Maryland tives are: to develop and implement better subgrid-scale Paola Passalacqua, Graduate Student Researcher models to accurately account for the effect of the non- Josh Rubin, Undergraduate Student Researcher resolved scales (smaller than grid size) on the dynamics of Mark B. Sielaff, Supercomputing Institute Undergraduate the resolved turbulent fields; to develop improved Intern James R. Stoll, Graduate Student Researcher boundary conditions for the simulations, based on results Jean-Francois Vinuesa, Supercomputing Institute Research from wind tunnel experiments as well as numerical Scholar experiments; to develop parameterizations for the inter- Feng Wan, Graduate Student Researcher actions between turbulence and chemical transformations Kyung Mi Won, Research Associate in turbulent boundary layer flows; and to increase the

2006 Annual Research Report of the Supercomputing Institute 165 UM TC–Saint Anthony Falls Laboratory

Charles C. S. Song, Fellow Large-Scale Computation of “Large Re-Small M” Industrial and Environmental Flows

his group continued its development of large- ventilation. The group has developed a virtual single- scale flow computation methods and computer phase approach for natural cavities with no ventilation Tcodes for scientific and engineering applications. and a two-phase approach for ventilated cavities. The The researchers deal with complex industrial and envi- group is now developing a two-phase approach for natu- ronmental subsonic turbulent flows. The weakly com- ral cavities occurring in water containing dissolved pressible flow equations are solved with finite volume incondensable gas. In this model, water and water vapor method. are treated as virtual single-phase fluids following a Recent work has focused on developing computer reversible process while the dissolved gas follows an irre- codes for unsteady cavitating flows with and without versible process. The researchers are also continuing their simulations of ventilated and non-ventilated cavitating flows, and are simulating interaction between micro-bub- Research Group bles and small-scale turbulence for the purpose of drag Xiang Ying Chen, Research Associate reduction. Jianming He, Research Associate Qiao Qin, Graduate Student Researcher

Heinz G. Stefan, Associate Fellow Simulations and Analysis of Physical, Chemical, and Biological Processes Affecting Water Quality in Freshwater Systems his research group is developing deterministic, distribution of wind stresses on lake surfaces for incorpo- unsteady, year-round water quality and habitat ration into these simulations. Tsimulation models. The ongoing objective is to A second, related project is the study of mass transfer develop, expand and apply computational methods processes at natural sediment/water interfaces such as which link hydrology, hydrodynamics, water chemistry, found in rivers, lakes and estuaries. This research involves and biological processes in lakes and streams. These flow and mass transfer simulations to investigate penetra- dynamic models simulate water temperature and dis- tive dispersion and uptake/release of solutes in various solved oxygen in various classes of water systems. During sedimentary matrices, including the effects of surface the past year group members have studied specifically the waves, hyporheic flows and boundary layers. A third project has been the development of an integrated deterministic simulation model for runoff tem- Research Group and Collaborator peratures in watersheds. This project requires the integra- William Herb, Research Associate tion of hydrologic processes with heat transfer processes Makoto Higashino, Faculty Collaborator over a wide range of spatial and temporal scales in a wide Ben Janke, Graduate Student Researcher range of environmental settings. It also includes the Eric Novotny, Graduate Student Researcher study of the effects of man-made systems on heat transfer Qin Qian, Graduate Student Researcher in aquatic environments. James Thill, Graduate Student Researcher A fourth project is the statistical analysis of stream flow and temperature characteristics to find indicators of climate change.

166 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Computer Science and Engineering

Daniel L. Boley, Fellow Data Preprocessing for Gene Expression Analysis

icroarray technology generates large quantities project uses very high-dimensional data, the first prepro- of data from which gene expression analysis cessing step involves a dimensional reduction step of the Mcan be performed. Finding useful and reliable original data. A second project involves training a sup- methodologies to explore the relationships between genes port vector machine classifier based on the SCOP pro- or to reveal patterns of biological significance involves tein sequence dataset. many processing steps. The data pre-processing step has become a necessity before any interpretation of data can begin, because there are many sources of systematic variation in microarray experiments that affect the measured gene expression levels. These researchers are focusing on the crucial tasks of gene expression data normalization and transformation to infer meaningful comparisons of expression levels and to select genes for further analysis and data mining. In Research Group one project, they are using Supercomputing Institute Ham Ching Lam, Graduate Student Researcher resources to conduct matrix factorization. Because this

David H. Du, Fellow Address Caching in Peer-to-Peer Overlay Networks

ynamic address caching in peer-to-peer systems defines shortcuts through the overlay that short- Research Group Dens the object lookup path to the requested des- Jim Diehl, Graduate Student Researcher tination and increases overlay network connectivity. Dingshan He, Graduate Student Researcher These researchers investigated how to optimize the Yingping Lu, Graduate Student Researcher caching based on limited cache space at each node. Xianbo Zhang, Research Associate

2006 Annual Research Report of the Supercomputing Institute 167 UM TC–Department of Computer Science and Engineering

Tian He, Principal Investigator Achieving Balanced and Flexible Military Surveillance at Scale

ireless sensor networks (WSNs) have a large performance goals through a cross-layer design, subject confluence of characteristics that make them to the multi-dimensional resource constraints, such as Wunique both in terms of their technical limited power, bandwidth, computation, and memory, requirements and in potential applications. The objective available in physical sensor devices. The researchers are of this work is to support the next generation of extreme- using multi-objective optimization, which requires exten- ly large-scale military surveillance using WSNs. This sive computation, to exploit this high-dimensional design project is aimed at developing a balanced and flexible space. Because of the computational needs of this proj- architecture and a physical implementation. The main ect, the researchers must use Supercomputing Institute challenge is how to reconcile and/or trade off concurrent resources.

Research Group Yu Gu, Graduate Student Researcher Joengmin Hwang, Graduate Student Researcher

George Karypis, Principal Investigator Scalable Algorithms for Graph Partitioning, Data Mining, and Bioinformatics

he Karypis group’s research focuses on four areas: ability; developing better scoring methods for sequence developing better machine learning algorithms alignment, sequence-structure search methods, and statis- Tbased on support vector machines by designing tically derived potential functions that are designed to kernel functions that capture the characteristics of pro- capture the sequence-structure conservation present in teins and chemical compounds and improving their scal- protein sequences; developing better optimization algorithms and methodologies for ab initio structure prediction; and developing better feature extraction algorithms Research Group for chemical compounds that utilize topological and geo- Kevin DeRonne, Graduate Student Researcher metric substructures. This work builds on the group’s Christopher Kauffman, Graduate Student Researcher earlier work on highly effective and scalable graph parti- Michihiro Kuramochi, Graduate Student Researcher tioning algorithms, clustering algorithms for high-dimen- Huzefa Rangwala, Graduate Student Researcher sional datasets and scalable-pattern discovery algorithms, Shilad Sen, Graduate Student Researcher and developing algorithms for protein structure predic- Nikil Wale, Graduate Student Researcher tion, remote homology prediction, and rational drug Ying Zhao, Graduate Student Researcher design.

168 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Computer Science and Engineering

Vipin Kumar, Fellow High-Performance Data Mining

he objective of this research is to develop novel, provide analysts and domain scientists with automated high-performance data mining algorithms and tools that facilitate some of the steps needed for hypothe- Ttools for mining large-scale datasets that arise in a sis generation and evaluation. variety of applications. Some examples are: large biological databases that can be analyzed to better understand various biological processes underlying them; gigabyte Research Group and Collaborator datasets collected by earth-observing satellites that need Shyam Boriah, Graduate Student Researcher to be processed to find potentially useful patterns and to Varun Chandola, Graduate Student Researcher better understand global-scale changes in biosphere Eric Eilertson, Graduate Student Researcher processes; data generated by scientific simulations that Rohit Gupta, Graduate Student Researcher can be used to gain insight into the underlying physical Ravi Janardan, Faculty Collaborator processes; data obtained through monitoring traffic net- Benjamin W. Mayer, Graduate Student Researcher works to detect illegal network activities; collections of Aysel Ozgur, Graduate Student Researcher text and hypertext analyzed to extract relevant informa- Gaurav Pandey, Graduate Student Researcher Sanjay Ranka, Department of Computer and tion. The key technical challenges in mining these Information Science, University of Florida, datasets include: high volume, dimensionality, and het- Gainesville, Florida erogeneity; spatio-temporal aspects of the data; possible Gyorgy Simon, Graduate Student Researcher skewed class distribution; distributed nature of the data; Michael S. Steinbach, Graduate Student Researcher and the complexity in converting raw collected data into Pang Tan, Research Associate high-level functions. High-performance data mining is essential to analyze the growing amount of data and to

2006 Annual Research Report of the Supercomputing Institute 169 UM TC–Department of Computer Science and Engineering

Yousef Saad, Fellow PARSEC, p-ARMS, and Applications

he Saad group is working on two distinct and Chelikowsky from the University of Texas at Austin, the broad projects. In the first, the group aims at group has developed a highly effective method based on Tdeveloping novel techniques for electronic struc- real space representation. The code, called Pseudopoten- ture calculations. In collaboration with Professor James tial Algorithm for Real Space Energy Calculations (PAR- SEC), has recently enabled calculations with thousands of atoms (including a 10,000-atom silicon cluster) with Research Group and Collaborators modest computational resources (fewer than 48 proces- Lee B. Ballard, Supercomputing Institute sors). The success of this code is in great part due to Undergraduate Intern effective eigensolvers and methods that take a different Konstantinos Bekas, Research Associate look at diagonalization in the standard density functional Sheehan Bernie, Research Associate theory approach. In addition, the researchers are develop- Matthias Bollhoefer, University of Berlin, Berlin, ing faster, more robust methods for the geometry opti- Germany mization and mixing problems. The group has recently Russ Burdick, Graduate Student Researcher investigated different eigenvalue solvers, as well as meth- James R. Chelikowsky, Department of Chemistry and ods which avoid the computation of eigenvalues. Biochemistry, University of Texas, Austin, Texas The second project is in the area of numerical linear Michael R. Frasca, Supercomputing Institute algebra. The researchers are investigating robust precon- Undergraduate Intern Shivariju Gowda, Graduate Student Researcher ditioning techniques for solving general large sparse lin- Pascal Henon, Research Associate ear systems of equations. Team members have developed Manasi Joshi, Graduate Student Researcher a software code called the Parallel Algebraic Recursive Efi Kokiopoulou, Graduate Student Researcher Multilevel Solvers (pARMS) which was made available Na Li, Graduate Student Researcher publicly in 2001 (See www.cs.umn.edu/~saad). Since ZhongZe Li, Research Associate then, they have developed new methods, including the Scott MacLachlan, Research Associate Parallel Hierarchical Interface Decomposition Algorithm Daniel Osei-Kuffor, Graduate Student Researcher (PHIDAL) and a more recent version of ARMS which Suzanne Shontz, Supercomputing Institute Research uses the “restrictive” Schwarz approach. Scholar Masha Sosonkina, Faculty Collaborator Nicholas J. Voshell, Supercomputing Institute Undergraduate Intern Yunkai Zhou, Research Associate

170 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Computer Science and Engineering

Shashi Shekhar, Fellow High-Performance Spatial Data Mining

he main objective of this work is to develop high- few million points. These researchers focus on developing ly scalable spatial data mining techniques such as new SAR parameter estimation algorithms and paralleliz- Tthe Spatial Auto-Regression (SAR) model. SAR ing those to meet this challenge. parameter estimation is computationally challenging due the need to compute complex functions (e.g. log determinant) of very large matrices, with trillions of elements. Current SAR parameter estimation algorithms are not scalable and take hours of computation for small problems with a few thousand spatial locations. There is a Research Group need, however, to find scalable parameter estimation Mete Celik, Graduate Student Researcher techniques to scale up to medium and large datasets, such as satellite and aerial imagery, which typically have a

Jon B. Weissman, Principal Investigator Community Services

he Community Services project is constructing next-generation middleware and systems software Research Group Tfor dynamic grid services. A focus of this project Zhaoxin Ding, Graduate Student Researcher is the definition of an adaptive grid service and a system Darin England, Graduate Student Researcher architecture to support a fully dynamic grid service life- Colin Gan, Graduate Student Researcher cycle. Dynamic grid services are an important substrate Taruq Islam, Graduate Student Researcher to support collaboration. Seonho Kim, Graduate Student Researcher These researchers deployed dynamic grid services onto Byoung-Dai Lee, Graduate Student Researcher workstations in the Scientific Development and Nathan Mukesh, Graduate Student Researcher Laksman Abburi Rao, Graduate Student Researcher Visualization Laboratory. In their grid testbed, the labo- Murali Sangubhatla, Graduate Student Researcher ratory acts as a compute provider. The researchers have Jason Sonnek, Graduate Student Researcher demonstrated this grid testbed to various visiting speak- Rahul Trivedi, Graduate Student Researcher ers and researchers. Durgaprasad Velagaleti, Graduate Student Researcher Feng Wang, Graduate Student Researcher

2006 Annual Research Report of the Supercomputing Institute 171 UM TC–Department of Computer Science and Engineering

Pen-Chung Yew, Principal Investigator Performance Analysis and Optimization of Molecular Dynamics Simulation Tools

hese researchers analyzed the performance bottlenecks of molecular dynamics modeling tools on a Tuniprocessor machine and on multiprocessor cluster. The researchers compiled tools using an open research compiler for an Itanium machine and monitor the performance issues. They then identified the potential bottlenecks and applied compiler optimization schemes.

Research Group Harish Barathvajasankar, Graduate Student Researcher

Zhi-Li Zhang, Principal Investigator Profiling Internet Backbone Traffic: Behavior, Models, and Applications

his project explores the design and implementa- information-theoretic techniques to automatically discov- tion issues of a real-time behavior profiling sys- er significant events based on the communication pat- Ttem for high-speed internet links. The profiling terns of end-hosts. The group is demonstrating the oper- system uses flow-level information generated from ational feasibility of this system by implementing it and “always-on” packet monitors, and uses data mining and performing extensive benchmarking of central processing unit (CPU) and memory costs using packet-level traces from OC-48 backbone links. They are developing new filtering algorithms to improve the robustness of the sys- Research Group tem against sudden explosive growth in the number of Antonio J. Estepa Alonso, Graduate Student Researcher flows—and consequently CPU and memory require- Yu Jin, Graduate Student Researcher ments—during denial-of-service attacks or worm out- Guor-Huar Lu, Graduate Student Researcher breaks. Finally, the group is developing an event analysis Haldane R. Peterson, Graduate Student Researcher engine to track interesting or suspicious network events Mukund Srinvasan, Graduate Student Researcher over time, and a simple yet comprehensive event specifi- Kuai Xu, Graduate Student Researcher cation language that allows a user to extract information on events of interest.

172 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Electrical and Computer Engineering

Rhonda Franklin Drayton, Principal Investigator Use of Photonic Gap Modeling in Integrated Packaging

n order for information networks to provide fast, easy interconnect (i.e., low dispersion and low attenuation) access to large amounts of data, system design com- and suppress the poor qualities associated with coupling Iplexity inherently increases. At the same time, the between designs in close proximity to each other. The ability to preserve signal integrity becomes increasingly group is using resources at the Scientific Development difficult. At the circuit level, signal integrity is affected and Visualization Laboratory to model such designs in mainly by changes in signal speed and signal strength as order to develop propagation models that can be used to it travels through the specific design. In order to have develop lumped element models for integrated circuit timely access to data, operation frequency is typically design. increased, but this can have dire effects on signal intensity. Usually, single-frequency operation is desirable within a specific system. Research Group This project investigates the use of photonic bandgap Emile Davies-Venn, Graduate Student Researcher design approaches to tailor substrate environments to Isaac Itotia, Graduate Student Researcher Hosaeng Kim, Graduate Student Researcher suppress cross-talk between interconnects in close prox- Ethan Miller, Graduate Student Researcher imity. The aim is to identify substrate augmentation designs that preserve the good qualities of an isolated

Anand Gopinath, Associate Fellow Modeling of Optical and Microwave Structures

hese researchers are involved in modeling projects whose computational requirements necessitate Research Group and Collaborator use of the supercomputers. These projects T Kang-Hyun Baek, Graduate Student Researcher include: modeling photonic band gap structures using Jang-Uk Lee, Kookmin University, Seoul, South Korea finite difference time domain codes; designing an inte- Jaewon Kim, Graduate Student Researcher grated optical coupler modulator/filter with linear Jaesang Oh, Graduate Student Researcher response; modeling coils for magnetic resonance imaging Christopher C. Olson, Graduate Student Researcher using integral equation methods; and a new project this Heather Orser, Graduate Student Researcher year, modeling metamaterials for microwave antennas Hyung-Suk You, Graduate Student Researcher and lenses.

2006 Annual Research Report of the Supercomputing Institute 173 UM TC–Department of Electrical and Computer Engineering

Ramesh Harjani, Principal Investigator High-Speed Communication Circuit Design

his work focuses on the design of high-speed wired and wireless communication circuits in Tadvanced silicon integrated circuit technologies. The computation requirements for circuit simulations of many of these circuits are quite extensive, and the simulations are not easily performed on single workstations. Using the supercomputers allows this work to be accomplished in hours rather than weeks.

Research Group M. Reza Ahmadi, Graduate Student Researcher Kin-Joe Sham, Graduate Student Researcher

Heiko O. Jacobs, Principal Investigator Computer Modeling of Electrostatically Directed Self-Assembly of Silicon Nanoparticles in Argon Media he theory behind the derivation of Brownian osition process of silicon nanoparticles suspended in motion can be traced to its earliest form at the argon media as part of the process called nanoxerography. Tbeginning of the 19th century. Critical aspects of The model takes into account several different parame- this widely used fundamental theory were developed ters, including: gas rarefication of the silicon nanoparti- through the work of Einstein, Brown, Schultze, cles; electrostatic attraction and repulsion; and substrate Ornstein, and others in their dealings with gas kinetics. charge pattern geometry. Results are presented with a Their findings consolidate into a concrete statistical time-step analysis showing the dependency of the deposi- analysis from which computational modeling was built. tion pattern to both the physical parameters and the geo- This research is based on the constructs made by these metrical consideration of the simulation. The researchers scientists. These researchers simulated a self-directed dep- compared these results to experimental work to demonstrate the reliability and accuracy of the model.

Research Group Thomas J. Hatch, Graduate Student Researcher

174 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Electrical and Computer Engineering

Mostafa Kaveh, Principal Investigator Genomic Microarray Data Clustering

eoxyribonucleic acid (DNA) microarray tech- the genes are informative, and therefore the quality and nology is critical in genomic research. Data reliability of common clustering algorithms, such as K- Dfrom microarray experiments is arranged in a means hierarchical and self-organizing maps, may not be data matrix, where each gene corresponds to one row and high enough for biological interpretation purposes or each condition to one column. Each entry of this data have high computational complexity. These researchers matrix represents the expression level of a gene under a used projection and dimensionality reduction techniques, specific condition or time sample point. The process of such as the discrete cosine transform and singular value transforming this abundance of information into mean- decomposition, to cluster the microarray gene-expression ingful biological information is a major goal of gene data. expression data analysis. Clustering techniques have proven to be helpful in understanding gene function, gene regulation, and cellular processes. Due to the large Research Group number of genes involved in microarray data, not all of Hossein Zare, Graduate Student Researcher

David J. Lilja, Fellow The Impact of Emerging Technologies on the Design of Computer Systems

he overall goal of this research is to develop mining spatial data, such as that obtained from geo- processor systems that satisfy a desired set of con- graphic information systems. Tstraints. These constraints typically require non- obvious trade-offs in performance, power consumption, cost, and reliability. The Lilja group is particularly interested in how changes in the underlying technology, such Research Group as the trend towards smaller feature sizes in very-large- Zain M. Asgar, Undergraduate Student Researcher scale integration circuits, affects how computer systems Ying Chen, Graduate Student Researcher should be designed. They are working on several projects Benjamin J. Dodson, Supercomputing Institute in this broad area, including a study of the impact of soft Undergraduate Intern errors on processors constructed with deep sub-micron Lieven Eeckhout, Research Associate and nanoscale devices, the development of techniques to Chris J. Hescott, Graduate Student Researcher control transistor leakage currents in processors using Baris Kazar, Graduate Student Researcher sleep transistors, the development of a program-profiling Sreekuamar V. Kodakara, Graduate Student Researcher tool to improve simulation efficiency and dynamic per- Drew Ness, Graduate Student Researcher formance optimization, and the development of tech- Resit Sendag, Graduate Student Researcher niques for automatically classifying the benchmark pro- Keqiang Wu, Graduate Student Researcher Joshua J. Yi, Graduate Student Researcher grams used to evaluate the performance of computer systems. They are also developing parallel algorithms for

2006 Annual Research Report of the Supercomputing Institute 175 UM TC–Department of Electrical and Computer Engineering

Ned Mohan, Principal Investigator Investigation of Nonlinear Mutual Coupling in Switched Reluctance Motors

ynamic modeling of a switched reluctance used finite element analysis (FEA) to obtain static char- machine (SRM) usually assumes independent acteristics and flux linkage and torque for the designs, Doperation of each phase. Since SRMs are mostly which have very small differences in geometry. Even used with simultaneous excitation of two or more phases, small differences in the geometry of the stator pole of it is necessary to account for mutual couplings between SRMs lead to significant changes in the static characteris- different phases in the presence of magnetic saturation. tics, emphasizing the need for accurate modeling and These researchers have formulated a dynamic model for FEA. The SRM design has been finalized, and the motor simultaneous excitation of two phases and have designed has been fabricated. The researchers are performing FEA three machines to study non-linear mutual effects. They on the final design. Once this is complete, they will experimentally verify the dynamic model of the SRM; the dynamic model will be used to obtain the optimum Research Group control parameters for the machine. Nitin B. Bhiwapurkar, Graduate Student Researcher Amit Kumar Jain, Graduate Student Researcher Rinkle Surend, Graduate Student Researcher

Jaijeet Roychowdhury, Principal Investigator

SPICE++

his group is developing a next-generation circuit and mixed-physics simulator called SPICE++. TThey are using the supercomputers to speed up prototyping algorithm development within SPICE++.

Research Group Jie Chen, Graduate Student Researcher Angan Das, Graduate Student Researcher Ning Dong, Graduate Student Researcher Brian Fett, Graduate Student Researcher Ali Gorji, Graduate Student Researcher Ting Mei, Graduate Student Researcher Shweta Srivastava, Graduate Student Researcher Yayun Wan, Graduate Student Researcher Jia Zou, Graduate Student Researcher

176 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Electrical and Computer Engineering

P. Paul Ruden, Associate Fellow Properties of Semiconductor Materials and Devices

hese researchers are working on the electronic structure and related properties of semiconductor materials and novel devices. Recent research by T Research Group and Collaborator this group has centered on electron transport simulations for large band-gap III-nitride materials using the Monte John D. Albrecht, Air Force Research Laboratory, Carlo technique. The current focus is the creation of Wright-Patterson Air Force Base, Ohio device models for large gap semiconductor devices, in Jeff Balk, Graduate Student Researcher Mohammad Kauser, Graduate Student Researcher particular III-nitride sensors and devices fabricated from Dominic Schroepfer, Graduate Student Researcher organic materials. The researchers are also beginning Isaiah Steinke, Graduate Student Researcher Monte Carlo calculations for carbon nanotubes and have Mahammad Yunus, Graduate Student Researcher recently begun work on electron spin transport in large gap semiconductors.

Sachin S. Sapatnekar, Principal Investigator Computer-Aided Analysis and Optimization of Very-Large-Scale Integration Designs

hermal effects have become increasingly impor- algorithms; one uses a table look-up approach to acceler- tant in the design of high-performance integrated ate the evaluation of Green function and the other is Tcircuits, due to the high power dissipation caused based on the concept of frequency domain computa- by the increasing clock frequencies and die sizes. Physical tions. design, which determines the positions of the logical units and wires of a chip, plays an important role in determining the thermal profile of a circuit, so this is the focus of this group’s work. Specifically, they are determining the optimal, thermal-aware placement of logical block of a circuit. At the microarchitecture level, this requires several cycle accurate simulations on standard benchmark programs, where each simulation can take several hours to complete. Research Group The researchers are developing efficient and accurate Sagar Nookala, Graduate Student Researcher Green function based thermal simulation algorithms that Yong Zhan, Graduate Student Researcher can be used in chip design. They have implemented two

2006 Annual Research Report of the Supercomputing Institute 177 UM TC–Department of Electrical and Computer Engineering

Guillermo R. Sapiro, Principal Investigator Statistical Characterization of Protein Ensembles

hen structural fluctuations or measurement observed conformations (“ensemble”). Following a differ- errors should be accounted for, a single rigid ent approach, these researchers are introducing a frame- Wstructure may not be enough to represent a work for estimating probability density functions in very protein. One approach to solving this problem is to rep- high dimensions and applying it to represent ensembles resent the possible conformations as a discrete set of of folded proteins.

Research Group Anish Mohan, Graduate Student Researcher Diego Rother, Graduate Student Researcher

Randall H. Victora, Fellow Micromagnetic Simulations of Head and Media for High-Density Magnetic Recording

urrent magnetic recording technology is tives is to record the media perpendicularly, which may approaching several new technical barriers that require significant technological changes. These Cmay limit the further increase of hard disk researchers have developed micromagnetic models that recording density. Examples of these barriers include fun- simulate the characteristics of perpendicular recording damental limitations in the thermal stability and switch- media and recording heads. In recent work, the group ing speed of the magnetic domains. Instead of the cur- has predicted the switching behavior of exchange-cou- rent longitudinal recording method, one of the alterna- pled composite nanograins that are predicted to enable terrabit perpendicular magnetic recording and made further predictions about the switching behavior of an exchange-based system. They are continuing to work on Research Group exchange bias and composite media. They are also apply- Stephanie Hernandez, Graduate Student Researcher ing these simulations to designing a recording head that Manish Kapoor, Graduate Student Researcher is optimized for composite recording media and to study Jyotirmoy Saha, Graduate Student Researcher the issue of overwriting one signal with another. Xiao Shen, Graduate Student Researcher

178 2006 Annual Research Report of the Supercomputing Institute Um TC–Department of Geology and Geophysics

David A. Yuen, Fellow Large-Scale Numerical Modeling, Data Analysis and Mining, and Visualization in Geophysical and Biomedical Sciences he Yuen group’s research is focused toward a quantitative understanding of the earth’s interior Tfrom numerical modeling of complex physical- chemical and fluid-dynamical processes. Recently, the group has also applied these models to biomedical applications. They have engaged in scientific visualization, also called “visual computing,” and feature extraction. Many of the complicated phenomena with fine features must be visualized at high resolution in order to fully Research Group and Collaborators (continued) understand the nonlinear processes inherent in flow Daniel Goldstein, Supercomputing Institute Research Scholar Weronika Gorzyk, Swiss Federal Institute of Technology, problems. For this reason, the research requires the use of Zurich, Switzerland Supercomputing Institute resources. Cathy Hier-Majumder, Department of Terrestrial Magnetism, The specific research areas include: three-dimensional Carnegie Institute of Washington, Washington, D.C mantle convection with variable thermal conductivity Paul Jensen, Undergraduate Student Researcher Benjamin J. Kadlec, Supercomputing Institute and variable viscosity and phase change; discrete-particle Undergraduate Intern modeling, including molecular dynamics, dissipative-par- Masanori Kameyama, Japan Marine Science and Technology ticle dynamics, and fluid-particle models as applied to Center, Kanagawa, Japan multiphase flow in blood arteries and veins with ten mil- Motoyuki Kido, Faculty of Science, Kobe University, Kobe, lion particles; visualization and analysis of very large Japan Daniel G. Kigelman, Undergraduate Student Researcher datasets in both geophysics and biomedical sciences; and Marcin Kurdziel, Undergraduate Student Researcher numerical simulations of the earth’s lithosphere-mantle Yingchun Liu, Research Associate thermal-chemical system with complex nonlinear physics Zigg Lu, School of Computational Science, Florida State and multi-component nonlinear rheologies and thermo- University, Tallahassee, Florida Frank Lyness, Undergraduate Student Researcher dynamics. Marc Monnereau, CNE/CNRS, Toulouse, France Yuliya Palchuk, Undergraduate Student Researcher Jonathan Regele, Department of Geology and Geophysics, University of Colorado, Boulder, Colorado Research Group and Collaborators Klaus Regenauer-Lieb, Hohentengen, Germany Tom Arodz, AGH University of Science and Technology, Billy Richard, Centre National d’Etudes Spatiales, Paris, Krakow, Poland France Gretchen L. Beebe, Supercomputing Institute Undergraduate Michael Riedel, Project Group Thermodynamics, Intern GeoforschungsZentrum Potsdam, Potsdam, Germany Marie Behounokova, Charles University, Prague, Czech Kimberly Schramm, Graduate Student Researcher Republic Ekaterina Shukh, Supercomputing Institute Undergraduate Evan F. Bollig, Undergraduate Student Researcher Intern Allison Capel, Undergraduate Student Researcher Marina Shukh, Undergraduate Student Researcher Monica D. Christiansen, Supercomputing Institute Benjamin A. Sowell, Supercomputing Institute Undergraduate Intern Undergraduate Intern Cesar Da Silva, Department of Materials Physics, University Alexei Vezolainen, Department of Physics, New Mexico State of Sao Paulo, Sao Paulo, Brazil University, Las Cruces, New Mexico Megan Damon, Graduate Student Researcher Alain P. Vincent, CERCA, Montreal, Quebec, Canada Troy Dos Santos, Undergraduate Student Researcher Shuo Mark Wang, Supercomputing Institute Undergraduate Witold Dzwinel, Research Associate Intern Harsh Gadgil, Department of Computer Science, Indiana Chris Wijns, Commonwealth Scientific and Industrial University, Bloomington, Indiana Research Organisation, Australia Taras Gerya, Research Associate Lilli Yang, Undergraduate Student Researcher

2006 Annual Research Report of the Supercomputing Institute 179 UM TC–Department of Mechanical Engineering

Jane H. Davidson, Associate Fellow Thermal and Chemical Processes

hese researchers have been involved in three proj- tank with immersed tube or tube bundle exchangers. ects using supercomputing resources. The objec- Direct numerical simulation has been used to simulate Ttive of the first project is to simulate the transient single tube heat exchangers. The group’s current work flow structure and temperature field in a heat storage uses a porous media model to simulate tube bundle heat exchangers. The results will allow the researches to determine optimum geometries to enhance overall heat trans- Research Group and Collaborators fer rate. Junhong Chen, Department of Mechanical The second project aims to develop a numerical Engineering, University of Wisconsin, Milwaukee, model for ozone production in clean and humid air by Wisconsin direct current (DC) corona discharges from a thin wire. Dongsheng Huang, Research Associate The model is based on prior models of ozone production Mike Kingsley, Graduate Student Researcher by DC coronas in dry air, with modifications to incorpo- Zhihua Li, Graduate Student Researcher rate the effect of water vapor on the electrical characteris- Wei Liu, Graduate Student Researcher tics and the chemistry of the discharge. Yan Su, Graduate Student Researcher The final project, completed this year, involved con- Pengxiang Wang, Department of Mechanical vective heat transfer in novel heat exchangers made of Engineering, University of Wisconsin, Milwaukee, Wisconsin polymeric materials. The objective of this study was to determine the flow field and heat transfer in tube bundles of non-circular tubes.

Traian Dumitrica, Principal Investigator Structural Properties of Silicon Nanoparticles

his research focuses on the stability and optical form a detailed surface passivation study using tight- properties of silicon nanoparticles. One objective binding and ab initio calculations. Energy comparison in Tis to gain more insight into thermodynamic this case is subtle as the formal composition may change aspects such as energetics, shapes, and structures. A gen- with cluster size and the formation energy computed per eralized Wulff construction will provide the base point atom bears little significance. The researchers compare for evaluating different structures and selecting the most the molar (per atom) Gibbs free energies of formations stable (magic) ones. Next, the researchers will study the for clusters with different compositions. Thus, the rela- occurrences of order-to-order and order-to-disorder tran- tive stability depends on the constituent chemical poten- sitions by varying the temperature. Finally, they will per- tials, which in turn represent the environmental conditions. Further, this study aims to establish the influence of contaminants on the optical properties of these parti- Research Group cles. Toni Carlson, Graduate Student Researcher Evgeni Kalyuzhny, Graduate Student Researcher Paolo Valentini, Graduate Student Researcher

180 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Mechanical Engineering

Arthur G. Erdman, Principal Investigator Investigations Into Urinary Incontinence

hese researchers have been working on two proj- a simplified numerical analysis model of the female pelvis ects related to urinary incontinence. The first was using the finite element method, which enables them not Tto develop an improved device to help male only to explain the causes of the problems but also to patients with this condition. In the United States alone, provide guides for the cure. The first step involves inves- there are approximately four million males who struggle tigating urinary incontinence in elite female athletes to with urinary incontinence. One of the three options of figure out why and how the problem occurs and to find treatment is to use an external urethra clamping device. out the effect of each component in the female pelvis on Current devices available on the market, however, often the problem. fail to perform satisfactorily and patients complain of leaking and discomfort. The objective of this project was to characterize the penile structure, build an analytical Research Group and Collaborator model, and eventually develop an improved device. Seoggwan Kim, Research Associate In a new project, the researchers are investigating the Jerry Timm, Faculty Collaborator causes of female urinary incontinence. They are creating

Sean C. Garrick, Associate Fellow Large-Scale Simulation of Nanoparticle Development and Growth in Turbulent Flows

his research draws upon expertise in the fields of computational fluid dynamics, aerosol dynamics, Tchemistry, and physics to develop computational Research Group and Collaborator tools to simulate particle formation and growth in turbu- Chris Bergstedt, Graduate Student Researcher lent reacting flows. The methodology unites the latest Takumi Hawa, Research Associate mathematical and phenomenological models with robust Shantanu Jathar, Graduate Student Researcher simulation techniques, thus creating a new regime of Mehrzad Khakpour, Graduate Student Researcher computational flow/chemistry. This new approach will Soo Hyung Kim, Research Associate facilitate the prediction and control of nanoscale particles Juha Kurkela, Research Associate Saurav Mitra, Graduate Student Researcher production for materials processing. Dibyendu Mukherjee, Graduate Student Researcher Specific projects for this group include: large-eddy Nathan Murfield, Graduate Student Researcher simulation (LES) of a chemically reacting co-flow round Prahalad Parthangal, Graduate Student Researcher jet, in order to validate the LES results based on a previ- Jouni Pyykonen, Research Associate ous experiment with the same flow/chemical fields; Katherine Ruzicka, Undergraduate Student Researcher investigation of particle shape effects in the simulation of Nelson Settumba, Graduate Student Researcher the growth of titania nanoparticles; simulation of particle Shekar Sonwane, Research Associate growth, agglomeration, and breakage into smaller parti- Guanghai Wang, Graduate Student Researcher cles in fluid flows; development of a subgrid-scale model Patrick Wells, Research Associate for nanoparticle formation and growth processes to use Michael R. Zachariah, Department of Mechanical Engineering, University of Maryland, College Park, in LES simulations; and investigation of the validity of a Maryland new computational method accounting for nanoparticle nucleation and condensation.

2006 Annual Research Report of the Supercomputing Institute 181 UM TC–Department of Mechanical Engineering

Steven L. Girshick, Fellow Modeling Plasma Synthesis of Materials

hese researchers are investigating plasma process- transport in semiconductor processing systems; synthesis ing and plasma chemistry in three contexts of of nanostructured materials in a thermal plasma expan- Tpractical importance: particle formation and sion process; and particle synthesis and surface passivation of nanoenergetic materials. These projects involve the development of computer models in concert with Research Group and Collaborators ongoing experiments. Key issues include the detailed Jami Hafiz, Graduate Student Researcher chemistry that governs film growth, and the nucleation, Vijay Kodimala, Graduate Student Researcher growth, and transport of particles in plasmas. Feng Liao, Graduate Student Researcher Bo Liu, Graduate Student Researcher Rajesh Mukherjee, Graduate Student Researcher Soonam Park, Graduate Student Researcher Lavanya Ravi, Graduate Student Researcher Masaya Shigeta, Research Associate Maren Van Otterloo, Graduate Student Researcher Xiaoliang Wang, Graduate Student Researcher Sarah Warthesen, Graduate Student Researcher

Richard J. Goldstein, Associate Fellow Heat Transfer in Gas Turbine Passages; Rayleigh-Bernard Convection

hese researchers are using supercomputing validate the numerical simulation. Once they have resources for two projects. In the first, they are assessed the predictive capabilities of the code, the Tcomputing the flow and heat transfer on the researchers will perform simulations to design new lead- blade and bottom endwall surfaces of a linear gas turbine ing-edge modifications with the objective of reducing cascade. The geometry and flow conditions match those fluid dynamic losses and heat transfer. of the linear cascade located in the Heat Transfer The second project uses the method of Chebyshev Laboratory of the Mechanical Engineering Department, collocation, which has been shown to be ideal for simu- from which detailed experimental results are available to lating problems involving hydrodynamic stability and transition to turbulence, to study turbulent Rayleigh- Benard convection. The researchers are interested in the Research Group global heat transfer behavior, represented in terms of the Kalyanjit Ghosh, Graduate Student Researcher Nusselt number as a power-law function of the Rayleigh Willard Hanson, Graduate Student Researcher number. The simulations will try to resolve the contro- Sangjo Han, Graduate Student Researcher versy regarding the value of the exponent in the power- Kaustubh Kulkarni, Graduate Student Researcher law relationship. Marco Papa, Graduate Student Researcher Vinod Srinivasan, Graduate Student Researcher Justin E. Waldron, Graduate Student Researcher

182 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Mechanical Engineering

Joachim V. Heberlein, Associate Fellow Emil Pfender, Co-Principal Investigator Plasma Computation

lasma processing is increasingly being used to fine grid resolution in a two- or three-dimensional geom- develop new materials processing technologies and etry, and thus requires the computing resources available Pimprove existing ones. Process models may be used at the Supercomputing Institute. as design tools to simulate complex phenomena, such as magneto-fluid-dynamic interactions, turbulence, and particle breakup and transport, that take place in processes such as wire-arc spraying, plasma deposition, and plasma spraying. These researchers have developed a computer code that accurately calculates thermodynamic and transport Research Group properties of different plasma mixtures and are currently Srikumar Ghorui, Research Associate modifying it to also allow simulation of non-equilibrium He-Ping Li, Research Associate conditions. These transport properties are used to simu- Juan Pablo Trelles, Graduate Student Researcher late the various processes listed above. This research Nicole Wagner, Graduate Student Researcher involves the iterative or transient solution of a large set of Giovanni Zelioli, Graduate Student Researcher strongly coupled non-linear equations, often with a very

Uwe R. Kortshagen, Associate Fellow Highly Realistic Modeling of Low-Pressure Processing Plasmas

hese researchers investigate new approaches for group is beginning to couple plasma-chemical models to fast realistic modeling of processing plasmas both detailed plasma models. Tat low temperatures and atmospheric pressures. Finally, the researchers have begun to model atmos- One focus of this research is the accurate prediction of pheric pressure glow discharges with two-dimensional the electronic energy distribution function. In this area, time-dependent fluid codes. the researchers use a highly realistic Monte Carlo approach, based on first principles, to accurately determine the electron energy distribution function in a low- pressure plasma. These results will provide new insights into the physics of electron transport processes both in Research Group configuration and in energy space. Ameya Bapat, Graduate Student Researcher A second focus is the study of the chemical nucleation Upendra Bhandarkar, Graduate Student Researcher of nanometer-sized particles in plasmas, namely the Ying Dong, Graduate Student Researcher chemical nucleation of clusters. Here, the researchers are Lorenzo Mangolini, Graduate Student Researcher developing plasma-chemical reaction mechanisms that Peng Zhang, Graduate Student Researcher include neutral as well as ion-neutral chemistry. The

2006 Annual Research Report of the Supercomputing Institute 183 UM TC–Department of Mechanical Engineering

Perry Y. Li, Principal Investigator Design of Advanced Fluid Power Components and Systems

major research thrust in the Fluid Power Control pump output, resulting in an energy efficient, compact Laboratory is the design of fluid power compo- power supply; an unstable valve that uses steady and Anents using mechatronic principles where sensing unsteady flow forces to improve the agility of a spool, and feedback control are integrated into the design. thus making the valve have higher bandwidth or flow These researchers are currently designing three compo- rating without using a large solenoid actuator; and an nents: a software-enabled variable displacement pump integrated production qualification test sensor, a micro- system that uses pulse-width modulation control of a electro-mechanical-system-based sensor that makes use of high-speed on/off valve to modulate the flow of the existing flow geometries in components to measure flow, pressure, and temperature. Hence, extra pressure loss can be avoided. Research Group The group is performing computational fluid dynam- Charlie Groepper, Graduate Student Researcher ics calculations as part of the design effort. Michael B. Rannow, Graduate Student Researcher Haink Tu, Graduate Student Researcher Qinghui Yuan, Graduate Student Researcher

Susan C. Mantell, Principal Investigator Jane H. Davidson, Associate Fellow Finite Element Analysis Modeling of Composite Perforated Plates and an Advanced Energy-Efficient Roof System hese researchers have been involved in two proj- found good agreement. This project was completed dur- ects that use finite element analysis (FEA) modeling the past year. Ting. In the first, they investigated the mechanical The purpose of the second project is to develop an behavior of perforated chopped fiber reinforced plates. innovative residential roof with the primary objective of These plates serve as a manifold for polymer heat creating a more energy-efficient building envelope. The exchangers, where each perforation would be connected goal is to design, build, and evaluate a one-piece modular to a tube carrying pressurized fluid. The researchers roof panel that uses a composite material or laminated developed an FEA modeling technique to find the effec- structure manufactured in a continuous process. The tive modulus of elasticity of perforated plates. They com- researchers are using FEA to predict the failure modes pared this technique with experimental results, and and stresses of various designs.

Research Group Michael Eggen, Research Associate Yvonne Miller, Graduate Student Researcher

184 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Mechanical Engineering

Virgil A. Marple, Principal Investigator Electrodynamic Focusing of Aerosols

oncentration of aerosols from a large volume of Previous work investigated the static fields for differ- air into a small sample volume is essential in ent electrodes and the use of non-uniform electrostatic Cincreasing the sensitivity of their detection. The fields for dielectrophoretic focusing of aerosols. After use of electrodynamics forces to achieve particle focusing selecting suitable electrode configurations and shapes and thereby concentrating them was the prime objective from the electrostatic studies, the researchers plan to of this project. The researchers are studied the resulting study forces on charged particle in electrodynamic fields. electrostatic fields from different electrode shapes and configurations for their suitability for focusing aerosols. They used software available at the Scientific Research Group Development and Visualization Laboratory. Barnard A. Olson, Research Associate Kumaragovindhan Santhanakrishnan, Graduate Student Researcher

Peter H. McMurry, Principal Investigator Numerical Analysis of Particle Transport Through Various Aerosol Instruments

umerical simulations of the flow field and parti- researchers are attempting to improve the performance of cle transport in an aerosol instrument can pro- a DMA, which classified charged particles according to Nvide useful information on the performance of their electrical mobility, by modeling the Brownian diffu- the instrument and help to optimize its design. These sion of aerosols within a laminar flow field. In the final researchers are using the software package FLUENT and its area, the group has developed guidelines for designing supporting software to calculate flow and particle motion aerodynamic lens systems that can focus particles less in various aerosol instruments. These include a Thermal than 30 nm, for applications such as particle delivery in Desorption Chemical Ionization Mass Spectrometer mass spectrometer and micro-fabrications. (TDCIMS), a differential mobility analyzer (DMA), and an aerodynamic lens system. The TDCIMS measures the chemical composition of Research Group particles as small as 4 nm by collecting charged aerosols Hyo Keun Ahn, Graduate Student Researcher on a metal filament by means of electrostatic disposition. Mark Emery, Graduate Student Researcher The goal of this work is to optimize the parameters such Kenjiro Iida, Graduate Student Researcher as flowrate, filament length, and electric field, and to cal- Xiaoliang Wang, Graduate Student Researcher culate the corresponding particle efficiency. The

2006 Annual Research Report of the Supercomputing Institute 185 UM TC–Department of Mechanical Engineering

David Y. H. Pui, Associate Fellow Dynamic Filtration Simulation of Pleated Filter Cartridges Under Pulse-Jet Cleaning in a Baghouse he pulse-jet-cleaned dust collector (or baghouse) tion can be found in the literature. These researchers are has been developed and applied to air contamina- performing a detailed investigation of the operation prin- Ttion control since the late 1950s. In addition to ciples of pleated filter cartridges in a pulse-jet-cleaned the conventional flat-sheet fabric filters (i.e., filter bags), dust collector. the pleated filters (i.e., filter cartridges) have been adopt- Confirmed by the experimental data, this group’s ed extensively in pulse-jet-cleaned dust collectors, three-dimensional numerical models were capable of pre- because of their larger filtration surface and lower operat- dicting overpressures across filters developed from a high- ing costs. However, the fundamental operating principle speed pulse-jet. The main purpose is to obtain the sur- of pleated filter cartridges in a pulse-jet-cleaned dust col- face static pressures on filter surfaces from the numerical lector is not well understood, and only limited informa- models, and to relate them to cleaning efficiency. The numerical results demonstrated that the models can explain the pressure evolution of pleated filter cartridges Research Group during pulse-jet cleaning. With the numerical models, Christof Asbach, Research Associate the group studied the effect of pleat ratio (defined as the Hee-Siew Han, Research Associate ratio of pleat height over pleat pitch) on cleaning effi- Seong Chan Kim, Research Associate ciency and the behavior of duct cake removal during Liming Lo, Graduate Student Researcher pulsing. The results show that a pleat ratio of 4.0 is criti- Weon Gyu Shin, Graduate Student Researcher cal to cleaning modes, which is the same as experimental Sho Takagaki, Graduate Student Researcher results. Investigations of dust cake removal during pulse- Se-Jin Yook, Graduate Student Researcher jet cleaning indicated that the pressure ramp-up rate is an important factor influencing cleaning efficiency.

186 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Mechanical Engineering

Terrence W. Simon, Associate Fellow Simulations of Turbulent Flow and Heat Transfer in Power and Propulsion Systems

hese researchers use Reynolds Averaged Navier- Stokes (RANS) and large-eddy simulation (LES) Research Group and Collaborators Tto study turbulent and transitional flows in aero- Asghar Afshari, Department of Mechanical dynamics and power and propulsion systems. Recent Engineering, Michigan State University, East activities include: large-eddy simulation of flow in a Lansing, Michigan square duct with heat transfer and rotation; simulation of Debashish Burman, Graduate Student Researcher pipe, rod bundle, and annular passage flows with large Farhad A. Jaberi, Department of Mechanical property variations and buoyancy effects (including Engineering, Michigan State University, East supercritical fluids); simulations of film cooling flows. Lansing, Michigan Another small portion of the work is the simulation of Joon Lee, Department of Mechanical Engineering, Wayne State University, Detroit, Michigan porous media in support of the group’s measurements of Yuanhong Li, Department of Mechanical Engineering, thermal dispersion. Iowa State University, Ames, Iowa The long-term objective of this research is twofold. Kunlun Liu, Department of Mechanical Engineering, The first goal is to evaluate the accuracy of RANS, LES, Iowa State University, Ames, Iowa and subgrid turbulence models by comparing predicted Richard Pletcher, Department of Mechanical results with experimentally measured ones. The second is Engineering, Iowa State University, Ames, Iowa to contribute to the physical understanding of flows and Zhaohui Qin, Department of Mechanical Engineering, transition in aerodynamics and power and propulsion Iowa State University, Ames, Iowa systems. Joshua Quinnell, Graduate Student Researcher Wen Wang, Department of Mechanical Engineering, Iowa State University, Ames, Iowa Xiaohang Wang, Department of Mechanical Engineering, Iowa State University, Ames, Iowa Zhi Wang, Department of Mechanical Engineering, Michigan State University, East Lansing, Michigan Bin Zhu, Department of Mechanical Engineering, Michigan State University, East Lansing, Michigan

2006 Annual Research Report of the Supercomputing Institute 187 UM TC–Department of Mechanical Engineering

Patrick J. Starr, Principal Investigator One-Dimensional and Three-Dimensional Modeling of Dynamic Fluid Flow in a Four- Stroke Multi-Cylinder Spark-Ignition Engine his project consists of using industry-standard configuration in that it utilizes a 20 mm intake air orifice one-dimensional and three-dimensional modeling and a multi-port fuel injection. Tsoftware to improve engine performance by The researchers are investigating cyclinder-to-cylinder increasing volumetric efficiency. The computer model air distribution, taper/curvature of intake manifold run- and its calibration are based on a four-cylinder, four- ner, and pulsed choked flow through an orifice/venturi stroke motorcycle engine. The engine differs from a stock restrictor. They are comparing the results of computer simulations with dynamometer runs.

Research Group Mark R. Claywell, Research Associate Dillon J. Hodapp, Undergraduate Student Researcher Donald Horkheimer, Undergraduate Student Researcher Tyler Kuhlmann, Undergraduate Student Researcher Garrett R. Stockburger, Research Associate

Paul J. Strykowski, Principal Investigator Terrence W. Simon, Associate Fellow Computational Modeling of Flow and Heat Transfer in a Heat Exchanger; Engineering Model of Wide Cleft Palate Deformity hese researchers are conducting a numerical study effective transport properties. The database includes the of fluid flow and heat transfer in a heat exchanger permeability, Forchheimer, and thermal dispersion ten- Tconfiguration using a model based on spatial sors, as well as the heat transfer coefficients. In the averaging theorem. The shell-side flow passage is treated micro-scale, a unit cell is analyzed by imposing a varying as a porous medium with anisotropic effective properties. mean flow direction relative to the unit cell and a varying They utilized a unit cell model to construct a database of Reynolds number. In the macro-model analysis, the velocity and temperature distributions in the heat exchanger configuration are obtained by solving the vol- Research Group and Collaborators ume-averaged equations supplemented with effective Aiman Alshare, Graduate Student Researcher properties. The obtained results from the combined Guus B. Jacobs, Department of Mechanical and models are validated by direct numerical simulation. Industrial Engineering, University of Illinois, In a new project, these researchers are investigating Chicago, Illinois whether volmer flaps, a method of repairing wide cleft Deborah Kacmarynski, Graduate Student Researcher Farzad Mashayek, Department of Mechanical and palate deformities in children, causes significant obstruc- Industrial Engineering, University of Illinois, tion in nasal pathways. They are building physical and Chicago, Illinois computer models of volmer flap repairs and comparing the results.

188 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Mechanical Engineering

Kumar K. Tamma, Fellow Computational Mechanics and Multi-Disciplinary Applications to High-Performance Supercomputing his project is concerned with the development of unified computational methodologies, solution Research Group and Collaborators Talgorithms and finite elements, and discontinu- Bayram Alakus, Graduate Student Researcher ous Galerkin and meshless modeling/analysis strategies Shumaila Anwer, Graduate Student Researcher for rigid-flexible multi-body dynamics, contact-impact- Matthew Arrebato, Undergraduate Student Researcher penetration, electromagnetics, multi-disciplinary flow- Antonio F. Avila, Department of Mechanical thermal-structural problems, and micro/nano-scale effects Engineering, Universidade Federal de Minas Gerais, in heat conduction. The philosophy and rationale of this Minas Gerais, Brazil work is based on employing a common numerical Sameer Bhapkar, Graduate Student Researcher Jesus Carrero, Graduate Student Researcher methodology for each of the individual disciplines in Winston Chuck, United Defense, Minneapolis, conjunction with common computational algorithms for Minnesota applicability to supercomputing systems in solving large- Peter N. Chung, U. S. Army Research Laboratory, scale engineering problems. Various research activities Aberdeen, Maryland include: development of new time integration computa- Qunsheng Cao, Research Associate tional algorithms for transient/dynamic problems; devel- Sukru Guzey, Graduate Student Researcher opment of effective finite element-based methodologies Bhanu Hariharan, Graduate Student Researcher that can be used in multi-disciplinary problems; new Andrew Hoitink, Graduate Student Researcher physically correct contact models for penetration and Amit Jain, Graduate Student Researcher impact problems; and application of finite element meth- Brian Johnson, Undergraduate Student Researcher Jared J. Johnson, Graduate Student Researcher ods in manufacturing simulations to provide a paradigm Ramdev Kanapady, Research Associate for virtual manufacturing. The application areas include Christopher D. Kauffman, Undergraduate Student a wide range of engineering problems involving multi- Researcher physics and space/time domain decomposition with Yu Liang, Research Associate interface to graph partitioning techniques. The overall Yvonne Miller, Graduate Student Researcher efforts focus attention on providing new, effective, and Ram V. Mohan, U. S. Army Research Laboratory, robust approaches for not only improving the existing Aberdeen, Maryland capabilities for applicability to supercomputing environ- Nam D. Ngo, Graduate Student Researcher ments, but also towards providing an accurate under- Aniruddha Sadhale, Graduate Student Researcher standing of the physics and mechanics relevant to multi- Sukhpreet Singh Sandhu, Research Associate Dale Shires, U. S. Army Research Laboratory, disciplinary engineering problems. Aberdeen, Maryland Anak Somkanae, Undergraduate Student Researcher Siddharth Srinivasan, Graduate Student Researcher Jing Wang, Research Associate Delonia Wiggins, Graduate Student Researcher Ming Zang, Graduate Student Researcher Nan Zhang, Research Associate Xiangmin Zhou, Graduate Student Researcher

2006 Annual Research Report of the Supercomputing Institute 189 UM TC–Department of Physics

Paul A. Crowell, Principal Investigator Micromagnetic Studies of Spin Dynamics in Magnetic Nanoparticles

mall ferromagnetic grains are the building blocks of This research project focuses on two problems. First, storage media, and these researchers are studying the group addresses the real-time dynamics of particles Sarrays of thin film magnetic nanostructures as pro- with an inhomogeneous magnetic microstructure. totypical patterned media. The dynamics of these systems Typical examples include magnetic vortices and other are influenced by the interplay of short-ranged exchange structures showing topological defects such as domain interactions and longer-range magneto-static interactions. walls. Second, the group examines the stability of small The characteristic frequencies are in the gigahertz range magnetic particles under pulsed excitation as well as high and damping times for excitations are typically a few amplitude continuous-wave excitation. This aspect of the nanoseconds. work addresses applications such as ultrafast switching and the stability of storage media. The researchers use the supercomputers to perform real-time micromagnetic sim- Research Group ulations to address spin-wave dynamics in inhomoge- Mun Chan, Graduate Student Researcher neous media. The results are used to interpret time- Robert Compton, Graduate Student Researcher resolved Kerr microscopy measurements. Jooho Park, Graduate Student Researcher David Toyli, Undergraduate Student Researcher

Eric D. Ganz, Principal Investigator Quantum Chemistry Studies of Hydrogen Storage in Metal Organic Frameworks

ecently, a new concept for hydrogen storage has the binding energy of the crystal. The researchers used been demonstrated that involves storing hydrogen Moeller-Plesset many-body perturbation theory to calcu- Rgas in a porous solid material. In particular, metal late the binding energy for hydrogen on the metal organ- organic frameworks have been developed that are inex- ic framework materials, and used grand canonical Monte pensive to manufacture, lightweight, and stable. Carlo simulations to calculate the sorption as a function These researchers use quantum chemistry methods to of temperature and pressure. A wide range of structures is study the hydrogen-storage properties of these materials. possible with metal organic frameworks, and the group The gravimetric and volumetric storage efficiency can be also studied the fundamental design principles for creat- increased by increasing the surface area of by increasing ing the storage devices. This research should contribute to the realization of a portable, efficient, and safe storage method for hydrogen gas. Research Group James Klassen, Undergraduate Student Researcher Julia Ortony, Undergraduate Student Researcher Tatsuhiko Sagara, Graduate Student Researcher

190 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Physics

Alexander Y. Grosberg, Fellow Entropy of Polymeric Knots and Its Dependence on Polymer Flexibility

hile it is known that the probability of obtaining a ring with no knots upon polymer Research Group and Collaborators Wchain random closure decays exponentially Longhua Hu, Graduate Student Researcher with the number of segments, this fact is not understood. Rhonald Lua, Graduate Student Researcher Researchers also do not understand the characteristic Nathan Moore, Graduate Student Researcher number of segments involved in the exponential depend- Shay Rapaport, Department of Physics, Bar Ilan ence, which is unexpectedly large at around 300 seg- University, Israel ments. These researchers studied these important entrop- Motohiko Tanaka, National Institute for Fusion ic properties of polymeric knots by simulating knots for Science, Toki, Japan polymers with a variety of segment lengths, distribution, and flexibility mechanisms.

2006 Annual Research Report of the Supercomputing Institute 191 UM TC–Department of Physics

J. Woods Halley, Fellow Numerical Studies of Fluids and Disordered Solids

hese researchers are continuing their computational research in the fields of electrochemical interfaces, disordered polymers, and Bose- T Research Group and Collaborators (continued) Einstein condensed systems. The computational methods You Lin, Department of Physics, University of South used include direct dynamics, classical molecular dynam- Florida, Tampa, Florida ics, hydrodynamics, continuum mechanics, and Monte Dang Dinh Long, Department of Physics, University Carlo simulation. The group is developing several new of Alberta, Edmonton, Alberta, Canada methods, including self-consistent tight binding molecu- Yaroslav Lutsyshyn, Graduate Student Researcher lar dynamics and temporally renormalized molecular Dat Nguyen, Graduate Student Researcher dynamics in the course of this research. Scott J. Reckinger, Supercomputing Institute Undergraduate Intern James R. Rustad, Department of Geology, University of California, Davis, California Patrick Schelling, Department of Physics, University of South Florida, Orlando, Florida Herbert Shore, Department of Physics, San Diego Research Group and Collaborators State University, San Diego, California Jun Chung, Graduate Student Researcher Alexander Tchernatinsky, Research Associate Larry Curtiss, Argonne National Laboratory, Argonne, Nacir Tit, Department of Physics, University of the Illinois United Arab Emirates, Al-Ain, United Arab Emirates Yuhua Duan, National Energy Technology Laboratory, Mark Williams, Department of Physics, Northeastern Department of Energy, Pittsburgh, Pennsylvania University, Boston, Massachusetts Serkan Erdin, Argonne National Laboratory, Argonne, Aaron Wynveen, Department of Physics, University Illinois College, London, United Kingdom Lingling Jia, Research Associate Peter Zapol, Argonne National Laboratory, Argonne, Robert Joynt, Department of Physics, University of Illinois Wisconsin, Madison, Wisconsin Weilin Zhang, Graduate Student Researcher Keith Lidke, Sandia National Laboratory, Min Zhuang, Department of Physics, University of Albuquerque, New Mexico Montreal, Montreal, Quebec, Canada

192 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Physics

Shaul Hanany, Associate Fellow Probing the Big Bang With the Cosmic Microwave Background Radiation

he Hanany group is probing the origin of the using the supercomputers to perform physical optics Universe with observations of the cosmic analysis to explore the optical performance of their Tmicrowave background (CMB) radiation. The designs and for mission-planning and pipeline-develop- group is in the process of design and construction of a ment tasks. balloon payload called EBEX that promises to yield information about the universe at times as short as 10–35 seconds after the big bang. The group is also par- Research Group and Collaborators ticipating in a study for a National Aeronautics and Prashanth Jonnalagadda, Graduate Student Researcher Space Administration mission called EPIC to measure Michael Milligan, Graduate Student Researcher Nicolas Ponthieu, Institute Astrophysique Spatiale, the polarization of the CMB. Both of these efforts prom- Orsay, France ise to yield strong constraints on models of the origin Jiun-Huei Proty Wu, Physics Department, National and evolution of the universe. The design efforts on Taiwan University, Taipei, Taiwan EBEX and EPIC require significant computing power; Ilan S. Sagiv, Staff the researchers are performing finite element analysis to See-Chew Soon, Graduate Student Researcher identify the mechanical requirements of the telescope Kyle Zilic, Undergraduate Student Researcher reflectors, support structures, and gondola. They are also

Norton M. Hintz, Principal Investigator Nuclear Reaction Calculations

he basic nucleon-nucleon interaction is well known for free nucleons (neutrons and protons). TThis interaction, however, is modified, in a still- unknown way, when the nucleons are in the nuclear medium. This is important for nuclear structure and astrophysical calculations. This project analyzed data the Principal Investigator took during the 1980s and 90s at Research Group Los Alamos. This data, on the scattering of protons off Michael A. Franey, Research Associate nuclei, can be used to extract information on the medium modification of the nucleon-nucleon interaction.

2006 Annual Research Report of the Supercomputing Institute 193 UM TC–Department of Physics

Robert L. Lysak, Associate Fellow Numerical Investigations of Solar Wind-Magnetosphere-Ionosphere Coupling

his project is centered on several problems involv- applying the group’s three-dimensional model for the ing the coupling of mass, momentum, and ener- propagation of compressional and shear Alfvén waves Tgy between the solar wind, magnetosphere, and through the auroral ionosphere and atmosphere by look- ionosphere. This work involves both the development of ing at the excitation and propagation of waves propagat- new codes and the modification and use of existing codes ing in the so-called ionospheric waveguide, and by look- to address the problem of solar wind-magnetosphere-ion- ing at the detailed structure of the ionosphere including osphere coupling. Specific areas of research include: collisional effects; developing and modifying a model for magnetospheric wave propagation in the magnetosphere to a code in spherical geometry to model atmospheric Research Group and Collaborators wave propagation in order to study the so-called James Crumley, Department of Physics, St. John’s Schumann resonances; investigation of the dynamics of University, Collegeville, Minnesota the magnetospheric tail using a three-dimensional version Eun-Hwa Kim, Astronomy and Space Science, Kyung- of the total variance diminishing magnetohydrodynamic Hee University, Yongin, Kyunggi, Korea code developed by the Thomas Jones group in the Dong-Hun Lee, Astronomy and Space Science, Kyung- Department of Astronomy; and considering the effects of Hee University, Yongin, Kyunggi, Korea a kinetic description of electrons in the auroral zone. Yan Song, Research Associate Jesse Woodroffe, Graduate Student Researcher

Oriol T. Valls, Fellow Numerical Studies on Superconducting/Magnetic Structures and on the Superconducting Vortex Lattice Phase Diagram hese researchers continued their investigations superconducting and ferromagnetic materials, using a into two areas: proximity effects in heterostruc- numerical method they have developed to solve the exact Ttures involving superconductors and ferromag- microscopic equations for such systems. In the second nets, and phase diagram and density structure of super- area, the researchers study the phase diagram of type II conducting vortex systems in the presence of pinning superconductors in the vortex state, in the presence of centers. In the first area, the group studies the behavior both a magnetic fields and pinning centers. They use of high-quality multilayers and superlattices composed of numerical minimization of the appropriate free energy function (in terms of the time-averaged density variables) to find the free energy from which the phase diagram is Research Group and Collaborators obtained. The density structure at each minimum yields Chandan Dasgupta, Faculty Collaborator the correlation functions and the nature (crystal, glass, or Paul Barsic, Graduate Student Researcher liquid) of the phase. Klaus Halterman, China Lake Research Center, China Lake, California Igor Zutic, State University of New York, Buffalo, New York

194 2006 Annual Research Report of the Supercomputing Institute UM TC–Theoretical Physics Institute

Philippe de Forcrand, Adjunct Fellow Quantum Chromodynamics at Finite Density

ne prediction of quantum chromodynamics date: they consider an imaginary chemical potential µI, (QCD) is that quarks are confined at low tem- for which traditional Monte Carlo methods apply, and Operature, but that a quark-gluon plasma forms determine the critical temperature Tc(µI). The result is fit to a truncated Taylor series followed by analytic continu- above some temperature Tc. Current experiments on heavy-ion collisions may provide evidence for this plas- ation to real µ. Information about the canonical ensemble, at fixed baryon number, can also be extracted, thus ma, so it is important to predict Tc. The critical tempera- providing a framework for an ab initio calculation of ture Tc (µ) depends on the relative excess of matter over antimatter in the heavy-ion collision, or equivalently on nuclear interactions. the quark chemical potential m. Unfortunately, lattice QCD simulations can only directly probe the case µ = 0, because otherwise the notorious “sign problem” prevents Collaborator Monte Carlo sampling over a positive measure. These Owe Philipsen, Institute for Theoretical Physics, researchers are pursuing an approach that is free of the Westfaelische Wilhelms-Universität, Münster, sign problem and that gives the most accurate results to Germany

UM TC–School of Mathematics

Bernardo Cockburn, Fellow Numerical Methods for Partial Differential Equations

hese researchers are involved in three projects for equation model problems. The researchers use approxi- which they are using the supercomputers. In the mations given by the discontinuous Galerkin method Tfirst, they are using finite element methods to with polynomials of degree k and a post-processing tech- obtain approximations to the viscosity solution of nique. Their approximations converge to the true func- Hamilton-Jacobi equations. Using an a posteriori error tional value at order 4k + 1 and 4k in ODE and convec- estimate and algorithm to computer new mesh of the tion equations, respectively. They are now investigating computational domain from the old, the researchers the adaptivity of this method. compute approximations whose L∞— error is within a prescribed tolerance, while keeping the computational effort minimal. Research Group In the second project, the group has developed a new Yanlai Chen, Graduate Student Researcher hybridized method to efficiently solve second order ellip- Bo Dong, Graduate Student Researcher tic problems. The method allows for a very easy imple- Deepa Gupta, Graduate Student Researcher mentation of variable-degree approximations. Johnny Guzman, Research Associate The final project deals with obtaining superconvergent Ryuhei Ichikawa, Graduate Student Researcher approximations of linear functions, considering ordinary Haiying Wang, Graduate Student Researcher differential equations (ODE) and convection-diffusion

2006 Annual Research Report of the Supercomputing Institute 195 UM TC–School of Mathematics

Dennis A. Hejhal, Fellow Computational Aspects of Analytic Number Theory

his research group continued its computational ning on the IBM SP and SGI Altix supercomputers. analyses of high frequency eigenfunctions of the Also, using the Fourier coefficients obtained from this TLaplacian on fuschsian groups. During this year, program, they have conducted statistical analyses of these they have optimized their code so that it is suitable for coefficients of a more refined nature than previously car- applications wherein the underlying multiplier system ried out. has arbitrary real weight. One such application would be to the L-functions L(s,f) associated with such eigenfunctions. They have been working on getting this code run-

Collaborators Barry N. Rackner, Bridge Communications, St. Paul, Minnesota James Z. Wang, Information Technology, Pennsylvania State University, State College, Pennsylvania

Mitchell B. Luskin, Fellow Richard D. James, Co-Principal Investigator Numerical Tools for Active Martensitic Thin Films; Parallelization and Optimization of the Multiscale Quasicontinuum Methods he computation of active thin films is essential to active thin films. The goal of the research was to develop the development of micromachines for wide- the ability to simulate the behavior of shape memory Tranging applications from medicine to aerospace. materials that undergo a martensitic transformation. These researchers developed computational methods for A new project begun this year involved the quasicon- nonlinear partial differential equations that model the tinuum (QC) method, which is a multiscale computa- dynamics of the austenitic-martensitic transformation in tional technique used to study problems in materials physics involving simultaneous multiple spatial scales. The method retains atomistic resolution where necessary, Research Group and Collaborator grading out to a continuum elsewhere. Typically, using Marcel Arndt, Research Associate this method results in a computational savings of two to Pavel Belík, Research Associate three orders of magnitude relative to standard brute-force Matthew Dobson, Graduate Student Researcher atomistic techniques. Although this method is standard Ellad Tadmor, Faculty Collaborator Huang Tang, Graduate Student Researcher in the modeling community, it has never been optimized Steve Whalen, Graduate Student Researcher or parallelized. These researchers are developing an opti- Tianyu Zhang, Graduate Student Researcher mal parallelized version of the QC method suitable for studying large-scale materials problems.

196 2006 Annual Research Report of the Supercomputing Institute UM TC–School of Mathematics

Wei-Ming Ni, Principal Investigator Reaction-Diffusion Model of Bacterial Colony Patterns

hese researchers are running a reaction-diffusion model for bacterial colony patterns with different Tgrowth rates. They hope to find dense branching Research Group morphology or diffusion-limited aggregation patterns, as Yu-Wen Chiu, Graduate Student Researcher observed in experiments. The group is using the Supercomputing Institute laboratories for this project.

Andrew Odlyzko, Principal Investigator Statistical Analyses of Zeros and the Riemann Zeta Function

here is active research going on around the world data, and they have tested them on subsets of the data. on the (so far largely speculative) connection They are now applying these algorithms to the entire Tbetween the Riemann zeta function from pure dataset in order to see how well actual data fits the specu- number theory and random matrices that arise in quan- lative predictions. tum chaos studies. In particular, analogies have been drawn between the behavior of the zeta function on the critical line and some matrix models that have led to new conjectures, not approachable from number theoretic viewpoints, about the asymptotics of the moments of the zeta function on the critical line. The aim of this project is to obtain numerical data to check these conjectures. These researchers have developed a database of over 20 billion zeros of the Riemann zeta Research Group functions and related values, most near zero number Ghaith Hiary, Graduate Student Researcher 1023. They have also developed algorithms for efficient computation of moments of the zeta function from this

2006 Annual Research Report of the Supercomputing Institute 197 UM TC–School of Mathematics

Hans G. Othmer, Fellow Mathematical Modeling of Actin Dynamics and Cell and Tissues Mechanics

ell and tissue movement is an integral part of interactions with their surroundings, and understanding many biological processes, such as large-scale tis- how they are controlled in space and time to produce Csue rearrangements or translocations that occur cell-level movement is a major challenge. during embryogenesis and angiogenesis. Movement These researchers are continuing their research on cell entails force generation within cells and mechanical and tissue movement by investigating cell cytoskeleton dynamics, the mechanics of cell movement, and the mechanics of tumor growth. Other research areas Research Group include: development of a three-dimensional model that Jifeng Hu, Graduate Student Researcher may explain seemingly counterintuitive patterns on the Minchul Kang, Graduate Student Researcher dorsal surface of Drosophila; development of a continu- Yang-Jin Kim, Graduate Student Researcher um mechanics software that will be used to simulate and Chang Hyeong Lee, Graduate Student Researcher analyze the dynamics of a variety of biomechanical com- Anastasios Matzavinos-Toumasis, Research Associate Magdalena Stolarska, Supercomputing Institute ponents of eukarotic cells, such as F-actin networks Research Scholar involved in the process of force generation at the leading Nicoleta Tarfulea, Graduate Student Researcher edge of motile cells; and formulation of a master equa- David Umulis, Graduate Student Researcher tion in the framework of stochastic chemical kinetics, Xiaoqiang Wang, Research Associate characterizing the distribution of length and nucleotide Chuan Xue, Graduate Student Researcher profiles of actin filaments.

Fernando L. Reitich, Principal Investigator High-Order Methods for Compuational Electromagnetics and Acoustics

hese researchers have developed a variety of efficient numerical techniques for the simulation of Research Group and Collaborators Telectromagnetic- and acoustic-wave scattering Akash Anand, Graduate Student Researcher processes in the time and frequency domains. Their novel Qunsheng Cao, College of Information Science and procedures are based on effective, high-order treatments Technology, Nanjing University of Aeronautics and of integral and differential formulations of the scattering Astronautics, Nanjing, China problem. Their initial work on a wide array of test cases YoungAe Han, Department of Applied and demonstrated the viability of the newly developed Computational Mathematics, California Institute of schemes for scattering simulations, and it also proved Technology, Pasadena, California that they offer the potential for substantial improvement McKay Hyde, Department of Computational and Applied Mathematics, Rice University, Houston, in simulation capabilities over currently available meth- Texas ods. The confirmation of these advantages for practical, Ramdev Kanapady, Faculty Collaborator realistic geometric arrangements at frequencies of inter- Catalin Turc, Department of Applied and est, however, demands the use of supercomputing Computational Mathematics, California Institute of resources. The researchers are using the supercomputers Technology, Pasadena, California to improve and expand their current codes to efficiently run simulations of practical interest.

198 2006 Annual Research Report of the Supercomputing Institute UM TC–School of Mathematics

Fadil Santosa, Principal Investigator Ophthalmic Lens Design and Simulation

his project concerned the design of progression what the patient sees through a particular lens. The next addition lenses, which are worn by patients with step was to devise an optimization method that allowed Tpresbyopia. Progressive lenses need to accommo- the researchers to design lenses with specific desirable date both far-vision correction as well as near-vision cor- attributes. rection. Unlike bifocal lenses, progressive lenses change power smoothly from far to near vision. The physical properties of the lenses are well modeled by geometrical optics. Most design procedures further simplify the Research Group and Collaborator optics, reducing it to designing a surface with prescribed Gerard Awanou, Research Associate mean curvature. Dacian Daescu, Research Associate In this project, the researchers designed lenses based Stephen A. DeSalvo, Supercomputing Institute on optical principles. They first investigated the proper- Undergraduate Intern ties of a lens using geometrical optics. In particular, they Anton Leykin, Graduate Student Researcher built a tool whereby they could simulate what a patient Mihalis Sigalas, Agilent Laboratories, Palo Alto, with presbyopia sees. The tool allowed them to assess the California corrective properties of a lens, and especially simulate

UM TC–Institute for Mathematics and Its Applications

Arnd Scheel, Principal Investigator Mathematics of Imaging Science

he Institute for Mathematics and Its Applications great opportunity to significantly contribute to advances (IMA) is hosting a program aimed at the synthe- in imaging science. Tsis of the problems at the interface between mathematics, imaging science, and computer vision. Imaging science is highly interdisciplinary, naturally con- Research Group necting mathematical sciences with a variety of applica- Gerard Awanou, Research Associate tion areas. Mathematical areas that have contributed to Evgeniy Bart, Research Associate this field include harmonic analysis, partial differential Brian DiDonna, Research Associate Sookyung Joo, Research Associate equations and integral geometry, calculus of variations, Chiu Yen Kao, Research Associate probability theory, statistics, and learning theory. Richard Kollar, Research Associate Historically, interchange of ideas among researchers com- Matthias Kurzke, Research Associate ing from different applications has been impeded by bar- Frederic Legoll, Research Associate riers of jargon and culture. By bringing together a range Xiantao Li, Research Associate of researchers end emphasizing the underlying mathe- Peter Philip, Research Associate matical structures and algorithms in the highly interdisci- Xiaoqiang Wang, Research Associate plinary atmosphere of the IMA, this program creates a

2006 Annual Research Report of the Supercomputing Institute 199 UM TC–Department of Dermatology

Mimi Cho, Principal Investigator Marna E. Ericson, Co-Principal Investigator Characterization of Keratinocyte Populations in Vitiligo Patients

itiligo is a disease caused by the absence of and may play a role in vitiligo. Using blister samples melanocytes in the epidermis. Its pathogenesis is from affected and non-affected skin, the researchers are Vmultifactorial and treatments are marginal with a performing gene expression investigation by microarray 50–60% response rate that does not guarantee full repig- analysis to study the role of the epidermis in vitiligo. mentation. Understanding the pathogenesis of vitiligo will allow better targets for treatment. One of the most effective treatments is ultraviolet light therapy. The hair follicle contains melanocyte reservoirs in the outer root sheath and dermal papillae. Interestingly, the inactive melanocytes are protected from the effects of vitiligo and are activated by light therapy. These cells have been studied histologically and biochem- ically but have not been studied by characterization of their global gene expression. These researchers theorize that other cells in the epidermis, primarily keratinocytes, also influence the microenvironment for the melanocytes

UM TC–Department of Laboratory Medicine and Pathology

Donald P. Connelly, Principal Investigator The Impact of Bone Marrow Biopsy Diagnostic Discordance on Clinical Decision- Making; Blood Utilization Collaborative hese researchers are using the Computational informatics point of view. Genetics Laboratory for two projects. The first is The second study involves one of the basic problems Ta three-phase project. In the first phase, the encountered by blood bank medical directors, the need researchers are measuring bone marrow diagnostic discor- to find reasonable sources of community standards for dance among the hematopathology, cytogenetics, and blood usage data. Such sources do not exist, at least not flow cytometry laboratory cases. The second phase on a large scale. The goal of this study is to create a data- involves categorizing these discordances by several meth- base of blood usage data across specialties and indications ods, while the third looks at how discordance impacts in order to create information normalized to patient and clinical decision-making with a case vignette study. Each other factors. phase looks at clinical decision-making from a health

Research Group Andrea Pitkus, Graduate Student Researcher Amar Subramanian, Research Associate

200 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Laboratory Medicine and Pathology

Lynda B. M. Ellis, Principal Investigator Seeking the Vertebrate Secretome

ecreted proteins (the secretome) make up approxi- These researchers have developed csP, a technique that mately 10–20% of the vertebrate proteome, control uses protein domain classification instead of signal Scell-cell interactions, and are major targets for drug sequence identification to predict secreted proteins. They discovery. Secreted protein prediction has traditionally are using Supercomputing Institute resources along with relied on N-terminal signal sequence identification. this technique for their research. These techniques assume predictions are based on full- length protein sequences and performance significantly Research Group decreases when analyzing N-terminally incomplete Mark J. Fischbach, Undergraduate Student Researcher sequences, such as protein sequences encoded by Yogesh Kale, Graduate Student Researcher expressed sequence tags. Truncated signal peptides may Eric Klee, Graduate Student Researcher reduce the sensitivity, and N-terminal truncations near Kyong-Jin Shim, Graduate Student Researcher transmembrane domains may reduce the specificity, of Carlos Sosa, Research Associate these techniques.

Michael A. Farrar, Principal Investigator Regulation of Lymphocyte Development and Activation by STAT5

he transcription factor STAT5 plays a key role in the mechanism by which STAT5 drives T cell homeosta- the development of both B and T lymphocytes. sis. TThese researchers have demonstrated that activa- Finally, STAT5 plays a key role in promoting the tion of this transcription factor is sufficient to restore development of a subset of T cells, called suppressor T lymphocyte development in the absence of the cytokine cells, which play an important role in preventing autoim- IL7. They are using STAT5 chromatin immunoprecipita- munity. The group is identifying STAT5 target genes tion assays and gene microarrays to identify STAT5 tar- that regulate suppressor T cell development and func- get genes required for this process. These studies should tional activity. shed light on the molecular mechanisms that entrain lymphocyte development. Research Group STAT5 also plays an important role in regulating Matt Burchill, Graduate Student Researcher numbers of mature T cells. The cytokine IL7 is impor- Linxi Li, Graduate Student Researcher tant in ensuring that T cell numbers remain relatively Leo McNamara, Research Associate constant (referred to as T cell homeostasis). The John Szarejko, Graduate Student Researcher researchers have identified two genes, bcl-xL and pim-1, Jianying Yang, Graduate Student Researcher as key target genes in this process and are characterizing

2006 Annual Research Report of the Supercomputing Institute 201 UM TC–Department of Laboratory Medicine and Pathology

William B. Gleason, Fellow Computational Approaches to Understanding Biomolecular Structure and Function

hese researchers are continuing their work on a period include: the use of parallel processing for the number of projects using Supercomputing interpretation of mass spectral data and for drug dock- TInstitute resources. Projects of interest during this ing; production of three-dimensional models for all known fibroblast growth factors using homology modeling followed by, in some cases, molecular dynamics simulations; simulation of the binding of heparin and Research Group heparin-like molecules to proteins; simulation of the Leila Albers, Research Associate Jack Anderson, Undergraduate Student Researcher binding of anti-cancer drugs to tyrosine kinases, taking Jason Bjork, Graduate Student Researcher into account their dynamic behavior; molecular simula- Pooja Chakrabarty, Undergraduate Student Researcher tion of the binding of Congo Red (and analogs) to the Eric Eccleston, Research Associate human immunodeficiency virus protease; and simulation Mona Majid, Undergraduate Student Researcher of the dynamics of sulfated-carbohydrate containing Elliot McSherry, Graduate Student Researcher polymers, based on poly(methyl methacrylate), in order Caroline Nibbe, Undergraduate Student Researcher to determine the likelihood of their similarity to heparin. Evgenia (Jane) Shveldize, Supercomputing Institute Undergraduate Intern Lee G. Stanek, Graduate Student Researcher Derek Straka, Undergraduate Student Researcher

Myron D. Gross, Principal Investigator Deoxyribonucleic Acid Repair Genes and Breast Cancer Risk

hese researchers are using supercomputing resources to identify potentially important single Tnucleotide polymorphisms in the nucleotide exci- sion repair (NER) pathway. They are also studying the interactions between different genes in the NER pathway and their relationship to breast cancer risk.

Research Group Jennifer Hayes, Research Associate Poonguzhali Kailash, Research Associate Waseem Khaliq, Graduate Student Researcher Chris Lessard, Research Associate Bharat Thyagarajan, Graduate Student Researcher

202 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Laboratory Medicine and Pathology

Franz Halberg, Associate Fellow Germaine G. Cornélissen, Co-Principal Investigator Assessment of Physiologic Chronomes From Womb to Tomb

trokes and other adverse vascular events are major The researchers use supercomputing resources to: ana- cripplers at an estimated yearly cost of over $30 bil- lyze beat-to-beat records for resolving chronobiologic and Slion. These researchers are developing a system for chaotic endpoints; automatically update reference stan- the chronobiologic analysis of cardiovascular records with dards as added data accumulate; detect the earliest risk by focus on disease prevention, but also addressing the ques- means of chronome alterations; and follow up at-risk tion of the optimal kind and scheduling of treatment. individuals longitudinally by means of control charts. Ambulatory devices are used in different geographic locations to monitor blood pressure for seven days at the out- set. Chronobiologic analyses of such records serve first and foremost to improve screening, diagnosis, and treat- Research Group and Collaborator ment, but also to assess how environmental factors affect Dewayne Hillman, Graduate Student Researcher human physiology, notable heart rate and blood pressure. Miguel A. Revilla, Department of Applied and Computational Mathematics, Faculty of Sciences, University of Valladolid, Valladolid, Spain

Stephen S. Hecht, Associate Fellow Biochemistry, Biology, and Carcinogenicity of Tobacco-Specific N-Nitrosamines

hese researchers are studying the cytochrome this research is to use these models as tools to construct P450-mediated bioactivation of the tobacco car- potent and specific inhibitors of nitrosamine bioactiva- Tcinogen, 4-(methylnitrosamino)-1-(3-pyridyl)-1- tion. Such inhibitors would ideally reduce its carcino- butanone (NNK). This nitrosamine causes lung tumors genicity. in all animal models in which it has been tested and is a putative human lung carcinogen in tobacco products. In vitro metabolism assays have revealed that closely related cytochrome P450 enzymes (P450s), both within and between species, exhibit markedly variable regioselectivity for the metabolism of NNK. Recent work by this group has attempted to elucidate the structural basis for these biochemical data. They have also constructed homology Research Group models of P450 2A enzymes, for which crystal structures Yanbin Lao, Graduate Student Researcher are not currently available. The researchers are now Siyi Zhang, Graduate Student Researcher broadening their studies with the homology models to other carcinogenic nitrosamines. The ultimate goal of

2006 Annual Research Report of the Supercomputing Institute 203 UM TC–Department of Laboratory Medicine and Pathology

John H. Kersey, Principal Investigator Gene Deregulation in MLL-Fusion Gene Leukemia

nfant leukemia and secondary leukemias are associat- identify those genes that deregulated in specific cell com- ed with translocations involving the MLL gene. partments. These data will help identify downstream IThese researchers are investigating the molecular effects that are specific to a given fusion gene in a specific pathogenesis of leukemia caused by these MLL-fusion cell type. This information will significantly add to the genes. They are studying animal models of two of these understanding of the molecular pathogenesis of these dis- fusion genes, MLL-AF4 and MLL-AF9. They are com- orders, which will then help in the development of newer paring the gene expression profiles of various hematopoi- therapeutic strategies. etic progenitor/stem cells derived from MLL-AF4 and MLL-AF9 mice to wild-type counterparts in order to

Research Group Suzanne Grindle, Research Associate Ashish Kumar, Research Associate

Matthew F. Mescher, Principal Investigator Gene Array Analysi of CD8 T Lymphocyte Activation

D8 T lymphocytes are the “killer cells” of the form gene array analysis to determine the genes that are immune system, and can recognize and eliminate regulated by the third signal cytokines. Studies so far Cvirus-infected cells and tumor cells. In order to have revealed several families of regulated genes and have carry out this function, the naive cells must first be stim- identified candidate transcription factors that may play ulated in an antigen-specific manner to proliferate and key regulatory roles in proliferation, survival, and differ- undergo a differentiation process to develop effector entiation of the cells. The group is performing additional function. Naive CD8 T lymphocytes require three signals gene array analyses to determine changes in expression to become fully activated: antigen, costimulation, and a patterns when these candidate molecules are absent, third signal that can be provided by IL-12 or Type I using T cells from mice with selective gene knockouts. interferon. Using artificial antigen-presenting cells to provide antigen and costimulation, the researchers per-

Research Group Pujya Agarwal, Graduate Student Researcher

204 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Laboratory Medicine and Pathology

Harry T. Orr, Principal Investigator Microarray Analysis of SCA1

pinocerebellar ataxia type 1 (SCA1) is a progressive ment for the disease. The researchers are using software neurodegenerative disease caused by the expansion available through the Supercomputing Institute laborato- Sof a polyglutamine repeat in the disease protein, ries for their analyses. ataxin-1. To understand the basic mechanism involved in SCA1 pathology, these researchers are using microarray technology to analyze the pattern of gene expression in a conditional mouse model in which the expression of mutant ataxin-1 in cerebellar Purkinje cells can be controlled by a tetracycline-regulated system. They are screening two groups of these mice (treated and untreated) at twelve weeks of age as well as two groups (treated Research Group and untreated) of twelve-week-old wild-type animals. Heliane Serra, Research Associate Genes capable of reversing the pathology will be useful in understanding SCA1 and in developing therapeutic treat-

Sherif Tawfic, Principal Investigator Study of CD10 in Prostatic Adenocarcinoma

rostate cancer is the most common non-skin This project studied a large number of cases to exam- malignancy and the second leading cause of cancer ine the potential use of CD10 expression as a diagnos- Pdeath in men in the United States. Molecules that tic/prognostic marker, and to examine the level of regula- are differentially expressed in prostate cancer and/or nor- tion of CD10 expression in prostatic adenocarcinoma. mal glands have the potential to be used as diagnostic/ The project used resources at the Basic Sciences prognostic markers, to enhance the understanding of the Computing Laboratory to show the three-dimensional pathogenesis and to help in developing specific therapies. distribution of the tumor within the gland. Preliminary data have shown that CD10, a cell-surface enzyme that inactivates several biologically active peptides, is downregulated in low-grade prostatic adenocarcinoma and in its precursor lesion. The decline of CD10 in the precursor lesion indicates that CD10 downregula- tion temporally precedes the development of prostatic adenocarcinoma and may be involved in the process of oncogenesis.

2006 Annual Research Report of the Supercomputing Institute 205 UM TC–Department of Laboratory Medicine and Pathology

Michael Y. Tsai, Principal Investigator Gene Expression Profile of People With High HDL and Low HDL

he serum concentration of cholesterol in high- ciated with enzymes such as paraoxonase, lethicin choles- density lipoprotein (HDL) is an inverse predictor terol acyltransferase, and apolipoproteins apo A-1 and Tof future cardiovascular disease, with evidence apo A-2. HDL’s anti-inflammatory and antithrombotic mounting that therapies that increase HDL concentra- functions are associated with inhibition of expression of tion are antiatherogenic. The best-known antiatherogenic cellular adhesion molecules. Recently discovered vasopro- function of HDL particles relates to their ability to protective mechanisms of HDL include enhanced nitric mote the efflux of cholesterol from cells. They also have oxide production and improved endothelium-dependent antioxidant, antiinflammatory, and antithrombotic prop- relaxation erties, however. Antioxidant properties of HDL are asso- These researchers extract ribonucleic acid (RNA) from people with either a high or low HDL level, and compare their gene expression profiles. The researchers are using resources at the Computational Genetics Research Group Laboratory and the Scientific Development and Valerie L. Arends, Research Associate Visualization Laboratory for this work. Jing Cao, Graduate Student Researcher

206 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Medicine

Timothy W. Behrens, Principal Investigator Discovery of Biomarkers for Rheumatic Diseases

he goal of this research project is to integrate a variety of cutting-edge discovery technologies in Research Group and Collaborator (continued) Torder to discover novel biomarkers that will be Jason Bauer, Graduate Student Researcher clinically useful in one of the two major rheumatic dis- Dianna Crawford, Graduate Student Researcher eases, rheumatoid arthritis and systemic lupus erythe- Karl Espe, Staff matosus. These technologies include broad gene expres- Emily C. Gillespie, Graduate Student Researcher sion profiling using deoxyribonucleic acid microarrays, Clarence Gillett, Graduate Student Researcher Thearith Koeuth, Staff combined with novel approaches to multi-parameter Chieko Kyogoku, Graduate Student Researcher analysis of cell surface and soluble proteins relevant to Anojinie Nagahawatte, Graduate Student Researcher inflammatory disease states. The group used the Lydia Najera, Research Associate Computational Genetics Laboratory and the Basic Steven M. Offer, Graduate Student Researcher Science Computing Laboratory for their research. Ward Ortmann, Staff Laura Ramsey, Graduate Student Researcher Peter Rodine, Staff Research Group and Collaborator Brian Schram, Research Associate Franak Batliwalla, Division of Biology and Human Catherine Slattery, Staff Genetics, North Shore University Hospital, Mark Stenglein, Graduate Student Researcher Manhasset, New York Beth Ziemba, Graduate Student Researcher

Peter B. Bitterman, Principal Investigator Elucidating the Rules of Translation Control

n the past ten years, a growing body of literature has documented that messenger ribonucleic acid transla- Research Group and Collaborators Ition is an important control point, especially in Deanna Diebold, Research Associate embryonic development, regulation of cell growth, and Flora Fan, Graduate Student Researcher differentiation and tumorigenesis. The goal of this study Craig Henke, Faculty Collaborator is to identify the elements and the rules of translational Ola Larsson, Research Associate control. The Bitterman laboratory uses polyribosome Shunan Li, Research Associate assay, gene expression profiling, and data-mining meth- David Perlman, Faculty Collaborator ods to further the understanding of translation control, Karen A. Smith, Research Associate which will enable them to study in detail various aspects of health and disease.

2006 Annual Research Report of the Supercomputing Institute 207 UM TC–Department of Medicine

Jeffrey J. Connaire, Principal Investigator Mark E. Rosenberg, Co-Principal Investigator The Role of Multipotent Renal Progenitor Cells in Recovery After Acute Renal Failure

ecovery of renal function following acute renal and used multiphoton microscopy to localize the destina- failure is dependent on the replacement of necrot- tion of these cells both in fixed sections and in vivo. After Ric tubular cells with functioning renal epithelium. simple localization, phenotypic changes in the cells can These researchers have isolated and characterized a multi- be assessed using immunohistochemical techniques. The potent progenitor cell from adult kidney, and speculate group used Supercomputing Institute resources to facili- that these cells are the source of regenerating cells follow- tate data analysis by volume reconstruction in three and ing acute renal failure. The cells are called multipotent four dimensions. renal progenitor cells (MRPCs). The researchers performed laboratory experiments with MRPCs and evalutated the effect the cells may have on recovery of renal function. They characterized the homing of the cells to kidney post mortem and in vivo

William C. Duane, Principal Investigator Regulation of Ileal Bile Acid Transport Gene

ile acids are major catabolic products of choles- tion. They have also found that transactivation potential terol that hold cholesterol in solution in bile and partially migrates with very-low-density lipoprotein, low- Bfacilitate fat absorption in the intestine. They are density lipoprotein, and high-density lipoprotein, espe- reabsorbed in the terminal ileum by the apical sodium cially the latter. dependent bile acid transporter (ASBT). ASBT levels are The researchers are now continuing their studies of critical for conserving bile acid and regulating the return these findings. These experiments should advance the of bile acid to the liver. These researchers have found that understanding of in vivo regulation of ASBT gene expres- human serum transactivates the promoter of the human sion. They may also provide a novel approach to deter- ASBT gene, and that cortisol, lysophosphatidic acid, and mining how genetic regulation by transcription factors certain epidermal growth factor-related peptides are con- governs functioning of the human organism, both in stituents of serum they have found to induce transactiva- health and disease.

Research Group Wendy Xiong, Staff

208 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Medicine

Patrick M. Gaffney, Principal Investigator Gene Expression Profiling in Head and Neck Cancers

olecular studies of squamous cell carcinoma of gesting that modulation of tumor-specific immune the head and neck (HNSCC) have demon- responses provide evidence for a new gene expression- Mstrated multiple genetic abnormalities. In based biomarker of local treatment failure in HNSCC. order to identify gene expression signatures that may serve as biomarkers, these researchers have studied 41 squamous cell carcinoma tumors and 13 healthy oral mucosal biopsy samples with microarray analysis. Several gene expression signatures were readily identifiable in the HNSC tumors, including signatures associated with proliferation, extracellular matrix production, cytokine/ chemokine expression, and immune response. Of partic- Research Group ular interest was the association of a gene expression sig- Matt Ginos, Research Associate nature enriched for genes involved in tumor invasion and Ketan Patel, Graduate Student Researcher metastasis with patients experiencing locally recurrent Michaela Tsai, Graduate Student Researcher disease. Notably, these tumors also demonstrated a Sonja Volker, Research Associate marked absence of an immune response signature, sug-

Kalpna Gupta, Principal Investigator Opioids Stimulating Angiogenesis and Tumor Growth

hese researchers studied angiogenesis in tumors with image analysis using multi-photon laser Tscanning microscopy. They created three-dimensional renditions of images of blood vessels, nerves, and Research Group lymph vessels. The researchers used resources at the Basic Niroopshankar Ammbashankar, Graduate Student Sciences Computing Laboratory and the Digital Researcher Technology Computational Biology Laboratory for this work.

2006 Annual Research Report of the Supercomputing Institute 209 UM TC–Department of Medicine

Jennifer L. Hall, Principal Investigator Genomics Analysis of Cardiovascular Disease

goal of the Hall laboratory is to use genomics- taken at the time of implant and explant of an assist based strategies to define novel genes and signal- device. The researchers are using data generated from Aing networks in multiple cardiovascular diseases. these studies to put forth new hypotheses into networks A primary focus has been to build a compendium of governing the reversal and recovery of heart failure. genomics data from paired human heart failure samples

Research Group Neeta Adhikari, Research Associate Suzanne Grindle, Research Associate Ami Mariash, Research Associate

Robert P. Hebbel, Principal Investigator Genetic Heterogeneity of Endothelial Cell Gene Expression

hese researchers are testing the idea that clinical lial genetic phenotype. The researchers are using phenotype of human vascular disease is, in part, resources at several of the Supercomputing Institute’s lab- Tdetermined by genetic determinants of endothe- oratories for this project. lial cell biology. To test this hypothesis, they are applying microarray technology to analyze blood outgrowth endothelial cells as reporter cells of constitutive endothe-

Research Group and Collaborators Vidya D. Bodempudi, Research Associate Judy Enenstein, Faculty Collaborator Kalpna Gupta, Faculty Collaborator Taryn Hall, Graduate Student Researcher Aixiang Jiang, Research Associate Peng Wei, Graduate Student Researcher

210 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Medicine

Ajay Israni, Principal Investigator Long-Term Deterioration of Kidney Allograft Function (DeKAF)

nd stage renal disease (ESRD) is a growing and DeKAF study will undergo kidney allograft biopsies for a expensive problem in the United States, costing in deterioration of renal function defined by greater than Eexcess of $25 billion in 2002 alone. For treating 25% persistent increase in serum creatinine from a base- ESRD, kidney transplantation is more cost-effective than line established at three months post-transplant or new long-term dialysis. Despite improvements in one-year onset proteinuria. The DeKAF study is designed to clas- kidney allograft survival, late graft loss (LGL) persists as a sify causes of CGD, using clinical information and biop- major clinical problem. sy findings. The researchers are using Supercomputing Both immune and nonimmune mechanisms con- Institute resources to help determine how genetic predis- tribute to chronic allograft dysfunction (CGD) and sub- position may help to explain the outcomes defined in the sequent LGL. Although many correlates of allograft DeKAF study. function are now known, there remains extensive unex- plained variation in occurrence of LGL. These researchers are using a genetic epidemiology Collaborator approach, using an ongoing, large, prospective cohort of Scott Selby, Minnesota Medical Research Foundation, kidney transplant recipients enrolled in a study funded Minneapolis, Minnesota by the National Institutes of Health. All subjects in the

Sagarika Kanjilal, Principal Investigator Vivek Kapur, Co-Principal Investigator Comparative Cancer Genomics

his group’s research is focused on elucidating The group is using resources at the Computational basic mechanisms of cancer pathogenesis and Genetics Laboratory to store and analyze batches of Tprogression using molecular and comparative sequence files and microarray datasets, both from genomic approaches. The project can be categorized into Affymetrix GeneChip and custom cDNA array experi- three thematic areas: identification of molecular markers ments. Further work will involve visualizing, accessing, and gene-expression profiles in tumor development and and querying the information using existing or custom progression; characterization of the cancer genome software tools. through analyses of human and feline tumor carrier deoxyribonucleic acid (cDNA) libraries and cat bacterial artificial chromosome libraries; and elucidation of molec- Research Group ular response to chemotherapeutic agents and discovery Nilanjana Banerji, Research Associate of novel drug targets.

2006 Annual Research Report of the Supercomputing Institute 211 UM TC–Department of Medicine

Richard A. King, Principal Investigator Marshall I. Hertz, Co-Principal Investigator Gene Expression Microarrays in Lung Rejection

bliterative bronchiolotis (OB) is a fibroprolifera- gene expression associated with acute rejection and also tive process that represents the most significant patterns that can serve as biomarkers of risk for OB. The Olimiting factor for long-term survival in lung researchers are using resources at the Supercomputing transplant recipients. OB occurs unpredictably and is Institute laboratories to load, normalize, and analyze undetectable in a preclinical state. In addition, the major their data. risk factor for OB is acute rejection, which can only be diagnosed by invasive lung biopsies. Therefore, these researchers are using microarrays to identify patterns of

Research Group Todd Berryman, Staff Lisa Bolin, Research Associate Vincent Gimino, Research Associate Jeffrey Lande, Graduate Student Researcher Jagadish Patil, Research Associate

Cary N. Mariash, Principal Investigator Molecular Mechanisms Regulating Mammalian Lipogenesis

n understanding of the regulation of lipid synthe- mechanism by which the S14 protein stimulates lipogen- sis is critical to understanding the causes and esis. They used bioinformatics software at the Atreatment of diseases such as obesity. These Computational Genetics Laboratory for this project. researchers recently developed a mouse model lacking the Spot 14 (S14) protein. This protein correlates with de novo fatty acid synthesis in liver, fat, and mammary tissue. To understand factors that are responsible for de novo lipogenesis, these researchers tried to determine the

Research Group Lance Augustin, Research Associate

212 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Medicine

Anna M. Masellis, Principal Investigator Gene Array Analysis of Bone Marrow Stromal Cells in Multiple Myeloma

n multiple myeloma, the bone marrow microenviron- stromal cells uniquely express genes compared to their ment is abnormal and plays a role in disease status normal age-matched donor controls that may impact the Iand response to chemotherapeutic treatment. growth and function of the bone marrow microenviron- Effective disease management will ultimately depend not ment. These researchers’ ultimate goal is to broaden their only on the elimination of tumor cells but also on the understanding of the involvement of the bone marrow reestablishment of a bone marrow environment that sup- microenvironment in myeloma pathogenesis and to ports normal cell growth. These researchers have used determine whether clinical response in myeloma can be their established in vitro cell culture systems to identify attributed, in part, to the impact of therapy on bone genes differentially expressed in bone marrow stromal marrow mesenchymal cell function. cells derived from myeloma patients compared to healthy donor bone marrow stromal cells. They found approximately 34 genes differentially expressed in myeloma bone Research Group and Collaborator marrow stromal cells, comprising cytokines/growth fac- Nandita Bose, Research Associate tors, transcription factors, cell signal transduction pro- Suzanne Grindle, Research Associate teins, and components of the extracellular matrix. The preliminary data indicate that myeloma bone marrow

Jeffrey S. Miller, Principal Investigator Use of Gene Arrays to Understand the Biology of Human Natural Killer Cells

espite progress made in the understanding of natural killer (NK) cell development, the molec- Dular mechanisms directing differentiation of NK cells and killer-immunoglobin receptor acquisition during development are poorly understood. These Research Group researchers are using the Computational Genetics Todd Lenvik, Staff Laboratory and the Laboratory for Large-Scale Data Feng Xiao, Research Associate Analysis to investigate the differentiation of human NK cells using microarray analysis.

2006 Annual Research Report of the Supercomputing Institute 213 UM TC–Department of Medicine

Kathy L. Moser, Principal Investigator Gene Expression Profiling of Rheumatic Autoimmune Disorders

hese researchers used the Computational salivary glands. The researchers hypothesized that SS Genetics Laboratory for two closely related proj- patients have characteristic gene expression profiles that Tects. The first used gene expression profiling to may reflect underlying pathophysiologic processes. They investigate Sjögren’s Syndrome (SS), a chronic autoim- used microarray technologies to examine the expression mune disease that preferentially affects the lachrymal and of thousands of genes simultaneously in cells from SS patients. The second project investigated Antiphospholipid Research Group and Collaborators Syndrome (APS), a condition where the immune system Aaron Becker, Research Associate mistakenly produces autoantibodies that bind to various Eshrat Emamian, Graduate Student Researcher phospholipids, resulting in clinical manifestations such as Martha Grandits, Research Associate recurrent clotting, strokes, and spontaneous miscarriages. Amber Leiran, Research Associate The researchers worked to assess the activity of thousands Joanlise Leon, Graduate Student Researcher of genes simultaneously and to identify gene expression Carolyn Meyer, Research Associate signatures that are specifically associated with APS. This Paula Ramos, Graduate Student Researcher Nelson Rhodus, Faculty Collaborator could provide important new opportunities for designing Barbara Segal, Faculty Collaborator more effective diagnostic tools and therapies for APS.

Erik J. Peterson, Principal Investigator Gene Expression in Profiling Peripheral Blood Leukocytes in Psoriatic Arthritis Patients soriatic arthritis (PsA) is a systemic inflammatory aids in diagnosis as well as distinguishes PsA patients condition featuring polyarthritis associated with from patients with other types of inflammatory arthritis. Pskin psoriasis. Skin psoriasis affects about 2% of These researchers prepared a pilot study of gene expres- the Caucasian U. S. population and arthritis occurs in sion profiles in peripheral blood from PsA patients. They about 5–7% of patients with psoriasis. Apart from clini- are currently analyzing the data to determine genes that cal indicators, few biomarkers are available to aid in the may be a factor in PsA. They plan to compare their gene diagnosis and management of PsA. These researchers are list with lupus and rheumatoid arthritis datasets to deter- interested in determining a gene expression signature that mine if there is a unique gene signature that differenti- ates PsA from other inflammatory diseases.

Research Group Lindsey Fostel, Research Associate Felipe Mendez, Research Associate Angela Stoeckman, Research Associate Liangxing Zou, Research Associate

214 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Medicine

Keith M. Skubitz, Principal Investigator Gene Expression in Sarcoma and Other Malignancies

his project centers primarily around differences in gene expression in various malignant conditions Tand will provide major support to the muscu- loskeletal tumor program at the University of Minnesota. The projects uses software available at the Computa- tional Genetics Laboratory.

Clifford J. Steer, Principal Investigator Betsy J. Kren, Co-Principal Investigator Sleeping Beauty Transposon System for Gene Therapy of Sickle Cell Disease

his project aims to develop a gene therapy method for treating sickle cell disease. The Tresearchers are designing and optimizing a β or γ globin–Sleeping Beauty (SB) vector. The next step is in Research Group vitro expression testing and genome integration analysis. Jianhui Zhu, Research Associate The group will then perform in vivo studies of β/γ globin–SB using a mouse model of sickle cell disease.

2006 Annual Research Report of the Supercomputing Institute 215 UM TC–Department of Medicine

Patricia E. Tam, Principal Investigator Enterovirus Infection as an Environmental Trigger of Chronic Disease

he Tam laboratory studies mechanisms of pathogenesis. RNA folding algorithms suggest that one enterovirus pathogenesis in a mouse model where determinant may affect the secondary structure of the 5’ Tinfection with a myopathic strain of coxsack- untranslated region in viral genomic RNA. Other deter- ievirus leads to the development of chronic inflammatory minants are located in the capsid and have been predict- muscle disease. They have developed a panel of amyo- ed to act as T cell epitopes. Although the acute infections pathic coxsackieviruses that infect muscle but do not caused by myopathic and amyopathic viruses appear sim- cause chronic disease. Sequencing and reverse genetics ilar, differences in the way they interact with the muscle has identified four viral genetic differences that mediate itself and/or the immune system may ultimately lead to the development of chronic muscle disease. In a related project, gene expression microarrays are Research Group being used to identify genes and pathways that are differ- Jaime Nugent, Research Associate entially regulated in persistently-infected muscle. These Maribeth Sandager, Research Associate studies will advance the field of coxsackievirus biology by Wade Schulz, Undergraduate Student Researcher providing a global picture of the molecular events that Melissa Weber-Sanders, Research Associate occur during acute and persistent infection.

Anthony Varghese, Principal Investigator Structural Basis of Redox Sensitivity of Voltage-Gated Potassium Channels

on channels are a class of proteins responsible for per- known. This project’s aim is to use molecular-biology mitting flow of ions through cell membranes. techniques to isolate specific areas of potassium channels IVoltage-gated potassium channels are ion channels that may be responsible for redox control. that are selectively permeable to potassium and activated by changes in the cell transmembrane potential difference. In addition to cell electrical potentials, potassium channels are regulated by other ions and cellular second messages. This research project focuses on uncovering the role of cellular redox (reduction-oxidation) status in regulating potassium channels. Redox regulation of ion channels is an important signaling mechanism in the modulation of cell function by oxygen levels in the lung, heart, and neuroendocrine cells of the adrenal glands, carotid body, and neuroepithelial bodies. The mechanistic basis of regulation of potassium channels by redox state is not

216 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Microbiology

Paul R. Bohjanen, Principal Investigator Analysis of T Cell Gene Expression and mRNA Decay

hese researchers use Affymetrix microarrays to measure messenger ribonucleic acid (mRNA) decay rates in human T lymphocytes under dif- T Research Group and Collaborator ferent conditions of stress or activation. This has includ- Sharon Chen, Faculty Collaborator ed T cell receptor-mediated stimulation, infection with Rachel Ogilvie, Graduate Student Researcher viruses, or treatment with ionizing radiation. They have Nuzha Tahoe, Research Associate also compared mRNA decay in normal or malignant T Irina Vlasova, Supercomputing Institute Research cells. Their findings suggest that mRNA decay is an Scholar important level of gene regulation in response to envi- Richard Walsh, Research Associate ronmental conditions. They are using software available Darlisha Williams, Staff through the Supercomputing Institute, such as David Boulware, Research Associate GENESPRING and PATHWAYASSIST to facilitate interpretation and presentation of their microarray results.

P. Patrick Cleary, Principal Investigator Innate Immune Response to Streptococcus pyogenes Infection in Nasal-Associated Lymphoid Tissue by Microarray Analysis treptococcus pyogenes causes pharyngitis in children induction of inflammatory responses to the bacteria as and adults at well as sequelae such as rheumatic several cells express C5a receptors, such as macrophages, S fever and streptococcal toxic shock syndrome. neutrophils, memory B-cells, and T-cells. These Infection of human tonsils can be modeled by studies of researchers are using the Computational Genetics nasal-associated lymphoid tissue (NALT). The goal of Laboratory for this project. this project is to determine the early response to S. pyogenes by the NALT and whether this response is altered in the presence or absence of streptococcal virulence factors, such as M protein and SCPA, which are mechanisms that S. pyogenes uses to avoid early host defenses. M proteins are fibronectin- and laminin-binding proteins that promote invasion of streptococci into epithelial cells. M proteins also interfere with deposition of C3b opsonin Research Group and activation of the alternative complement pathway. Kendra Hyland, Research Associate Streptococci encode a serese protease called SCPA that cleaves C5a, a complement protein. C5a is critical for

2006 Annual Research Report of the Supercomputing Institute 217 UM TC–Department of Microbiology

Dana Davis, Principal Investigator Iron Uptake Systems in Candida albicans

he ability to acquire iron from the host is critical determine how different forms of iron limitation affect for Candida albicans pathogenicity. Since differ- expression of the iron uptake systems. They took a simi- Tent iron sources require different uptake systems, lar approach to elucidate how Rim101p, Afg2p, and cells regulate expression of the correct uptake system for Pir1p govern these transcriptional responses. The group a different iron source. These researchers conducted used the Basic Sciences Computing Laboratory, the whole-genome transcriptional profiling experiments to Computational Genetics Laboratory, and the Scientific Development of Visualization Laboratory for this research. Research Group Yong-Un Baek, Research Associate Katie Ballering, Graduate Student Researcher David Simmons, Staff

Gary M. Dunny, Principal Investigator Microarray Analysis of Enterococcus faecalis Gene Expression

nterococci are part of the normal intestinal bacter- genes differentially expressed when the organisms adapt ial flora of humans. They can also cause serious from growth in liquid culture to biofilm growth on sur- Einfections in immune-compromised hospital faces. patients. These researchers used genomic deoxyribonucleic acid microarrays to study regulation of genes important in causing infections. In particular, they studied

Research Group Christopher Kristich, Research Associate

218 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Microbiology

Ashley T. Haase, Principal Investigator Functional Genomic Analysis of the Response of HICV-1 Infected Lymphatic Tissue to Anti-Retroviral Therapy hile it is known that highly active anti-retro- of infection. Based on the decreased expression after viral therapy (HAART) curtails HIV-1 treatment of mediators and moderators of immune acti- W(human immunodeficiency virus) replication vation and defenses, this group is working on a model in in lymphatic tissues, and partially reverses the pathologi- which the treatment of mediators and moderators cal damage associated with infection, the genes that account for HIV-1 infection’s slow dynamics before treat- mediate these pathological and reparative processes ment. Anti-inflammatory agents alone or in combination remain largely unknown. This group used microarrays to with HAART could have a role in treating HIV-1 infec- profile gene expression in serial lymph node biopsies tion, by tipping this balance to mitigate pathology and before and after treatment. The reduced expression after promote lymphatic tissue healing. treatment of numerous type I and II interferon system, natural killer cell, and other innate immunity system genes points to a surprisingly prominent role for innate Research Group and Collaborator immunity in limiting HIV-1 replication before treat- Winston Cavert, Faculty Collaborator ment. Because these genes were expressed in patients in Qingsheng Li, Research Associate later as well as acute stages of infection, innate immunity may significantly contribute to host defenses at all stages

Marc K. Jenkins, Principal Investigator CD4 T Cell Biology

D4 T cells produce lymphokines when their anti- and inhibit deleterious T cell responses such as autoim- gen receptors bind to foreign peptides displayed munity and graft rejection. Con the surface of other cells, so-called antigen- presenting cells. The lymphokines produced by CD4 T cells regulate many aspects of the immune response, including antibody production and the microbicidal Research Group activities of other cells. The Jenkins laboratory has devel- Drew Catron, Research Associate oped a system in which the activation status of CD4 T Jason Hataye, Graduate Student Researcher cells of known specificity can be monitored by flow Stephen Huddleston, Research Associate cytometry, immunohistology, or confocal microscopy in Andrea Itano, Research Associate James McLachlan, Research Associate vivo. They have used this system to define the roles of James Moon, Research Associate several lymphokines and surface receptors in the in vivo Kathryn Pape, Research Associate activation of CD4 T cells and antigen-presenting cells as Lori Schneider, Graduate Student Researcher they occur in the lymphoid tissues. By studying the acti- Jennifer Walter, Staff vation of CD4 T cells in the body, the researchers hope Traci Zell, Research Associate to gain information that can be used to improve vaccines

2006 Annual Research Report of the Supercomputing Institute 219 UM TC–Department of Microbiology

Russell C. Johnson, Principal Investigator Human Granulocytic Ehrlichiosis: North Central United States

he goal of these researchers is to characterize Deer from the southern U. S. have been reported to aspects of the epizootiology of the agent of be infected with an Ehrlichia or Anaplasma species other THuman Granulocytic Ehrlichiosis (HGE), now than that of the HGE agent. The researchers are working known as Anaplasma phagocytophilum, in the north-cen- to determine if the deer Ehrlichia is capable of being tral United States. They will document the presence of amplified by their primers. Sequencing the p44 the HGE agent in deer from areas of Minnesota endemic nucleotide of the deer Ehrlichia may show significant for HGE. Deoxyribonucleic acid (DNA) extracted from variation from that of the HGE agent. The 16s riboso- white-tailed deer are analyzed by polymerase chain reac- mal DNA (rDNA) of the deer Ehrlichia is only 94% tion amplification using primers for the p44 300 base identical with that of the HGE agent. The researchers are pair segment, which is unique to A. phagocytophilum. in the process of investigating and comparing the 16s rDNA of deer Ehrlichia with that of the HGE agent. The group is using several Supercomputing Institute laboratories for this project. Research Group Yaning Xu, Research Associate

220 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Microbiology

Vivek Kapur, Principal Investigator Investigations on Bacterial and Viral Pathogens: Pathogenomics

he focus of this research program is to understand the basic processes by which bacteria and Research Group and Collaborators Tviruses cause disease and how their hosts respond Agot Aakra, Laboratory of Microbial Gene Technology, to infection. To address this problem, the researchers Agricultural University of Norway, Aas, Norway apply genomics tools, including whole-genome sequenc- Alongkorn Amonsin, Research Associate ing, expression profiling using microarrays, and pro- Tanong Asawakarn, Research Associate teomics, to characterize microbial pathogens and the host Nilanjana Banerji, Research Associate response to infection. The group has sequenced several Sohail Babar Butt, Graduate Student Researcher bacterial genomes, including Lawsonia intracellularis, Brett Dearing, Visiting Researcher Staphylococcus aureus, and Mycobacterium avium subsp. Scott Dennis, Visiting Researcher paratuberculosis. They plan to continue to use Supercom- Archana Deshpande, Research Associate Mugdha Deshpande, Graduate Student Researcher puting Institute resources for annotation of more Monica Dozier, Visiting Researcher genomes of bacterial and viral pathogens, for analysis of Heather Haemig, Staff microarray data on gene expression and comparative Lisa Herron, Graduate Student Researcher genomics, and to investigate strain differentiation within Michael Hobbs, Faculty Collaborator species. Kuljeet Kaur, Research Associate T. Rajendra Kumar, Faculty Collaborator Lingling Li, Graduate Student Researcher Xia Li, Staff Barbara J. May, Research Associate Georg Mellitzer, National Institute of Health and Medical Research, University of Strasbourg, Strasbourg, France Shirin Munir, Research Associate Athipoo Nuntaprasert, Research Associate Garret Olson, Graduate Student Researcher Cecilia Serrano, Visiting Researcher Sushmita Singh, Research Associate Youvraj Sohni, Staff Rachel Surber, Staff Cesar Tapia-Esquivel, Visiting Researcher Nathan Treff, Department of Surgery, University of Wisconsin, Madison, Wisconsin George Ude, Visiting Researcher Laura Wonderling, Staff Qing Zhang, Research Associate

2006 Annual Research Report of the Supercomputing Institute 221 UM TC–Department of Microbiology

Patrick M. Schlievert, Principal Investigator Marnie L. Peterson, Co-Principal Investigator Staphylococcus aurens and Group A Streptococcal Interaction With Human Epithelial Cells hese researchers are using microarray analysis to chemokines will be released by the epithelial cells in study the interaction of human epithelial cells response to bacterial superantigens and hemolysins that T(both lung and vaginal) with both Staphylococcus allow the toxins to penetrate mucosal barriers. aurens and Group A Streptococci. These two organisms The researchers are using the Computational Genetics have the capacity to cause toxic shock syndromes Laboratory and the Basic Sciences Computing through their interactions with these cells. The responses Laboratory for this project. of treated cells are compared with the control untreated cells. The researchers hypothesize that cytokines and

Research Group Mandy Helvig, Graduate Student Researcher George Konstantinides, Staff Matthew Schaefers, Staff Kristi Strandberg, Graduate Student Researcher Tim Tripp, Research Associate

Peter Southern, Principal Investigator Human Organ Cultures and Microbial Infections at Epithelial Surfaces

hese researchers are using human organ cultures they have recognized that the external infectious agents and populations of human cells to examine trans- applied in the laboratory can interact with microbes that Tmission and primary microbial infections at are already present on the tissue surface or within the tis- mucosal surfaces. This work originated with the develop- sue at the time of surgical removal. They have devised a ment of experimental systems to understand human multi-microscope approach to reconstruct infectious immunodeficiency virus (HIV) transmission, but they processes and are using resources at the Basic Sciences have also examined other infectious agents such as differ- Computing Laboratory for this work. In particular, they ent viruses, bacteria, and fungi. As an additional feature, have used software available at the laboratory to develop three-dimensional surface reconstructions from confocal microscopy z-series datasets. Research Group Julie Horbul, Graduate Student Researcher Barrie Miller, Graduate Student Researcher

222 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Microbiology

Kenneth D. Vernick, Principal Investigator Pathogenomics of Malaria-Host Interactions

hese researchers are using the Computational Genetics Laboratory for analysis of functional Research Group Tgenomic, genetic, and proteomic data relating to Fred Oduol, Research Associate host response to malaria infection. Jun Li, Research Associate Michelle Riehle, Research Associate Jianning Xu, Research Associate

UM TC–Department of Neurology

Christopher M. Gomez, Principal Investigator Genetics of Dominantly Inherited Spinocerebellar Ataxias

he dominantly inherited spinocerebellar ataxias male infertility. In addition to this family, the researchers (SCAs) are a clinically and genetically heteroge- are also studying several pure ataxia families. They are Tneous group of neurodegenerative disorders char- using the Computational Genetics Laboratory to per- acterized by progressive imbalance, dysarthria, and inco- form linkage-wide genome analyses in all the families. ordination. Genetically distinct subtypes differ clinically, due in part to involvement of extracerebellar neuronal populations. These researchers have identified a five-generation family with progressive ataxia in which all affect- Research Group ed males are infertile. Identification of the gene responsi- Guo-Yun Yu, Research Associate ble for this unique phenotype may shed additional light onto the pathogenesis of ataxia, mental retardation, and

2006 Annual Research Report of the Supercomputing Institute 223 UM TC–Department of Neurology

William R. Kennedy, Principal Investigator Quantification of Nerves in Skin and the Gastrointestinal Tract

hese researchers use immunohistochemical and subjects and subjects with neuropathy caused by diabetes confocal methods to visualize fine nerve endings and other factors. The researchers are using the Basic Tin the superficial dermis and epidermis of skin Sciences Computing Laboratory and the Scientific and the mucosa of the gastrointestinal tract. The density Development and Visualization Laboratory for this proj- of nerve fibers appears to diminish in subjects with neu- ect. ropathy. The group is using image analysis methods to quantify the number of nerve fibers in cohorts of normal

Research Group Christina Brakken-Thal, Staff Joy Brown, Research Associate Gwen Crabb, Staff Shawn Foster, Staff Jeanne Nelson, Research Associate Mona Selim, Research Associate

UM TC–Department of Neuroscience

Bagrat Amirikian, Principal Investigator Neuronal Structure With Coherent Properties

he long-term goal of this research project is to are working on a three-dimensional lattice model that elucidate a relationship between the structure and allows for a fundamentally novel approach to studying Tfunction of fundamental distinct areas in the directional operations performed in the motor cortex by neocortex, in general, and the motor cortex, in particular, providing means for explicit exploration of the link by a combination of theoretical methods with experi- between the underlying local cortical structure and global mental approaches. The researchers are working to collective properties of interacting cells that are substrates advance the understanding of whether and how the spa- of this structure. The model will allow the researchers to tio-structural constraints on intrinsic connectivity affect bridge theoretical frameworks and experimental data in the segregation of neurons into functional modules. They the domain of very large-scale simulations of networks of simplified neurons.

Research Group Pavlos Gourtzelidis, Research Associate Douglas Hart, Graduate Student Researcher Thomas Naselaris, Graduate Student Researcher

224 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Neuroscience

W. Dale Branton, Principal Investigator Molecular Modeling of Cysteine Knot Proteins

large number of small, highly disulfide-bonded, relatively small (circa 40 AA) size of the proteins, will protein neurotoxins have been isolated or charac- allow development of useful models of the unknown Aterized from spider venoms. The Branton labora- structures. Such models could lead to better understand- tory has characterized two such proteins. These proteins ing of the structural basis for the broad spectrum of share a tight network of disulfide bonds, roughly six action of the toxin molecules and insight into key struc- amino acids between each disulfide crosslink, on average. ture-function relationships for the neuronal ion channel Using previously determined three-dimensional struc- targets of the toxin proteins. tures of other, related cysteine knot proteins, this researcher is developing computer-assisted models for the basic three-dimensional structures of families of toxic molecules. It is possible that the constraints placed on the structures by the disulfide bonds, coupled with the

Jon Gottesman, Principal Investigator Robert F. Miller, Co-Principal Investigator Monte Carlo Modeling of a Retinal Ribbon Synapse

hese researchers simulated neurotransmitter diffu- tribute to stimulus-evoked release of multiple vesicles. sion, ligand-receptor interactions, and ligand- This conforms to physiological observations. Ttransporter interactions in three-dimensional The researchers quantified the sources of variability in space. This project extended previous work performed on neural responses after they completed the simulation desktop computers, and implemented a complex spatial runs and subsequent analysis. They also have published a geometry to more accurately represent the relationships new model of both the pre- and postsynaptic cell that between transmitter release sites, post-synaptic receptors, allowed them to begin to study the release of multiple transmitter transporters, and a more complex extracellu- vesicles from a single ribbon site in an effort to character- lar space. ize the response of the synapse to light-evoked activity. Prior simulations of single vesicular release events, including a tonic concentration of transmitter in the simulation space, have demonstrated that this tonic level Research Group and Collaborator plays a substantial role in the amplitude and threshold of Tom Bartol, Computational Neurobiology Laboratory, postsynaptic processes. Furthermore, the researchers have Salk Institute for Biological Studies, La Jolla, discovered that NMDA receptors can be located as close California as 250 nm from the site of vesicle release without Josh Mrazek, Undergraduate Student Researcher responding to a single exocytotic event, but will con-

2006 Annual Research Report of the Supercomputing Institute 225 UM TC–Department of Neuroscience

Alexander E. Kalyuzhny, Principal Investigator Immunohistochemical Study of Interactions of Opioid Receptors With GABA-ergic Systems his research focused on investigating interactions quantification of profiles, which co-express several target of opioid- and GABA-ergic neurotransmitter sys- proteins. This work helped to understand cellular mecha- Ttems within the descending antinociceptive nisms underlying antinoception so more efficient thera- brainstem circuits, including PAG, RVM, and dorsal pies can be developed to treat pain. horn spinal cord. To study these interactions, the researcher employed multi-color fluorescence immuno- histochemistry on cryostast sections of rat brain in combination with retrograde tract-tracing techniques to label spinally projecting neurons. Stained brain tissues were analyzed using both conventional fluorescence and confocal microscopy. In some cases, the researcher performed

Naoko Koyano, Principal Investigator Steven C. McLoon, Co-Principal Investigator Analysis of Gene Cascade Regulating Vertebrate Neurogenesis

fundamental question in developmental neurobi- cascade initiated by neurogenin, a basic helix-loop-helix ology is how multipotential progenitor cells dif- transcription factor. They overexpressed neurogenin Aferentiate appropriately as specified by temporal under various conditions in Xenopus embryos, prepared and topographic coordinates to construct the intricate complementary deoxyribonucleic acid (cDNA) probes composition of neurons and glia. This project investi- from them, and analyzed gene expression profiles on gates the functions of transcription factors regulating this Xenopus cDNA microarrays. They identified numbers of process. neurogenin targets and are further examining individual In order to dissect the gene cascade used in neuronal downstream pathways using the microarray. The group differentiation, these researchers examined the genetic plans to use data-mining techniques to analyze the data in detail. Other projects include differentiation of retinal cells Research Group and stem cell manipulation using various molecular biol- Josh Aaker, Staff ogy techniques. The researchers are using the Basic David Hernandez, Undergraduate Student Researcher Sciences Computing Laboratory and the Computational Hyun-Jin Yan, Graduate Student Researcher Genetics Laboratory for this work.

226 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Neuroscience

Tongbin Li, Principal Investigator Support Vector Regression Approach to Capturing Peptide Sequence Characteristics

he primary structure (sequence) determines crucial properties of short peptides such as their Tbinding affinities with histocompatibility complex molecules, and some categories of enzymes, such as protein kinases, phosphotases, and proteases. How to quantitatively represent features of a peptide pattern required for these reactions is a challenging problem. Research Group These researchers are using the support vector regression Wuming Gong, Research Associate method to attack this problem, because of its demon- Jian Guo, Research Associate strated superiority in generalization/prediction perform- Wen Liu, Research Associate Xiangshan Meng, Research Associate ance among available machine learning tools. Preliminary Yongliang Ren, Research Associate exploration using a set of peptide array data suggests that Feng Xiao, Research Associate a good performance can be achieved with reasonably small sizes of peptide binding data.

Teresa A. Nick, Principal Investigator Mechanisms of Vocal Learning in the Zebra Finch

ird song allows investigation of critical periods in sensorimotor behavior. As in humans, zebra finch- Bes learn their vocalizations from a tutor during a restricted period. These researchers have found that during the sensorimotor “babbling” phase of development, playback of tutor song selectively activates a brain area devoted to song production, but only during the wake state. During sleep, this same brain area is most activated Research Group by the bird’s own song. These sensory responses provide Murtaza Adam, Undergraduate Student Researcher clues to the mechanisms that sculpt sensorimotor behav- Shane Crandall, Staff ior. These researchers are investigating the functions of Dan Cygnar, Undergraduate Student Researcher auditory-evoked and spontaneous activity in the developing song system.

2006 Annual Research Report of the Supercomputing Institute 227 UM TC–Department of Neuroscience

A. David Redish, Principal Investigator Electrode Localization Through Reconstruction of Three-Dimensional Patch/Matrix Anatomy hese researchers study the behavior of striatal cells should process different information. The researchers in awake, behaving rats—they record the firing of could detect the compartments and detect the positions Tstriatal neurons and ask what information is car- of the electrodes that record the firing, but could not tell ried by those firing patterns. They have technology, con- which electrode corresponded to which marker. They sisting of 12 individual electrodes, that allows them to used visualization resources at Supercomputing Institute record from large ensembles of 50 striatal cells simultane- laboratories to create a three-dimensional structure that ously, yet separately. The stratum consists of a complex, allowed them to determine the exact paths of the elec- interdigitated structure called patch and matrix. trodes and to see the three-dimensional structure of Although these two “components” consist of similar cell patch/matrix. types, they have different input and output pathways and

Research Group Deborah Bang, Graduate Student Researcher

Martin W. Wessendorf, Principal Investigator Heterodimerization of Opioid Receptors

airs of different g-protein coupled receptors have ferent types of receptors. Resolution could in principle be been reported to heterodimerize. By doing so, they improved by deconvolving the confocal images, however. Pshould exist within a few nanometers of each The researchers used the resources of the Basic Sciences other. If these receptors do in fact heterodimerize, it Computing Laboratory to deconvolve such images. should be possible to use light microscopy to detect sin- Obtaining higher-resolution images will improve their gle structures in the central nervous system that are ability to test which receptors, if any, may exist as het- labeled for both receptors. erodimers and to determine their distributions. These researchers have been able to detect single structures at the limit of resolution by confocal microscopy (i.e., smaller than 0.3 mm) that are labeled for two dif-

Research Group Ming Gu, Graduate Student Researcher

228 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Neuroscience

George L. Wilcox, Fellow Development of a Scalable, Parallelization Surrogate Partitioning Algorithm for Large- Scale Multivariate Analysis he Wilcox group is interested in developing scala- that will facilitate batch data analysis on these two paral- ble, parallelizable partitioning algorithms for lel architectures. Tlarge-scale multivariate data analysis. They developed a surrogate-based algorithm for multivariate partitioning multichannel data acquisitions from whole-head Research Group and Collaborators magnetoencephalographic recordings from human brain. Elhabib Benlhabib, Research Associate Component mixtures discovered by partitioning are Anne Bertelsen, Department of Neurology, University compared with linear cross-correlogram analyses of the of Haukeland Hospital, Bergen, Norway whole-head sensor map display to reveal commonalities Carolyn Fairbanks, Faculty Collaborator between a subset of the distribution components and the Chip Hart, Graduate Student Researcher observed linear interaction structure. Hoang-Oanh Nguyen, Research Associate The group’s recent effort was geared towards porting Marius Poliac, Poliac Research Corporation, Burnsville, the datasets to the IBM SP and the Netfinity Cluster to Minnesota compare performance metrics across architectures, while Laura Stone, Research Associate Pradyumna Upadrashta, Graduate Student Researcher also incorporating instruction-level and loop-level paral- lelism into the code. They adapted single-processor code

UM TC–Department of Neurosurgery

Stephen J. Haines, Principal Investigator Three-Dimensional Surface Reconstruction of Brain Stem Neurovascular Relations

ertain anatomic relationships between the nerves Development and Visualization Laboratory. Scans from and vessels of the brain stem are known to have normal patients and from patients with trigeminal neu- Can etiologic relationship to clinical conditions, ralgia will be processed and evaluated against clinical such as trigeminal neuralgia and hemifacial spasm. It has information. not been possible to reliably predict the presence of the clinical syndrome from interpretation of two-dimensional scans of these anatomic relationships. It is possible that a three-dimension surface reconstruction of the neurovascular relationship will allow reliable identification of patients with these clinical conditions from the imaging data alone. To this end, this project takes existing magnetic resonance scanning data and processes it using image-processing programs available through the Scientific

2006 Annual Research Report of the Supercomputing Institute 229 UM TC–Department of Orthpaedic Surgery

Jack L. Lewis, Principal Investigator Narendra K. Simha, Co-Principal Investigator Cartilage Biomechanics

hese researchers are examining the inelastic and focuses on structure-function models for cartilage; here failure response of cartilage with the goal of the researchers are developing multi-scale simulations to Tunderstanding the cartilage disease processes like study the consequences of nanoscale biomolecular osteroarthritis. They use finite element methods to deter- changes on tissue-level properties. mine appropriate test protocols for quantifying inelastic and fracture properties on the microscale and to perform parametric studies to understand the influence of inelastic deformation on the fracture response. Another goal

Research Group Sidharth Chiravaramath, Graduate Student Researcher

UM TC–Department of Otolaryngology

John H. Anderson, Principal Investigator Motor Learning and Eye-Hand Coordination in Patients With Cerebellar Ataxia

he control and adaptation of gaze and eye-hand The goal of this project is to determine when visual- coordination is dependent on the cerebellum. motor learning becomes compromised or abolished as THereditary, neurodegenerative diseases that affect the severity of the disease increases in genetic subtypes of the cerebellum cause postural instability, uncoordinated spinocerebellar ataxia and Friedreich’s ataxia. Patients will limb movements, and abnormal eye movements. In addi- be tested in an upper-limb pointing task wherein the tion, there is a decreased ability for adaptive motor learn- mapping of the patient’s visual space to a physical, body- ing. centered space is altered. The researchers are using Supercomputing Institute resources to develop three- dimensional visual environments that will be used to test Research Group the patients with the pointing task and to simulate what Chris Fuller, Staff the patients see.

230 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Otolaryngology

Steven K. Juhn, Principal Investigator Structure of Stereocilia Extracellular Links and Morphology of Hair Bundles

tereocilia are connected together by extracellular ocilia links is performed using transmission electron links, which are involved in mechanoelectrical microscopy methods of protein crystallography and com- Stransduction, force transmission across the bundle, puter image analysis. The researchers are using resources and maintenance of the hair bundle structure. Despite at Supercomputing Institute laboratories for this project. various studies, there is much that is poorly understood about the organization of the links and their properties. The objective of this project is to obtain more detailed information about the structure, properties, and function of the stereocilia links and their relationship to abnormalities of the stereocilia bundle caused by acoustic trauma. The specific aims of this research are to study the structure of stereocilia links and the structure of the side Research Group link and its relationship to abnormalities of the stereocil- Vladimir Tsuprun, Research Associate ia bundle caused by acoustic trauma, and underlying hearing dysfunction. The structural study of the stere-

Jizhen Lin, Principal Investigator Id1 Mutant for Squamous Cell Cancer Progression

quamous cell carcinoma (SCC) is a significant The researchers are investigating the molecular mecha- health issue worldwide. In the United States, it nisms of the Id1 mutant in the progression and malig- Safflicts more than 200,000 people each year. nancy of SCC. This study will not only improve under- Despite optimal treatment with surgery, irradiation, and standing of the molecular mechanisms of the carcinogen- chemotherapy, disease recurrence and progression esis and angiogenesis of SCC but will also provide a remains a challenging issue. There is a compelling need foundation for innovative treatment. for innovative therapeutic interventions on those patients at high risk for recurrence and death. Development of SCC involves mutations of genes that are involved in cell growth control or tumor suppression. These researchers have discovered that Id1, a member of the inhibitor of differentiation (Id) family, which is involved in cell proliferation and angiogenesis, is mutated Research Group and Collaborator in head and neck SCC patients and this mutant could Frank G. Ondrey, Faculty Collaborator play a role in the carcinogenesis and angiogenesis of Wei Pan, Research Associate SCC.

2006 Annual Research Report of the Supercomputing Institute 231 UM TC–Department of Pediatrics

Bruce R. Blazar, Principal Investigator Angela Panoskaltsis-Mortari, Co-Principal Investigator Identification of Gene Expression in Type II Pneumocytes

eratinocyte growth factor (KGF) is a potent are performing microarray analysis on KGF receptor-pos- mediator of epithelial cell proliferation, as well as itive cells in the lung. Ka growth factor for type II pneumocytes. It has The researchers hypothesize that they will find increas- also demonstrated cytoprotective properties against es in expression of genes involved in deoxyribonucleic chemotherapy and radiation-induced injury. Investiga- acid repair, surfactant production, alveolar fluid clear- tions into the role of KGF in the lung have observed ance, and other protective processes. They think they increased lung surfactant levels, increased alveolar fluid may also see a decrease in expression of apoptotic genes. clearance, and decreased hyperoxic injury of type II After characterization of genes important for protection pneumocytes. In order to further evaluate the mechanism by KGF, the researchers may be able to investigate possi- of KGF-induced protection of the lung, these researchers ble avenues for increasing the therapeutic benefit of KGF treatment.

Research Group Andrew Price, Staff Kevin Tram, Staff

Elizabeth G. Ingulli, Principal Investigator Simulation With Self-Peptide MHC Class-II Ligands

elf-peptide MHC class-II ligands (self-ligands) are ignore their specific antigen. The researchers believe that required for thymic selection of a functional and self-ligand deprivation leads to a defect in CD4 T cell Sself-tolerant T cell repertoire. Recent evidence sug- motility. They used in vivo video microscopy and soft- gests that self-ligands are also crucial for T cell activation ware available at the Basic Sciences Computing in the periphery. These researchers have observed a pro- Laboratory to aid in their research. gressive defect in CD4 T cell activation, proliferation, and interaction with antigen-presenting dendritic cells in the secondary lymphoid tissue after prolonged periods of self-ligand deprivation. Although antigen-specific CD4 T cells and antigen-presenting dendritic cells are present in the secondary lymphoid tissue, CD4 T cells seem to

Research Group Ursula B. Fischer, Research Associate

232 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Pediatrics

Michael Mauer, Principal Investigator Youngki Kim, Co-Principal Investigator Microarray Studies of Skin Fibroblasts in Type I Diabetes

iabetic nephtopathy (DN) is the leading cause two groups: one a “fast-track” group (high risk of DN) of kidney failure and was responsible for 44% of and one a “slow-track” group (low risk of DN). They are Dall the new cases of kidney failure in the United also testing whether diabetes per se, compared to con- States in 2001. These researchers are studying cultured trols, influences these cells and whether identical twins skin fibroblast (SF) and renal proximal epithelial cells discordant for diabetes have similar or different cell (PTEC) from type I diabetic patients in order to better behaviors. understand the differences in behavior of these in The researchers are using the Basic Sciences patients with and without DN. They are testing the Computing Laboratory and the Computational Genetics hypothesis that there are inherent cellular differences Laboratory for this project. between type I diabetic patients with or without DN and that these differences are genetically determined and are associated with altered SF and/or PTEC gene expression. Research Group The goal is to use microarray techniques to test for gene Paul Walker, Research Associate expression differences in total ribonucleic acid isolated Chunmei Huang, Research Associate from SF and PTEC from type I diabetes patients that have been structurally and functionally polarized into

Alfred F. Michael, Principal Investigator Clifford E. Kashtan, Co-Principal Investigator Mass Spectrometry of Glomerular Proteins

he glomerulus constitutes the cells and basement membranes of the capillary filter. This is the site Tof immunologic and biochemical injury in disease. This study examines proteins and peptides isolated from animal and human glomeruli (either whole or via Collaborator laser capture) using proteomic techniques. The Bing Zhou, Faculty Collaborator researchers are using the Scientific Development and Visualization Laboratory for this work.

2006 Annual Research Report of the Supercomputing Institute 233 UM TC–Department of Pediatrics

Julie A. Ross, Principal Investigator Dietary Influences on Gene Expression in Offspring

olate supplementation around the time of pregnan- imprinting has carcinogenic consequences, provides evi- cy has been consistently associated with a reduced dence whereby childhood ALL could be initiated in Frisk of neural tube defects in children. There is also utero as a result of folate deficiency. This exploratory a growing body of evidence that periconceptual vitamin study is evaluating associations between maternal dietary supplementation and diets rich in folate protect against folate and gene expression in offspring. The researchers childhood cancers, including childhood acute lym- are investigating whether maternal dietary supplementa- phoblastic leukemia (ALL). The mechanisms for this pro- tion with various folate levels (control, deficient, or over- tective effect are unknown. The requirement for folate in supplemented) influences gene expression in B lineage deoxyribonucleic acid methylation, however, together cells obtained from the bone marrow and spleen in off- with data showing that hypomethlation and loss of spring. This project will provide evidence regarding nutritional modification of the expression of specific genes that may be important in hematopoiesis and/or leukemogenesis. Research Group Kimberly J. Johnson, Graduate Student Researcher

Scott B. Selleck, Principal Investigator Molecular and Genetic Analysis of Synapse Development

hese researchers are interested in the genes and NMJ. They are conducting morphological studies using molecules governing synapse development plas- fluorescent-tagged antibodies and confocal microscopy. Tticity. The Drosophila neuromuscular junction Specific antibodies are used to visualize presynaptic pro- (NMJ) is one of their model systems. The group is using teins, post-synaptic components such as neurotransmitter resources at the Basic Sciences Computing Laboratory receptors, and cytoskeletal proteins critical for synapse and the Digital Technology Computational Biology formation and stabilization. Laboratory to analyze synapse size and structure, to determine how specific genes affect the assembly of the

Research Group Hong Ge, Graduate Student Researcher Yi Ren, Graduate Student Researcher

234 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Pediatrics

Xianzheng Zhou, Principal Investigator Stable Gene Transfer and Expression in Human Primary T Cells by the Sleeping Beauty Transposon System he Sleeping Beauty (SB) transposon system is a stable gene expression in human PBLs, confirming that non-viral deoxyribonucleic acid (DNA) delivery catalytic DDE domain is necessary for transposition in Tssytem in which a transposase directs integration human primary T cells. of an SB transposon into TA-dinucleotide sites in the genome. To determine whether the SB transposon can mediate integration and long-term transgene expression Research Group in human primary T cells, the group nucleofected freshly Preetinder Bassi, Undergraduate Student Researcher isolated peripheral blood lymphocytes (PBLs) without Suet Choi, Undergraduate Student Researcher prior activation with SB vectors carrying a DsRed Hongfeng Guo, Research Associate reporter gene. They confirmed that delivery of SB trans- Kari Haley, Undergraduate Student Researcher posase-encoding plasmid in trans effectively mediated Xin Huang, Research Associate stable gene expression in primary T cells. Further, the Johnthomas Kang, Research Associate transposase mutant construct was incapable of mediating

UM TC–Department of Pharmacology

Duanqing Pei, Principal Investigator Regulation of Membrane-Type Matrix Metalloproteinases by Trafficking in Cancer Cells he goal of this project was to integrate studies of AP-2 adaptins. The third aim of the project was to define membrane type 1 matrix metalloproteinase the regulatory role of trafficking on MT1-MMP and T(MT1-MMP) and membrane type 3 matrix met- MT3-MMP mediated cell growth and invasion within or alloproteinase (MT3-MMP) to test whether tumor cells through three-dimensional type 1 collagen matrix. modulate their invasiveness by controlling the trafficking The results from this research may yield insights into of membrane-type matrix metalloproteinases (MT- how tumor cells gain a growth and invasive advantage by MMPs) through their cytoplasmic domains. The project regulating MT-MMP trafficking. Such insights may lead had three specific aims. The first was to define the traf- to the development of novel drugs for therapy and ficking of MT1-MMP and MT3-MMP from cell surface chemoprevention of cancer. to the clathrin coated vesicles, early endosomes, late endosomes, trans-Golgi networks, and lysosome, and to characterize the impact of growth factors and extracellu- Research Group lar matrix on their trafficking. The second was to define Ping Cui, Research Associate Kris England, Research Associate the role of cytoplasmic domains of MT1-MMP and Ping Wang, Research Associate MT3-MMP in mediating their trafficking and character- Xing Wang, Research Associate ize their interactions with cellular components including

2006 Annual Research Report of the Supercomputing Institute 235 UM TC–Department of Pharmacology

Li-Na Wei, Principal Investigator Nuclear Receptor Interacting Protein 1 in Vitamin A Signaling Pathways

he retinoids—vitamin A—exert a wide variety of by recruiting coactivators in the presence of retinoic acid effects on biological processes and are commonly (RA) and corepressors in its absence. Nuclear receptor Tused for preventive and therapeutic purposes. interacting protein 1 (NRIP1) is a novel corepressor that Their action is mediated primarily by two families of represses gene expression in the presence of hormones. nuclear receptors, retinoic acid receptors (RAR) and These researchers address the mechanisms of NRIP1, retinoid receptors (RXR), which regulate gene expression and have three goals in doing so. The first goal is to vig- orously examine the molecular basis of NRIP1 interaction with holo-RAR/RXR. The second goal is to examine Research Group the molecular basis of NRIP1 complex to a typical lig- Jing Bi, Graduate Student Researcher and-dependent coactivator complex, SRC-1, with regards Yixin Chen, Research Associate to the efficiency of their interaction with receptors and Maria Farooqui, Research Associate their specific associate proteins. The third goal is to Ying He, Graduate Student Researcher address the physiological relevance of RA-dependent Xinli Hu, Research Associate corepressor activity of NRIP1. The ultimate goal is to Shaukat Khan, Research Associate Guanghin Li, Research Associate determine in the unique property of NRIP1 bears a Song Wook Park, Research Associate physiological relevance in terms of the specificity of vitamin A on a particular gene promoter.

W. Gibson Wood, Principal Investigator Statins, Gene Expression, and the Brain

he cholesterol-lowering drugs known as statins the cerebral cortex of mice and that the three statins have been reported to lower the risk of develop- crossed the blood-brain barrier. Ting Alzheimer’s disease. It is unclear, however, as These researchers used Supercomputing Institute to whether the apparent efficacy of statins is simply due resources to help test their hypothesis that statins have to lowering cholesterol levels, as these drugs also have cholesterol-independent effects on brain gene expression cholesterol-independent effects. These researchers’ recent that are neuroprotective, and that a mechanism of this laboratory results show that lovastatin, pravastatin, and neuroprotection is regulation of apoptosis by the Bci-2 simvastatin had pleiotropic effects of gene expression in pathway. They also tested whether active transport mechanisms contribute to the movement of statins into and out of the brain. Research Group Tammy Butterick, Graduate Student Researcher Urule Igbavboa, Research Associate Leslie N. A. Johnson, Graduate Student Researcher Ximena Rossello, Graduate Student Researcher

236 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Physical Medicine and Rehabilitation

Paula M. Ludewig, Principal Investigator Biomechanically Based Shoulder Rehabilitation Strategies

he long-term objective of this research is to devel- also help the researchers determine the effects of abnor- op and test the effectiveness of biomechanically mal kinematics on the available volume of the subacro- Tbased rehabilitation strategies for improving mial space, providing insight into how specific kinematic upper extremity function and reducing pain and disabili- deviations create impingement of soft tissue structures. ty in persons with shoulder pathologies related to abnor- Supercomputing Institute software is being used to mal shoulder movement patterns. The project has two model and visualize the three-dimensional bone struc- main goals. In the first, the researchers are collecting full- tures and animate motion. shoulder complex kinematics during arm elevation from healthy and symptomatic patients, which will be used in a state-of-the-art shoulder model to describe the three- Research Group dimensional function of the muscles to compare the dif- Edward L. Gonda, Staff ferent muscles and their relative abilities to contribute to Daniel R. Hassett, Graduate Student Researcher or reduce kinematic deviations. The second goal is to use Vandana Phadke, Graduate Student Researcher imaging data in combination with the kinematic data to Danielle Becker, Graduate Student Researcher animate the imaging data for highly accurate human Bryan M Armitage, Graduate Student Researcher movement descriptions. These data in combination will

Robert P. Patterson, Principal Investigator Modeling of Electric Potentials in Human Thorax

his project investigates various electrical measure- fluid and fat measurement, and electrical impedance ments in the body. Three-dimensional models of tomography. Tthe human thorax are generated from magnetic Recent work has focused on measuring pulmonary resonance images. These images are segmented and all edema using both internal pacemaker leads and external tissues are assigned a corresponding electrical resistivity. electrodes. Current paths through the body may then be studied by placing electrodes in the thorax model and solving the resulting forward problem. This group’s finite difference Research Group models consist of 3.8 million elements. Applications Andres Belalcazar, Graduate Student Researcher include design of implantable pacemakers and defibrilla- Fei Yang, Research Associate tor electrode systems, impedance cardiography, body

2006 Annual Research Report of the Supercomputing Institute 237 UM TC–Department of Physiology

Jürgen F. Fohlmeister, Associate Fellow Impulse Characteristics of the Encoder of Retinal Ganglion Cells in a Comparison With the Squid Axon his project analyzes nerve impulse trains elicited propagation function of axons, appear to suppress this from retinal ganglion cells (RCGs) of the cat and potential function of membrane capacitance. Phase-plot Trabbit and compares them with similar data from analyses, which yield the precise magnitudes of current the tiger salamander and with the Hodgkin-Huxley flowing during impulses, show a high degree of similarity model to determine the complement and magnitudes of in the complement of ion channels that underlie the active ion currents and to study effects of changing tem- impulse waveforms among RCGs of the amphibian and perature. Among the numerous functions of membrane mammalian preparations. Among the quantitative differ- capacitance in shaping impulse waveforms and determin- ences is a substantially smaller Ca-current in rabbit ing their amplitudes, its presence determines the mini- RCGs relative to both tiger salamander and cat. These mum conductances necessary for excitation. It may also results and this analysis will be extended to the full mor- be the basis for extending the dynamic range of impulse- phology of RCGs, which involved non-uniform channel frequency responses, that is, the basis relative to which densities and a great enlargement in excitation phenome- these central neurons optimize their ion channel densities na. for their information integration-function. The excessive- ly large (by about a factor of four) ion conductances of the Hodgkin-Huxley model, while suitable for the spike-

Doris A. Taylor, Principal Investigator Cell Transplantation for Cardiovascular Repair

re-clinical and clinical studies suggest that trans- of the cells. They have found that transplanting a mixed plantation of bone marrow- or tissue-derived stem population of marrow-derived cells that can adopt a Pcells can improve global cardiac function. No myogenic phenotype improves regional contractility and quantitative assessment of regional systolic contraction diastolic relaxation in failing myocardium. Transplanting and correlation with phenotype has yet been made, how- cardiac-derived stem cells that can adopt both a myo- ever. These researchers used their models of infarcted rab- genic and vascular phenotype appear to be equally if not bit or rat myocardium for intracardiac transplantation of more potent. a mixed population of bone marrow-derived cells and assessed both regional function and myogenic conversion

Research Group Jonathan McCue, Graduate Student Researcher Harald Ott, Research Associate Xiangrong Xin, Graduate Student Researcher

238 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Psychiatry

S. H. Fatemi, Principal Investigator Genotyping of Brain Response to Psychotropic Medications

hese researchers are analyzing the chronic effects Biology Laboratory, and the Medicinal Chemistry/ of psychotropic medications on gene expression Supercomputing Institute Visualization-Workstation Tprofiles in adult male rats using microarray, Laboratory. quantitative polymerase chain reaction, and western blot- ting techniques. The added information will be of significance in the treatment of major psychiatric illnesses. The researchers are using several Supercomputing Institute Research Group laboratories for this project, including the Basic Sciences Timothy Folsom, Research Associate Computing Laboratory, the Computational Genetics Teri Reutiman, Research Associate Laboratory, the Digital Technology Computational

UM TC–Department of Radiology

Mark J. Conroy, Principal Investigator Textural Qualities of Mitochondria Images

hese researchers analyze the textural qualities of scanning electron microscope images of mito- Tchondria. The morphological properties of hepa- tocyte mitochrondria should have different quantitative textural values than those in hemorrhagic shock. The techniques the researchers develop as well as the presumed correlation will provide insight into the oxygen consumption limitations of the cells associated with massive organ failure due to hemorrhagic shock. The researchers used the Medicinal Chemistry/Supercom- Research Group puting Institute Visualization-Workstation Laboratory David Jahangir, Undergraduate Student Researcher and the Scientific Development and Visualization Laboratory for this project.

2006 Annual Research Report of the Supercomputing Institute 239 UM TC–Department of Radiology

Noam Harel, Principal Investigator Patrick J. Bolan, Co-Principal Investigator Visualization of Cortical Microvascular System Using High-Resolution Magnetic Resonance Imaging unctional magnetic resonance imaging (fMRI) is architecture is needed. These researchers are creating the chief method for studying human brain func- three-dimensional visualizations of microvascular sys- Ftion in vivo. The technique relies on the fact that, tems. Three-dimensional reconstruction and visualization during increase in neuronal activity, there is a localized of the vascular volume will provide much-need informa- increase in blood flow. Oxygenated blood that rushes to tion about the spatial organization of the cortical the active region alters the MRI signal and consequently microvascular system, including vessel sizes, orientations, allows visualization of the localized brain regions “at and densities. This will enhance the ability to design work.” Thus, the detection of changes in neuronal activi- image acquisition techniques and improve the interpreta- ty is closely tied to the underlying vascular organization. tion of fMRI signals. To improve the spatial specificity of fMRI, better understanding of cortical vascular and microvascular

Research Group Nathaniel Powell, Staff

Pierre-Gilles Henry, Principal Investigator Metabolic Modeling of Isotropic Turnover in the Brain

he aim of this project is to directly measure neu- These researchers are assessing the reliability and accu- rotransmission activity in the brain in vivo. To do racy of current modeling approaches using Monte Carlo Tthis, the researchers measure the rate of incorpo- simulations. The fitting procedure will be repeated with ration of an isotopic tracer into brain metabolites using different noise to determine the distribution of fitted nuclear magnetic resonance and analyze the resulting parameters. Simulations are performed under different turnover curve with a sophisticated metabolic model to conditions by varying noise level in experimental data, by calculate metabolic fluxes. Metabolic models consist of a adding more constraints in the model, or by including stiff system of differential equations. These sets of equa- more experimental data in the fitting procedure. The tions are solved numerically, then parameters in the result will be a better understanding of how much meta- model are adjusted to fit experimental data using least- bolic information can be extracted from isotopic square fitting. turnover curves using complex metabolic models.

Research Group Alexander Shestov, Research Associate

240 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Surgery

Peter S. Dahlberg, Principal Investigator Gene Expression in Thoracic Oncology

he incidence of esophageal adenocarcinoma that are regulated by ERBB2 at the level of protein trans- (EAC) has risen dramatically in the last two lation. Tdecades. As with other malignancies, changes in Another area of investigation of the Thoracic gene expression play a key role in the development and Oncology Laboratory is the evaluation of surgical stress progression of other tumors. on the immune system. Investigators are analyzing the This project involved characterizing tumors that con- effect of minimally invasive surgical approaches on gene tain amplified ERBB2 genes, a situation which occurs expression in cancer and cancer patients. approximately 20% of the time. Comparison of nucleic acid expression, as determined by microarray analysis, of tumors and normal esophageal mucosa has allowed these researchers to map the genes that are co-amplified with ERBB2 in tumors and in cell lines. They are also looking at changes that occur in the precursor of pre-malignant Research Group Barrett’s esophageal cells to adenocarcinoma. In Ganesh Dahal, Research Associate esophageal cancer, these investigators are also using Bryan A. Whitson, Research Associate microarray analysis of gene expression to identify genes

Lester F. Harris, Principal Investigator Leonard S. Schultz, Co-Principal Investigator Dynamic Simulations of Solvated Protein-DNA Complexes and Protein Folding Studies hese researchers are conducting experiments The researchers are also computing PME periodic investigating the mechanism(s) of a genetic boundary solvated dynamic simulations on several other Tswitch controlled by deoxyribonucleic acid steroid receptor/DNA complexes. These studies include (DNA) regulatory proteins. They are interested in steroid DNA containing various hormone response elements hormone receptor protein interactions with DNA in the (cognate and non-cognate) in complex with members of pathogenesis of breast cancer. The researchers have previ- the steroid receptor superfamily of proteins, particularly ously reported on a mechanism describing how these the estrogen, glucocorticoid, retinoic acid, and proges- DNA regulatory proteins recognize and bind to their terone receptors. specific sites on DNA. They are conducting Particle Mesh Ewald (PME) periodic boundary molecular dynamics simulations in solvent to investigate hydrogen Research Group bonding, van der Waals, and long-range electrostatic Pamela D. Popken-Harris, Research Associate interactions between amino acids of the DNA regulatory Michael R. Sullivan, Research Associate proteins and nucleotides of their cognate DNA binding sites.

2006 Annual Research Report of the Supercomputing Institute 241 UM TC–Department of Surgery

Bernhard J. Hering, Principal Investigator Mixed Chimerism in Non-Human Primates

ixed chimerism is a platform strategy to: per- donor lymphocyte infusions for the treatment of hemato- mit transplantation without the need for logical and selective non-hematological malignancies. To Mchronic immunosuppression; control autoreac- be clinically useful in these treatments, stable mixed tivity in autoimmune disorders; alleviate clinical symp- chimerism must have minimal toxicity; to make it more toms in hemoglobinopathies, genetically based immun- widely applicable in transplantation, major histocompati- odeficiencies, and enzymatic deficiencies; and reduce risk bility complex barriers must be transgressed. These of graft-versus-host-disease through subsequent same- researchers have made several steps towards achieving these goals. Because of the complexity of the research protocol and the desirability of sharing the information Research Group with other researchers, this group is using resources at Tor Aasheim, Research Associate Supercomputing Institute laboratories to build a robust Sue Clemmings, Research Associate computerized electronic information system for this proj- Melanie Graham, Research Associate ect. Maria Hardstedt, Research Associate Tun Jie, Research Associate Kevin Larson, Staff

Paul A. Iaizzo, Principal Investigator Differential Gene Expression Analysis of Cell Culture and Animal Studies

he objective of this study is to explore potential The researchers are also using mass spectrometry, pro- biomarkers that may be discovered by various tein computation modeling, and linkage programs to Texperimental studies facilitation at Medtronic, interpret data obtained from initial experiments in Inc. The researchers have used Affymetrix gene chip genomics and proteomics studies. technology to investigate differential gene expression in cell culture and animal studies. They are now using the Supercomputing Institute’s microarray data analysis and statistical program to effectively analyze the raw data for basic research in cardiovascular medicine.

Collaborator Jocelyn Clark-Greuel, Medtronic, Inc., Fridley, Minnesota

242 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Surgery

David E. R. Sutherland, Principal Investigator Pancreatic Resection and Autologous Islet Transplant to Treat Painful Chronic Pancreatitis ancreatectomy can alleviate pain in patients with chronic pancreatitis, and autologous islet trans- Pplant lowers the surgical diabetes risk from this procedure. These researchers are investigating the use of Research Group and Collaborator autologous islet transplant in patients undergoing pri- Tun Jie, Research Assistant mary pancreatic resection for the treatment of refractory Takashi Kobayashi, Visiting Researcher pain associated with small duct chronic pancreatitis. Ann Marie Papas, Staff They are using the Computational Genetics Laboratory for this project.

UM TC–Department of Therapeutic Radiology

Daniel A. Vallera, Principal Investigator Optimizing Construction of Single-Chain Fv Antibodies That Recognize Human Leukemia Cells hese researchers are primarily interested in antibody targeting of human cancer with antibodies Tas a replacement for non-specific chemotherapy. In order to enhance their ability to selectively bind tumors in vivo, it is important to enhance antibody bind- Research Group ing avidity. These researchers clone single-chain Fv (sFv) Hua Chen, Staff antibodies that bind tumors, then use molecular model- David Kuroki, Staff ing programs to construct three-dimensional models of Yanqun Shu, Staff the projected tertiary structures of sFvs. Using other pro- Andy Sicheneder, Staff grams, the researchers locate likely areas in the molecule Brad Stish, Graduate Student Researcher in which cysteines can be introduced to stabilize the Liz Taras, Staff Deborah Todhunter, Staff structure. Once located, the sFvs are mutated and used Vincent Vallera, Undergraduate Student Researcher in in vitro and in vivo assays to determine whether efficacy and pharmacokinetics have been improved.

2006 Annual Research Report of the Supercomputing Institute 243 UM TC–Department of Urologic Surgery

Kenneth S. Koeneman, Principal Investigator Targeting New Therapeutics for Lethal Phenotypes of Prostate Cancer

elomerase activity is seen in greater than 90% of ovirus and mini-dose taxotere in a murine model of human prostate cancer. Inhibition of telomerase intraosseous human prostate cancer. The researchers are Thas long been postulated as a novel mechanism using the Basic Science Computing Laboratory, the for tumor eradication. This project aims to test the Medicinal Chemistry/Supercomputing Institute effectiveness of recently developed serum-stable anti- Visualization-Workstation Laboratory, and the Scientific sense oligonucleotides to the messenger ribonucleic acid Development and Visualization Laboratory for this proj- template of telomerase, as well as in combination with ect. tissue-specific, cytolytic replication-competent aden-

Research Group Yingming Li, Research Associate

Carl S. Smith, Principal Investigator Dynamics of Urethral Sphincter Activity

ynamical analysis is a mathematical tool that Furthermore, despite the apparent system complexity, a provides a powerful alternative to traditional dynamical analysis can reveal a series of simple rules that Dbiologic signal processing. Traditional approach- govern the system’s behavior. This study examines the es quantitate and characterize signals by parameters such electromyographic signal present in the urethral striated as frequency, amplitude, and waveform in an effort to muscle during bladder filling. discover the underlying relationships within the system under study. A dynamical approach utilizes the same time-dependent information but constructs a visual picture, an attractor, of the nature of interaction found with the system that generated the signal. This is an extraordi- nary unexpected result in dynamical analysis; for the first time, there is a technique that allows a glimpse at the richness of structures that create the biologic signal.

244 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Urologic Surgery

Robert M. Sweet, Principal Investigator The Institute for Simulated Learning Assessment and Novel Development

he use of simulation in medical procedures is now being proven as a valid and economically Research Group and Collaborators Tsound method for training medical students and John P. Abraham, Department of Engineering, residents. These researchers are using Supercomputing University of St. Thomas, St. Paul, Minnesota Institute resources to build, test, and validate medical Peter Oppenheimer, Human Interface Technology simulators to train cognitive and procedural skills and Laboratory, University of Washington, Seattle, applications of virtual reality to clinical medicine. They Washington are using existing simulation platforms and building new Ephraim M. Sparrow, Faculty Collaborator modules on these platforms as well as developing new Nick Whitehead, Graduate Student Researcher simulation software tools.

Gerald W. Timm, Principal Investigator Flow Dynamics of Stented/Unstented Superficial Femoral Artery

his group is investigating methods of monitoring in vivo movement of the superficial femoral Tartery and to use the information they gain to improve stent design. The main objectives of this project are to model in vivo movement of the artery with and without the stent and find solutions to designing a frac- Research Group and Collaborator ture-safe stent. In order to model the movement and Santhi Elayaperumal, Undergraduate Student fluid flow of the artery with and without the stent’s pres- Researcher ence, the group is analyzing imaging scans and applying Jeff Hammerstrom, Undergraduate Student Researcher finite element analysis to the problem. Gregory Lee, Undergraduate Student Researcher Jianlu Ma, ev3 Incorporated, Plymouth, Minnesota A second project involves characterizing how rigidity Brian Pederson, Undergraduate Student Researcher is attained and maintained in thin-walled pressurized ves- Ngoc-Linh Pham, Undergraduate Student Researcher sels and how measurement of wall collapse can serve as a diagnostic tool.

2006 Annual Research Report of the Supercomputing Institute 245 UM TC–Department of Developmental and Surgical Sciences

Massimo Costalonga, Principal Investigator Study of the Pathogenesis of Periodontitis in Vivo in a Mouse Model

hese researchers used Supercomputing Institute laboratory resources to stably transform TPorphyromonas gingivalis with a series of genes, namely modified hen egg lysozyme, E Alpha, and ovalbumin. Their objective was to study the pathogenesis of periodontitis in vivo in a mouse model.

Research Group Leonidas Batas, Staff Lori Fischer, Staff Zhenfen Zhao, Staff

UM TC–Department of Diagnostic and Biological Sciences

Dwight L. Anderson, Principal Investigator Modeling the ATPase Core of the φ29 Bacteriophage Protein gp16

he φ29 bacteriophage protein gp16 participates ATP, suggest the ATPase core of gp16 has a β-strand in the packaging of viral deoxyribonucleic acid structure identical to that of TrwB, but differs in the T(DNA) into the phage capsid. Amino acid align- lengths of loops and α-helices that connect these strands. ment and secondary structure prediction of analogs for Structural modeling of the gp16 ATPase core onto the this protein suggest a structural similarity to the ATPase TrwB template requires the deletion of a TrwB domain, core of the hexameric protein TrwB, a bacterial protein modification in the lengths of loops and helices, and the involved in cell-to-cell DNA translocation. Alignment of fitting of the model into a hexameric ring. Generation of the predicted secondary structure for gp16 with the crys- a model for the gp16 ATPase core will guide future tal structure of TrwB, along with a concurrent alignment mutagenesis experiments designed to identify DNA of amino acids involved in the sensing and hydrolysis of binding residues and to modify structural elements affecting rates of ATP hydrolysis.

Research Group Rockney Atz, Staff

246 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Diagnostic and Biological Sciences

James R. Fricton, Principal Investigator Sandra L. Myers, Co-Principal Investigator Temporomandibular Joint Disorder Implant Registry and Repository

emporomandibular joint disorders (TMJs) are allow researchers to advance the understanding and common disorders causing facial pain, headaches, increase the successful treatment of TMJD. In particular, Tclicking, locking, and diminished functioning in those patients who need TMJ implants in the future will the jaw. In some cases, there is degeneration of the tem- benefit from the increased understanding of TMJ disor- poromandibular joint structure (bone and articulated ders generated by the tissues and data made available. cartilage) leading to pain, dysfunction, and destructive changes in the joint. These researchers have created the National Institute Research Group and Collaborators of Dental and Craniofacial Research’s TMJ Implant Patricia Carlson, Research Associate Registry and Repository (TIRR) to improve the under- Mike Davin, Staff standing and care of patients with temporomandibular Nancy Hardie, Faculty Collaborator muscle and joint disorders (TMJD). The TIRR asks both Wenjun Kang, Graduate Student Researcher patients and clinicians to contribute clinical information Lois Kehl, Faculty Collaborator and biological specimens from patients who are having John Look, Research Associate surgery with TMJ disorders. Wei Ouyang, Graduate Student Researcher With the help of doctors and patients, this project will

Raj Gopalakrishnan, Principal Investigator Anna Petryk, Co-Principal Investigator Twisted Gastrulation and Bone Development

one morphogenic proteins (BMPs) are critical for The objective of this project is to determine the func- most stages of osteoblast differentiation, such as tion of Tsg in bone by performing static and dynamic osteoblast lineage commitment from precursor histomorphometry and micro-CT analysis in long bones B +/+ -/- cells, maintenance of differentiated state of already com- of Tsg and Tsg mice. The parameters being investi- mitted osteoblasts, and matrix mineralization. Tsg is an gated include skeletal area, bone volume to total volume, extracellular protein that has both pro-BMP and anti- trabecular thickness, trabecular number, trabecular sepa- BMP functions. However, the role of Tsg and its possible ration, bone surface to volume ratio, osteoblast surface, regulation of BMP signaling during postnatal bone mineral apposition rate, and bone formation rate. development are not known. Toward this end, these researchers are studying mice that have a targeted deficiency of the Tsg gene. Tsg-/- mice in 129Sv/Ev back- Research Group ground show decreased bone density, reduced cortical Ann Carlson, Staff thickness, and defective osteoblast differentiation com- Lei Li, Research Associate pared to wild-type mice, suggesting a role for Tsg as a Julio Sotillo, Graduate Student Researcher positive regulator of bone formation.

2006 Annual Research Report of the Supercomputing Institute 247 UM TC–Department of Diagnostic and Biological Sciences

Mark C. Herzberg, Principal Investigator Oral Epithelial Cells: Innate Immune “Gatekeeper” of HIV

he oral mucosal epithelium is directly exposed to how they are then able to transfer virus to susceptible tar- human immunodeficiency virus (HIV) during at- get cells. They are particularly interested in the intracel- Trisk sexual activity and through breast-feeding. lular events that promote or inhibit the stages of HIV Unlike the intestinal epithelium, the oral mucosa is infre- infection and replication. The group is using the Basic quently considered to be a locus of primary HIV infec- Sciences Computing Laboratory and the Scientific tion. These researchers are interested in the interaction of Development and Visualization Laboratory for their HIV with oral epithelial cells, specifically, how HIV research. binds to and productively infects oral epithelial cells and

Research Group Kristin H. Gebhard, Staff Brian D. McAdams, Staff Karen Ross, Research Associate Anjalee Vacharaksa, Graduate Student Researcher

Ching-Chang Ko, Principal Investigator Computational Prediction of Bone Adaptation Around a Dental Implant

he amount and architecture of bone growth sur- previous experimental data to develop a mathematical rounding a dental implant depends on the local model for prediction of bone adaptation. They used Tmechanical environment. Developing a quantita- three-dimensional finite element models that require a tive relationship between stress-strain and bone adapta- great deal of computing power to deal with the large tion would provide useful information for the design of number of elements and the iterative processes per- implants. These researchers previously created a load- formed. Since the model is too large for standard desktop controlled model to assess adaptation patterns of an computers, the group used resources of the implant-bone interface. For this project, they used their Supercomputing Institute.

Research Group Heng-Li Huang, Research Associate

248 2006 Annual Research Report of the Supercomputing Institute UM TC–Department of Diagnostic and Biological Sciences

Patrick W. Mantyh, Principal Investigator Molecular Mechanisms of Bone Cancer Pain

he overall goal of this project is to gain a better understanding of the factors that generate and Tmaintain bone cancer pain due to a mixed tumor, i.e., one that induces both bone destruction and formation. The researchers examined how peripheral factors such as tumor growth, bone destruction, and sympathetic neurons excite or modulate sensory neurons and thus contribute to bone cancer pain. They also examined how inputs from sensory fibers that innervate the tumor-bearing bone alter the cellular and neurochemical characteristics of the spinal cord and dorsal column nuclei and thus Research Group contribute to central sensitization. While the present Joseph Ghilardi, Research Associate project focused on bone cancer pain, these experiments Kyle Halvorson, Staff may also provide insight into non-osseous types of cancer Christopher M. Peters, Graduate Student Researcher pain and aid in the development of novel strategies for controlling cancer pain in humans.

Joel D. Rudney, Principal Investigator Extracrevicular Invasion by Periodontal Pathogens

major goal of this project is to determine whether mucosal cells taken directly from the mouth con- Atain intracellular oral bacteria. Fluorescent probes to conserved and species-specific regions of bacterial 16S ribosomal ribonucleic acid are used to label bacteria associated with human buccal epithelial cells. The researchers then use confocal microscopy to collect z-stacks of cells that appear to contain intracellular bacteria. Using software available at the Basic Sciences Computing Research Group Laboratory, the researchers can create three-dimensional Ruoqiong Chen, Staff reconstructions to confirm that the labeled bacteria are actually present within the bounds of the cell membrane.

2006 Annual Research Report of the Supercomputing Institute 249 UM TC–Division of Biostatistics

Patricia M. Grambsch, Principal Investigator James D. Neaton, Co-Principal Investigator Interim Monitoring of Randomized Clinical Trials With Multiple Endpoints

any clinical trials have multiple outcomes and The boundaries control the overall type 1 error with con- formal interim monitoring guidelines that sideration of the endpoint correlations through multi- Mconsider them can be useful to Data and variate integration. The results show that the boundaries Safety Monitoring Committees. These researchers have from the new decision rules depend on the correlation developed an approach for stopping trials that takes into between the two outcomes. For low to moderate correla- account cases where there is not a clear difference tion, critical values based on the O’Brien Fleming error between a safety and efficacy endpoint, or where there is spending function that consider the correlation are lower interest in more than one disease outcome. They consid- than those that do not. The researchers also carried out er trials with two treatments and develop sets of two extensions of current bivariate sequential tests to allow boundaries, a higher and a lower one, permitting one more interim looks and to consider the correlation endpoint to be primary and other supportive or second- between endpoints. Current works involves comparing ary, with or without pre-specifying which one is primary. the new approach to two important competitors, the O’Brien generalized least squares approach and an ad hoc version of the new approach in terms of statistical power Collaborator and robustness to mis-specified correlation. Yanli Zhao, Lilly Company, Indianapolis, Indiana

Na Li, Principal Investigator Selection of Single Nucleotide Polymorphisms for Evaluating Gene-Phenotype Associations Using Haplotypes type of genetic marker, single nucleotide poly- informative than single SNPs, but using more SNPs may morphisms (SNPs), is increasingly commonly introduce more noise. These researchers developed a sta- Atyped to detect the association between candidate tistical method to select an optimal subset of SNPs that genes and disease traits of interest in a population sam- can be used to assess the association between the gene ple. For SNPs that are located on the same chromosome and the trait. Because of the large model space to search and hence are more likely to be transmitted together and the use of cross-validation and permutation, the from generation to generation, they form the so-called method is computationally intensive. The researchers haplotypes. Multi-SNP haplotypes tend to be more used simulated datasets to investigate the operational properties of the method.

Research Group Meijuan Li, Graduate Student Researcher

250 2006 Annual Research Report of the Supercomputing Institute UM TC–Division of Biostatistics

Wei Pan, Principal Investigator Statistical Analysis of Genomic and Proteomic Data

hese researchers developed new statistical methods and software to analyze large amounts of Research Group multiple types of genomics and proteomic data. T Peng Wei, Graduate Student Researcher These data result from high-throughput biotechnologies such as microarrays. The researchers used the Supercomputing Institute laboratories for this project.

UM TC–Division of Environmental Health Sciences

Lisa A. Peterson, Principal Investigator Environmental Carcinogenesis

hese researchers are interested in the chemical mechanism of carcinogenesis induced by environ- Tmental chemicals. They are characterizing the products formed when carcinogens and/or their metabolites modify important biomolecules such as deoxyribonucleic acid (DNA) and proteins. They are also performing exploratory molecular modeling experiments to Research Group understand how DNA repair proteins accommodate Li Li, Research Associate DNA adducts at their active sites. These studies will pro- Renee Mijal, Research Associate vide preliminary data required to more fully explore Choua Vu, Staff structural issues affecting DNA repair by human variant repair proteins in a DNA sequence dependent manner.

2006 Annual Research Report of the Supercomputing Institute 251 UM TC–Division of Environmental Health Sciences

Peter C. Raynor, Principal Investigator Supercomputer Modeling of Airborne Particle Filtration

ibrous filters are important tools for controlling lar cross-sections can improve filter performance. The exposure to potentially hazardous particles. New specific aims are to: develop flow fields for air moving Fsynthetic fibers with irregular cross-sectional shapes past two-dimensional arrays of irregularly shaped filter may improve filter performance beyond the capabilities fibers; model the movement of particles through the flow of filters made with conventional fibers. The objective of fields; and calculate the efficiency of particle collection this project is to determine how much fibers with irregu- by the fibers. The researchers use the computational fluid dynamics software program FIDAP on the supercomputers for this work. Research Group This research will provide the first analysis of the pos- Seung Won Kim, Graduate Student Researcher sible advantages of using irregularly shaped fibers in fil- Ji Young Park, Graduate Student Researcher ters. With this new information, filter manufacturers may be able to produce filters that can protect people better than is possible now.

UM TC–Division of Epidemiology and Community Health

James S. Pankow, Principal Investigator Michael B. Miller, Co-Principal Investigator Genetic Epidemiology of Cardiovascular Disease and Associated Risk Factors

his research project seeks to detect, localize, and Research Group and Collaborator characterize genes involved in the development of Suzette Bielinski, Graduate Student Researcher Tcardiovascular disease (CVD) and its associated Soon Young Jang, Graduate Student Researcher risk factors (e.g., diabetes, high blood pressure, elevated Adele Jiang, Graduate Student Researcher cholesterol, etc.). Recent technological advances in Joanlise Leon, Graduate Student Researcher molecular biology and genetics have provided new Na Michael Li, Faculty Collaborator opportunities to explore the genetic architecture of com- Gregg Lind, Graduate Student Researcher plex diseases and traits such as CVD. Genetic epidemio- Yuhong Liu, Graduate Student Researcher logical research on such traits, however, requires data on Amy Lynch, Graduate Student Researcher thousands of individuals, hundreds of genetic markers, James Peacock, Research Associate and complex statistical models that are computationally Laura Rasmussen, Graduate Student Researcher Richard Sherva, Graduate Student Researcher demanding. Supercomputing resources are used to con- Weihong Tang, Research Associate struct models with high order gene-gene or gene-envi- Joel Wu, Graduate Student Researcher ronment interactions that cannot be practically evaluated otherwise, and to conduct simulation experiments.

252 2006 Annual Research Report of the Supercomputing Institute Bethel University

College of Arts and Sciences Department of Chemistry Rollin A. King ...... 254

Macalester College

Department of Chemistry Keith T. Kuwata ...... 254

2006 Annual Research Report of the Supercomputing Institute 253 Bethel University–Department of Chemistry

Rollin A. King, Principal Investigator Hydrogen Bonding to Dye Molecules in Ground and Electrically Excited States

fter electronic excitation of the dye Coumarin- cause of this break. These researchers are performing 102 (C102), infrared laser pulses tuned to its car- electronic structure computations to investigate the Abonyl stretch appear to reveal an impulsive cleav- nature of the C102 hydrogen bond in both the ground age of the hydrogen bond formed with phenol or chloro- and excited S1 states of the dye. In recent work, they form molecules within 200 fs of excitation. Hydrogen- have used density functional and coupled cluster theories bond breaking between C102 and aniline has also been to determine ground- and excited-state structures and observed within 250 fs, with reformation of the bond dipole moments of C102 and related model compounds. taking 30 ps. Other researchers do not agree about the They are now focusing on the hydrogen-bond breaking process in an attempt to determine if the bond-breaking potential is purely or nearly dissociative. Research Group Kerri Jaye Grove, Undergraduate Student Researcher

Macalester College–Department of Chemistry

Keith T. Kuwata, Principal Investigator Computational Kinetics of Oxidation Intermediates in the Troposphere

ydrocarbons released into the earth’s atmosphere calculations to predict the rates of these reactions. The are rapidly converted to oxygenated species that initial focus of the study is the reactions of carbonyl Hundergo either unimolecular reactions or bimol- oxides formed in alkene oxonolysis. The researchers are ecular reactions with water. The short lifetimes of these addressing fundamental atmospheric questions, such as molecules make direct experimental studies of reaction the ability of carbonyl oxides to generate free radicals and kinetics problematic. These researchers are using their impact on aerosol loading in the atmosphere. They Supercomputing Institute resources to perform accurate are also seeking to validate density functional theory electronic structure and variational transition state theory methods against more demanding composite electronic structure theory approaches.

Research Group Brianna Kujala, Undergraduate Student Researcher Julia Stanfield, Undergraduate Student Researcher

254 2006 Annual Research Report of the Supercomputing Institute Mayo Clinic CCollegeampus of Medicine

Advanced Genomic Technology Center Sreekumar Raghavakaimal ...... 256 Department of Molecular Pharmacology and Experimental Therapeutics Yuan-Ping Pang ...... 256 Department of Neuroscience and Neurology Charles L. Howe ...... 257 Department of Orthopedic Research Gobinda Sarkar and Mark W. Bolander ...... 257 Department of Physiology Steven M. Sine ...... 258 Division of Cardiovascular Disease Iftikhar J. Kullo ...... 258

2006 Annual Research Report of the Supercomputing Institute 255 Mayo Clinic College of Medicine–Advanced Genomic Technology Center

Sreekumar Raghavakaimal, Principal Investigator Microarray Data Analysis

hese researchers are involved with data analysis of profiles in samples subjected to different treatments; ana- four main types of microarray projects. These lyzing gene expression profiles over a time course (for Tprojects include: determining gene expression example, embryo development or cell cycle); studying changes in gene expression profiles in samples with different genotypes; and analyzing gene expression profiles Research Group and Collaborators in different tissue or cell types. The researchers use soft- Kathleen Bartemes, Research Associate ware available at Supercomputing Institute laboratories Unnikrishnan Gopinathan, Faculty Collaborator to aid in their analyses. Paul Streg, Faculty Collaborator William Johnson, Faculty Collaborator Christopher Kolbert, Staff Alexey Leontovich, Staff Michael W. Lin, Staff

Mayo Clinic College of Medicine–Department of Molecular Pharmacology and Experimental Therapeutics

Yuan-Ping Pang, Associate Fellow In Silico Drug Design

his project’s goal is to develop and apply compu- chemical databases. This group has developed the tational (in silico) methods for determining three- Cationic Dummy Atom Approach for molecular dynam- Tdimensional structures of drug targets from ics simulations of metalloproteins and small-molecule genetic codes and identifying drug candidates from inhibitor leads of Severe Acute Respiratory Syndrome (SARS) virus protease using the information from the SARS genome and multiple molecular dynamics simulations. The researchers are further testing the practicality Research Group of their in silico methods in identifying small-molecule Paramita Dasgupta, Research Associate inhibitor leads of calcium-bound neuraminidase of Avian Alfonso Garcia Sosa, Research Associate Candace Kash, Staff Flu (H5N1) virus, West Nile Virus protease, botulinum Kevin J. Langenwalter, Research Associate neurotoxin serotype A light chain, Bacillus anthracis Isidro Merino, Research Associate lethal factor, XIAP, and BLyS. Successful completion of John Streiff, Research Associate these projects will lead to in silico approaches that com- Jason Thompson, Research Associate plete experimental approaches in drug discovery, and Qi Wang, Graduate Student Researcher ultimately result in therapeutics for treating cancers and infectious diseases.

256 2006 Annual Research Report of the Supercomputing Institute Mayo Clinic College of Medicine–Department of Neuroscience and Neurology

Charles L. Howe, Principal Investigator Modeling the Signaling Endosome Hypothesis

he signaling endosome hypothesis in its broadest walk from the plasma membrane. Because, however, the interpretation states that all cells, regardless of equations for diffusion are not vectorial, they only pro- Tsize or architecture, compartmentalize signals vide a measure of average root mean square particle generated by transmembrane receptor tyrosine kinases movement without specifying direction. In contrast, into membrane-bounded organelles of endocytic origin. facilitated transport of signaling endosomes is inherently These signal transduction platforms are long-lived, self- vectorial and nucleus-directed because of the intrinsic regenerating transport vehicles that utilize cytoplasmic properties of the microtubule network within cells. In motor proteins such as dyenin to move a signal from the order to quantify the efficiency of transport versus diffu- plasma membrane to the nucleus along microtubules. sion, this researcher modeled the diffusion of several The traditional model for signal transduction from the known signal transduction molecules as a random walk plasma membrane depends upon simple diffusion of sig- from the plasma membrane to the nucleus. naling molecules through the cytoplasm, with signals reaching the nucleus essentially as the result of a random

Mayo Clinic College of Medicine–Department of Orthopedic Research

Gobinda Sarkar, Principal Investigator Mark W. Bolander, Co-Principal Investigator Tumor Endothelial Marker Sequences

his group employed sequence alignment (paired and/or multiple) strategies to discover nucleotide Research Group sequences among various tumor endothelial T Dinakar Desai, Research Associate marker genes. They used the Basic Sciences Computing Alok Srivastava, Research Associate Laboratory and the Computational Genetics Laboratory for this work.

2006 Annual Research Report of the Supercomputing Institute 257 Mayo Clinic College of Medicine–Department of Physiology

Steven M. Sine, Principal Investigator Molecular Dynamics Study of the Gating Mechanism of the Nicotinic Acetylcholine Receptor his group’s overall research aims to understand expanding their studies of the nicotinic receptor in com- with atomic precision how synaptic receptors putational simulations by incorporating it into a defined Tchange conformation to produce a biological membrane surrounded by explicit solvent molecules and response. Such knowledge is crucial for understanding ions, and employing a series of molecular dynamics sim- synaptic transmission in normal and disease states and ulations to identify conformational changes that link for design of therapeutic drugs. The researchers are binding of the natural neurotransmitter to opening of the intrinsic ion channel. This project will provide the first glimpse of the working mechanism of a biologically Collaborator significant signaling protein. Hai-Long Wang, Faculty Collaborator

Mayo Clinic College of Medicine–Division of Cardiovascular Disease

Iftikhar J. Kullo, Principal Investigator Patterns of Population Differentiation of Candidate Genes for Atherosclerotic Vascular Disease in Three Ethnic Groups enetic variation may only be adaptive in certain may be evidence for different selective pressures across environments and less favored in others, which populations. Gwould balance and maintain variation across dif- In this project, the researchers are assessing the pat- ferent environments of populations, resulting in, for terns of population differentiation of candidate genes for example, geographic clines in allele frequencies. If func- atherosclerotic cardiovascular diseases (ASCVD) in three tional variation exhibits significantly different patterns of ethnic groups. Based on the patterns of population dif- geographic variation compared to neutral variation, this ferentiation of these genes, they want to identify the candidate genes for ASCVD that may be under local selection. Such information will provide insights into the dif- Research Group ferent susceptibility towards atherosclerotic cardiovascular Keyue Ding, Research Associate disease among different ethnic groups.

258 2006 Annual Research Report of the Supercomputing Institute Metropolitan State University

College of Arts and Sciences Department of Information and Computer Sciences Jigang Liu ...... 260

2006 Annual Research Report of the Supercomputing Institute 259 Metropolitan State University–Department of Information and Computer Science

Jigang Liu, Principal Investigator Performance Evaluation of Parallel Computational Geometry Algorithms

he goal of this project is to create an experimental environment for analyzing and evaluating the Tperformance of parallel computational geometry algorithms. The environment has three major components: a data-acquiring system, a communication system, and a computation system. The data-acquiring system will be established using graphic user interface technology so that the user can freely define the scenarios for testing and evaluation purposes. The communication system is based on the Unix PC mechanism using TCP/IP protocols and works as a connection component between the data-acquiring and computation systems. The computation system is dedicated to the implementation of the existing and newly developed parallel computation geometry algorithms on the IBM SP supercomputer and the Linux cluster.

260 2006 Annual Research Report of the Supercomputing Institute Minnesota State University, Mankato

College of Business

Department of Management Rakesh Kawatra ...... 262

College of Science, Engineering, and Technology

Department of Computer and Information Sciences David J. Haglin ...... 262 Department of Mechanical and Civil Engineering Deborah K. Nykanen ...... 263 Patrick A. Tebbe ...... 263

2006 Annual Research Report of the Supercomputing Institute 261 Minnesota State University–Department of Management

Rakesh Kawatra, Principal Investigator A Multiperiod Hop-Constrained Telecommunication Network Designed Problem

he multiperiod hop-constrained telecommunica- value h; and some terminal nodes are activated at the tion design problem consists of scheduling the beginning of the planning horizon while the remaining Tinstallation of links in a network so as to connect terminal nodes are activated over time. The researcher a set of terminal nodes N = {2,3,...... n} to a central node has formulated this as an integer programming problem with minimal present value of expenditure such that: and is using a Lagrangian relaxation-based branch each terminal node j has exactly one entering link; for exchange heuristic to find a feasible solution. each terminal node j, a unique path from the central node to j exists; the number of links from the central node to each terminal node t is limited to a predefined

Minnesota State University–Department of Computer and Information Sciences

David J. Haglin, Principal Investigator High-Performance Computing and Statistical Disclosure Control

iven a data set of personal information presumed within. While this approach provides an accurate score to be “anonymized” by removing uniquely iden- for each record, it clearly suffers from combinatorial Gtifying features, identifying records at high risk explosion. of identity breach by finding rare patterns such as a 16- Because of the growing need to protect the privacy of year-old with a marital status of “widow” can help the personal information even though there are clear advan- process of statistical disclosure control. If there are multi- tages to releasing this type of information for legitimate ple occurrences of a 16-year-old widow, perhaps adding research needs, it is important to improve algorithms and the feature of “number-of-children” will produce a pat- investigate effective parallelization strategies for this NP- tern of three feature-values that is unique. Each record Complete (Non-deterministic Polynomial time- can be scored according to the number of unique pat- Complete) problem. This project will involve investigat- terns of various sizes (number of attributes) contained ing the scalability of current algorithms on a Linux cluster for comparison to other types of parallel computation architectures. Research Group Anna Manning, Research Associate

262 2006 Annual Research Report of the Supercomputing Institute Minnesota State University–Department of Mechanical and Civil Engineering

Deborah K. Nykanen, Principal Investigator Topographical Influence on the Multi-Scale Statistical Properties of Precipitation

he ultimate goal of this project is to characterize topography and address: whether spatial and space-time the space-time scaling and dynamics of convec- scaling exists as a common feature in convective oro- Ttive precipitation, especially in mountainous ter- graphic presentation; at what spatial and temporal scales rain, and to develop downscaling methods to transfer do meteorological and orographic controls manifest precipitation fields from one scale to another. Space-time themselves in the space-time variability of convective pre- scale gaps continue to exist between distributed hydro- cipitation fields; and how meteorological forcings and logic models and numerical weather prediction forecasts. geographic location impact trends in orographic influ- This study attempts to address the open research prob- ences on the multi-scale statistical properties of convec- lem of scaling organized thunderstorms and convection tive precipitation. in mountainous terrain down to 1–4 km scales. The key objective of the study is to investigate the meteorological and orographic influence on the space-time scaling and dynamics of convective precipitation over complex

Patrick A. Tebbe, Principal Investigator Three-Dimensional Study of Asymmetric and Unsteady Convection in Physical Vapor Transport he physical vapor transport (PVT) process is used have on product quality. While the process is inherently to produce certain specialty semiconductor mate- three-dimensional and time varying, numerical studies Trials, such as mercury iodide or mercurous chlo- have been largely limited to two-dimensional or steady- ride. Product quality is dependent on achieving a uni- state approximations because of computational limita- form growth rate at the crystalline surface. The growth tions on convention computer hardware. This project rate is in turn influenced by a complex combination of uses the supercomputers to benchmark a three-dimen- thermal, fluid, and chemical phenomena. sional, transient PVT model. The overall objective of this research is to examine the asymmetric and unsteady convection patterns that result in the PVT process and determine the influence they

2006 Annual Research Report of the Supercomputing Institute 263 St. Cloud State University

College of Science and Engineering Department of Chemistry Daniel D. Gregory and Mohammad Mahroof-Tahir ...... 265 Department of Computer Science Jie Hu ...... 265

264 2006 Annual Research Report of the Supercomputing Institute St. Cloud State University–Department of Chemistry

Daniel D. Gregory, Principal Investigator Mohammad Mahroof-Tahir, Co-Principal Investigator Development of Insulin Mimetics: Characterization of Vanadium-Flavonoid Complexes Using Density Functional Theory iabetes mellitus is one of the most widespread with solid and solution phase data to help develop a diseases in the world. It is a metabolic as well as more comprehensive relationship of the structure of Dhormonal disorder characterized by relative or vanadium complexes and their biological activity. This absolute lack of insulin. Several vanadium-containing may help achieve the ultimate goal of developing new compounds can serve as insulin mimics in the treatment vanadium-containing compounds that could be used to of diabetes, but it is unknown what electronic or struc- treat diabetes. tural features are important for biological activity. These researchers investigated the chemical structure of several vanadium complexes using density functional theory. The main goal was to develop the three-dimensional structure around the vanadium atom as a function Research Group of ligand structure. All of the ligands are symmetric and Luke Roskop, Undergraduate Student Researcher anti-symmetric flavonoid derivatives. The researchers used results from the computational work in conjunction

St. Cloud State University–Department of Computer Science

Ji Hue, Principal Investigator Parallel Implementation of Self-Organizing Map Algorithms and Independent Component Analysis Algorithms hese researchers used resources of the Supercom- as given by electroencephalogram, feature analysis, and puting Institute for two projects during this peri- image analysis; this means that a faster algorithm for ICA Tod. One project investigated a parallel implemen- becomes important. These researchers implemented such tation of one of the variants of the Self-Organizing Map an algorithm on a parallel machine in order to improve (SOM), Asynchronous Self-Organizing Map, which has its efficiency. proven to be efficient in theory. The goal of this project was to implement the Asynchronous SOM algorithm on a distributed multiple-memory system by using the MPI parallel programming paradigm, to compare the performance with previous experimental results and to further explore the possibility of improving the algorithm. The second project dealt with independent compo- Research Group nent analysis (ICA), which was originally developed to Jing Cheng, Graduate Student Researcher deal with blind signal separation problems. Recent inter- Biao Xu, Graduate Student Researcher est in ICA has resulted in the development of interesting Liqiang Zhang, Graduate Student Researcher applications, such as electrical recordings of brain activity

2006 Annual Research Report of the Supercomputing Institute 265 University of St. Thomas

School of Engineering John P. Abraham, Ephraim M. Sparrow, and Robert M. Sweet ...... 267

266 2006 Annual Research Report of the Supercomputing Institute University of St. Thomas–School of Engineering John P. Abraham, Associate Fellow Ephraim M. Sparrow, Co-Principal Investigator Robert M. Sweet, Co-Principal Investigator Numerical Investigation of Biological Fluid Flow

ccurate numerical simulations of fluid flow in lation. This group has recently partnered with the newly biological system such as arteries, airway passages, formed Simulation Program at the University of Aand the urethra are necessary for understanding a Minnesota Medical School to bridge the two disciplines. number of biological phenomena. Applications include The long-term goal of the project is the creation of virtu- blood-flow simulations that can help predict blood clots, al-reality simulations that will enable medical students to airflow simulations to help develop therapies for sleep practice surgery in a computational environment before apnia, and simulations of bio-fluid in the urethra, which operating on humans. may play a critical role in developing intra-urethral stents. In all these cases, simulating this fluid flow is Research Group complicated by the fact that the walls that bound the Paul Chevalier, Graduate Student Researcher flow passage are not stationary, but rather move as the Dean Hacker, Undergraduate Student Researcher fluid passes through the channels. This interaction Jimmy Tong, Graduate Student Researcher between fluid and the participating boundary is one of Christi Saari, Graduate Student Researcher the most difficult of all simulation problems to solve. Sandra Sparr, Graduate Student Researcher A key feature of this project is the incorporation of Nick Whitehead, Graduate Student Researcher new medical imaging techniques to computational simu-

2006 Annual Research Report of the Supercomputing Institute 267 Index and Bibliography Index and Bibliography

Index of Principal Investigators Abraham, John P...... 267 Clarke, Duncan J...... 95 Abrahamsen, Mitchell S...... 113 Cleary, P. Patrick ...... 217 Aldrich, Courtney ...... 61 Cockburn, Bernardo ...... 195 Amin, Elizabeth A...... 142 Conklin, Kathleen F...... 96 Amirikian, Bagrat ...... 224 Connaire, Jeffrey J...... 208 Anderson, Dwight L...... 246 Connelly, Donald P...... 200 Anderson, James A...... 63 Conner, Sean D...... 96 Anderson, John H...... 230 Conroy, Mark J...... 239 Armitage, Ian M...... 82 Conti-Fine, Bianca M...... 84 Arndt, Roger E. A...... 164 Cornélissen, Germaine G...... 203 Arnold, William A...... 158 Costalonga, Massimo ...... 246 Banaszak, Leonard J...... 83 Cramer, Christopher J...... 144 Barany, George ...... 142 Crouch, Steven L...... 159 Barker, Lucia P...... 44 Crowell, Paul A...... 190 Barocas, Victor H...... 126 Dahlberg, Peter S...... 241 Basak, Subhash C...... 43 Davidson, Jane H...... 180, 184 Behrens, Timothy W...... 207 Davis, Dana ...... 218 Beitz, Alvin J...... 114 Davis, H. Ted ...... 131, 139 Berman, Judith G...... 95 de Forcrand, Philippe ...... 195 Bernardo, Rex N...... 64 Derby, Jeffrey J...... 131 Bernlohr, David ...... 83 Distefano, Mark D...... 145 Bielinsky, Anja-Katrin ...... 84 Dong, Zigang ...... 47 Bitterman, Peter B...... 207 Drayton, Rhonda Franklin ...... 173 Blank, David A...... 143 Drewes, Lester R...... 44 Blazar, Bruce R...... 232 Du, David H...... 167 Bohjanen, Paul R...... 217 Duane, William C...... 208 Bolan, Patrick J...... 240 Dumitrica, Traian ...... 180 Bolander, Mark W...... 257 Dunny, Gary M...... 218 Boley, Daniel L...... 167 Eckstein, Zvi ...... 101 Bradeen, James M...... 68 Efange, S. Mbua Ngale ...... 107 Branton, W. Dale ...... 225 Egeland, Byron R...... 101 Candler, Graham V...... 121 Ekker, Stephen C...... 97 Carr, Robert W...... 129 Elliott, Ryan S...... 121 Chang, Leng Chee ...... 39 Ellis, Lynda B. M...... 201 Chelikowsky, James R...... 130 Elmquist, William F...... 104 Cho, Mimi ...... 200 Erdman, Arthur G...... 181

270 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Index of Principal Investigators (continued) Ericson, Marna E...... 200 Gulliver, John S...... 165 Fahrenkrug, Scott C...... 66 Gupta, Kalpna ...... 209 Fallon, Ann M...... 67 Gute, Brian D...... 43 Fan, David P...... 97 Guzina, Bojan ...... 159 Farrar, Michael A...... 201 Haase, Ashley T...... 219 Fatemi, S. H...... 239 Haglin, David J...... 262 Ferguson, David M...... 108 Haines, Stephen J...... 229 Fohlmeister, Jürgen F...... 238 Hajjar, Jerome F...... 160 Fosdick, Roger L...... 122 Halberg, Franz ...... 203 Foufoula, Efi ...... 164 Hall, Jennifer L...... 210 French, Catherine W...... 162, 163 Halley, J. Woods ...... 192 Fricton, James R...... 247 Hanany, Shaul ...... 193 Frisbie, C. Daniel ...... 132 Harel, Noam ...... 240 Gaffney, Patrick M...... 209 Harjani, Ramesh ...... 174 Gantt, J. Stephen ...... 77 Harris, Lester F...... 241 Ganz, Eric D...... 190 Hays, Thomas S...... 98 Gao, Jiali ...... 146, 147, 154 He, Bin ...... 127 Garrick, Sean C...... 181 He, Tian ...... 168 Garvin, David F...... 64 Hebbel, Robert P...... 210 Gibson, Susan I...... 77 Heberlein, Joachim V...... 183 Girshick, Steven L...... 182 Hecht, Stephen S...... 203 Gladfelter, Wayne L...... 147 Hejhal, Dennis A...... 196 Glazebrook, Jane ...... 78 Hendrickson, Eric A...... 85 Gleason, William B...... 202 Henry, Pierre-Gilles ...... 240 Goldstein, Richard J...... 182 Hering, Bernhard J...... 242 Gomez, Christopher M...... 223 Hertz, Marshall I...... 212 Gopalakrishnan, Raj ...... 247 Herzberg, Mark C...... 248 Gopinath, Anand ...... 173 Hiller, John R...... 42 Gottesman, Jon ...... 225 Hillmyer, Marc A...... 148 Goyal, Arun ...... 43 Hintz, Norton M...... 193 Grambsch, Patricia M...... 250 Hondzo, Miki ...... 165 Grant, David J. W...... 112 Hooper, Alan B...... 86 Gregory, Daniel D...... 265 Howe, Charles L...... 257 Griffin, Timothy J...... 85 Hoye, Thomas R...... 148 Grosberg, Alexander Y...... 191 Hozalski, Raymond M...... 160 Gross, Myron D...... 202 Hu, Jie ...... 265

2006 Annual Research Report of the Supercomputing Institute 271 Index and Bibliography

Index of Principal Investigators (continued) Hu, Wei-Shou ...... 133 Kistler, H. Corby ...... 68 Iaizzo, Paul A...... 242 Ko, Ching-Chang ...... 248 Ingulli, Elizabeth G...... 232 Koeneman, Kenneth S...... 244 Israni, Ajay ...... 211 Kortshagen, Uwe R...... 183 Jacobs, Heiko O...... 174 Koyano, Naoko ...... 226 James, Ashley ...... 122 Kren, Betsy J...... 215 James, Richard D...... 196 Kroll, Daniel M...... 105 Jansa, Sharon A...... 74 Kullo, Iftikhar J...... 250 Jenkins, Marc K...... 219 Kumar, Satish ...... 134 Ji, Yinduo ...... 114 Kumar, Vipin ...... 169 Johnson, Paul E...... 119 Kuwata, Keith T...... 254 Johnson, Rodney L...... 108 Lanyon, Scott M...... 74 Johnson, Russell C...... 220 Largaespada, David A...... 98 Jones, Thomas W...... 125 Lefebvre, Paul A...... 79 Joseph, Daniel D...... 123 Leo, Perry H...... 124 Juhn, Steven K...... 231 Leopold, Doreen G...... 149 Kalyuzhny, Alexander E...... 226 Leopold, Kenneth R...... 150 Kanjilal, Sagarika ...... 211 Lewis, Jack L...... 230 Kannan, Mathur S...... 115 Li, Na ...... 250 Kapur, Vivek ...... 211, 221 Li, Perry Y...... 184 Karim, Christine B...... 86 Li, Tongbin ...... 227 Karypis, George ...... 168 Li, William ...... 119 Kashtan, Clifford E...... 233 Lilja, David J...... 175 Kass, Steven R...... 149 Lin, Jizhen ...... 231 Katagiri, Fumiaki ...... 78 Lipscomb, John D...... 88 Kaveh, Mostafa ...... 175 Liu, Jigang ...... 260 Kawatra, Rakesh ...... 262 Live, David ...... 88 Kazlauskas, Romas ...... 87 Ludewig, Paula M...... 237 Kaznessis, Yiannis N...... 134 Luskin, Mitchell B...... 196 Kennedy, William R...... 224 Lysak, Robert L...... 194 Kersey, John H...... 204 Macosko, Chris W...... 135 Khodursky, Arkady ...... 87 Mahesh, Krishnan ...... 125 Kim, Youngki ...... 233 Mahroof-Tahir, Mohammad ...... 265 King, Richard A...... 212 Mann, Kent R...... 150 King, Rollin A...... 254 Mantell, Susan C...... 184 Kiprof, Paul ...... 40 Mantyh, Patrick W...... 249

272 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Index of Principal Investigators (continued) Marasteanu, Mihai ...... 161 Myers, Sandra L...... 247 Mariash, Cary N...... 212 Nachtsheim, Christopher J...... 119 Marks, M. David ...... 79 Nelsestuen, Gary L...... 90 Marple, Virgil A...... 185 Neaton, James D...... 250 Martin, Bruce L...... 82 Nemykin, Viktor N...... 40 Masellis, Anna M...... 213 Ni, Wei-Ming ...... 197 Matsuo, Hiroshi ...... 89 Nick, Teresa A...... 227 Mauer, Michael ...... 233 Nieber, John L...... 72 May, Georgiana ...... 75 Norris, David J...... 137 Maynard, Jennifer A...... 135 Nykanen, Deborah K...... 263 Mayo, Kevin H...... 89 O’Connor, Michael B...... 99 McCall, Brian P...... 118 Odde, David J...... 127 McClurg, Richard B...... 136 Odlyzko, Andrew ...... 197 McCormick, Alon V...... 136 Ohlendorf, Douglas H...... 90 McFadden, Joseph P...... 75 Okazaki, Taichiro ...... 161 McLaughlin, David J...... 80 Orr, Harry T...... 205 McLoon, Seven C...... 226 Othmer, Hans G...... 198 McMurry, Peter H...... 185 Pan, Wei ...... 251 McNeill, Kristopher ...... 151 Pang, Yuan-Ping ...... 256 Mescher, Matthew F...... 204 Pankow, James S...... 252 Michael, Alfred F...... 233 Panoskaltsis-Mortari, Angela ...... 232 Mickelson, James R...... 115 Patterson, Robert P...... 237 Miller, Jeffrey S...... 213 Pedersen, Ted ...... 41 Miller, Michael B...... 252 Pei, Duanqing ...... 235 Miller, Robert F...... 225 Penn, R. Lee ...... 152 Mogilevskaya, Sofia G...... 159 Peterson, Erik J...... 214 Mohan, Ned ...... 176 Peterson, Lisa A...... 251 Moro, Andrea ...... 102 Peterson, Marnie L...... 105, 222 Morse, David C...... 137 Petryk, Anna ...... 247 Moser, Kathy L...... 214 Pfender, Emil ...... 183 Muehlbauer, Gary J...... 64 Phillips, Ronald L...... 65 Murphy, Sharon E...... 60 Porté-Agel, Fernando ...... 165 Murtaugh, Michael P...... 116 Portoghese, Philip S...... 109 Musier-Forsyth, Karin M...... 151 Pui, David Y. H...... 186 Muthyala, Ramaiah ...... 109 Pusey, Anne E...... 76 Myers, Jr., Samuel L...... 120 Raghavakaimal, Sreekumar ...... 256

2006 Annual Research Report of the Supercomputing Institute 273 Index and Bibliography

Index of Principal Investigators (continued) Ramaswamy, Shri ...... 103 Semmens, Michael J...... 162 Ranum, Laura P. W...... 99 Shekhar, Shashi ...... 171 Raynor, Peter C...... 252 Sheppard, Eric S...... 102 Redish, A. David ...... 228 Shield, Carol K...... 163 Regal, Jean F...... 45 Siders, Paul D...... 41 Regal, Ronald R...... 45 Siegel, Ronald A...... 112 Reineccius, Gary A...... 72 Siepmann, J. Ilja ...... 153 Reitich, Fernando L...... 198 Silflow, Carolyn D...... 79 Retzel, Ernest F...... 61 Simha, Narendra K...... 230 Rines, Howard W...... 65 Simon, Terrence W...... 187, 188 Roberts, Jeffrey T...... 147 Sine, Steven M...... 258 Rosenberg, Mark E...... 208 Skinner, Pamela J...... 116 Ross, Julie A...... 234 Skubitz, Keith M...... 215 Rother, Michael A...... 39 Smith, Carl S...... 244 Rougvie, Ann E...... 100 Smith, Kevin P...... 66 Roychowdhury, Jaijeet ...... 176 Somers, David A...... 66 Ruden, P. Paul ...... 177 Song, Charles C. S...... 166 Rudney, Joel D...... 249 Sosonkina, Masha ...... 42 Rutherford, Mark S...... 45 Southern, Peter ...... 222 Saad, Yousef ...... 130, 170 Sparrow, Ephraim M...... 267 Sachs, Jonathan N...... 128 Springer, Nathan M...... 80 Sadowsky, Michael J...... 71 Sreevatsan, Srinand ...... 118 Samac, Deborah A...... 69 Srienc, Friedrich ...... 73 Santosa, Fadil ...... 199 St. Peter, John ...... 106 Sapatnekar, Sachin S...... 177 Stankovich, Marian T...... 154 Sapiro, Guillermo R...... 178 Starr, Patrick J...... 188 Sarkanen, Simo ...... 104 Steer, Clifford J...... 215 Sarkar, Gobinda ...... 257 Stefan, Heinz G...... 166 Scheel, Arnd ...... 199 Steffenson, Brian J...... 69 Schlievert, Patrick M...... 222 Stein, Andreas ...... 154 Schmidt, Lanny D...... 138 Straka, Robert J...... 106 Schmidt-Dannert, Claudia ...... 91 Strykowski, Paul J...... 188 Schultz, Arturo ...... 162 Sturla, Shana J...... 110 Schultz, Leonard S...... 241 Sugita, Shinya ...... 76 Scriven, L.E...... 138, 139 Suryanarayanan, Raj ...... 113 Selleck, Scott B...... 234 Sutherland, David E. R...... 243

274 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Index of Principal Investigators (continued) Sweet, Robert M...... 245, 267 Warren, John Robert ...... 103 Szabo, Les J...... 70 Wei, Li-Na ...... 236 Tam, Patricia E...... 216 Weiblen, George D...... 82 Tamma, Kumar K...... 189 Weiss, Douglas J...... 117 Taton, T. Andrew ...... 155 Weissman, Jon B...... 171 Tawfic, Sherif ...... 205 Wentzcovitch, Renata M...... 141 Taylor, Doris A...... 238 Wessendorf, Martin W...... 228 Tebbe, Patrick A...... 263 Westendorf, Jennifer J...... 60 Thill, Christian A...... 67 Wilcox, George L...... 229 Thomas, David D...... 92 Wilmot, Carrie M...... 94 Tiffin, Peter L...... 81 Wood, W. Gibson ...... 236 Timm, Gerald W...... 245 Xing, Chengguo ...... 111 Towle, Howard C...... 93 Yew, Pen-Chung ...... 172 Tracy, Tim ...... 107 York, Darrin M...... 110, 157 Tretyakova, Natalia ...... 110 Young, Nevin D...... 70 Truhlar, Donald G...... 111, 156 Yuen, David A...... 179 Tsai, Michael ...... 206 Zhang, Zhi-Li ...... 172 Tsapatsis, Michael ...... 140 Zhou, Xiangzheng ...... 235 Vallera, Daniel A...... 243 Zhu, Xiaoyang ...... 158 Valls, Oriol T...... 194 Van Ness, Brian G...... 100 VandenBosch, Kathryn A...... 81 Varghese, Anthony ...... 216 Vaughan, J. Thomas ...... 128 Veglia, Gianluigi ...... 157 Verfaillie, Catherine M...... 62 Vernick, Kenneth D...... 223 Victora, Randall H...... 178 Vince, Robert ...... 62 Voller, Vaughan R...... 163 von Keitz, Marc G...... 73 Wackett, Lawrence P...... 93 Wagner, Carston R...... 111 Walcheck, Bruce K...... 117 Walters, Kylie J...... 94 Wang, Dong ...... 71

2006 Annual Research Report of the Supercomputing Institute 275 Index and Bibliography

Bibliography UMSI Research Reports, January 1, 2004 through April 30, 2006 (arranged alphabetically by field of study)

The list below contains papers, presentations, books, and book chapters that have resulted from research performed using Supercomputing Institute resources. Most UMSI Research Reports are eventually published in peer-reviewed literature. Papers that have already been published show the literature citation. Papers listed only as UMSI reports will, in most cases, be published, but had not been published at the time this bibliography was finalized. Further information of these projects is available from the principal investigators, whose names appear in bold print. Instructions for obtaining copies of UMSI research reports can be found on our Web site: www.msi.umn.edu/cgi-bin/reports/searchv2.html

Some reports are also listed in our Computational Biology (CB) or Virtual Laboratory for Earth and Planetary Materials (VLab) series and are identified with CB or VLab numbers in their citations. See the Web site for additional information.

Aerospace Engineering and Mechanics 2004/10 “Simulations of Laminar Pulsatile Flow Through an Axisymmetric Sudden Expansion,” X. Yang and A. J. James, University of Minnesota Supercomputing Institute Research Report UMSI 2004/10, February 2004. 2004/36 “Modeling the Effect of Shock Unsteadiness in Shock-Wave Turbulent Boundary Layer Interactions,” K. Sinha, K. Mahesh, and G. V. Candler, University of Minnesota Supercomputing Institute Research Report UMSI 2004/36, April 2004. 2004/49 “Detached Eddy Simulation of Supersonic Base Flow With Bleed,” P. Subbareddy and G. V. Candler, AIAA Paper 2004-66, presented at the 42nd AIAA Aerospace Sciences Meeting and Exhibit, Reno, Nevada, January 5–8, 2004. 2004/50 “Numerical Studies of Laser-Induced Energy Deposition for Supersonic Flow Control,” R. Kandala and G. V. Candler, AIAA Journal, 42, p. 2266 (2004). 2004/51 “A Cartesian Grid Method for Simulations of Viscous Flows Around Complex and Moving Solid Objects,” J.-E. Emblemsvåg, R. Suzuki, and G. V. Candler, University of Minnesota Supercomputing Institute Research Report UMSI 2004/51, April 2004. 2004/110 “Study of Trajectories of Jets in Crossflow Using Direct Numerical Simulations,” S. Muppidi and K. Mahesh, University of Minnesota Supercomputing Institute Research Report UMSI 2004/110, July 2004. 2004/141 “A Stokes Theorem for Second Order Tensor Fields and Its Implications in Continuum Mechanics,” R. Fosdick and G. Royer-Carfagni, International Journal of Non-Linear Mechanics, 40, p. 381 (2005).

276 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2004/142 “Chemomechanical Equilibrium of Bars,” M. Buonsanti, R. Fosdick, and G. Royer-Carfagni, University of Minnesota Supercomputing Institute Research Report UMSI 2004/142, August 2004. 2004/143 “Upstream Entrainment in Numerical Simulations of Spatially Evolving Round Jets,” P. C. Babu and K. Mahesh, Physics of Fluids, 16, p. 3699 (2004). 2004/234 “Nonlinear Theory of Self-Similar Crystal Growth and Melting,” S. Li, J. S. Lowengrub, P. H. Leo, and V. Cristini, Journal of Crystal Growth, 267, p. 703 (2004). 2004/235 “Nonlinear Stability Analysis of Self-Similar Crystal Growth: Control of the Mullins-Sekerka Instability,” S. Li, J. S. Lowengrub, P. H. Leo, and V. Cristini, University of Minnesota Supercomputing Institute Research Report UMSI 2004/235, December 2004. 2004/291 “A Surfactant-Conserving Volume-of-Fluid Method for Interfacial Flows With Insoluble Surfactant,” A. J. James and J. Lowengrub, Journal of Computational Physics, 201, p. 685 (2004). 2005/15 “Direct Numerical Simulation of Turbulent Jets in Crossflow,” S. Muppidi and K. Mahesh, University of Minnesota Supercomputing Institute Research Report UMSI 2005/15, February 2005. 2005/55 “Numerical Study of the Steady State Uniform Flow Past a Rotating Cylinder,” J. C. Padrino and D. D. Joseph, University of Minnesota Supercomputing Institute Research Report UMSI 2005/55, May 2005. 2005/56 “Migration of a Sphere in Tube Flow,” B. H. Yang, J. Wang, D. D. Joseph, H. H. Hu, T-W. Pan, and R. Glowinski, University of Minnesota Supercomputing Institute Research Report UMSI 2005/56, May 2005. 2005/81 “Stress Induced Cavitation for the Streaming Motion of a Viscous Liquid Past a Sphere,” J. C. Padrino, D. D. Joseph, T. Funada, and J. Wang, University of Minnesota Supercomputing Institute Research Report UMSI 2005/81, May 2005. 2005/140 “Local and Global Injective Solutions of the Rotationally Symmetric Sphere Problem,” A. R. Aguiar, University of Minnesota Supercomputing Institute Research Report UMSI 2005/140, August 2005. Agronomy and Plant Genetics 2004/182 “Power of In Silico Mapping of Quantitative Trait Loci Via a Mixed-Model Approach in Hybrid Crops,” J. Yu, M. Arbelbide, and R. Bernardo, University of Minnesota Supercomputing Institute Research Report UMSI 2004/182, October 2004 and CB 2004-51. 2005/251 “Quantitative Trait Loci for Multiple Disease Resistance in Wild Barley,” S. J. Yun, L. Gyenis, P. M. Hayes, I. Matus, K. P. Smith, B. J. Steffenson, and G. J. Muehlbauer, Crop Science, 45, p. 2563 (2005) and CB 2005-72. Astronomy 2004/11 “The Extreme-Ultraviolt Emission in the Coma Cluster of Galaxies and the Underlying Source of This Radiation,” S. Bowyer, E. J. Korpela, M. Lampton, and T. W. Jones, The Astrophysical Journal, 605, p. 168 (2004). 2004/111 “3-D Simulations of Turbulent Compressible Stellar Convection,” P. R. Woodward, D. H. Porter, and M. Jacobs, University of Minnesota Supercomputing Institute Research Report UMSI 2004/111, July 2004.

2006 Annual Research Report of the Supercomputing Institute 277 Index and Bibliography

Bibliography (continued) 2004/112 “Obtaining and Predicting Parallel Performance for Explicit Hydrocodes: The PPM Parallel Computing Model,” P. R. Woodward, S. E. Anderson, and D. H. Porter, University of Minnesota Supercomputing Institute Research Report UMSI 2004/112, July 2004. 2004/113 “Three Dimensional Simulation of Convective Motions in Giant Stars,” M. Jacobs, D. Porter, and P. R. Woodward, University of Minnesota Supercomputing Institute Research Report UMSI 2004/113, July 2004. 2004/114 “Initial Experiences With Grid-Based Volume Visualization of Fluid Flow Simulations on PC Clusters,” D. H. Porter, P. R. Woodward, and A. Iyer, University of Minnesota Supercomputing Institute Research Report UMSI 2004/114, July 2004. 2004/115 “Cluster Computing in the SHMOD Framework on the NSF TeraGrid,” P. R. Woodward, S. E. Anderson, D. H. Porter, and A. Iyer, University of Minnesota Supercomputing Institute Research Report UMSI 2004/115, July 2004. 2004/207 “Efficiency of Nonlinear Particle Acceleration at Cosmic Structure Shocks,” H. Kang and T. W. Jones, University of Minnesota Supercomputing Institute Research Report UMSI 2004/207, November 2004. 2004/208 “Kinematics of X-Ray-Emitting Components in Cassiopeia A,” T. DeLaney, L. Rudnick, R. A. Fesen, T. W. Jones, R. Petre, and J. A. Morse, The Astrophysical Journal, 613, p. 343 (2004). 2004/209 “3D Simulations of Radio Galaxy Evolution in Cluster Media,” S. M. O’Neill, P. Shearer, I. L. Tregillis, T. W. Jones, and D. Ryu, University of Minnesota Supercomputing Institute Research Report UMSI 2004/209, November 2004. Accepted for publication, Journal of The Korean Astronomical Society. 2004/210 “Ultra High Energy Cosmic Rays and Clusters,” T. W. Jones, University of Minnesota Supercomputing Institute Research Report UMSI 2004/210, November 2004. Accepted for publication, Journal of The Korean Astronomical Society. 2005/16 “MHD Simulations of Relic Radio Bubbles in Clusters,” T. W. Jones and D. S. De Young, University of Minnesota Supercomputing Institute Research Report UMSI 2005/16, February 2005. Accepted for publication, The Astrophysical Journal. 2005/114 “3D Simulations of MHD Jet Propagation Through Uniform and Stratified External Environments,” S. M. O’Neill, I. L. Tregillis, T. W. Jones, and D. Ryu, University of Minnesota Supercomputing Institute Research Report UMSI 2005/114, August 2005. Accepted for publication, The Astrophysical Journal. 2005/145 “An Efficient Numerical Scheme for Simulating Particle Acceleration in Evolving Cosmic-Ray Modified Shocks,” T. W. Jones and H. Kang, Astroparticle Physics, 24, p. 75 (2005). 2006/21 “Numerical Studies of Diffusive Shock Acceleration at Spherical Shocks,” H. Kang and T. W. Jones, University of Minnesota Supercomputing Institute Research Report UMSI 2006/21, March 2006. Bio-based Products 2005/190 “Towards a Mechanism for Macromolecular Lignin Replication,” S. Sarkanen and Y.-R. Chen, 59th Appita Proceedings, 2, p. 407 (2005) and CB 2005-52. Biochemistry, Molecular Biology and Biophysics 2004/13 “Acylation of SC4 Dodecapeptide Increases Bactericidal Potency Against Gram-Positive Bacteria, Including Drug-Resistant Strains,” N. A. Lockwood, J. R. Haseman, M. V. Tirrell, and K. H. Mayo, Biochemical Journal, 378, p. 93 (2004) and CB 2004-2.

278 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2004/27 “Specificity Determinants for Lipids Bound to β-Barrel Proteins,” A. J. Reese and L. J. Banaszak, Journal of Lipid Research, 45, p. 232 (2004) and CB 2004-5. 2004/28 “Multi-Conformational States in Phosphoglycerate Dehydrogenase,” J. K. Bell, G. A. Grant, and L. J. Banaszak, Biochemistry, 43, p. 3450 (2004) and CB 2004-6. 2004/236 “Aqueous Sample in an EPR Cavity: Sensitivity Considerations,” Y. E. Nesmelov, A. Gopinath, and D. D. Thomas, Journal of Magnetic Resonance, 167, p. 138 (2004). 2004/247 “Letter to the Editor: Chemical Shift Assignments of the (Poly)ubiquitin-Binding Region of the Proteasome Subunit S5a,” Q. Wang and K. J. Walters, Journal of Biomolecular NMR, 30, p. 231 (2004) and CB 2004-67. 2004/248 “Ubiquitin Family Proteins and Their Relationship to the Proteasome: A Structural Perspective,” K. J. Walters, A. M. Goh, Q. Wang, G. Wagner, and P. M. Howley, Biochimica et Biophysica Acta, 1695, p. 73 (2004) and CB 2004-68. 2004/262 “Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3- Dioxygenases,” M. W. Vetting, L. P. Wackett, L. Que, Jr., J. D. Lipscomb, and D. H. Ohlendorf, Journal of Bacteriology, 186, p. 1945 (2004) and CB 2004-74. 2004/290 “Biophysical Analyses of Designed and Selected Mutants of Protocatechuate 3,4-Dioxygenase,” C. K. Brown, M. W. Vetting, C. A. Earhart, and D. H. Ohlendorf, Annual Review of Microbiology, 58, p. 555 (2004) and CB 2004/80. 2005/28 “Phospholamban Pentamer Quaternary Conformation Determined by In-Gel Fluorescence Anisotropy,” S. L. Robia, N. C. Flohr, and D. D. Thomas, Biochemistry, 44, p. 4302 (2005) and CB 2005-10. 2005/31 “Structure of S5a Bound to Monoubiquitin Provides a Model for Polyubiquitin Recognition,” Q. Wang, P. Young, and K. J. Walters, University of Minnesota Supercomputing Institute Research Report UMSI 2005/31, April 2005 and CB 2005-12. Publication in press, Journal of Molecular Biology. 2005/39 “Organelle and Translocatable Forms of Glyoxysomal Malate Dehydrogenase—The Effect of the N- Terminal Presequence,” B. Cox, M. M. Chit, T. Weaver, C. Gietl, J. Bailey, E. Bell, and L. Banaszak, FEBS Journal, 272, p. 643 (2005) and CB 2005-13. 2005/69 “Subtilisin-Catalyzed Resolution of N-Acyl Arylsulfinamides,” C. K. Savile, V. P. Magloire, and R. J. Kazlauskas, Journal of the American Chemical Society, 127, p. 2104 (2005) and CB 2005-18. 2005/71 “Molecular Basis of Perhydrolase Activity in Serine Hydrolases,” P. Bernhardt, K. Hult, and R. J. Kazlauskas, Angewandte Chemie International Edition, 44, p. 2 (2005) and CB 2005-19. 2005/89 “Unexpected Subtilisin-Catalyzed Hydrolysis of a Sulfinamide Bond in Preference to a Carboxamide Bond in N-Acyl Sulfinamides,” P. F. Mugford, V. P. Magloire, and R. J.Kazlauskas, Journal of the American Chemical Society, 127, p. 6536 (2005) and CB 2005-23. 2005/152 “Arginase Activity Differs With Allergen in the Effector Phase of Ovalbumin- vs Trimellitic Anhydride- Induced Asthma,” A. L. Greene, M. S. Rutherford, R. R. Regal, G. H. Flickinger, J. A. Hendrickson, C. Giulivi, M. E. Mohrman, D. G. Fraser, and J. F. Regal, University of Minnesota Supercomputing Institute Research Report UMSI 2005/152, September 2005, and CB 2005-37. Accepted for publication, Toxicological Sciences.

2006 Annual Research Report of the Supercomputing Institute 279 Index and Bibliography

Bibliography (continued) 2005/179 “Roles of the Equatorial Tyrosyl Iron Ligand of Protocatechuate 3,4-Dioxygenase in Catalysis,” M. P. Valley, C. K. Brown, D. L. Burk, M. W. Vetting, D. H. Ohlendorf, and J. D. Lipscomb, Biochemistry, 44, p. 11024 (2005) and CB 2005-47. 2005/238 “Structure of the Streptococcal Cell Wall C5a Peptidase,” C. K. Brown, Z.-Y. Gu, Y. V. Matsuka, S. S. Purushothaman, L. A. Winter, P. P. Cleary, S. B. Olmsted, D. H. Ohlendorf, and C. A. Earhart, Proceedings of the National Academy of Sciences, 102, p. 18391 (2005) and CB 2005-67. 2005/239 “Structure of Peptide Sex Pheromone Receptor PrgX and PrgX/pheromone Complexes and Regulation of Conjugation in Enterococcus faecalis,” K. Shi, C. K. Brown, Z.-Y. Gu, B. K. Kozlowicz, G. M. Dunny, D. H. Ohlendorf, and C. A. Earhart, Proceedings of the National Academy of Sciences, 102, p. 18596 (2005) and CB 2005-68. 2005/240 “Structure of Catechol 1,2-dioxygenase From Pseudomonas arvilla,” C. A. Earhart, M. W. Vetting, R. Gosu, I. Michaud-Soret, L. Que Jr., and D. H. Ohlendorf, Biochemical and Biophysical Research Communications, 338, p. 198 (2005) and CB 2005-69. 2005/250 “Directed Evolution of Bacillus Subtilis Lipase A by Use of Enantiomeric Phosphonate Inhibitors: Crystal Structures and Phage Display Selection,” M. J. Dröge, Y. L. Boersma, G. van Pouderoyen, T. E. Vrenken, C. J. Rüggeberg, M. T. Reetz, B. W. Dijkstra, and W. J. Quax, ChemBioChem, 6, p. 1 (2005) and CB 2005/71. 2005/256 “Lipid Metabolism and Adipokine Levels in Fatty Acid-Binding Protein Null and Transgenic Mice,” A. V. Hertzel, L. A. Smith, A. H. Berg, G. W. Cline, G. I. Shulman, P. E. Scherer, and D. A. Bernlohr, American Journal of Physiology–Endocrinology and Metabolism, 290, p. 814 (2005), DOI: 10.1152/ajpen- do.00465.2005 and CB 2005-75. 2006/26 “Manganese-Substituted Carbonic Anhydrase as a New Peroxidase,” K. Okrasa and R. J. Kazlauskas, Chemistry–A European Journal, 12, p. 1587 (2006) and CB 2006-3. 2006/35 “Expression, Purification, Crystallization and Preliminary X-ray Diffraction of a Novel Nitrosomonas europaea Cytochrome, Cytochrome P460,” B. O. Elmore, A. R. Pearson, C. M. Wilmot, and A. B. Hooper, University of Minnesota Supercomputing Institute Research Report UMSI 2006/35, April 2006 and CB 2006-6. Accepted for publication, Acta Crystallographica. Biomedical Engineering 2004/153 “Affine vs. Non-Affine Fibril Kinematics in Collagen Networks: Theoretical Studies of Network Behavior,” P. L. Chandran and V. H. Barocas, University of Minnesota Supercomputing Institute Research Report UMSI 2004/153, September 2004 and CB 2004-43. 2004/154 “Microfluidic Pumping by Non-Reciprocating Motion of a Spherical Particle in a Square Duct: Theoretical Analysis,” D. A. Nordsletten, M. S. Stay, and V. H. Barocas, University of Minnesota Supercomputing Institute Research Report UMSI 2004/154, September 2004. 2005/24 “Deterministic Material-Based Averaging Theory Model of Collagen Gel Micromechanics,” P. L. Chandran and V. H. Barocas, University of Minnesota Supercomputing Institute Research Report UMSI 2005/24, March 2005 and CB 2005-8. 2005/196 “Thin-Film Coupled Fluid-Solid Analysis of Flow Through the Ahmed Glaucoma Drainage Device,” M. S. Stay, T. Pan, J. D. Brown, B. Ziaie, and V. H. Barocas, Journal of Biomechanical Engineering, 127, p. 776 (2005) and CB 2005-57.

280 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2006/39 “A Cortical Potential Imaging Study From Simultaneous Extra- and Intra-Cranial Electrical Recordings by Means of the Finite Element Method,” Y. Zhang, L. Ding, W. van Drongelen, K. Hecox, D. Frim, and B. He, University of Minnesota Supercomputing Institute Research Report UMSI 2006/39, April 2006. Publication in press, NeuroImage. 2006/40 “Estimation of Number of Independent Brain Electric Sources From the Scalp EEGs,” X. Bai and B. He, University of Minnesota Supercomputing Institute Research Report UMSI 2006/40, April 2006. Biostatistics 2004/179 “Comparison of Numerical Algorithms for Bivariate Sequential Tests Based on Marginal Criteria,” Y. Zhao, P. M. Grambsch, and J. D. Neaton, University of Minnesota Supercomputing Institute Research Report UMSI 2004/179, October 2004 and CB 2004-49. Publication in press, Computational Statistics and Data Analysis. 2005/21 “Model Selection For Clustered Recurrent Event Data Using Nested Gamma Frailty Models,” X. Zhi, L. E. Eberly, and P. M. Grambsch, University of Minnesota Supercomputing Institute Research Report UMSI 2005/21, February 2005 and CB 2005-6. 2005/254 “A Population Association Study of Angiotensinogen Polymorphisms and Haplotypes With Left Ventrical Phenotypes,” L. J. Rasmussen-Torvik, K. E. North, C. C. Gu, C. E. Lewis, J. B. Wilk, A. Chakravarti, Y.-P. C. Chang, M. B. Miller, N. Li, R. B. Devereux, and D. K. Arnett, Hypertension, 46, p. 1294 (2005) and CB 2005-73. Cancer Center 2004/244 “Molecular Modelling of CYP2A Enzymes: Application to Metabolism of the Tobacco-Specific Nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK),” J. R. Jalas, M. Seetharaman, S. S. Hecht, and S. E. Murphy, Xenobiotica, 34, p. 515 (2004) and CB 2004-66. Center for Drug Design 2005/232 “Rationally Designed Nucleoside Antibiotics That Inhibit Siderophore Biosynthesis of Mycobacterium tuberculosis,” R. V. Somu, H. Boshoff, C. Qiao, E. M. Bennett, C. E. Barry III, and C. C. Aldrich, Journal of Medicinal Chemistry, ASAP Article (2005) and CB 2005-63. Chemical Engineering and Materials Science 2004/17 “Crystal Growth: Crystal Growth, Bulk (Theory and Models),” J. J. Derby, University of Minnesota Supercomputing Institute Research Report UMSI 2004/17, February 2004. 2004/18 “Modeling of Crystal Growth Processes,” J. J. Derby and A. Yeckel, presented at ISSCG-12, The Twelfth International Summer School on Crystal Growth, Berlin, Germany, August 1–7, 2004. Published in Proceedings (Elsevier Science B.V., 2004). 2004/19 “Feasibility Study of Cadmium Zinc Telluride Growth Using a Submerged Heater in a Vertical Bridgman System,” A. Yeckel and J. J. Derby, Journal of Electronic Materials, 33, p. 488 (2004). 2004/20 “Quantum Confinement in Phosphorus-Doped Silicon Nanocrystals,” D. V. Melnikov and J. R. Chelikowsky, Physical Review Letters, 92, art. no. 046802 (2004). 2004/21 “Electronic Structure of Clusters and Nanocrystals,” J. R. Chelikowsky and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2004/21, February 2004.

2006 Annual Research Report of the Supercomputing Institute 281 Index and Bibliography

Bibliography (continued) 2004/22 “Viscosities of Liquid CdTe Near Melting Point From Ab Initio Molecular Dynamics Calculations,” E. Ko, M. M. G. Alemany, and J. R. Chelikowsky, Journal of Chemical Physics, 121, p. 942 (2004). 2004/23 “Modeling Slitting of Magnetic Tapes,” R. H. Andruet, R. F. Cook, and W. R. Qualls, University of Minnesota Supercomputing Institute Research Report UMSI 2004/23, February 2004.

2004/37 “Akimotoite to Perovskite Phase Transition in MgSiO3,” R. M. Wentzcovitch, L. Stixrude, B. B. Karki, and B. Kiefer, Geophysical Research Letters, 31, art. no. L10622, DOI: 10.1029/2004-GL019704 (2004). 2004/41 “Computer Modelling of Bulk Crystal Growth,” A. Yeckel and J. J. Derby, in Bulk Crystal Growth of Electronic, Optical, and Optoelectronic Materials, edited by P. Capper (Hoboken, New Jersey: John Wiley and Sons, 2005). 2004/57 “Equation of State and Elasticity of FeSi,” R. Caracas and R. M. Wentzcovitch, Geophysical Research Letters, 31, art. no. L20603, DOI: 10.1029/2004GL0196614 (2004). 2004/62 “Simulation of the N-Terminus of HIV-I Glycoprotein 41000 Fusion Peptide in Micelles,” A. Langham and Y. Kaznessis, University of Minnesota Supercomputing Institute Research Report UMSI 2004/62, April 2004 and CB 2004-16. 2004/63 “Conformational Mapping of the N-Terminal Peptide of HIV-1 gp41 in Lipid Detergent and Aqueous Environments Using 13C-Enhanced Fourier Transform Infrared Spectroscopy,” L. M. Gordon, P. W. Mobley, W. Lee, S. Eskandari, Y. Kaznessis, M. A. Sherman, and A. J. Waring, Protein Science, 13, p. 1012 (2004) and CB 2004-17. 2004/64 “Numerical Simulation of Stochastic Gene Circuits,” H. Salis and Y. Kaznessis, University of Minnesota Supercomputing Institute Research Report UMSI 2004/64, April 2004 and CB 2004-18. 2004/65 “Inferring Gene Regulatory Relationships by Combining Target-Target Pattern Recognition and Regulator-Specific Motif Examination,” H. Wei and Y. Kaznessis, University of Minnesota Supercomputing Institute Research Report UMSI 2004/65, April 2004 and CB 2004-19.

2004/68 “Elasticity of Post-Perovskite MgSiO3,” T. Tsuchiya, J. Tsuchiya, K. Umemoto, and R. M. Wentzcovitch, Geophysical Research Letters, 31, art. no. L14603 (2004) and VLab 2004-1. 2004/76 “Molecular Crystal Global Phase Diagrams: 1. Method of Construction,” J. A. Mettes, J. B. Keith, and R. B. McClurg, Acta Crystallographica Section A, 60, p. 621 (2004) and CB 2004-21. 2004/79 “Non-Linear Reduction for Kinetic Models of Metabolic Reaction Networks,” Z. P. Gerdtzen, P. Daoutidis, and W.-S. Hu, Metabolic Engineering, 6, p. 140 (2004) and CB 2004-23. 2004/82 “A Diffusion-Reaction Model for DNA Microarray Assays,” C. Gadgil, A. Yeckel, J. J. Derby and W.-S. Hu, Journal of Biotechnology, 114, p. 31 (2004) and CB 2004-26. 2004/84 “Large Scale Gene Expression Profiling of Metabolic Shift of Mammalian Cells in Culture,” R. Korke, M. de Leon Gatti, A. L. Y. Lau, J. W. E. Lim, T. K. Seow, M. Ching, M. Chung, W.-S. Hu, Journal of Biotechnology, 107, p. 1 (2004) and CB 2004-28.

2004/88 “Equation of State and Stability of CaSiO3 Under Pressure,” R. Caracas and R. Wentzcovitch, G. D. Price, and J. Brodholt, University of Minnesota Supercomputing Institute Research Report UMSI 2004/88, June 2004. Accepted for publication, Geophysical Research Letters. 2004/92 “Low High Density Transformations in Ice,” K. Umemoto and R. Wentzcovitch, University of Minnesota Supercomputing Institute Research Report UMSI 2004/92, July 2004.

282 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2004/93 “Structural and Vibrational Properties of Ice VIII Under Decompression,” K. Umemoto and R. Wentzcovitch, University of Minnesota Supercomputing Institute Research Report UMSI 2004/93, July 2004.

2004/98 “Phase Transition in MgSiO3 Perovskite in the Earth’s Lower Mantle,” T. Tsuchiya, J. Tsuchiya, K. Umemoto, and R. M. Wentzcovitch, Earth and Planetary Science Letters, 224, p. 241 (2004) and VLab 2004-2. 2004/117 “Analysis of the Growth of Cadmium Zinc Telluride in an Electrodynamic Gradient Freeze Furnace Via a Self-Consistent, Multi-Scale Numerical Model,” A. Pandy, A. Yeckel, M. Reed, C. Szeles, M. Hainke, G. Muller, and J. J. Derby, University of Minnesota Supercomputing Institute Research Report UMSI 2004/117, July 2004. 2004/183 “Brownian Dynamics Algorithm for Bead-Rod Semiflexible Chain With Anisotropic Friction,” A. Montesi, D. C. Morse, and M. Pasquali, University of Minnesota Supercomputing Institute Research Report UMSI 2004/183, October 2004. 2004/205 “Molecular Crystal Global Phase Diagrams,” J. B. Keith, J. A. Mettes, and R. B. McClurg, Crystal Growth and Design, 4, p. 1009 (2004).

2004/211 “Co1-xFexS2: A Tunable Source of Highly Spin-Polarized Electrons,” L. Wang, K. Umemoto, R. M. Wentzcovitch, T. Y. Chen, C. L. Chien, J. G. Checkelsky, J. C. Eckert, E. D. Dahlberg, and C. Leighton, University of Minnesota Supercomputing Institute Research Report UMSI 2004/211, November 2004. 2004/212 “Multi-Disciplinary Impact of the Deep Mantle Post-Perovskite Phase Transition,” T. Lay, D. Heinz, M. Ishii, S.-H. Shim, J. Tsuchiya, T. Tsuchiya, R. Wentzcovitch, and D. Yuen, EOS, Transactions, American Physical Union, 86, p. 1 (2005) and VLab 2004-5. 2004/214 “On the Validity of Boundary Layer Analysis for Flow and Mass Transfer Caused by Rotation During the Solution Growth of Large, Single Crystals,” B. Vartak, A. Yeckel, and J. J. Derby, University of Minnesota Supercomputing Institute Research Report UMSI 2004/214, November 2004. 2004/219 “Theoretical Reinvestigation of the Isostructural Transformation in Ice VIII,” K. Umemoto and R. M. Wentzcovitch, University of Minnesota Supercomputing Institute Research Report UMSI 2004/219, November 2004. Publication in press, Physical Review B. 2004/220 “Time-Dependent, Three-Dimensional Flow and Mass Transport During Solution Growth of Potassium Titanyl Phosphate,” B. Vartak, A. Yeckel, and J. J. Derby, University of Minnesota Supercomputing Institute Research Report UMSI 2004/220, November 2004. 2004/222 “Fixed-Point Convergence of Modular, Steady-State Heat Transfer Models Coupling Multiple Scales and Phenomena for Melt Crystal Growth,” A. Pandy and J. J. Derby, University of Minnesota Supercomputing Institute Research Report UMSI 2004/222, December 2004. 2004/224 “Introduction to Organic Thin Film Transistors and Design of n-Channel Organic Semiconductors,” C. R. Newman, C. D. Frisbie, D. A. da Silva Filho, J.-L. Brédas, P. C. Ewbank, and K. R. Mann, Chemical Materials, 16, p. 4436 (2004). 2004/281 “Simulation of Ordered Packed Beds in Chromatography,” M. R. Schure, R. S. Maier, D. M. Kroll, and H. T. Davis, Journal of Chromatography A, 1031, p. 79 (2004).

2006 Annual Research Report of the Supercomputing Institute 283 Index and Bibliography

Bibliography (continued) 2004/285 “Convective Heat and Mass Transport in Novel Bridgman Configurations for Cadmium Zinc Telluride Growth,” A. Yeckel and J. J. Derby, presented at XXI ICTAM, Warsaw, Poland, August 15–21, 2004. 2004/286 “The Feedback Control of the Vertical Bridgman Crystal Growth Process by Crucible Rotation: Two Case Studies,” P. Sonda, A. Yeckel, J. J. Derby, and P. Daoutidis, Computers and Chemical Engineering, 29, p. 887 (2004). 2004/287 “Analysis of Flow-Induced, Step-Bunching Instabilities During the Growth of Crystals From Liquid Solutions,” B. Dai, Y.-I. Kwon, and J. J. Derby, presented at XXI ICTAM, Warsaw, Poland, August 15- 21, 2004. 2004/288 “Experimental and Numerical Analysis of Coupled Interfacial Kinetics and Heat Transport During the Axial Heat Flux Close to the Phase Interface (AHP) Growth of BGO Single Crystals,” S. V. Bykova, V. D. Golyshev, M. A. Gonik, V. B. Tsvetovsky, V. I. Deshko, A. Ya. Karvatskii, A.V. Lenkin, S. Brandon, O. Weinstein, A. Virozub, J. J. Derby, A. Yeckel, P. Sonda, Journal of Crystal Growth, 266, p. 246 (2004). 2004/289 “A Visualization System for Mineral Elasticity,” B. B. Karki and R. Chennamsetty, Visual Geosciences, Springer-Verlag, ISSN 1610-2924, November 2004 and VLab 2004-11. 2004/292 “Electronic Structure and Spin Polarization of MnGaP,” L. Kronik, M. Jain, and J. R. Chelikowsky, Applied Physics Letters, 85, p. 2014 (2004). 2004/293 “Ab Initio Calculations for the Photoelectron Spectra of Vanadium Clusters,” S. Li, M. M. G. Alemany, and J. R. Chelikowsky, Journal of Chemical Physics, 121, p. 5893 (2004). 2005/12 “Accurate Hybrid Stochastic Simulation of a System of Coupled Chemical or Biochemical Reactions,” H. Salis and Y. Kaznessis, Journal of Chemical Physics, 122, art. no. 054103 (2005) and CB 2005-2. 2005/13 “Protegrin Structure-Activity Relationships: Using Homology Models of Synthetic Sequences to Determine Structural Characteristics Important for Activity,” N. Ostberg and Y. Kaznessis, Peptides, 26, p. 197 (2005) and CB 2005-3. 2005/27 “The Orthorhombic Fddd Network in Triblock and Diblock Copolymer Melts,” C. A. Tyler and D. C. Morse, University of Minnesota Supercomputing Institute Research Report UMSI 2005/27, March 2005. 2005/29 “Computing Charge Densities With Partially Reorthogonalized Lanczos,” C. Bekas, Y. Saad, M. L. Tiago, and J. R. Chelikowsky, University of Minnesota Supercomputing Institute Research Report UMSI 2005/29, April 2005. 2005/44 “Physicochemical and Residue Conservation Calculations to Improve the Ranking of Protein-Protein Docking Solutions,” Y. Duan, B. V. B. Reddy, and Y. N. Kaznessis, Protein Science, 14, p. 316 (2005) and CB 2005-16. 2005/45 “Molecular Dynamics Simulations of Helical Antimicrobial Peptides in SDS Micelles: What Do Point Mutations Achieve?,” H. Khandelia and Y. N. Kaznessis, University of Minnesota Supercomputing Institute Research Report UMSI 2005/45, April 2005 and CB 2005-17. 2005/60 “Spherical-Tip Indentation of Viscoelastic Material,” L. Cheng, X. Xia, L. E. Scriven, and W. W. Gerberich, Mechanics of Materials, 37, p. 213 (2005).

2005/76 “Ab Initio Simulations of Non-Stoichiometric CdxTe1-x Liquids,” E. Ko, M. Alemany, J. J. Derby, and J. R. Chelikowsky, University of Minnesota Supercomputing Institute Research Report UMSI 2005/76, May 2005.

284 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2005/85 “Suppression of Flow Oscillations in a Vertical Bridgman Crystal Growth System,” P. Sonda, A. Yeckel, J. J. Derby, and P. Daoutidis, University of Minnesota Supercomputing Institute Research Report UMSI 2005/85, May 2005. 2005/96 “Efficient Computation of the Coupling Matrix in Time-Dependent Density Functional Theory,” E. Lorin de la Grandmaison, S. B. Gowda, Y. Saad, M. L. Tiago, and J. R. Chelikowsky, University of Minnesota Supercomputing Institute Research Report UMSI 2005/96, June 2005. 2005/106 “Lubrication Flow Between a Cavity and a Flexible Wall,” X. Yin and S. Kumar, Physics of Fluids, 17, art. no. 063101 (2005). 2005/118 “Developing Quantitative, Multi-Scale Models For Microgravity Crystal Growth,” J. J. Derby, Y.-I. Kwon, A. Pandy, P. Sonda, A. Yeckel, T. Jung, and G. Müller, University of Minnesota Supercomputing Institute Research Report UMSI 2005/118, August 2005.

2005/123 “Vibrational and Thermodynamic Properties of MgSiO3 Postperovskite,” J. Tsuchiya, T. Tsuchiya, and R. M. Wentzcovitch, Journal of Geophysical Research, 110, art. no. B02204 (2005) and VLab 2005-8.

2005/124 “CaSiO3 Perovskite at Lower Mantle Pressures,” R. Caracas, R. Wentzcovitch, G. David Price, and J. Brodholt, Geophysical Research Letters, 32, art. no. L06306 (2005) and VLab 2005-9. 2005/125 “Theoretical Study of the Isostructural Transformation in Ice VIII,” K. Umemoto and R. M. Wentzcovitch, Physical Review B, 71, art. no. 012102 (2005) and VLab 2005-10.

2005/129 “Post-Rh2O3(II) Transition and the High P,T Phase Diagram of Alumina,” J. Tsuchiya, T. Tsuchiya, and R. M. Wentzcovitch, University of Minnesota Supercomputing Institute Research Report UMSI 2005/129, August 2005 and VLab 2005-14. Publication in press, Physical Review B.

2005/131 “Transition from the Rh2O3(II)-to-CaIrO3 Structure and the High-Pressure-Temperature Phase Diagram of Alumina,” J. Tsuchiya, T. Tsuchiya, and R. M. Wentzcovitch, Physical Review B, 72, art. no. 020103- 1 (2005) and VLab 2005-17. 2005/132 “A New and Efficient Approach to Time-Dependent Density-Functional Perturbation Theory for Optical Spectroscopy,” B. Walker, A. M. Saitta, R. Gebauer, and S. Baroni, University of Minnesota Supercomputing Institute Research Report UMSI 2005/132, August 2005 and VLab 2005-18.

2005/133 “Theoretical Determination of the Structures of CaSiO3 Perovskites,” R. Caracas and R. Wentzcovitch, University of Minnesota Supercomputing Institute Research Report UMSI 2005/133, August 2005 and VLab 2005-19. 2005/222 “On the Effects of Furnace Gradients on Interface Shape During the Growth of Cadmium Zinc Telluride in EDG Furnaces,” L. Lun, A. Yeckel, M. Reed, C. Szeles, P. Daoutidis, and J. J. Derby, University of Minnesota Supercomputing Institute Research Report UMSI 2005/222, December 2005. 2005/231 “Decreasing Lateral Segregation in Cadmium Zinc Telluride Via Ampoule Tilting During Vertical Bridgman Growth,” L. Lun, A. Yeckel, P. Daoutidis, and J. J. Derby, University of Minnesota Supercomputing Institute Research Report UMSI 2005/231, December 2005. 2005/241 “Size-Dependent Spintronic Properties of Dilute Magnetic Semiconductor Nanocrystals,” X. Huang, A. Makmal, J. R. Chelikowsky, and L. Kronik, Physical Review Letters, 94, art. no. 236801-1 (2005). 2005/242 “Ab Initio Absorption Spectra of Ge Nanocrystals,” G. Nesher, L. Kronik, and J. R. Chelikowsky, Physical Review B, 71, art. no. 035344-1 (2005).

2006 Annual Research Report of the Supercomputing Institute 285 Index and Bibliography

Bibliography (continued) 2005/243 “Surface Passivation Method for Semiconductor Nanostructures,” X. Huang, E. Lindgren, and J. R. Chelikowsky, Physical Review B, 71, art. no. 165328-1 (2005). 2005/244 “Ab Initio Calculations of the Photoelectron Spectra of Transition Metal Clusters,” S. Li, M. M. G. Alemany, and J. R. Chelikowsky, Physical Review B, 71, art. no. 165433-1 (2005). 2005/245 “Real-Space Pseudopotential Calculations of the Ground-State and Excited-State Properties of the Water Molecule,” M. Lopez del Puerto, M. L. Tiago, I. Vasiliev, and J. R. Chelikowsky, Physical Review A, 72, art. no. 052504-1 (2005). 2005/246 “First-Principles GW-BSE Excitations in Organic Molecules,” M. L. Tiago and J. R. Chelikowsky, Solid State Communications, 136, p. 333 (2005). 2005/252 “Surfactant Effects on Buoyancy-Driven Viscous Interactions of Deformable Drops,” M. A. Rother, A. Z. Zinchenko, and R. H. Davis, University of Minnesota Supercomputing Institute Research Report UMSI 2005/252, April 2006. Publication in Press, Colloids and Surfaces A. 2006/22 “Mass Transfer Limitations at Crystallizing Interfaces in an Atomic Force Microscopy Fluid Cell: A Finite Element Analysis,” D. Gasperino, A. Yeckel, B. K. Olmsted, M. D. Ward, and J. J. Derby, University of Minnesota Supercomputing Institute Research Report UMSI 2006/22, March 2006. Submitted to Langmuir. 2006/31 “Instability of Creeping Flow Past a Deformable Wall: The Role of Depth-Dependent Modulus,” V. Gkanis and S. Kumar, Physical Review E, 73, art. no. 026307 (2006). 2006/37 “The Fraction Contributions of Elementary Modes to the Metabolism of Escherichia coli and Their Estimation From Raction Entropies,” A. P. Wlaschin, C. T. Trinh, R. Carlson, and F. Srienc, University of Minnesota Supercomputing Institute Research Report UMSI 2006/37, April 2006, and CB 2006-7. Chemistry 2004/3 “Pseudorotation of Natural and Chemically Modified Biological Phosphoranes: Implications for RNA Catalysis,” C. Silva López, O. Nieto Faza, B. A. Gregersen, X. Lopez, A. R. de Lera, and D. M. York, ChemPhysChem, 5, p. 1266 (2004) and CB 2004-1. 2004/4 “Theoretical Study of the Vinyl Allene Oxide to Cyclopent-2-en-1-one Rearrangement: Mechanism, Torquoselectivity, and Solvent Effects,” C. Silva López, O. Nieto Faza, D. M. York, and A. R. de Lera, Journal of Organic Chemistry, 69, p. 3635 (2004). 2004/52 “Many-Body Force Field Models Based Solely on Pairwise Coulomb Screening Do Not Simultaneously Reproduce Correct Gas-Phase and Condensed-Phase Polarizability Limits,” T. J. Giese and D. M. York, Journal of Chemical Physics, 21, p. 9903 (2004). 2004/53 “Structure and Binding of Mg(II) Ions and Di-Metal Bridge Complexes With Biological Phosphates and Phosphoranes,” E. Mayaan, K. Range, and D. M. York, Journal of Biological Inorganic Chemistry, 9, p. 807 (2004) and CB 2004-11. 2004/54 “A Smooth Solvation Method for d-Orbital Semiempirical Calculations of Biological Reactions: Application to RNA Transphosphorylation,” J. Khandogin, B. A. Gregersen, W. Thiel, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2004/54, April 2004 and CB 2004-12.

286 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2004/55 “Hybrid QM/MM Study of Thio Effects in Transphosphorylation Reactions: The Role of Solvation,” B. A. Gregersen, X. Lopez, and D. M. York, Journal of the American Chemical Society, 125, p. 7504 (2004) and CB 2004-13. 2004/56 “Variational Transition State Theory and Multidimensional Tunneling for Simple and Complex Reactions in the Gas Phase, Solids, Liquids, and Enzymes,” D. G. Truhlar, University of Minnesota Supercomputing Institute Research Report UMSI 2004/56, April 2004 and CB 2004-14. To be published as a chapter in Isotope Effects in Chemistry and Biology, edited by H. Limbach and A. Kohen (New York: Marcel Dekker, Inc., 2005). 2004/58 “Ensemble-Averaged Variational Transition State Theory With Optimized Multidimensional Tunneling for Enzyme Kinetics and Other Condensed-Phase Reactions,” D. G. Truhlar, J. Gao, M. Garcia-Viloca, C. Alhambra, J. Corchado, M. Luz Sanchez, and T. D. Poulsen, International Journal of Quantum Chemistry, 100, p. 1136 (2004) and CB 2004-15. 2004/67 “Pyridylpyrrolides as Alternatives to Cyclometalated Phenylpyridine Ligands: Synthesis and Characterization of Luminescent Zinc and Boron Pyridylpyrrolide Complexes,” J. J. Klappa, S. A. Geers, S. J. Schmidtke, L. A. MacManus-Spencer, and K. McNeill, Dalton Transactions, 2004, p. 833 (2004) and CB 2004-20. 2004/70 “Simulation Studies on the Effects of Mobile-Phase Modification on Partitioning in Liquid Chromatography,” C. D. Wick, J. I. Siepmann, and M. R. Schure, Analytical Chemistry, 76, p. 2886 (2004). 2004/71 “Binary Phase Behavior and Aggregation of Dilute Methanol in Supercritical Carbon Dioxide: A Monte Carlo Simulation Study,” J. M. Stubbs and J. I. Siepmann, Journal of Chemical Physics, 121, p. 1525 (2004). 2004/101 “Time Resolved Direct Probing of the Change in the Local Solvent Response Following Excitation of a Solute,” D. F. Underwood and D. A. Blank, University of Minnesota Supercomputing Institute Research Report UMSI 2004/101, July 2004. 2004/116 “Balancing Reactor Fluid Dynamics and Deposition Kinetics to Achieve Compositional Variation in Combinatorial Chemical Vapor Depositions,” B. Xia, R. C. Smith, T. L. Moersch, and W. L. Gladfelter, Applied Surface Science, 223, p. 14 (2004). 2004/121 “Molecular Modeling of Environmentally Important Processes: Reduction Potentials,” A. Lewis, J. A. Bumpus, D. G. Truhlar, and C. J. Cramer, Journal of Chemical Education, 81, p. 596 (2004). 2004/122 “Small Basis Sets for Calculations of Barrier Heights, Energies of Reaction, Electron Affinities, Geometries, and Dipole Moments,” B. J. Lynch and D. G. Truhlar, Theoretical Chemistry Accounts, 111, p. 335 (2004). 2004/123 “Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree-Fock Wave Functions With Molecular Mechanics,” J. Pu, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry A, 108, p. 632 (2004). 2004/124 “Benchmark Results for Hydrogen Atom Transfer Between Carbon Centers and Validation of Electronic Structure Methods for Bond Energies and Barrier Heights,” A. Dybala-Defratyka, P. Paneth, J. Pu, and D. G. Truhlar, Journal of Physical Chemistry A, 108, p. 2475 (2004). 2004/125 “How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations,” M. Garcia-Viloca, J. Gao, M. Karplus, and D. G. Truhlar, Science, 303, p. 186 (2004) and CB 2004-36.

2006 Annual Research Report of the Supercomputing Institute 287 Index and Bibliography

Bibliography (continued) 2004/126 “Validation of Theoretical Methods for the Structure and Energy of Aluminum Clusters,” N. E. Schultz, G. Staszewska, P. Staszewski, and D. G. Truhlar, Journal of Physical Chemistry B, 108, p. 4850 (2004). 2004/127 “Army Ants Algorithm for Rare Event Sampling of Delocalized Nonadiabatic Transitions by Trajectory Surface Hopping and the Estimation of Sampling Errors by the Bootstrap Method,” S. Nangia, A. W. Jasper, T. F. Miller III, and D. G. Truhlar, Journal of Chemical Physics, 120, p. 3586 (2004). 2004/128 “Calculation of Converged Rovibrational Energies and Partition Function for Methane Using Vibrational-Rotational Configuration Interaction,” A. Chakraborty, D. G. Truhlar, J. M. Bowman, and S. Carter, Journal of Chemical Physics, 121, p. 2071 (2004). 2004/129 “Predicting Adsorption Coefficients at Air-Water Interfaces Using Universal Solvation and Surface Area Models,” C. P. Kelly, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry B, 108, p. 12882 (2004). 2004/130 “Class IV Charge Model for the Self-Consistent Charge Density-Functional Tight-Binding Method,” J. A. Kalinowski, B. Lesyng, J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A, 108, p. 2545 (2004). 2004/131 “Non-Born-Oppenheimer Trajectories With Self-Consistent Decay of Mixing,” C. Zhu, A. W. Jasper, and D. G. Truhlar, Journal of Chemical Physics, 120, p. 5543 (2004). 2004/132 “Tests of Second-Generation and Third-Generation Density Functionals for Thermochemical Kinetics,” Y. Zhao, J. Pu, B. J. Lynch, and D. G. Truhlar, Physical Chemistry Chemical Physics, 6, p. 673 (2004). 2004/133 “Development and Assessment of a New Hybrid Density Functional Model for Thermochemical Kinetics,” Y. Zhao, B. J. Lynch, and D. G. Truhlar, Journal of Physical Chemistry A, 108, p. 2715 (2004). 2004/134 “Efficient Molecular Mechanics for Chemical Reactions: Multiconfiguration Molecular Mechanics Using Partial Electronic Structure Hessians,” H. Lin, J. Pu, T. V. Albu, and D. G. Truhlar, Journal of Physical Chemistry A, 108, p. 4112 (2004). 2004/135 “New Universal Solvation Model and Comparison of the Accuracy of the SM5.42R, SM5.43R, C-PCM, D-PCM, and IEF-PCM Continuum Solvation Models for Aqueous and Organic Solvation Free Energies and for Vapor Pressures,” J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A, 108, p. 6532 (2004). 2004/136 “Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) With Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method,” J. Pu, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry A, 108, p. 5454 (2004). 2004/137 “Doubly Hybrid Meta DFT: New Multi-Coefficient Correlation and Density Functional Methods for Thermochemistry and Thermochemical Kinetics,” Y. Zhao, B. J. Lynch, and D. G. Truhlar, Journal of Physical Chemistry A, 108, p. 4786 (2004). 2004/138 “Analytic Potential Energy Functions for Aluminum Clusters,” A. W. Jasper, P. Staszewski, G. Staszewska, N. E. Schultz, and D. G. Truhlar, Journal of Physical Chemistry B, 108, p. 8996 (2004). 2004/139 “Introductory Lecture: Nonadiabatic Effects in Chemical Dynamics, A,” W. Jasper, C. Zhu, S. Nangia, and D. G. Truhlar, Faraday Discussions, 127, p. 1 (2004).

288 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2004/140 “Hybrid Meta Density Functional Theory Methods for Thermochemistry, Thermochemical Kinetics, and Noncovalent Interactions: The MPW1B95 and MPWB1K Models and Comparative Assessments for Hydrogen Bonding and Van Der Waals Interactions,” Y. Zhao and D. G. Truhlar, Journal of Physical Chemistry A, 108, p. 6908 (2004). 2004/147 “The Magnitude of Hyperconjugation in Ethane: A Perspective From Ab Initio Valence Bond Theory,” Y. Mo, W. Wu, L. Song, M. Lin, Q. Zhang, and J. Gao, Angewandte Chemie International Edition, 43, p. 1986 (2004). 2004/148 “Solvent and Protein Effects on the Vibrational Frequency Shift and Energy Relaxation of the Azide Ligand in Carbonic Anhydrase,” M. Garcia-Viloca, K. Nam, C. Alhambra, and J. Gao, Journal of Physical Chemistry B, 108, p. 13501 (2004) and CB 2004-38. 2004/149 “A QM/MM Study of a Nucleophilic Aromatic Substitution Reaction Catalyzed by 4-chlorobenzoyl- CoA Dehalogenase,” D. Xu, H. Guo, J. Gao, and Q. Cui, Chemical Communications, 7, p. 892 (2004) and CB 2004-39. 2004/150 “A Combined QM/MM Approach to Protein-Ligand Interactions: Polarization Effects of the HIV-1 Protease on Selected High Affinity Inhibitors,” C. Hensen, J. C. Hermann, K. Nam, S. Ma, J. Gao, and H.-D. Holtje, Journal of Medicinal Chemistry, 47, p. 6673 (2004) and CB 2004-40. 2004/151 “Homology Modeling and Molecular Dynamics Simulations of the Mu Opioid Receptor in a Membrane-Aqueous System,” Y. Zhang, Y. Y. Sham, R. Rajamani, J. Gao, and P. S. Portoghese, ChemBioChem, 6, p. 1 (2005) and CB 2004-41. 2004/152 “QM/MM Studies of Enzyme Catalyzed Dechlorination of 4-Chlorobenzoyl-CoA Provide Insight Into Reaction Energetics,” D. Xu, Y. Wei, J. Wu, D. Dunaway-Mariano, H. Guo, Q. Cui, and J. Gao, Journal of the American Chemical Society, 126, p. 13649 (2004) and CB 2004-42. 2004/155 “Following the Solvent Directly During Ultrafast Excited State Proton Transfer,” S. J. Schmidtke, D. F. Underwood, and D. A. Blank, Journal of the American Chemical Society, 126, p. 8620 (2004). 2004/156 “2-(2-Pyridyl)pyrroles: Part I. Structure and Energetics of Pyridylpyrroles, Their Dimers, Complexes and Excited States,” S. J. Schmidtke, L. A. MacManus-Spencer, J. J. Klappa, T. A. Mobley, K. McNeill, and D. A. Blank, Physical Chemistry Chemical Physics, 6, p. 3938 (2004). 2004/157 “2-(2-Pyridyl)pyrroles: Part II. Spectroscopic Investigation of Pyridylpyrrole Alcohol Complexes,” L. A. MacManus-Spencer, S. J. Schmidtke, D. A. Blank, and K. McNeill, Physical Chemistry Chemical Physics, 6, p. 3948 (2004). 2004/161 “Effect of Meta Electron-Donating Groups on the Electronic Structure of Substituted Phenyl Nitrenium Ions,” A. H. Winter, D. E. Falvey, and C. J. Cramer, Journal of the American Chemical Society, 126, p. 9661 (2004). n+ 2004/162 “Mixed Metal Bis(µ-oxo) Complexes with [CuM(µ-O)2] (M = Ni(III) or Pd(II)) Cores,” N. W. Aboelella, J. T. York, A. M. Reynolds, K. Fujita, C. R. Kinsinger, C. J. Cramer, C. G. Riordan, and W. B. Tolman, Chemical Communications, 15, p. 1716 (2004). 2004/163 “Isotactic Polymers With Alternating Lactic Acid and Oxetane Subunits From the Endoentropic Polymerization of a 14-Membered Ring,” D.Zhang, J. Xu, L. Alcazar-Roman, L. Greenman, C. J. Cramer, M. A. Hillmyer, and W. B. Tolman, Macromolecules, 37, p. 5274 (2004).

2006 Annual Research Report of the Supercomputing Institute 289 Index and Bibliography

Bibliography (continued) 2004/164 “298 K Enthalpies of Formation of Monofluorinated Alkanes: Theoretical Predictions for Methyl, Ethyl, Isopropyl and Tert-butyl Fluoride,” B. L. Kormos, J. F. Liebman, and C. J. Cramer, Journal of Physical Organic Chemistry, 17, p. 656 (2004). 2004/165 “Rapid Quantum Mechanical Models for the Computational Estimation of C-H Bond Dissociation Energies as a Measure of Metabolic Stability,” J. L. Lewin and C. J. Cramer, Molecular Pharmaceutics, 1, p. 128 (2004) and CB 2004-44. 2004/166 “Computation of Equilibrium Oxidation and Reduction Potentials for Reversible and Dissociative Electron-Transfer Reactions in Solution,” P. Winget, C. J. Cramer, and D. G. Truhlar, Theoretical Chemistry Accounts, 112, p. 217 (2004). 2004/167 “Structural and Dynamic Variations in DNA Hexamers Containing T-T and F-F Single and Tandem Internal Mispairs,” E. C. Sherer and C. J. Cramer, Theoretical Chemistry Accounts, 111, p. 311 (2004) and CB 2004-45. 2004/172 “Lithiated Hydrocarbons, Their Conjugate Bases, and Corresponding Radicals: A Computational Study of RLi (R = CH3, CH3CH2, CH2=CH, and HC=C),” L. M. Pratt and S. R. Kass, Journal of Organic Chemistry, 69, p. 2123 (2004). 2004/173 “Pseudorotation Barriers of Biological Oxyphosphorances: A Challenge for Simulations of Ribozyme Catalysis,” C. Silva Lopez, O. Nieto Faza, A. Rodriguez de Lera, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2004/173, October 2004 and CB 2004-46. 2004/174 “Ellipticity: A Convenient Tool to Characterize Electrocyclic Reactions,” C. Silva López, O. Nieto Faza, F. P. Cossío, D. M. York, and A. Rodriguez de Lera, University of Minnesota Supercomputing Institute Research Report UMSI 2004/174, October 2004. 2004/176 “Simulating the Vapour-Liquid Equilibria of Large Cyclic Alkanes,” J.-S. Lee, C. D. Wick, J. M. Stubbs, and J. I. Siepmann, University of Minnesota Supercomputing Institute Research Report UMSI 2004/176, October 2004. Accepted for publication, Molecular Physics. 2004/177 “Transferable Potentials for Phase Equilibria. 6. United-Atom Description for Ethers, Glycols, Ketones, and Aldehydes,” J. M. Stubbs, J. J. Potoff, and J. I. Siepmann, Journal of Physical Chemistry B, 108, p. 17596 (2004). 2004/188 “A Smooth Solvation Method for d-Orbital Semiempirical Calculations of Biological Reactions I: Implementation,” J. Khandogin, B. A. Gregersen, W. Thiel, M. Karplus, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2004/188, October 2004 and CB 2004-55. 2004/189 “A Smooth Solvation Method for d-Orbital Semiempirical Calculations of Biological Reactions II: Application to Phosphoryl Transfer Reactions,” B. A. Gregersen, J. Khandogin, W. Thiel, M. Karplus, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2004/189, October 2004 and CB 2004-56. 2004/190 “Variational Electrostatic Projection (VEP) Methods for Efficient Modeling of the Macromolecular Electrostatic and Solvation Environment in Activated Dynamics Simulations,” B. A. Gregersen and D. M. York, Journal of Physical Chemistry B, 109, p. 536 (2005).

2004/197 “Microwave Observation of H3N-S O3...H2O Using a Concentric, Dual-Injection Nozzle Source,” S. W. Hunt, C. S. Brauer, M. B. Craddock, K. J. Higgins, A. M. Nienow, and K. R. Leopold, Chemical Physics, 305, p. 155 (2004).

290 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2004/227 “New Effective Core Method (Effective Core Potential and Valence Basis Set) for Al Clusters and Nanoparticles and Heteronuclear Al-Containing Molecules,” N. E. Schultz and D. G. Truhlar, Journal of Chemical Theory and Computation, 1, p. 41 (2005). 2004/228 “Coherent Switching with Decay of Mixing: An Improved Treatment of Electronic Coherence for Non- Born-Oppenheimer Trajectories,” C. Zhu, S. Nangia, A. W. Jasper, and D. G. Truhlar, Journal of Chemical Physics, 121, p. 7658 (2004).

2004/229 “Accurate Vibrational-Rotational Partition Functions and Standard-State Free Energy Values for H2O2 From Monte Carlo Path-Integral Calculations,” V. Audette Lynch, S. L. Mielke, and D. G. Truhlar, Journal of Chemical Physics, 121, p. 5148 (2004). 2004/230 “Use of Block Hessians for the Optimization of Molecular Geometries,” J. Pu and D. G. Truhlar, University of Minnesota Supercomputing Institute Research Report UMSI 2004/230, December 2004. Publication in press, Journal of Chemical Theory and Computation. 2004/231 “Multi-Coefficient Extrapolated Density Functional Theory for Thermochemistry and Thermochemical Kinetics,” Y. Zhao, B. J. Lynch, and D. G. Truhlar, Physical Chemistry Chemical Physics, 7, p. 43 (2005). 2004/232 “The 6-31B(d) Basis Set and the BMC-QCISD and BMC-CCSD Multi-Coefficient Correlation Methods,” B. J. Lynch, Y. Zhao, and D. G. Truhlar, Journal of Physical Chemistry A, 109, p. 1643 (2005). 2004/233 “Conical Intersections and Semiclassical Trajectories: Comparison to Accurate Quantum Dynamics and Analyses of the Trajectories,” A. W. Jasper and D. G. Truhlar, Journal of Chemical Physics, 122, p. 44101 (2005). 2004/242 “Sensitivity of Molecular Dynamics Simulations to the Choice of the X-ray Structure Used to Model an Enzymatic Reaction,” M. Garcia-Viloca, T. D. Poulsen, D. G. Truhlar, and J. Gao, Protein Science, 13, p. 2341 (2004) and CB 2004-64.

2004/249 “Modeling the Peroxide/Superoxide Continuum in 1:1 Side-on Adducts of O2 with Cu,” B. F. Gherman and C. J. Cramer, Inorganic Chemistry, 43, p. 7281 (2004). 2004/250 “Interactions of Alkyltin Salts with Biological Dithiols: Dealkylation and Induction of a Regular b-Turn Structure in Peptides,” B. A. Buck, A. Mascioni, C. J. Cramer, and G. Veglia, Journal of the American Chemical Society, 126, p. 14400 (2004) and CB 2004-69. 2004/251 “Dioxygen Activation at a Single Cooper Site: Structure, Bonding, and Mechanism of Formation of 1:1 Cu-02 Adducts,” N. W. Aboelella, S. V. Kryatov, B. F. Gherman, W. W. Brennessel, V. G. Young, Jr., R. Sarangi, E. V. Rybak-Akimova, K. O. Hodgson, B. Hedman, E. I. Solomon, C. J. Cramer, and W. B. Tolman, Journal of the American Chemical Society, 126, p. 16896 (2004) and CB 2004-70. 2004/252 “Correlating Acidities, Electron Affinities, and Bond Dissociation Energies. Measure One, Get All Three!,” A. Fattahi and S. R. Kass, Journal of Organic Chemistry, 69, p. 9176 (2004). 2004/273 “Stability of Carboxonium Ions,” S. R. Miller, S. Krasutsky, and P. Kiprof, Journal of Molecular Structure (Theochem), 674, p. 43 (2004). 2004/283 “Liquid Water From First Principles: Investigation of Different Sampling Approaches,” I-F. W. Kuo, C. J. Mundy, M. J. McGrath, J. I. Siepmann, J. VandeVondele, M. Sprik, J. Hutter, B. Chen, M. L. Klein, F. Mohamed, M. Krack, and M. Parrinello, Journal of Physical Chemistry B, 108, p. 12990 (2004).

2006 Annual Research Report of the Supercomputing Institute 291 Index and Bibliography

Bibliography (continued) 2005/11 “An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations,” K. Nam, J. Gao, and D. M. York, Journal of Chemical Theory and Computation, 1, p. 2 (2005). 2005/20 “Hydrogen Atom Transfers in B12 Enzymes,” R. Banerjee, D. G. Truhlar, A. Dybala-Defratyka, and P. Paneth, University of Minnesota Supercomputing Institute Research Report UMSI 2005/20, February 2005 and CB 2005-5. Publication in press, chapter in Biological Aspects of Hydrogen Transfer, edited by R. Schowen and J. Klinman; Vol. 2 of Handbook of Hydrogen Transfer, edited by R. L. Schowen (Weinheim, Germany: Wiley-VCH, 2005). 2005/22 “Many-Body Tight-Binding Model for Aluminum Nanoparticles,” G. Staszewska, P. Staszewski, N. E. Schultz, and D. G. Truhlar, Physical Review B, 71, art. no. 045423 (2005). 2005/30 “High-Order Discretization Schemes for Biochemical Applications of Boundary Element Solvation and Variational Electrostatic Projection Methods,” B. A. Gregersen and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2005/30, April 2005 and CB 2005-11. Accepted for publication, Journal of Chemical Physics. 2005/33 “Oligomeric Rods of Alkyl- and Hydridogallium Imides,” B. L. Kormos, J. A. Jegier, P. C. Ewbank, U. Pernisz, V. G. Young, Jr., C. J. Cramer, and W. L. Gladfelter, Journal of the American Chemical Society, 127, p. 1493 (2005). 2005/34 “Density-Functional Theory and Hybrid Density-Functional Theory Continuum Solvation Models for Aqueous and Organic Solvents: Universal SM5.43 and SM5.43R Solvation Models for Any Fraction of Hartree-Fock Exchange,” J. D. Thompson, C. J. Cramer, and D. G. Truhlar, Theoretical Chemistry Accounts, 113, p. 107 (2005). 2005/35 “The Enthalpies of Formation of o-, m-, and p-Benzoquinone: Gas-Phase Ion Energetics, Combustion Calorimetry, and Quantum Chemical Computations Combined,” A. Fattahi, S. R. Kass, J. F. Liebman, M. A. R. Matos, M. S. Miranda, and V. M. F. Morais, University of Minnesota Supercomputing Institute Research Report UMSI 2005/35, April 2005. 2005/40 “Potential of Mean Force Calculation for the Proton and Hydride Transfer Reactions Catalyzed by Medium Chain Acyl-CoA Dehydrogenase: The Effect of Mutations on Enzyme Catalysis,” S. Bhattacharyya, S. Ma, D. G. Truhlar, M. T. Stankovich, and J. Gao, University of Minnesota Supercomputing Institute Research Report UMSI 2005/40, April 2005 and CB 2005-14. 2005/48 “The Nature of Iodine Oxygen Bonds in Hypervalent 10-I-3 Iodine Compounds,” P. Kiprof, ARKIVOC, iv, p. 19 (2005). 2005/87 “Measuring the Change in the Intermolecular Raman Spectrum during Dipolar Solvation,” D. F. Underwood and D. A. Blank, Journal of Physical Chemistry A, 109, p. 3295 (2005). 2005/97 “Simulating Vapor–Liquid Nucleation of Water: A Combined Histogram-Reweighting and Aggregation- Volume-Bias Monte Carlo Investigation for Fixed-Charge and Polarizable Models,” B. Chen, J. I. Siepmann, and M. L. Klein, Journal of Physical Chemistry A, 109, p. 1137 (2005). 2005/98 “Pressure Dependence of the Vapor–Liquid–Liquid Phase Behavior in Ternary Mixtures Consisting of n- Alkanes, n-Perfluoroalkanes, and Carbon Dioxide,” L. Zhang and J. I. Siepmann, Journal of Physical Chemistry B, 109, p. 2911 (2005).

292 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2005/99 “Vapor–Liquid and Vapor–Solid Phase Equilibria and United-Atom Benzene Models Near Their Triple Points: The Importance of Quadrupolar Interactions,” X. S. Zhao, B. Chen, S. Karaborni, and J. I. Siepmann, Journal of Physical Chemistry B, 109, p. 5368 (2005). 2005/100 “Elucidating the Vibrational Spectra of Hydrogen-Bonded Aggregates in Solution: Electronic Structure Calculations With Implicit Solvent and First-Principles Molecular Dynamics Simulations With Explicit Solvent for 1-Hexanol in n-Hexane,” J. M. Stubbs and J. I. Siepmann, Journal of American Chemical Society, 127, p. 4722 (2005). 2005/111 “Aspects of Glycosidic Bond Formation in Aqueous Solution: Chemical Bonding and the Role of Water,” J. M. Stubbs and D. Marx, Chemistry–A European Journal, 11, p. 2651 (2005) and CB 2005-30. 2005/115 “Effects of Field Orientation on the Driven Lattice Gas,” P. D. Siders, Journal of Statistical Physics, 119, p. 861 (2005). 2005/116 “A Charge-Scaling Implementation of the Variational Electrostatic Projection Method,” B. A. Gregersen and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2005/116, August 2005. 2005/126 “Improved Density Functionals for Water,” E. E. Dahlke and D. G. Truhlar, Journal of Physical Chemistry B, 109, p. 15677 (2005) and VLab 2005-11. 2005/128 “Simulating Fluid Phase Equilibria of Water From First Principles,” M. J. McGrath, J. I. Siepmann, I-F. W. Kuo, C. J. Mundy, J. VandeVondele, J. Hutter, F. Mohamed, and M. Krack, University of Minnesota Supercomputing Institute Research Report UMSI 2005/128, August 2005 and VLab 2005-13. 2005/134 “Molecular Simulation Study of the Bonded-Phase Structure in Reversed-Phase Liquid Chromatography With Neat Aqueous Solvent,” L. Zhang, L. Sun, J. I. Siepmann, and M. R. Schure, Journal of Chromatography A, 1079, p. 127 (2005). 2005/135 “Toward a Monte Carlo Program for Simulating Vapor-Liquid Phase Equilibria From First Principles,” M. J. McGrath, J. I. Siepmann, I-F. W. Kuo, C. J. Mundy, J. VandeVondele, M. Sprik, J. Hutter, F. Mohamed, M. Krack, and M. Parrinello, Computer Physics Communications, 169, p. 289 (2005). 2005/136 “Temperature Dependence of Hydrogen Bonding: An Investigation of the Retention of Primary and Secondary Alcohols in Gas-Liquid Chromatography,” L. Sun, C. D. Wick, J. I. Siepmann, and M. R. Schure, Journal of Physical Chemistry B, 109, p. 15118 (2005). 2005/141 “Variational Transition State Theory in the Treatment of Hydrogen Transfer Reactions,” D. G. Truhlar and B. C. Garrett, University of Minnesota Supercomputing Institute Research Report UMSI 2005/141, August 2005. To be published in Handbook of Hydrogen Transfer, edited by H. H. Limbach, J. T. Hynes, J. Klinman, and R. L. Schowen (VCH-Wiley). 2005/150 “Experimental Determination of the Heat of Hydrogenation of Phenylcyclobutadiene,” A. Fattahi, L. Lis, and S. R. Kass, Journal of the American Chemical Society, 127, p. 13065 (2005). 2005/151 “Zwitterion-Dianion Complexes and Anion-Anion Clusters with Negative Dissociation Energies,” S. R. Kass, Journal of the American Chemical Society, 127, p. 13098 (2005). 2005/153 “A Semiempirical Quantum Model for Hydrogen Bonded Nucleic Acid Base Pairs,” T. J. Giese, E. C. Sherer, C. J. Cramer, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2005/153, October 2005 and CB 2005-33. Publication in press, Journal of Chemical Theory and Computation.

2006 Annual Research Report of the Supercomputing Institute 293 Index and Bibliography

Bibliography (continued) 2005/154 “Improvement of Semiempirical Response Properties with Charge Dependent Response Density,” T. J. Giese and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2005/154, October 2005. Publication in press, Journal of Chemical Physics. 2005/162 “Kinetic Isotope Effects on Thio-Substituted Biological Phosphoryl Transfer Reactions From Density- Functional Theory,” Y. Liu, X. Lopez, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2005/162, October 2005 and CB 2005-41. 2005/163 “Theoretical Studies of Dissociative Phosphoryl Transfer in Interconversion of Phosphoenolpyruvate to Phosphonopyruvate: Solvent Effects, Thio Effects, and Implications for Enzymatic Reactions,” D. Xu, H. Guo, Y. Liu, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2005/163, October 2005 and CB 2005-42. 2005/164 “The Contribution of Phosphate-Phosphate Repulsions to the Free Energy of DNA Bending,” K. Range, E. Mayaan, L. J. Maher, III, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2005/164, October 2005 and CB 2005-43. 2005/165 “Benchmark Calculations of Proton Affinities and Gas Phase Basicities of Molecules Important in the Study of Biological Phosphoryl Transfer,” K. Range, D. Riccardi, Q. Cui, M. Elstner, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2005/165, October 2005 and CB 2005-44. 2005/166 “Simulations of Phosphoryl Transfer Reactions Using Multi-Scale Quantum Models,” B. A. Gregersen, T. J. Giese, Y. Liu, E. Mayaan, K. Nam, K. Range, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2005/166, October 2005 and CB 2005-45. 2005/167 “Density-Functional Study of the In-Line Mechanism of Methanolysis of Cyclic Phosphate and Thiophosphate Esters in Solution: Insight Into Thio Effects in RNA Transesterification,” Y. Liu, B. A. Gregersen, X. Lopez, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2005/167, October 2005 and CB 2005-46. 2005/168 “Influence of Polydispersity on the Self-Assembly of Diblock Copolymers,” N. A. Lynd and M. A. Hillmyer, Macromolecules, 38, p. 8803 (2005). 2005/172 “Demonstration of Tunable Reactivity for Meta-Benzynes,” J. J. Nash, K. E. Nizzi, A. Adeuya, M. J. Yurkovich, C. J. Cramer, and H. I. Kenttamaa, Journal of the American Chemical Society, 127, p. 5760 (2005).

2005/173 “Kinetics and DFT Studies on the Reaction of Copper(II) Complexes and H2O2,” T. Osako, S. Nagatomo, T. Kitagawa, C. J. Cramer, and S. Itoh, Journal of Biological Inorganic Chemistry, 10, p. 581 (2005). 2005/174 “Quantum Chemical Characterization of the Structural and Energetic Properties of HCN-BF3,” J. A. Phillips and C. J. Cramer, Journal of Chemical Theory and Computation, 1, p. 827 (2005). 2005/175 “Experimental and Theoretical Study of Stabilization of Delocalized Forms of Semibullvalenes and Barbaralanes by Dipolar and Polarizable Solvents. Observation of a Delocalized Structure That Is Lower in Free Energy Than the Localized Form,” M. Seefelder, M. Heubes, H. Quast, W. D. Edwards, J. R. Armantrout, R. Vaughan Williams, C. J. Cramer, A. C. Goren, D. A. Hrovat, and W. Thatcher Borden, Journal of Organic Chemistry, 70, p. 3437 (2005).

294 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2005/176 “The Electronic Spectra of 2-(2’-hydroxybenzoyl)pyrrole and 2-(2’-methoxybenzoyl)pyrrole: A Theoretical Study,” G. Ghigo, M. Ciofalo, L. Gagliardi, G. La Manna, and C. J. Cramer, Journal of Physical Organic Chemistry, 18, p. 1099 (2005). 2005/177 “Accurate Partial Atomic Charges for High-Energy Molecules Using Class IV Charge Models With the MIDI! Basis Set,” C. P. Kelly, C. J. Cramer, and D. G. Truhlar, Theoretical Chemistry Accounts, 113, p. 133 (2005). 2005/181 “Isobaric-Isothermal Monte Carlo Simulations From First Principles: Application to Liquid Water at Ambient Conditions,” M. J. McGrath, J. I. Siepmann, I-F. W. Kuo, C. J. Mundy, J. VandeVondele, J. Hutter, F. Mohamed, and M. Krack, ChemPhysChem, 6, p. 1894 (2005). 2005/183 “Probing Excited-State Dynamics and Intramolecular Proton Transfer in 1-Acylaminoanthraquinones via the Intermolecular Solvent Response,” S. J. Schmidtke, D. F. Underwood, and D. A. Blank, Journal of Physical Chemistry A, 109, p. 7033 (2005) and CB 2005-50. 2005/184 “Gold Nanorods Seed Coaxial, Cylinder-Phase Domains From Block Copolymer Solutions,” C. S. T. Laicer, T. Q. Chastek, T. P. Lodge, and T. A. Taton, University of Minnesota Supercomputing Institute Research Report UMSI 2005/184, October 2005. Publication in press, Journal of the American Chemical Society. 2005/186 “Transferable Potentials for Phase Equilibria. 7. Primary, Secondary, and Tertiary Amines, Nitroalkanes and Nitrobenzene, Nitriles, Amides, Pyridine, and Pyrimidine,” C. D. Wick, J. M. Stubbs, N. Rai, and J. I. Siepmann, Journal of Physical Chemistry B, 109, p. 18974 (2005). 2005/187 “Quantum Chemical and Master Equation Simulations of the Oxidation and Isomerization of Vinoxy Radicals,” K. T. Kuwata, A. S. Hasson, R. V. Dickinson, E. B. Petersen, and L. C. Valin, Journal of Physical Chemistry A, 109, p. 2514 (2005).

2005/193 “Characterization of a 1:1 Cu-02 Adduct Supported by an Anilido Imine Ligand,” A. M. Reynolds, B. F. Gherman, C. J. Cramer, and W. B. Tolman, Inorganic Chemistry, 44, p. 6989 (2005) and CB 2005-54. 2005/194 “Ab Initio Molecular Orbital and Density Functional Studies on the Solvolysis of Sarin and O,S- Dimethyl Methylphosphonothiolate, a VX-like Compound,” J. Seckute, J. L. Menke, R. J. Emnett, E. V. Patterson, and C. J. Cramer, Journal of Organic Chemistry, 70, p. 8649 (2005) and CB 2005-55. 2005/195 “Structures of Nonheme Oxoiron(IV) Complexes from X-ray Crystallography, NMR Spectroscopy, and DFT Calculations,” E. J. Klinker, J. Kaizer, W. W. Brennessel, N. L. Woodrum, C. J. Cramer, and L. Que, Jr., Angewandte Chemie International Edition, 44, p. 3690 (2005) and CB 2005-56.

2005/197 “Microscopic Origins for the Favorable Solvation of Carbonate Ether Copolymers in CO2,” C. D. Wick, J. I. Siepmann, and D. N. Theodorou, Journal of the American Chemical Society, 127, p. 12338 (2005). 2005/198 “Benchmark Calculations of Reaction Energies, Barrier Heights, and Transition-State Geometries for Hydrogen Abstraction From Methanol by a Hydrogen Atom,” J. Pu and D. G. Truhlar, Journal of Physical Chemistry A, 109, p. 773 (2005). 2005/199 “Benchmark Database of Barrier Heights for Heavy Atom Transfer, Nucleophilic Substitution, Association, and Unimolecular Reactions and Its Use to Test Theoretical Methods,” Y. Zhao, N. Gonzalez-Garcia, and D. G. Truhlar, Journal of Physical Chemistry A, 109, p. 2012 (2005).

2006 Annual Research Report of the Supercomputing Institute 295 Index and Bibliography

Bibliography (continued) 2005/200 “Quantum Mechanical Reaction Rate Constants by Vibrational Configuration Interaction: The OH + H2—H2O + H Reaction as a Function of Temperature,” A. Chakraborty and D. G. Truhlar, Proceedings of the National Academy of Sciences, 102, p. 6744 (2005). 2005/201 “Analytic Potential Energy Functions for Simulating Aluminum Nanoparticles,” A. W. Jasper, N. E. Schultz, and D. G. Truhlar, Journal of Physical Chemistry B, 109, p. 3915 (2005). 2005/202 “Temperature Dependence of Carbon-13 Kinetic Isotope Effects of Importance to Global Climate Change,” H. Lin, Y. Zhao, B. A. Ellingson, J. Pu, and D. G. Truhlar, Journal of the American Chemical Society, 127, p. 2830 (2005). 2005/203 “Redistributed Charge and Dipole Schemes for Combined Quantum Mechanical and Molecular Mechanical Calculations,” H. Lin and D. G. Truhlar, Journal of Physical Chemistry A, 109, p. 3991 (2005). 2005/204 “Generalized Hybrid Orbital Method for Combined Quantum Mechanical and Molecular Mechanical Calculations Based on Density Functional Theory and Hybrid Density Functional Theory,” J. Pu, J. Gao, and D. G. Truhlar, ChemPhysChem, 6, p. 1853 (2005). 2005/205 “Benchmark Databases for Nonbonded Interactions and Their Use To Test Density Functional Theory,” Y. Zhao and D. G. Truhlar, Journal of Chemical Theory and Computation, 1, p. 415 (2005). 2005/206 “Small Temperature Dependence of the Kinetic Isotope Effect for the Hydride Transfer Reaction Catalyzed by Escherichia coli Dihydrofolate Reductase,” J. Pu, S. Ma, J. Gao, and D. G. Truhlar, Journal of Physical Chemistry B, 109, p. 8551 (2005) and CB 2005-58. 2005/207 “Dependence of Transition State Structure on Substrate: The Intrinsic C-13 Kinetic Isotope Effect Is Different for Physiological and Slow Substrates of the Ornithine Decarboxylase Reaction Because of Different Hydrogen Bonding Structures,” D. Sicinska, D. G. Truhlar, and P. Paneth, Journal of the American Chemical Society, 127, p. 5414 (2005) and CB 2005-59. 2005/208 “Databases for Transition Element Bonding: Metal-Metal Bond Energies and Bond Lengths and Their Use To Test Hybrid, Hybrid Meta, and Meta Density Functionals and Generalized Gradient Approximations,” N. E. Schultz, Y. Zhao, and D. G. Truhlar, Journal of Physical Chemistry A, 109, p. 4388 (2005). 2005/209 “Design of Density Functionals That Are Broadly Accurate for Thermochemistry, Thermochemical Kinetics, and Nonbonded Interactions,” Y. Zhao and D. G. Truhlar, Journal of Physical Chemistry A, 109, p. 5656 (2005). 2005/210 “Non-Born-Oppenheimer Liouville-von Neumann Dynamics. Evolution of a Subsystem Controlled by Linear and Population-Driven Decay of Mixing With Decoherent and Coherent Switching,” C. Zhu, A. W. Jasper, and D. G. Truhlar, Journal of Chemical Theory and Computation, 1, p. 527 (2005). 2005/211 “Multicoefficient Extrapolated Density Functional Theory Studies of p···p Interactions: The Benzene Dimer,” Y. Zhao and D. G. Truhlar, Journal of Physical Chemistry A, 109, p. 4209 (2005). 2005/212 “Non-Born-Oppenheimer Molecular Dynamics,” A. W. Jasper, S. Nangia, C. Zhu, and D. G. Truhlar, Accounts of Chemical Research, ASAP Article (2005).

296 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2005/213 “High-Precision Quantum Thermochemistry on Nonquasiharmonic Potentials: Converged Path-Integral Free Energies and a Systematically Convergent Family of Generalized Pitzer-Gwinn Approximations,” V. Audette Lynch, S. L. Mielke, and D. G. Truhlar, Journal of Physical Chemistry A, 109, p. 10092 (2005). 2005/214 “How Well Can New-Generation Density Functional Methods Describe Stacking Interactions in Biological Systems,” Yan Zhao and D. G. Truhlar, Physical Chemistry Chemical Physics, 7, p. 2701 (2005) and CB 2005-60. 2005/215 “Infinite-Basis Calculations of Binding Energies for the Hydrogen Bonded and Stacked Tetramers of Formic Acid and Formamide and Their Use for Validation of Hybrid DFT and Ab Initio Methods,” Y. Zhao and D. G. Truhlar, Journal of Physical Chemistry A, 109, p. 6624 (2005). 2005/216 “How Well Can Density Functional Methods Describe Hydrogen Bonds to π Acceptors,” Y. Zhao, O. Tishchenko, and D. G. Truhlar, Journal of Physical Chemistry B, 109, p. 19046 (2005). 2005/217 “A New Algorithm for Efficient Direct Dynamics Calculations of Large-Curvature Tunneling and Its Application to Radical Reactions with 9–15 Atoms,” A. Fernández-Ramos and D. G. Truhlar, Journal of Chemical Theory and Computation, 1, p. 1063 (2005). 2005/218 “Electronic Decoherence Time For Non-Born-Oppenheimer Trajectories,” A. W. Jasper and D. G. Truhlar, Journal of Chemical Physics, 123, art. no. 064103 (2005). 2005/219 “SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters,” C. P. Kelly, C. J. Cramer, and D. G. Truhlar, Journal of Chemical Theory and Computation, 1, p. 1133 (2005). 2005/220 “Density Functionals for Inorganometallic and Organometallic Chemistry,” N. E. Schultz, Y. Zhao, and D. G. Truhlar, University of Minnesota Supercomputing Institute Research Report UMSI 2005/200, November 2005. Accepted for publication, Journal of Physical Chemistry A. 2005/221 “Exchange-Correlation Functional With Broad Accuracy for Metallic and Nonmetallic Compounds, Kinetics, and Noncovalent Interactions,” Y. Zhao, N. E. Schultz, and D. G. Truhlar, Journal of Chemical Physics, 123, art. no. 161103-1 (2005). 2005/224 “Decoherence in Combined Quantum Mechanical and Classical Mechanical Methods for Dynamics as Illustrated for Non-Born-Oppenheimer Trajectories,” D. G. Truhlar, University of Minnesota Supercomputing Institute Research Report UMSI 2005/224, December 2005. Chapter to be published in Quantum Dynamics of Complex Molecular Systems, edited by D. A. Micha and I. Burghardt (Chemical Physics Series of Springer-Verlag). 2005/247 “Variational Transition State Theory,” B. C. Garrett and D. G. Truhlar, in Theory and Applications of Computational Chemistry: The First Forty Years, edited by C. Dykstra et al. (Elsevier, 2005). 2005/248 “Quantum Chemical Characterization of the Structures, Thermochemical Properties, and Singlet-Triplet Splittings of Didehydroquinolinium and Didehydroisoquinolinium Ions,” J. J. Nash, H. I. Kenttämaa, and C. J. Cramer, Journal of Physical Chemistry A, 109, p. 10348 (2005) and CB 2005-70.

2005/249 “How Useful Are Vibrational Frequencies of Isotopomeric O2 Fragments for Assessing Local Symmetry? Some Simple Systems and the Vexing Case of a Galactose Oxidase Model,” C. R. Kinsinger, B. F. Gherman, L. Gagliardi, and C. J. Cramer, Journal of Biological Inorganic Chemistry, 10, p. 778 (2005).

2006 Annual Research Report of the Supercomputing Institute 297 Index and Bibliography

Bibliography (continued) 2005/253 “Quantum Chemical and Master Equation Studies of the Methyl Vinyl Carbonyl Oxides Formed in Isoprene Ozonolysis,” K. T. Kuwata, L. C. Valin, and A. D. Converse, Journal of Physical Chemistry A, 109, p. 10710 (2005). 2 2006/9 “Pseudo-Two-Dimensional Structures (HXYH)3n H6n (XY = GaN, SiC, GeC, SiSi, or GeGe; n = 1-3): Density Functional Characterization of Structures and Energetics,” B. L. Kormos, C. J. Cramer, and W. L. Gladfelter, Journal of Physical Chemistry A, 110, p. 494 (2006). 2006/10 “Large Gas-Solid Structural Differences in Complexes of Haloacetonitriles with Boron Trifluoride,” J. A. Phillips, J. A. Halfen, J. P. Wrass, C. C. Knutson, and C. J. Cramer, Inorganic Chemistry, 45, p. 722 (2006). 2006/11 “Models for Dioxygen Activation by the CuB Site of Dopamine β-Monooxygenase and Peptidylglycine α-Hydroxylating Monooxygenase,” B. F. Gherman, D. E. Heppner, W. B. Tolman, and C. J. Cramer, Journal of Biological Inorganic Chemistry, 11, p. 197 (2006) and CB 2006-1.

2006/12 “Theoretical Models on the Cu2O2 Torture Track: Mechanistic Implications for Oxytyrosinase and Small-Molecule Analogues,” C. J. Cramer, M. Wloch, P. Piecuch, C. Puzzarini, and L. Gagliardi, Journal of Physical Chemistry A, 110, p. 1991 (2006). 2006/13 “Adding Explicit Solvent Molecules to Continuum Solvent Calculations for the Calculation of Aqueous Acid Dissociation Constants,” C. P. Kelly, C. J. Cramer, and D. G. Truhlar, Journal of Physical Chemistry A, 110, p. 2493 (2006). 2006/23 “High-Spin and Low-Spin Iron(II) Complexes With Facially-Coordinated Borohydride Ligands,” M. P. Mehn, S. D. Brown, T. K. Paine, W. W. Brennessel, C. J. Cramer, J. C. Peters, and L. Que, Jr., Dalton Transactions, p. 1347 (2006).

2006/24 “Density Functional Characterization of Methane Metathesis with Cp*2MR (M = Sc, Y, Lu; R = Me, tBuCH2). Structural and Kinetic Consequences of Alkyl Steric Bulk,” N. L. Woodrum and C. J. Cramer, Organometallics, 25, p. 68 (2006). 2006/42 “QCRNA1.0: A Database of Quantum Calculations for RNA Catalysis,” T. J. Giese, B. A. Gregersen, Y. Liu, E. Mayaan, A. Moser, K. Range, O. Nieto Faza, C. Silva Lopez, A. Rodriguez de Lera, G. Schaftenaar, X. Lopez, T.-S. Lee, G. Karypis, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2006/42, April 2006 and CB 2006-11. 2006/43 “CHARMM Force Field Parameters for Simulation of Reactive Intermediates in Native and Thio- Substituted Ribozymes,” E. Mayaan, A. Moser, A. D. Mackerell, Jr., and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2006/43, April 2006 and CB 2006-12. 2006/44 “Nucleophilic Attack on Phosphate Diesters: A Density Functional Study of In-Line Reactivity in Dianionic, Monoanionic, and Neutral Systems,” X. Lopez, A. Dejaegere, F. Leclerc, D. M. York, and M. Karplus, University of Minnesota Supercomputing Institute Research Report UMSI 2006/44, April 2006 and CB 2006-13. 2006/45 “Transesterfication Thio Effects of Phosphate Diesters: Free Energy Barriers, Kinetic and Equilibrium Isotope Effects From Density-Functional Theory,” Y. Liu, B. A. Gregersen, A. Hengge, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2006/45, April 2006 and CB 2006-14.

298 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2006/46 “Multilevel and Density Functional Electronic Structure Calculations of Proton Affinities and Gas-Phase Basicities Involved in Biological Phosphoryl Transfer,” K. Range, C. Silva Lopez, A. Moser, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2006/46, April 2006 and CB 2006-15. 2006/47 “Normal Modes of Redox-Active Tyrosine: Conformation Dependence and Comparison to Experiment,” K. Range, I. Ayala, D. York, and B. A. Barry, University of Minnesota Supercomputing Institute Research Report UMSI 2006/76, April 2006 and CB 2006-16. Civil Engineering 2004/7 “A Scale-Dependent Dynamic Model for Scalar Transport in LES of the Atmospheric Boundary Layer,” F. Porté-Agel, Boundary-Layer Meteorology, 112, p. 81 (2004). 2004/38 “Computational Framework for the BIE Solution to Inverse Scattering Problems in Elastodynamics,” S. Nintcheu Fata, B. B. Guzina, and M. Bonnet, Computational Mechanics, 32, p. 370 (2003). 2004/39 “On the Spectral Analysis of Love Waves.” B. B. Guzina and A. I. Madyarov, University of Minnesota Supercomputing Institute Research Report UMSI 2004/39, April 2004. 2004/40 “A Linear Sampling Method for Near-Field Inverse Problems in Elastodynamics,” S. Nintcheu Fata and B. B. Guzina, Inverse Problems, 20, p. 713 (2004). 2004/94 “Coherent Structures and Subfilter-Scale Dissipation in LES: A Field Study,” M. A. Carper, and F. Porté-Agel, University of Minnesota Supercomputing Institute Research Report UMSI 2004/94, July 2004. 2004/95 “Experimental Investigation of the Turbulent Bubbly Wake in a Ventilated Flow,” M. Wosnik, T. Schauer, and R. E. A. Arndt, University of Minnesota Supercomputing Institute Research Report UMSI 2004/95, July 2004. 2004/97 “Time-Dependent Behavior of Concrete Integral Abutment Bridge,” C. French, C. Shield, and J. Huang, University of Minnesota Supercomputing Institute Research Report UMSI 2004/97, July 2004. 2004/99 “A Subgrid Model for Chemical Transformations in LES of the Atmospheric Boundary Layer,” J.-F. Vinuesa and F. Porté-Agel, University of Minnesota Supercomputing Institute Research Report UMSI 2004/99, July 2004. 2004/100 “Development of Stable Boundary Layer Parameterizations in Numerical Weather Prediction Models: A Scale-Dependent Dynamic LES Modeling Approach,” S. Basu, F. Porté-Agel, and E. Foufoula- Georgiou, University of Minnesota Supercomputing Institute Research Report UMSI 2004/100, July 2004. 2004/102 “Numerical Verification of a Time Domain Direct Boundary Integral Method for a Viscoelastic Plane With Circular Holes and Inclusions,” Y. Huang, S. L. Crouch, and S. G. Mogilevskaya, University of Minnesota Supercomputing Institute Research Report UMSI 2004/102, July 2004. 2004/118 “Effect of Column Stiffener Detailing and Weld Fracture Toughness on the Performance of Welded Moment Connections,” R. J. Dexter, J. F. Hajjar, and D. Lee, presented at the European Convention for Constructional Steelwork, Connections in Steel Construction V: Innovations in Steel Connections, Amsterdam, the Netherlands, June 3–4, 2004.

2006 Annual Research Report of the Supercomputing Institute 299 Index and Bibliography

Bibliography (continued) 2004/170 “On the Vertical Structure of Modeled and Observed Deep Convective Storms: Insights for Precipitation Retrieval and Microphysical Parameterization,” J. L. Smedsmo, E. Foufoula-Georgiou, V. Vuruputur, F. Kong, and K. Droegemeier, University of Minnesota Supercomputing Institute Research Report UMSI 2004/170, October 2004. 2004/193 “A New Metric for Comparing Precipitation Patterns With an Application to Ensemble Forecasts,” V. Venugopal, S. Basu, and E. Foufoula-Georgiou, University of Minnesota Supercomputing Institute Research Report UMSI 2004/193, October 2004. 2004/221 “Indicators of Climate Warming in Water Resources Data from Minnesota,” S. L. Johnson and H. G. Stefan, University of Minnesota Supercomputing Institute Research Report UMSI 2004/221, December 2004. 2004/240 “Revisiting the Local Scaling Hypothesis in Stably Stratified Atmospheric Boundary Layer Turbulence: An Integration of Field and Laboratory Measurements With Large-Eddy Simulations,” S. Basu, F. Porté- Agel, E. Foufoula-Georgiou, and J.-F. Vinuesa, University of Minnesota Supercomputing Institute Research Report UMSI 2004/240, December 2004. 2004/246 “Analysis of the Effects of Vertical Pre-Release Cracks on Prestressed Concrete Bridge Girders,” E. Baran, C. K. Shield, C. E. French, and T. A. Wyffels, PCI Journal, 49 (6), p. 114h (2004). 2004/263 “Generalized Hydraulic Geometry: Insights Based on Fluvial Instability Analysis and a Physical Model,” B. Dodov and E. Foufoula-Georgiou, Water Resources Research, 40, art. no. W12201 (2004). 2004/264 “Generalized Hydraulic Geometry: Derivation Based on a Multiscaling Formalism,” B. Dodov and E. Foufoula-Georgiou, Water Resources Research, 40, art. no. W06302 (2004). 2004/270 “Dependence of Lake Ice Covers on Climatic, Geographic and Bathymetric Variables,” G. Williams, K. L. Layman, and H. G. Stefan, Cold Regions Science and Technology, 40, p. 145 (2004). 2005/1 “Floodplain Morphometry Extraction From a High Resolution Digital Elevation Model: A Simple Algorithm for Regional Analysis Studies,” B. A. Dodov and E. Foufoula-Georgiou, University of Minnesota Supercomputing Institute Research Report UMSI 2005/1, January 2005. 2005/3 “A Dynamic Similarity Subgrid Model for Chemical Transformations in Large Eddy Simulation of the Atmospheric Boundary Layer,” J.-F. Vinuesa and F. Porté-Agel, University of Minnesota Supercomputing Institute Research Report UMSI 2005/3, January 2005. 2005/4 “Scale-Dependent Dynamic Models for LES: Surface Heterogeneity Effects,” R. Stoll and F. Porté-Agel, University of Minnesota Supercomputing Institute Research Report UMSI 2005/4, January 2005. 2005/51 “Sounding of Finite Solid Bodies By Way of Topological Derivative,” B. B. Guzina and M. Bonnet, University of Minnesota Supercomputing Institute Research Report UMSI 2005/51, May 2005. 2005/64 “A Methodology for Merging Multisensor Precipitation Estimates Based on Expectation-Maximization and Scale Recursive Estimation,” R. Gupta, V. Venugopal, and E. Foufoula-Georgiou, University of Minnesota Supercomputing Institute Research Report UMSI 2005/64, May 2005. 2005/84 “Fluvial Processes and Streamflow Variability: Interplay in the Scale-Frequency Continuum and Implications for Scaling,” B. Dodov and E. Foufoula-Georgiou, Water Resources Research, 41, cit. no. W05005, DOI: 10.1029/2004WR003408 (2005).

300 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2005/94 “Solute Transfer Into a Sediment Layer Under a Standing Water Wave: Numerical Solution of the 2-D Advection/Diffusion Equation and Derivation of a 1-D Dispersion Coefficient,” Q. Qian, V. Voller, and H. G. Stefan, University of Minnesota Supercomputing Institute Research Report UMSI 2005/94, June 2005. 2005/147 “Dynamics of Vertical Mixing in a Shallow Lake with Submersed Macrophytes,” W. R. Herb and H. G. Stefan, Water Resources Research, 41, cit. no. W02023 (2005) and CB 2005-35. 2005/148 “Seasonal Growth of Submersed Macrophytes in Lakes: The Effects of Biomass Density and Light Competition,” W. R. Herb and H. G. Stefan, University of Minnesota Supercomputing Institute Research Report UMSI 2005/148, September 2005, and CB 2005-36. Publication in press, Ecological Modelling. 2005/188 “Degradation of Drinking Water Disinfection Byproducts by Synthetic Goethite and Magnetite,” C. L. Chun, R. M. Hozalski, and W. A. Arnold, University of Minnesota Supercomputing Institute Research Report UMSI 2005/188, October 2005. Publication in press, Environmental Science & Technology. Computer Science and Engineering 2004/6 “Computation of Smallest Eigenvalues Using Spectral Schur Complements,” C. Bekas and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2004/6, January 2004. 2004/8 “pARMS: A Package for the Parallel Iterative Solution of General Large Sparse Linear Systems User’s Guide,” Y. Saad and M. Sosonkina, University of Minnesota Supercomputing Institute Research Report UMSI 2004/8, January 2004. 2004/21 “Electronic Structure of Clusters and Nanocrystals,” J. R. Chelikowsky and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2004/21, February 2004. 2004/33 “A Parallel Formulation of the Spatial Auto-Regression Model for Mining Large Geo-Spatial Datasets,” B. M. Kazar, S. Shekhar, D. J. Lilja, and D. Boley, presented at the 7th International Workshop on High Performance and Distributed Mining (HPDM 2004), Orlando, Florida, April 24, 2004. 2004/44 “Crout Versions of ILU Factorization With Pivoting for Sparse Symmetric Matrices,” N. Li and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2004/44, April 2004. 2004/72 “An Experimental Study of Communication Overhead for a Parallel Iterative Linear System Solver in Cluster Environments,” S. Storie and M. Sosonkina, University of Minnesota Supercomputing Institute Research Report UMSI 2004/72, May 2004. 2004/73 “Polynomial Filtering in Latent Semantic Indexing for Information Retrieval,” E. Kokiopoulou and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2004/73, May 2004 and VLab 2005-7. 2004/74 “A Parallel Mulilevel ILU Factorization Based on a Hierarchical Graph Decompostion,” P. Henon and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2004/74, May 2004. 2004/75 “Multilevel Preconditioners Constructed From Inverse-Based ILUs,” M. Bollhofer and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2004/75, May 2004. 2004/77 “SchurRAS: A Restricted Version of the Overlapping Schur Complement Preconditioner,” Z. Li and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2004/77, June 2004.

2006 Annual Research Report of the Supercomputing Institute 301 Index and Bibliography

Bibliography (continued) 2004/146 “Unsupervised Word Sense Discrimination by Clustering Similar Contexts,” A. Purandare and T. Pedersen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/146, August 2004. 2004/213 “PCA and Kernel PCA Using Polynomial Filtering: A Case Study on Face Recognition,” E. Kokiopoulou and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2004/213, November 2004. 2004/215 “Block Krylov-Schur Method for Large Symmetric Eigenvalue Problems,” Y. Zhou and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2004/215, November 2004. 2004/258 “Summary: Efficiently Summarizing Transactions for Clustering,” J. Wang and G. Karypis, University of Minnesota Supercomputing Institute Research Report UMSI 2004/258, April 2005. Accepted for publication, Knowledge and Information Systems. 2004/259 “Multi-Resource Aware Partitioning Algorithms for FPGAs With Heterogeneous Resources,” N. Selvakkumaran, A. Ranjan, S. Raje, and G. Karypis, presented at the 41st Design and Automation Conference (DAC), San Diego, California, June 7–11, 2004. Published in Proceedings. 2004/277 “Support Envelopes: A Technique for Exploring the Structure of Association Patterns,” M. Steinbach, P. N. Tan, and V. Kumar, presented at the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Seattle, Washington, August 22–25, 2004. Published in Proceedings. 2004/278 “Effective Localized Regression for Damage Detection in Large Complex Mechanical Structures,” A. Lazarevic, R. Kanapady, and C. Kamath, presented at the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Seattle, Washington, August 22–25, 2004. Published in Proceedings. 2004/279 “Generalizing the Notion of Support,” M. Steinbach, P.-N. Tan, H. Xiong, and V. Kumar, presented at the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Seattle, Washington, August 22–25, 2004. Published in Proceedings. 2004/280 “Exploiting A Support-Based Upper Bound of Pearsons Correlation Coefficient for Efficiently Identifying Strongly Correlated Pairs,” H. Xiong, S. Shekhar, P.-N. Tan, and V. Kumar, presented at the Tenth ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Seattle, Washington, August 22–25, 2004. Published in Proceedings. 2005/9 “Adapting Distributed Scientific Applications to Run-Time Network Conditions,” M. Sosonkina, University of Minnesota Supercomputing Institute Research Report UMSI 2005/9, February 2005. 2005/25 “Maximizing Semantic Relatedness to Perform Word Sense Disambiguation,” T. Pedersen, S. Banerjee, and S. Patwardhan, University of Minnesota Supercomputing Institute Research Report UMSI 2005/25, March 2005. 2005/29 “Computing Charge Densities With Partially Reorthogonalized Lanczos,” C. Bekas, Y. Saad, M. L. Tiago, and J. R. Chelikowsky, University of Minnesota Supercomputing Institute Research Report UMSI 2005/29, April 2005. 2005/36 “Multi-Objective Hypergraph Partitioning Algorithms for Cut and Maximum Subdomain Degree Minimization,” N. Selvakkumaran and G. Karypis, University of Minnesota Supercomputing Institute Research Report 2005/36, April 2005. Accepted for publication, IEEE Transactions on Computer Aided Design.

302 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2005/37 “Frequent Sub-Structure-Based Approaches for Classifying Chemical Compounds,” M. Deshpande, M. Kuramochi, N. Wale, and G. Karypis, University of Minnesota Supercomputing Institute Research Report 2005/37, April 2005 and CB 2005-32. Accepted for publication, IEEE Transactions on Knowledge and Data Engineering. 2005/38 “Clustering in Life Sciences,” Y. Zhao and G. Karypis, University of Minnesota Supercomputing Institute Research Report 2005/38, April 2005 and CB 2005-22. Accepted for publication, Molecular Biotechnology. 2005/42 “Filtered Conjugate Residual-Type Algorithms With Applications,” Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2005/42, April 2005. 2005/57 “Discovery of Patterns in Earth Science Data Using Data Mining,” P. Zhang, M. Steinbach, V. Kumar, S. Shekhar, P.-N. Tan, S. Klooster, and C. Potter, University of Minnesota Supercomputing Institute Research Report UMSI 2005/57, May 2005. Accepted for publication, New Generation of Data Mining Applications. 2005/67 “Intrusion Detection: A Survey,” A. Lazarevic, V. Kumar, and J. Srivastava, University of Minnesota Supercomputing Institute Research Report UMSI 2005/67, May 2005. 2005/68 “The MINDS—Minnesota Intrusion Detection System,” L. Ertöz, E. Eilertson, A. Lazarevic, P.-N. Tan, V. Kumar, J. Srivastava, and P. Dokas, University of Minnesota Supercomputing Institute Research Report UMSI 2005/68, May 2005. 2005/72 “RBA: An Integrated Framework for Regression Based on Association Rules,” A. Ozgur, P.-N. Tan, and V. Kumar, University of Minnesota Supercomputing Institute Research Report UMSI 2005/72, May 2005. 2005/73 “A Framework for Discovering Co-location Patterns in Data Sets With Extended Spatial Objects,” H. Xiong, S. Shekhar, Y. Huang, V. Kumar, X. Ma, and J. S. Yoo, University of Minnesota Supercomputing Institute Research Report UMSI 2005/73, May 2005. 2005/74 “HICAP: Hierarchical Clustering With Pattern Preservation,” H. Xiong, M. Steinbach, P.-N. Tan, and V. Kumar, University of Minnesota Supercomputing Institute Research Report UMSI 2005/74, May 2005. 2005/80 “Resolving Ambiguities in Biomedical Text With Unsupervised Clustering Approaches,” G. Savova, T. Pedersen, A. Purandare, and A. Kulkarni, University of Minnesota Supercomputing Institute Research Report UMSI 2005/80, May 2005 and CB 2005-21. 2005/82 “An Estimator for the Diagonal of a Matrix,” C. Bekas, E. Kokiopoulou, and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2005/82, May 2005. 2005/96 “Efficient Computation of the Coupling Matrix in Time-Dependent Density Functional Theory,” E. Lorin de la Grandmaison, S. B. Gowda, Y. Saad, M. L. Tiago, and J. R. Chelikowsky, University of Minnesota Supercomputing Institute Research Report UMSI 2005/96, June 2005. 2005/107 “MIQR: A Multilevel Incomplete QR Preconditioner for Large Sparse Least-squares Problems,” N. Li and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2005/107, July 2005. 2005/117 “Polynomial Filtered Lanczos Iterations With Applications in Density Functional Theory,” C. Bekas, E. Kokiopoulou, and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2005/117, August 2005 and VLab 2005-7. 2005/127 “Visualization of 3D Scientific Datasets Based on Interactive Clipping,” G. Khanduja and B. B. Karki, WSCG SHORT Papers, ISBN 80-903100-9-5, p. 33 (2005) and VLab 2005-12.

2006 Annual Research Report of the Supercomputing Institute 303 Index and Bibliography

Bibliography (continued) 2005/137 “Orthogonal Neighborhood Preserving Projections,” Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2005/137, August 2005. 2005/139 “POLSYS_GLP: A Parallel General Linear Product Homotopy Code for Solving Polynomial Systems of Equations,” H.-J. Su, J. M. McCarthy, M. Sosonkina, and L. T. Watson, University of Minnesota Supercomputing Institute Research Report UMSI 2005/139, August 2005. 2005/227 “Efficient Execution of Parallel Electronic Structure Calculations on SMP Clusters,” N. Ustemirov and M. Sosonkina, University of Minnesota Supercomputing Institute Research Report UMSI 2005/227, December 2005. 2005/228 “Parallel Solvers for Flexible Approximation Schemes in Multiparticle Simulation,” M. Sosonkina and I. Tsukerman, University of Minnesota Supercomputing Institute Research Report UMSI 2005/228, December 2005. 2005/229 “Concurrent Execution of Electronic Structure Calculations in SMP Environments,” N. Ustemirov, M. Sosonkina, M. S. Gordon, and M. Schmidt, University of Minnesota Supercomputing Institute Research Report UMSI 2005/229, December 2005. 2005/230 “Component-Based Iterative Methods for Sparse Linear Systems,” J. Jones, M. Sosonkina, and Y. Saad, Concurrency and Computation: Practice and Experience, 9, p. 1 (2005). 2006/15 “Numerical Methods for Electronic Structure Calculations of Materials,” Y. Saad, J. R. Chelikowsky, and S. M. Shontz, University of Minnesota Supercomputing Institute Research Report UMSI 2006/15, March 2006. 2006/16 “Orthogonal Neighborhood Preserving Projections: A Projection-Based Dimensionality Reduction Technique,” E. Kokiopoulou and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2006/16, March 2006. 2006/17 “A Greedy Strategy for Coarse-Grid Selection,” S. MacLachlan and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2006/17, March 2006. 2006/18 “On Correction Equations and Domain Decomposition for Computing Invariant Subspaces,” B. Philippe and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2006/18, March 2006. 2006/19 “Schur Complement Preconditioners for Distributed General Sparse Linear Systems,” Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2006/19, March 2006. 2006/20 “Face Recognition Using OPRA -faces,” E. Kokiopoulou and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2006/20, March 2006. 2006/27 “Acyclic Subgraph Based Descriptor Spaces for Chemical Compound Retrieval and Classification,” N. Wale and G. Karypis, University of Minnesota Supercomputing Institute Research Report UMSI 2006/27, March 2006. 2006/28 “Effective Optimization Algorithms for Fragment-Assembly Based Protein Structure Prediction,” K. W. DeRonne and G. Karypis, University of Minnesota Supercomputing Institute Research Report UMSI 2006/28, April 2006, and CB 2006-4. 2006/29 “Genomic View of Systemic Autoimmunity in MRLlpr Mice,” J. Liu, G. Karypis, K. L. Hippen, A. L. Vegoe, P. Ruiz, G. S. Gilkeson, and T. W. Behrens, Genes and Immunity, 7, p. 156 (2006) and CB 2006-5.

304 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2006/30 “Self-Consistent-Field Calculations Using Chebyshev-Filtered Subspace Iteration,” Y. Zhou, Y. Saad, M. L. Tiago, and J. R. Chelikowsky, University of Minnesota Supercomputing Institute Research Report UMSI 2006/30, April 2006. 2006/32 “A Chebyshev-Davidson Algorithm for Large Symmetric Eigenproblems,” Y. Zhou and Y. Saad, University of Minnesota Supercomputing Institute Research Report UMSI 2006/32, April 2006. 2006/42 “QCRNA1.0: A Database of Quantum Calculations for RNA Catalysis,” T. J. Giese, B. A. Gregersen, Y. Liu, E. Mayaan, A. Moser, K. Range, O. Nieto Faza, C. Silva Lopez, A. Rodriguez de Lera, G. Schaftenaar, X. Lopez, T.-S. Lee, G. Karypis, and D. M. York, University of Minnesota Supercomputing Institute Research Report UMSI 2006/42, April 2006 and CB 2006-11. Ecology, Evolution, and Behavior 2004/78 “Monophyly and Relationships of Wrens (Aves: Troglodytidae): A Congruence Analysis of Heterogenous Mitochondrial and Nuclear DNA Sequence Data,” F. K. Barker, Molecular Phylogenetics and Evolution, 31, p. 486 (2004) and CB 2004-22. 2004/81 “Phylogeny of Muroid Rodents: Relationships Within and Among Major Lineages as Determined by IRBP Gene Sequences,” S. A. Jansa, and M. Weksler, Molecular Phylogenetics and Evolution, 31, p. 256 (2004) and CB 2004-25. 2004/106 “Phylogeny and Diversification of the Largest Avian Radiation,” F. K. Barker, A. Cibois, P. Schikler, J. Feinstein, and J. Cracraft, Proceedings of the National Academy of Sciences, 101, p. 11040 (2004) and CB 2004-33. Diagnostic and Biological Sciences 2005/236 “Streptococci Dominate the Diverse Flora Within Buccal Cells,” J. D. Rudney, R. Chen, and G. Zhang, Journal of Dental Research, 84, p. 1165 (2005) and CB 2005-65. Economics 2004/169 “The Performance of the Pivotal-Voter Model in Small-Scale Elections: Evidence From Texas Liquor Referenda,” S. Coate, M. Conlin, and A. Moro, University of Minnesota Supercomputing Institute Research Report UMSI 2004/169, October 2004. Electrical and Computer Engineering 2004/9 “An Active Data-Aware Cache Consistency Protocol for Highly Scalable Data-Shipping DBMS Architectures,” K. Wu, P.-F. Chuang, and D. J. Lilja, University of Minnesota Supercomputing Institute Research Report UMSI 2004/9, January 2004. 2004/33 “A Parallel Formulation of the Spatial Auto-Regression Model for Mining Large Geo-Spatial Datasets,” B. M. Kazar, S. Shekhar, D. J. Lilja, and D. Boley, presented at the 7th International Workshop on High Performance and Distributed Mining (HPDM 2004), Orlando, Florida, April 24, 2004. 2004/34 “Enhancing the Memory Performance of Embedded Systems With the Flexible Sequential and Random Access Memory,” Y. Chen, K. Ranganathan, A. K. Puthenveetil, V. V. Pai, D. J. Lilja, and K. Bazargan, Lecture Notes in Computer Science, 3189, p. 88 (2004).

2006 Annual Research Report of the Supercomputing Institute 305 Index and Bibliography

Bibliography (continued) 2004/35 “State Pruning for Test Vector Generation for a Multiprocessor Cache Coherence Protocol,” Y. Chen, D. Abts, and D. J. Lilja, University of Minnesota Supercomputing Institute Research Report UMSI 2004/35, March 2004. 2004/69 “Self-Tuning Speculation for Maintaining the Consistency of Client-Cached Data,” K. Wu and D. J. Lilja, University of Minnesota Supercomputing Institute Research Report UMSI 2004/69, April 2004. 2004/108 “State Pruning for Generating Efficient Test Vectors,” Y. Chen, D. Abts, and D. J. Lilja, University of Minnesota Supercomputing Institute Research Report UMSI 2004/108, July 2004. 2004/217 “Characterizing and Comparing Prevailing Simulation Techniques,” J. J. Yi, S. V. Kodakara, R. Sendag, D. J. Lilja, and D. M. Hawkins, University of Minnesota Supercomputing Institute Research Report UMSI 2004/217, November 2004. 2004/236 “Aqueous Sample in an EPR Cavity: Sensitivity Considerations,” Y. E. Nesmelov, A. Gopinath, and D. D. Thomas, Journal of Magnetic Resonance, 167, p. 138 (2004). 2005/2 “The Applicability of Adaptive Control Theory to QoS Design: Limitations and Solutions,” K. Wu, D. J. Lilja, and H. Bai, University of Minnesota Supercomputing Institute Research Report UMSI 2005/2, January 2005. 2005/32 “Fast Computation of the Temperature Distribution in VLSI Chips Using the Discrete Cosine Transform and Table Look-up,” Y. Zhan and S. S. Sapatnekar, presented at the 10th Asia and South Pacific Design Automation Conference, Shanghai, China, January 18–21, 2005. 2005/46 “Exchange Coupled Composite Media for Perpendicular Magnetic Recording,” R. H. Victora and X. Shen, University of Minnesota Supercomputing Institute Research Report UMSI 2005/46, May 2005. 2005/54 “Microarchitecture-Aware Floorplanning Using a Statistical Design of Experiments Approach,” V. Nookala, Y. Chen, D. J. Lilja, and S. S. Sapatnekar, presented at the Design Automation Conference, Anaheim, California, June 13–17, 2005. 2005/138 “Effect of Intra-Granular Exchange on Exchange Coupled Composite Media,” M. Kapoor, X. Shen, and R. Victora, University of Minnesota Supercomputing Institute Research Report UMSI 2005/138, August 2005. 2005/143 “Accurate Statistical Approaches for Generating Representative Workload Compositions,” L. Eeckhout, R. Sundareswara, J. J. Yi, D. J. Lilja, and P. Schrater, presented at the IEEE International Symposium on Workload Characterization (IISWC), October 2005. 2005/169 “Large Scale Micromagnetic Simulation for the Exchange Interaction Between a Polycrystalline Antiferromagnet and a Ferromagnet,” J. Saha and R. H. Victora, University of Minnesota Supercomputing Institute Research Report UMSI 2005/169, October 2005. 2006/3 “Analyzing the Processor Bottlenecks in SPEC CPU 2000,” J. J. Yi, A. Joshi, R. Sendag, L. Eeckhout, and D. J. Lilja, University of Minnesota Supercomputing Institute Research Report UMSI 2006/3, January 2006. 2006/4 “Comparing Simulation Techniques for Microarchitecture-Aware Floorplanning,” V. Nookala, Y. Chen, D. J. Lilja, and S. S. Sapatnekar, University of Minnesota Supercomputing Institute Research Report UMSI 2006/4, January 2006.

306 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2006/6 “Evaluating the Efficacy of Statistical Simulation for Design Space Exploration,” A. Joshi, J. J. Yi, R. H. Bell Jr., L. Eeckhout, L. John, and D. Lilja, University of Minnesota Supercomputing Institute Research Report UMSI 2006/6, January 2006. Epidemiology and Community Health 2004/12 “Familial Aggregation and Genome-Wide Linkage Analysis of Carotid Artery Plaque: The NHLBI Family Heart Study,” J. S. Pankow, G. Heiss, G. W. Evans, P. Sholinsky, M. A. Province, H. Coon, R. C. Ellison, M. B. Miller, and B. Qaqish, University of Minnesota Supercomputing Institute Research Report UMSI 2004/12, February 2004. 2004/265 “Linkage Analysis of Diabetes Status Among Hypertensive Families—The Hypertension Genetic Epidemiology Network Study,” C. L. Avery, B. I. Freedman, G. Heiss, A. Kraja, T. Rice, D. Arnett, M. B. Miller, J. S. Pankow, C. E. Lewis, R. H. Myers, S. C. Hunt, L. Almasy, and K. E. North, Diabetes, 53, p. 3307 (2004) and CB 2004-75. 2004/266 “Evidence for a Gene on Chromosome 13 Influencing Postural Systolic Blood Pressure Change and Body Mass Index,” K. E. North, K. M. Rose, I. B. Borecki, A. Oberman, S. C. Hunt, M. B. Miller, J. Blangero, L. Almasy, and J. S. Pankow, Hypertension, 43, p. 780 (2004) and CB 2004-76. 2004/267 “Genome-Wide Linkage Analysis Replicates Susceptibility Locus for Fasting Plasma Triglycerides: NHLBI Family Heart Study,” D. K. Arnett, M. B. Miller, H. Coon, R. C. Ellison, K. E. North, M. Province, M. Leppert, and J. H. Eckfeldt, American Journal of Human Genetics, 115, p. 468 (2004) and CB 2004-77. 2005/110 “Further Evidence of a Quantitative Trait Locus on Chromosome 18 Influencing Postural Change in Systolic Blood Pressure: The Hypertension Genetic Epidemiology Network (HyperGEN) Study,” J. S. Pankow, D. M. Dunn, S. C. Hunt, M. F. Leppert, M. B. Miller, D. C. Rao, G. Heiss, A. Oberman, J.-M. Lalouel, and R. B. Weiss, American Journal of Hypertension, 18, p. 672 (2005) and CB 2005-29. 2005/254 “A Population Association Study of Angiotensinogen Polymorphisms and Haplotypes With Left Ventrical Phenotypes,” L. J. Rasmussen-Torvik, K. E. North, C. C. Gu, C. E. Lewis, J. B. Wilk, A. Chakravarti, Y.-P. C. Chang, M. B. Miller, N. Li, R. B. Devereux, and D. K. Arnett, Hypertension, 46, p. 1294 (2005) and CB 2005-73. 2005/255 “Genome-Wide Analysis for Loci Affecting Pulse Pressure: The Family Blood Pressure Program,” S. J. Bielinski, A. I. Lynch, M. B. Miller, A. Weder, R. Cooper, A. Oberman, Y.-D. I. Chen, S. T. Turner, M. Forange, M. Province, and Donna K. Arnett, Hypertension, 46, p. 1286 (2005) and CB 2005-74. Experimental and Clinical Pharmacology 2006/38 “Heteroactivator Effects on the Coupling and Spin State Equilibrium of CYP2C9,” C. W. Locuson, P. M. Gannett, and T. S. Tracy, University of Minnesota Supercomputing Institute Research Report UMSI 2006/38, April 2006 and CB 2006-8. Publication in press, Archives of Biochemistry and Biophysics. Genetics, Cell Biology, and Development 2004/226 “Impact of News Coverage, the Internet, the Difficulty of Getting Cigarettes, and Cigarette Prices on Smoking Time Trends,” D. P. Fan, L. D. Nordgren, and J. R. Finnegan Jr., University of Minnesota Supercomputing Institute Research Report UMSI 2004/226, December 2004 and CB 2004-62.

2006 Annual Research Report of the Supercomputing Institute 307 Index and Bibliography

Bibliography (continued) Geology and Geophysics 2004/1 “An Out-of-Core High-Resolution FFT Algorithm for Determining Large-Scale Features of Surface Potentials in Crystals,” M. Bakhos, A. P. Vincent, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/1, January 2004. 2004/5 “Interplay of Variable Thermal Conductivity and Expansivity on the Thermal Structure of Oceanic Lithosphere II,” S. Honda and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/5, January 2004. 2004/15 “Web-Cam’s Potential for Collaborative Activities in the Earth Sciences,” B. J. Kadlec, E. O. D. Sevre, D. A. Yuen, X. L. Yang, E. F. Bollig, Y. Wang, G. Erlebacher, and M. Rudolph, University of Minnesota Supercomputing Institute Research Report UMSI 2004/15, February 2004. 2004/16 “Pattern Recognition Techniques for Automatic Detection of Suspicious-Looking Anomalies in Mammograms,” T. Arodz, M. Kurdziel, E. O. D. Sevre, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/16, February 2004 and CB 2004-3. 2004/42 “Lithospheric Fault Zones Rejuvenated,” K. Regenauer-Lieb, B. E. Hobbs, H. Mulhaus, A. Ord, D. A. Yuen, and S. van der Lee, University of Minnesota Supercomputing Institute Research Report UMSI 2004/42, April 2004. 2004/43 “Probabilistic Tomography Maps Chemical Heterogeneities in the Lower Mantle,” J. Trampert, F. Deschamps, J. Resovsky, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/43, April 2004. 2004/45 “The Importance of Radiative Heat Transfer for Superplumes With a Deep Mantle Phase Transition,” C. Matyska and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/45, April 2004. 2004/66 “WEB-IS (Integrated System): An Overall View,” Y. Wang, E. F. Bollig, B. J. Kadlec, Z. A. Garbow, G. Erlebacher, D. A. Yuen, M. Rudolph, L. X. Yang, and E. O. D. Sevre, University of Minnesota Supercomputing Institute Research Report UMSI 2004/66, April 2004. 2004/144 “The Threshold Dependencies of Thermal Conductivity and Implications on Mantle Dynamics,” A. M. Hofmeister and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/144, September 2004 and VLab 2004-3. 2004/160 “Data Assimilation for Plume Models,” C. A. Hier Majumder, E. Belanger, S. DeRosier, D. A. Yuen, and A. P. Vincent, University of Minnesota Supercomputing Institute Research Report UMSI 2004/160, September 2004. 2004/168 “Modeling Mesoscopic Fluids With Discrete-Particles. Methods, Algorithms and Results,” W. Dzwinel, K. Boryczko, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/168, October 2004. 2004/175 “Aging in Hostile Environments Modeled by Cellular Automata With Genetic Dynamics,” W. Dzwinel and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/175, October 2004 and CB 2004-47. 2004/180 “Clustering and Visualization of Earthquake Data in a Grid Environment,” D. A. Yuen, B. J. Kadlec, E. F. Bollig, W. Dzwinel, Z. A. Garbow and C. da Silva, University of Minnesota Supercomputing Institute Research Report UMSI 2004/180, October 2004 and VLab 2004-4.

308 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2004/181 “A 3D Visualization System for Computer-Aided Mammogram Analysis,” T. Arodz, M. Kurdziel, T. Popiela, E. O. D. Sevre, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/181, October 2004 and CB 2004-50. 2004/184 “Challenges in the Visualization of a 2D Mantle Dynamics Simulation Using One Billion Tracers,” M. L. Rudolph, T. V. Gerya, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/184, October 2004. 2004/206 “Nonlinear Multi-Dimensional Scaling and Visualization of Earthquake Clusters Over Space, Time and Feature Space,” W. Dzwinel, D. A. Yuen, K. Boryczko, Y. Ben-Zion, S.Yoshioka, and T. Ito, University of Minnesota Supercomputing Institute Research Report UMSI 2004/206, November 2004 and VLab 2004- 10. 2004/212 “Multi-Disciplinary Impact of the Deep Mantle Post-Perovskite Phase Transition, “T. Lay, D. Heinz, M. Ishii, S.-H. Shim, J. Tsuchiya, T. Tsuchiya, R. Wentzcovitch, and D. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/212, November 2004. 2004/216 “The Influences of Temperature-Dependent Viscosity and Radiative Thermal Conductivity on Lower Mantle Dynamics With the Post-Perovskite Phase Change,” C. Matyska and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/216, November 2004 and VLab 2004-6. 2004/218 “Short Time-Scale Heating of the Earth’s Mantle by Ice-Sheet Dynamics,” L. Hanyk, C. Matyska, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/218, November 2004 and VLab 2004-7. 2004/223 “Shear-Induced Material Transfer Across the Core-Mantle Boundary Aided by the Post-Perovskite Phase Transition,” N. Petford, D. A. Yuen, T. Rushmer, J. Brodholt, and S. Stackhouse, University of Minnesota Supercomputing Institute Research Report UMSI 2004/223, December 2004 and VLab 2004-8. 2004/238 “From Point Defects to Plate Tectonic Faults,” K. Regenauer-Lieb, B. Hobbs, D. A. Yuen, A. Ord, Y. Zhang, H. B. Mulhaus, and G. Morra, University of Minnesota Supercomputing Institute Research Report UMSI 2004/238, December 2004 and VLab 2004-9. 2005/5 “Visualization and Analysis of Multi-Terabyte Geophysical Datasets in an Interactive Setting With Remote Webcam Capabilities,” B. J. Kadlec, D. A. Yuen, and G. Erlebacher, University of Minnesota Supercomputing Institute Research Report UMSI 2005/5, January 2005 and VLab 2005-1. 2005/6 “A Grid Framework for Visualization Services in the Earth Sciences,” G. Erlebacher, D. A. Yuen, E. F. Bollig, M. Pierce, and S. Pallickara, University of Minnesota Supercomputing Institute Research Report UMSI 2005/6, January 2005 and VLab 2005-2. 2005/7 “Quartz Rheology and Short-Timescale Crustal Instabilities,” K. Regenauer-Lieb and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2005/7, January 2005 and VLab 2005-3. 2005/10 “Simulated Tomographic Imagery of Cold Hydrous Upper-Mantle Plumes in the Mantle Wedge,” T. V. Gerya, J. A. D. Connolly, D. A. Yuen, W. Gorzcyk, and A. M. Capel, University of Minnesota Supercomputing Institute Research Report UMSI 2005/10, February 2005 and VLab 2005-4. 2005/43 “Tradeoffs in Chemical and Thermal Variations in the Post-Perovskite Phase Transition: Mixed Phase Regions in the Deep Lower Mantle,” F. J. Spera, D. A. Yuen, and G. Giles, University of Minnesota Supercomputing Institute Research Report UMSI 2005/43, April 2005 and VLab 2005-5.

2006 Annual Research Report of the Supercomputing Institute 309 Index and Bibliography

Bibliography (continued) 2005/50 “Efficient Adjoint Sensitivity Analysis for Flow and Transport in the Earth’s Crust and Mantle,” C. A. Hier Majumder, B. J. Travis, E. Bélanger, G. Richard, A. P. Vincent, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2005/50, May 2005 and VLab 2005-6. 2005/70 “River Systems With Complex Network Topology Modeled With Fine and Coarse Grained Cellular Automata,” P. Topa, W. Dzwinel, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2005/70, May 2005. 2005/113 “The Role of Water in Connecting Past and Future Episodes of Subduction,” S. van der Lee, K. Regenauer-Lieb, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2005/113, August 2005 and VLab 2005-15. 2005/130 “Adaptive Wavelets for Detecting Elastic Surface Waves in Marine Sediments,” A. Kritski, A. P. Vincent, D. A. Yuen, and T. Carlsen, University of Minnesota Supercomputing Institute Research Report UMSI 2005/130, August 2005 and VLab 2005-16. 2005/144 “Ensemble of Linear Models for Predicting Drug Properties,” T. Arodz, D. A. Yuen, and A. Z. Dudek, University of Minnesota Supercomputing Institute Research Report UMSI 2005/144, September 2005 and CB 2005-34. 2005/157 “VLab: Collaborative Grid Services and Portals to Support Computational Material Science,” M. Nacar, M. Aktas, M. Pierce, Z. Lu, G. Erlebacher, D. Kigelman, E. F. Bollig, C. De Silva, B. Sowell, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2005/157, October 2005 and VLab 2005-20. 2005/182 “Rapid Detection of Clusters of Microcalcifications in High-Resolution Mammograms,” K. Boryczko, M. Kurdziel, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2005/182, October 2005 and CB 2005-49. 2005/192 “Fe-Liquid Segregation in Deforming Planetesimals: Coupling Core-Forming Compositions With Transport Phenomena,” T. Rushmer, N. Petford, M. Humayun, and A. J. Campbell, University of Minnesota Supercomputing Institute Research Report UMSI 2005/192, October 2005 and VLab 2005-21. Publication in press, Earth and Planetary Science Letters. 2006/1 “Sensitivity Study of the Thermal State in the Lower Mantle by 3-D Convection With Post-Perovskite Phase Transition,” M. Kameyama and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2006-1, January 2006 and VLab 2006-1. 2006/2 “Unsolved Problems in the Lowermost Mantle,” K. Hirose, S. Karato, V. F. Cormier, J. P. Brodholt, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2006/2, January 2006. 2006/7 “A Multiscale Cellular Automata Model for Simulating Complex Transportation Systems,” P. Topa, W. Dzwinel, and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2006/7, February 2006. 2006/8 “Upper-Mantle Versus Lower-Mantle Plumes: Are They The Same?” C. Matyska and D. A. Yuen, University of Minnesota Supercomputing Institute Research Report UMSI 2006/8, February 2006. 2006/14 “Dynamics of Superplumes in the Lower Mantle,” D. A. Yuen, M. Monnereau, U. Hansen, M. Kameyama, and C. Matyska, University of Minnesota Supercomputing Institute Research Report UMSI 2006/14, February 2006 and VLab 2006-2.

310 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2006/33 “Tsunami and Earthquake Visualization Inspired by Light Interference,” X. Yuan, M. X. Nguyen, Y. Liu, D. A. Yuen, B. Chen, and Y. Shi, University of Minnesota Supercomputing Institute Research Report UMSI 2006/33, April 2006. Laboratory Medicine and Pathology 2004/119 “Hoxa9 Influences the Phenotype but Not the Incidence of Mll-AF9 Fusion Gene Leukemia,” A. R. Kumar, W. A. Hudson, W. Chen, R. Nishiuchi, Q.Yao, and J. H. Kersey, Blood, 103, p. 1823 (2004), and CB 2004-34. 2004/194 “In Vitro Circadian ANP Secretion by Gene Transferring Cells Encapsulated in Polycaprolactone Tubes: Gene Chronotherapy,” Z. Wang, L. Chen, C. Wan, Y. Qu, G. Cornélissen, and F. Halberg, Peptides, 25, p. 1259 (2004) and CB 2004-59. 2004/239 “Differential Gene Expression in Ovarian Carcinoma Identification of Potential Biomarkers,” K. Hibbs, K. M. Skubitz, S. E. Pambuccian, R. C. Casey, K. M. Burleson, T. R. Oegema Jr,. J. J. Thiele, S. M. Grindle, R. L. Bliss, and A. P. N. Skubitz, American Journal of Pathology, 165, p. 397 (2004) and CB 2004-63. 2004/244 “Molecular Modelling of CYP2A Enzymes: Application to Metabolism of the Tobacco-Specific Nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK),” J. R. Jalas, M. Seetharaman, S. S. Hecht, and S. E. Murphy, Xenobiotica, 34, p. 515 (2004). 2004/253 “A Chronomic Tree of Life: Ontogenetic and Phylogenetic ‘Memories’ of Primordial Cycles—Keys to Ethics,” F. Halberg, K. Otsuka, G. Katinas, R. Sonkowsky, P. Regal, O. Schwartzkopff, R. Jozsa, A. Olah, M. Zeman, E. E. Bakken, and G. Cornélissen, Biomedicine and Pharmacotherapy, 58, p. S1 (2004). 2004/254 “100 or 30 Years After Janeway or Bartter, Healthwatch Helps Avoid ‘Flying Blind’,” G. Cornélissen, F. Halberg, E. Bakken, R. B. Singh, K. Otsuka, B. Tomlinson, A. Delcourt, G. Toussaint, S. Bathina, O. Schwartzkopff, Z. Wang, R. Tarquini, F. Perfetto, G. Pantaleoni, R. Jozsa, P. A. Delmore, and E. Nolley, Biomedicine and Pharmacotherapy, 58, p. S69 (2004). 2004/255 “No Baseline for Blood Pressure in Ordinary Life: Another Case of Transient Chronome Alterations,” T. Sarabandi, J. Cohn, G. Cornélissen, F. Halberg, G. Katinas, J. Holte, O. Schwartzkopff, and K. Otsuka, Biomedicine and Pharmacotherapy, 58, p. S107 (2004) and CB 2004-73. 2004/256 “Franz Halberg: An Allo-(Auto)Biography,” O. Schwarzkopff, G. Cornélissen, and M. Sampson, presented at the Symposium on Chronobiology in Medicine, Dedicated to the 85th Anniversary of Professor Franz Halberg, Brno, Czech Republic, 2004. Published in Proceedings, edited by G. Cornélissen, R. Kenner, B. Fiser, and J. Siegelová. 2004/257 “Time Structures (Chronomes) in US and Around US: A Tribute to Franz Halberg,” G. Cornélissen, presented at the Symposium on Chronobiology in Medicine, Dedicated to the 85th Anniversary of Professor Franz Halberg, Brno, Czech Republic, 2004. Published in Proceedings, edited by G. Cornélissen, R. Kenner, B. Fiser, and J. Siegelová. Management 2004/245 “Design of a Degree-Constrained Minimal Spanning Tree With Unreliable Links and Node Outage Costs,” R. Kawatra and D. Bricker, European Journal of Operational Research, 156, p. 73 (2004).

2006 Annual Research Report of the Supercomputing Institute 311 Index and Bibliography

Bibliography (continued) Mathematics 2004/158 “A Computational Model for Martensitic Thin Films With Compositional Fluctuation,” P. Belík and M. Luskin, Mathematical Models and Methods in Applied Sciences, 14, p. 1585 (2004). 2004/159 “Computational Modeling of Softening in a Structural Phase Transformation,” P. Belik and M. Luskin, University of Minnesota Supercomputing Institute Research Report UMSI 2004/159, September 2004. 2004/186 “From Individual to Collective Behavior in Bacterial Chemotaxes,” R. Erban and H. G. Othmer, University of Minnesota Supercomputing Institute UMSI 2004/186, October 2004 and CB 2004-53. 2004/187 “From Signal Transduction to Spatial Pattern Formation in E. Coli: A Paradigm for Multi-Scale Modeling in Biology,” R. Erban and H. G. Othmer, University of Minnesota Supercomputing Institute UMSI 2004/187, October 2004 and CB 2004-54. 2004/199 “An Adaptive Method With Rigorous Error Control for the Hamilton-Jacobi Equations. Part I: The One-Dimensional Steady State Case,” B. Cockburn and B. Yenikaya, University of Minnesota Supercomputing Institute Research Report UMSI 2004/199, October 2004. 2004/234 “Nonlinear Theory of Self-Similar Crystal Growth and Melting,” S. Li, J. S. Lowengrub, P. H. Leo, and V. Cristini, University of Minnesota Supercomputing Institute Research Report UMSI 2004/234, December 2004. 2004/235 “Nonlinear Stability Analysis of Self-Similar Crystal Growth: Control of the Mullins-Sekerka Instability,” S. Li, J. S. Lowengrub, P. H. Leo, and V. Cristini, University of Minnesota Supercomputing Institute Research Report UMSI 2004/235, December 2004. 2005/14 “An Equation-Free Computational Approach for Extracting Population-Level Behavior From Individual- Based Models of Biological Dispersal,” R. Erban, I. G. Kevrekidis, and H. G. Othmer, University of Minnesota Supercomputing Institute UMSI 2005/14, February 2005 and CB 2005-4. 2005/52 “Existence of Energy Minimizers for Magnetostrictive Materials,” P. Rybka and M. Luskin, University of Minnesota Supercomputing Institute Research Report UMSI 2005/52, May 2005. 2005/93 “On the Calculation of Maass Cusp Forms,” D. A. Hejhal, University of Minnesota Supercomputing Institute Research Report UMSI 2005/93, June 2005. 2006/36 “The Γ-Convergence of a Sharp Interface Thin Film Model With Non-Convex Elastic Energy,” P. Belík and M. Luskin, University of Minnesota Supercomputing Institute Research Report UMSI 2006/36, April 2006. Accepted for publication, SIAM Journal on Mathematical Analysis. Mechanical Engineering 2004/14 “Large Eddy Simulation of Heated Vertical Annular Pipe Flow in Fully Developed Turbulent Mixed Convection,” J. Sang Lee, X. Xu, and R. H. Pletcher, International Journal of Heat and Mass Transfer, 47, p. 437 (2004). 2004/46 “A Global Model of Chemical Vapor Deposition of Silicon Dioxide by Direct-Current Corona Discharges in Dry Air Containing Octamethylcyclotetrasiloxane Vapor,” J. Chen and J. H. Davidson, Plasma Chemistry and Plasma Processing, 24, p. 511 (2004). 2004/47 “Heat Transfer Enhancement Using Shaped Polymer Tubes: Fin Analysis,” Z. Li, J. H. Davidson, and S. C. Mantell, Journal of Heat Transfer–Transactions of the ASME, 126, p. 211 (2004).

312 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2004/86 “Microscopic Simulation of Flow and Heat Transfer in Structured Isotropic and Anisotropic Porous Medium,” A. A. Alshare, P. J. Strykowski, T. W. Simon, University of Minnesota Supercomputing Institute Research Report 2004/86, June 2004. 2004/109 “Numerical and Experimental Study of Atmospheric Pressure Glows in Helium,” P. Zhang, C. Anderson, J. Heberlein, and U. Kortshagen, University of Minnesota Supercomputing Institute Research Report UMSI 2004/109, July 2004. 2004/201 “Large Eddy Simulation of the Effects of Inner Wall Rotation on Heat Transfer in Annular Turbulent Flow,” J. S. Lee, X.Xu, and R. H. Pletcher, Numerical Heat Transfer, Part A, 46, p. 323 (2004). 2004/202 “Large Eddy Simulation of Turbulent Forced Gas Flows in Vertical Pipes With High Heat Transfer Rates,” X. Xu, J. S. Lee, R. H. Pletcher, A. M. Shehata, and D. M. McEligot, International Journal of Heat and Mass Transfer, 47, p. 4113 (2004). 2004/203 “Numerical Study of the Effects of Rotation on Heat Transfer in Channels With and Without Ribs,” J. S. Lee, N. Meng, R. H. Pletcher, and Y. Liu, International Journal of Heat and Mass Transfer, 47, p. 4673 (2004). 2004/204 “A Procedure to Establish Inflow Conditions for LES of Spatially Developing Turbulent Boundary Layers,” K. Liu and R. H. Pletcher, in Proceedings of HT-FED2004, 2004 ASME Heat Transfer/Fluids Engineering Summer Conferences, Charlotte, North Carolina, July 11–15, 2004. 2004/225 “Effect of Relative Humidity on Electron Distribution and Ozone Production by DC Coronas in Air,” J. Chen and P. Wang, University of Minnesota Supercomputing Institute Research Report UMSI 2004/225, December 2004. 2004/241 “A DOS-Enhanced Numerical Simulation of Heat Transfer and Fluid Flow Through an Array of Offset Fins With Conjugate Heating in the Bounding Solid,” E. M. Sparrow, J. P. Abraham, and P. W. Chevalier, Journal of Heat Transfer, 126, p. 1 (2004). 2004/269 “Investigation of Intake Concepts for a Formula SAE Four-Cylinder Engine Using 1D/3D (Ricardo Wave/Vectis) Coupled Modeling Techniques,” M. R. Claywell, D. P. Horkheimer, and G. R. Stockburger, SAE International (2004). 2004/271 “Molecular Beam Mass Spectrometry System for Characterization of Thermal Plasma Chemical Vapor Deposition,” S. Park, F. Liao, J. M. Larson, S. L. Girshick, and M. R. Zachariah, Plasma Chemistry and Plasma Processing, 24, p. 353 (2004). 2004/274 “Two-Dimensional Space-Time-Resolved Emission Spectroscopy on Atmospheric Pressure Glows in Helium With Impurities,” C. Anderson, M. Hur, P. Zhang, L. Mangolini, and U. Kortshagen, Journal of Applied Physics, 96, p. 1835 (2004). 2004/275 “Effects of Current Limitation Through the Dielectric in Atmospheric Pressure Glows in Helium,” L. Mangolini, C. Anderson, J. Heberlein, and U. Kortshagen, Journal of Physics D: Applied Physics, 37, p. 1021 (2004). 2004/276 “Large Eddy Simulation of Turbulent Heat Transfer in a Square Duct,” Z. Qin and R. H. Pletcher, presented at the International Mechanical Engineering Congress and Exposition, Anaheim, California, November 13–19, 2004. Published in Proceedings.

2006 Annual Research Report of the Supercomputing Institute 313 Index and Bibliography

Bibliography (continued) 2005/18 “Numerical Simulation of Flow Field and Heat Transfer of Streamlined Cylinders in Crossflow,” Z. Li, J. Davidson and S. Mantell, presented at HT2005, 2005 ASME Summer Heat Transfer Conference, San Francisco, California, July 17–22, 2005. Published in Proceedings. 2005/19 “Friction Drag Resulting From the Simultaneous Imposed Motions of a Freestream and Its Bounding Surface,” J. P. Abraham and E. M. Sparrow, International Journal of Heat and Fluid Flow, 26, p. 289 (2005). 2005/53 “Atmospheric Pressure Glow Discharge Initiation From a Single Electron Avalanche,” P. Zhang and U. Kortshagen, IEEE Transactions on Plasma Science, 33, p. 318 (2005). 2005/58 “A Novel Nonlinearly Explicit Second-Order Accurate L-Stable Methodology for Finite Deformation: Hypoelastic/Hypoelasto-Plastic Structural Dynamics Problems,” X. Zhou, D. Sha, and K. K. Tamma, University of Minnesota Supercomputing Institute Research Report UMSI 2005/58, May 2005. 2005/59 “A New Unified Theory Underlying Time Dependent Linear First-Order Systems: A Prelude to Algorithms by Design,” X. Zhou and K. K. Tamma, University of Minnesota Supercomputing Institute Research Report UMSI 2005/59, May 2005. 2005/61 “A Compressible Finite Volume Formulation for Large Eddy Simulation of Turbulent Pipe Flows at Low Mach Number in Cartesian Coordinates,” X. Xu, J. Sang Lee, and R. H. Pletcher, Journal of Computational Physics, 203, p. 22 (2005). 2005/62 “Large Eddy Simulation of Turbulent Boundary Layers Subjected to Free-Stream Turbulence,” K. Liu and R. H. Pletcher, American Institute of Aeronautics and Astronautics Paper 2005-669, presented at the 43rd AIAA Aerospace Science Meeting and Exhibit, Reno, Nevada, January 10–13, 2005. 2005/63 “A Computational Analysis of the Radiative and Convective Processes Which Take Place in a Preheated/Non-Preheated Oven,” E. M. Sparrow and J. P. Abraham, University of Minnesota Supercomputing Institute Research Report UMSI 2005/63, May 2005. 2005/65 “Design, Analysis, and Synthesis of Generalized Single Step Single Solve and Optimal Algorithms for Structural Dynamics,” X. Zhou and K. K. Tamma, University of Minnesota Supercomputing Institute Research Report UMSI 2005/65, May 2005. 2005/66 “Transient Algorithms for Heat Transfer: General Developments and Approaches for Theoretically Generating Nth-Order Time Accurate Operators Including Practically Useful Second-Order Forms,” K. K. Tamma, X. Zhou, and D. Sha, University of Minnesota Supercomputing Institute Research Report UMSI 2005/66, May 2005. 2005/79 “Nanoparticle Coagulation via a Navier-Stokes/Nodal Methodology: Evolution of the Particle Field,” S. C. Garrick, K. E. J. Lehtinen, and M. R. Zachariah, University of Minnesota Supercomputing Institute Research Report UMSI 2005/79, May 2005. 2005/86 “Universal Solutions for the Streamwise Variation of the Temperature of a Moving Sheet in the Presence of a Moving Fluid,” E. M. Sparrow and J. P. Abraham, University of Minnesota Supercomputing Institute Research Report UMSI 2005/86, May 2005. Publication in press, International Journal of Heat and Mass Transfer. 2005/88 “Design and Relative Stability of Multicomponent Nanowires,” T. Dumitrica, V. Barone, M. Hua, and B. I. Yakobson, University of Minnesota Supercomputing Institute Research Report UMSI 2005/88, June 2005. Accepted for publication, NATO Science Series II: Mathematics, Physics and Chemistry.

314 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2005/95 “Natural Convective Flow and Heat Transfer in a Collector Storage With an Immersed Heat Exchanger: Numerical Study,” Y. Su and J. H. Davidson, University of Minnesota Supercomputing Institute Research Report UMSI 2005/95, June 2005. 2005/121 “Three-Dimensional Effects Inside a DC Arc Plasma Torch,” H.-P. Li and E. Pfender, IEEE Transactions on Plasma Science, 33, p. 400 (2005). 2005/122 “Three-Dimensional, Nonequilibrium Effects in a High-Intensity Blown Arc,” H.-P. Li, J. Heberlein, and E. Pfender, IEEE Transactions on Plasma Science, 33, p. 402 (2005). 2005/160 “Numerical Simulation of Nanoparticle Transport During Plasma-Enhanced Chemical Vapor Deposition,” S. J. Warthesen, U. R. Kortshagen, and S. L. Girshick, IEEE Transactions on Plasma Science, 33, p. 398 (2005). 2005/161 “Aerodynamic Focusing of Nanoparticles: II. Numerical Simulation of Particle Motion Through Aerodynamic Lenses,” X. Wang, A. Gidwani, S. L. Girshick, and P. H. McMurry, Aerosol Science and Technology, 39, p. 624 (2005). 2005/170 “Large Eddy Simulation of Discrete-Hole Film Cooling in a Flat Plate Turbulent Boundary Layer,” K. Liu and R. H. Pletcher, American Institute of Aeronautics and Astronautics AIAA 2005-4944, presented at the 38th AIAA Thermophysics Conference, Toronto, Ontario Canada, June 6–9, 2005.

2005/171 “Large Eddy Simulation of Supercritical CO2 Pipe Flow With Constant Wall Heat Flux,” X. Wang, X. Xu, and R. H. Pletcher, American Institute of Aeronautics and Astronautics AIAA 2005-4995, presented at the 17th AIAA Computational Fluid Dynamics Conference, Toronto, Ontario Canada, June 6–9, 2005. 2005/191 “Tissue Characterization for Improved External Penile Occlusive Device Design,” G. W. Timm, D. R. Wulfman, S. Kim, R. E. Hampton, S. Will, J. DiCosimo, and A. G. Erdman, Journal of Biomechanical Engineering, 127, p. 956 (2005) and CB 2005-53. 2006/5 “Simulation Results of Arc Behavior in Different Plasma Spray Torches,” J. P. Trelles and J. V. R. Heberlein, presented at the International Thermal Spray Conference and Exposition, Seattle, Washington, May 15–18, 2006. Medicinal Chemistry 2004/151 “Homology Modeling and Molecular Dynamics Simulations of the Mu Opioid Receptor in a Membrane-Aqueous System,” Y. Zhang, Y. Y. Sham, R. Rajamani, J. Gao, and P. S. Portoghese, ChemBioChem, 6, p. 1 (2005) and CB 2004-41. 2004/272 “Resummed Green-Kubo Relations for a Fluctuating Fluid-Particle Model,” T. Ihle, E. Tuzel, and D. M. Kroll, Physical Review E, 70, art. no. 035701-l (2004). 2004/281 “Simulation of Ordered Packed Beds in Chromatography,” M. R. Schure, R. S. Maier, D. M. Kroll, and H. T. Davis, Journal of Chromatography A, 1031, p. 79 (2004). 2005/156 “Synthesis of Pipecolic Acid-Based Spiro Bicyclic Lactam Scaffolds as β-Turn Mimics,” R. V. Somu and R. L. Johnson, Journal of Organic Chemistry, 70, p. 5954 (2005) and CB 2005-40. 2006/48 “Spectrophotometric Determination and Computaitonal Evaluation of the Rates of Hydrolysis of 9- Amino-Substituted Acridines,” J. R. Goodell, B. Svensson, and D. M. Ferguson, Journal of Chemical Information and Modeling, 46, p. 876 (2006) and CB 2006-17.

2006 Annual Research Report of the Supercomputing Institute 315 Index and Bibliography

Bibliography (continued) Medicine 2004/80 “The Use of Microarrays to Study Autoimmunity,” K. Moser, P. M. Gaffney, M. E. Grandits, E. S. Emamian, D. B. Machado, E. C. Baechler, N. L. Rhodus, and T. W. Behrens, Journal of Investigative Dermatology Symposium Proceedings, 9, p. 18 (2004) and CB 2004-24. 2004/90 “Modeling the Relationship Between LVAD Support Time and Gene Expression Changes in the Human Heart by Penalized Partial Least Squares,” X. Huang, W. Pan, S. Park, X. Han, L. W. Miller, and J. Hall, Bioinformatics, 20, p. 888 (2004) and CB 2004-30. 2004/91 “Expression Levels for Many Genes in Human Peripheral Blood Cells Are Highly Sensitive to Ex Vivo Incubation,” E. C. Baechler, F. M. Batliwalla, G. Karypis, P. M. Gaffney, K. Moser, W. A. Ortmann, K. J. Espe, S. Balasubramanian, K. M. Hughes, J. P. Chan, A. Begovich, S.-Y. P. Chang, P. K. Gregersen, and T. W. Behrens, Genes and Immunity, 5, p. 347 (2004) and CB 2004-31. 2004/96 “Identification of a Gene Expression Signature Associated With Recurrent Disease in Squamous Cell Carcinoma of the Head and Neck,” M. A. Ginos, G. P. Page, B. S. Michalowicz, K. J. Patel, S. E. Volker, S. E. Pambuccian, F. G. Ondrey, G. L. Adams, and P. M. Gaffney, Cancer Research, 64, p. 55 (2004) and CB 2004-32. 2004/239 “Differential Gene Expression in Ovarian Carcinoma Identification of Potential Biomarkers,” K. Hibbs, K. M. Skubitz, S. E. Pambuccian, R. C. Casey, K. M. Burleson, T. R. Oegema Jr,. J. J. Thiele, S. M. Grindle, R. L. Bliss, and A. P. N. Skubitz, American Journal of Pathology, 165, p. 397 (2004) and CB 2004-63. 2005/225 “In Vivo Assessment of the Relative Contributions of Deletion, Anergy, and Editing to B Cell Self- Tolerance,” K. L. Hippen, B. R. Schram, L. E. Tze, K. A. Pape, M. K. Jenkins, and T. W. Behrens, Journal of Immunology, 175, p. 909 (2005) and CB 2005-61. 2005/226 “Peripheral Blood Gene Expression Profiling in Rheumatoid Arthritis,” F. M. Batliwalla, E. C. Baechler, X. Xiao, W. Li, S. Balasubramanian, H. Khalili, A. Damle, W. A. Ortmann, A. Perrone, A. B. Kantor, P. S. Gulko, M. Kern, R. Furie, T. W. Behrens, and P. K. Gregersen, Genes and Immunity, 6, p. 388 (2005) and CB 2005-62. Microbiology 2004/196 “Reconstruction of Oral HIV Exposure. A Model System of Oral HIV Exposure Utilizing Human Palatine Tonsil Reveals Extensive Binding of HIV Infectivity With Limited Progression to Primary Infection,” D. Maher, X. Wu, T. Schacker, M. Larson, and P. Southern, University of Minnesota Supercomputing Institute Research Report UMSI 2004/196, October 2004 and CB 2004-60. Accepted for publication, Journal of Infectious Diseases. 2004/282 “Functional Genomic Analysis of the Response of HIV-1Infected Lymphatic Tissue to Antiretroviral Therapy,” Q. Li, T. Schacker, J. Carlis, G. Beilman, P. Nguyen, and A. T. Haase, Journal of Infectious Diseases, 189, p. 572 (2004) and CB 2004-79. 2005/109 “Coordinate Stabilization of Growth-Regulatory Transcripts in T Cell Malignancies,” I. A. Vlasova, J. McNabb, A. Raghavan, C. Reilly, D. A. Williams, K. A. Bohjanen, and P. R. Bohjanen, Genomics, 86, p. 159 (2005) and CB 2005-28.

316 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2005/112 “Ex Vivo Modeling of Oral HIV Transmission in Human Palatine Tonsil,” D. M. Maher, Z.-Q. Zhang, T. W. Schacker, and P. J. Southern, Journal of Histochemistry and Cytochemistry, 53, p. 631 (2005) and CB 2005-31. 2005/185 “HIV Binding, Penetration, and Primary Infection in Human Cervicovaginal Tissue,” D. Maher, X. Wu, T. Schacker, J. Horbul, and P. Southern, Proceedings of the National Academy of Sciences, 102, p. 11504 (2005) and CB 2005-51. Molecular Pharmacology and Experimental Therapeutics 2005/180 “Serotype-Selective, Small-Molecule Inhibitors of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A,” J. G. Park, P. C. Sill, E. F. Makiyi, A. T. Garcia-Sosa, C. B. Millard, J. J. Schmidt, and Y.-P. Pang, University of Minnesota Supercomputing Institute Research Report UMSI 2005/180, October 2005, and CB 2005-48. Publication in press, Bioorganic and Medicinal Chemistry. Neuroscience and Neurology 2004/145 “µ-Opioid Receptor Trafficking on Inhibitory Synapses in the Rat Brainstem,” K. N. Browning, A. E. Kalyuzhny, and R. A. Travagli, The Journal of Neuroscience, 24, p. 7344 (2004) and CB 2004-37. 2004/185 “A Computational Model of the Ribbon Synapse,” M. A. Sikora, J. Gottesman, and R. F. Miller, University of Minnesota Supercomputing Institute Research Report UMSI 2004/185, October 2004 and CB 2004-52. Accepted for publication, Journal of Neuroscience Methods. 2005/8 “The Expression and Function of MTG/ETO Family Proteins During Neurogenesis,” N. Koyano- Nakagawa and C. Kintner, Developmental Biology, 278, p. 22 (2005) and CB 2005-1. 2005/235 “Modeling the Signaling Endosome Hypothesis: Why a Drive to the Nucleus is Better Than a (Random) Walk,” C. L. Howe, Theoretical Biology and Medical Modelling, 2, p. 43 (2005) and CB 2005-64. Operations and Management Science 2004/59 “Optimal Foldover Plans for Two-Level Non-Regular Orthogonal Designs,” W. Li, D. K. J. Lin, and K. Q. Ye, University of Minnesota Supercomputing Institute Research Report UMSI 2004/59, April 2004. 2004/60 “Blocked Nonregular Two-Level Factorial Designs,” S.-W. Cheng, W. Li, and K. Q. Ye, University of Minnesota Supercomputing Institute Research Report UMSI 2004/60, April 2004. 2005/49 “Model Discrimination—Another Perspective on Model-Robust Designs,” B. A. Jones, W. Li, C. J. Nachtsheim, and K. Q. Ye, University of Minnesota Supercomputing Institute Research Report UMSI 2005/49, May 2005. Pharmaceutics 2004/191 “Solid-State Properties of Warfarin Sodium 2-Propanol Solvate,” A. R. Sheth, W. W. Brennessel, V. G. Young, Jr., F. X. Muller, and D. J. W. Grant, Journal of Pharmaceutical Sciences, 93, p. 2669 (2004) and CB 2004-57. 2004/192 “Relationships Between Crystal Structures and Thermodynamic Properties of Phenylbutazone Solvates,” T. Hosokawa, S. Datta, A. R. Sheth, and D. J. W. Grant, Crystal Engineering Communiations, 6, p. 243 (2004) and CB 2004-58. 2004/198 “Polymorphism in Piroxicam,” A. R. Sheth, S. Bates, F. X. Muller, and D. J. W. Grant, Crystal Growth and Design, 4, p. 1091 (2004) and CB 2004-61.

2006 Annual Research Report of the Supercomputing Institute 317 Index and Bibliography

Bibliography (continued) 2004/243 “Isostructurality Among Five Solvates of Phenylbutazone,” T. Hosokawa, S. Datta, A. R. Sheth, N. R. Brooks, V. G. Young, Jr., and D. J. W. Grant, Crystal Growth and Design, 4, p. 1195 (2004) and CB 2004-65. 2004/261 “Dehydration Kinetics of Piroxicam Monohydrate and Relationship to Lattice Energy and Structure,” A. R. Sheth, D. Zhou, F. X. Muller, and D. J. W. Grant, Journal of Pharmaceutical Sciences, 93, p. 3013 (2004) and CB 2004-72. 2005/23 “Measurement of Process-Dependent Material Properties of Pharmaceutical Solids by Nanoindentation,” X. Liao and T. S. Wiedmann, Journal of Pharmaceutical Sciences, 94, p. 79 (2005) and CB 2005-7. 2005/41 “Effect of Supersaturation on the Crystallization of Phenylbutazone Polymorphs,” S. Datta and D. J. W. Grant, Crystal Research and Technology, 40, p. 233 (2005) and CB 2005-15. 2005/78 “Mechanochromism of Piroxicam Accompanied by Intermolecular Proton Transfer Probed by Spectroscopic Methods and Solid-Phase Changes,” A. R. Sheth, J. W. Lubach, E. J. Munson, F. X. Muller, and D. J. W. Grant, Journal of American Chemical Society, 127, p. 6641 (2005) and CB 2005- 20. Pharmacology 2004/30 “Nonbonded Bivalence Approach to Cell-Permeable Molecules That Target DNA Sequences,” Y.-P. Pang, Bioorganic and Medicinal Chemistry, 11, p. 3063 (2004) and CB 2004-8. 2004/31 “Improved Loading and Cleavage Methods for Solid-Phase Synthesis Using Chlorotrityl Resins: Synthesis and Testing of a Library of 144 Discrete Chemicals as Potential Farnesyltransferase Inhibitors,” J. G. Park, K. J. Langenwalter, C. A. Weinbaum, P. J. Casey, Y.-P. Pang, Journal of Combinatorial Chemistry, 6, p. 407 (2004) and CB 2004-9. 2004/32 “ABCC9 Mutations Identified in Human Dilated Cardiomyopathy Disrupt Catalytic KATP Channel Gating,” M. Bienengraeber, T. M. Olson, V. A. Selivanov, E. C. Kathmann, F. O’Cochlain, F. Gao, A. B. Karger, J. D. Ballew, D. M. Hodgson, L. V. Zingman, Y.-P. Pang, A. E. Alekseev, and A. Terzic, Nature Genetics, 36, p. 1, DOI: 10.1038/ngXXX (2004) and CB 2004-10. 2004/260 “Three-Dimensional Model of a Substrate-Bound SARS Chymotrypsin-Like Cysteine Proteinase Predicted by Multiple Molecular Dynamics Simulations: Catalytic Efficiency Regulated by Substrate Binding,” Y.-P. Pang, Proteins: Structure, Function, and Bioinformatics, 57, p. 747 (2004) and CB 2004- 71. 2005/26 “Chronic Administration of Statins Alters Multiple Gene Expression Patterns in Mouse Cerebral Cortex,” L. N. Johnson-Anuna, G. P. Eckert, J. H. Keller, U. Igbavboa, C. Franke, T. Fechner, M. Schubert-Zsilavecz, M. Karas, W. E. Müller, and W. G. Wood, Journal of Pharmacology and Experimental Therapeutics, 312, p. 786 (2005) and CB 2005-9. Physical Medicine and Rehabilitation 2004/29 “Improved Lung Edema Monitoring With Coronary Vein Pacing Leads: A Simulation Study,” A. Belalcazar and R. P. Patterson, Physiological Measurement, 25, p. 475, DOI: 10.1088/0967- 3334/25/2/007 (2004) and CB 2004-7. 2005/155 “Lung Impedance Contributions to the Total Impedance Based on a FDM Model and Lead Field Theory,” R. Patterson and F. Yang, University of Minnesota Supercomputing Institute Research Report UMSI 2005/155, October 2005 and CB 2005-39.

318 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) Physics 2004/2 “Correlations Between the WMAP and MAXIMA Cosmic Microwave Background Anisotropy Maps,” M. E. Abroe, J. Borrill, P. G. Ferreira, S. Hanany, A. Jaffe, B. Johnson, A. T. Lee, B. Rabii, P. L. Richards, G. Smoot, R. Stompor, C. Winant, J. H. P. Wu, University of Minnesota Supercomputing Institute Research Report UMSI 2004/2, January 2004. 2004/48 “The Phase Diagram of Three-Flavor QCD for Small Baryon Densities,” P. de Forcrand and O. Philipsen, Progress of Theoretical Physics Supplement, 153, p. 127 (2004). 2004/61 “Magnetosphere-Ionosphere Coupling by Alfvén Waves at Mid-Latitudes,” R. L. Lysak, Journal of Geophysical Research–Space Physics, 109, art. no. A07201 (2004). 2004/85 “Melting and Structure of the Vortex Solid in Strongly Anisotropic Layered Superconductors With Random Columnar Pins,” C. Dasgupta, O. T. Valls, Physical Review B, 69, art. no. 214520 (2004). 2004/89 “Spin Waves in an Inhomogeneously Magnetized Stripe,” C. Bayer, J. P. Park, H. Wang, M. Yan, C. E. Campbell, and P. A. Crowell, Physical Review B, 69, art. no. 134401-1 (2004). 2004/103 “Nonperturbative Solution of Yukawa Theory and Gauge Theories,” J. R. Hiller, in Continuous Advances in QCD 2004, edited by T. Gherghetta (Singapore: World-Scientific, 2004), p. 515. 2004/104 “N = (1,1) Super Yang-Mills Theory in 1+1 Dimensions at Finite Temperature,” J. R. Hiller, Y. Proestos, S. Pinsky, and N. Salwen, Physical Review D, 70, art. no. 065012 (2004). 2004/105 “Improved Results for N = (2,2) Super Yang-Mills Theory Using Supersymmetric Discrete Light-Cone Quantization,” M. Harada, J. R. Hiller, S. Pinsky, and N. Salwen, Physical Review D, 70, art. no. 045015 (2004). 2004/107 “Stability of π Junction Configurations in Ferromagnet-Superconductor Heterostructures,” K. Halterman and O. T. Valls, Physical Review B, 70, art. no. 104516 (2004). 2004/171 “Computational Study of Hydrogen Binding by Metal-Organic Framework-5,” T. Sagara, J. Klassen, and E. Ganz, University of Minnesota Supercomputing Institute Research Report UMSI 2004/171, October 2004. 2004/195 “Propagation of Alfvén Waves at the Plasma Sheet Boundary Layer,” R. L. Lysak and Y. Song, University of Minnesota Supercomputing Institute Research Report UMSI 2004/195, October 2004. 2004/200 “Nonperturbative Solution of Yukawa Theory and Gauge Theories,” J. R. Hiller, presented at Light Cone 2004, Amsterdam, August 16–20, 2004. 2004/237 “QCD Phase Diagram at Small Baryon Densities From Imaginary µ: Status Report,” O. Philipsen and P. de Forcrand, University of Minnesota Supercomputing Institute Research Report UMSI 2004/237, December 2004. 2005/17 “Local Density of States and Order Parameter Configurations in Layered Ferromagnet-Superconductor Structures,” K. Halterman and O. T. Valls, University of Minnesota Supercomputing Institute Research Report 2005/17, February 2005. 2005/47 “Magnetosphere-Ionosphere Coupling by Alfvén Waves: Beyond Current Continuity,” R. L. Lysak and Y. Song, University of Minnesota Supercomputing Institute Research Report UMSI 2005/47, May 2005.

2006 Annual Research Report of the Supercomputing Institute 319 Index and Bibliography

Bibliography (continued) 2005/75 “Two-Dimensional Super Yang-Mills Theory Investigated With Improved Resolution,” J. R. Hiller, S. Pinsky, N. Salwen, and U. Trittmann, University of Minnesota Supercomputing Institute Research Report UMSI 2005/75, May 2005. 2005/77 “Binding Energies of Hydrogen Molecules to Isoreticular Metal-Organic Framework Materials,” T. Sagara, J. Klassen, J. Ortony, and E. Ganz, University of Minnesota Supercomputing Institute Research Report UMSI 2005/77, May 2005. 2005/83 “Phase Diagram of the Vortex System in Layered Superconductors With Strong Columnar Pinning,” C. Dasgupta and O. T. Valls, University of Minnesota Supercomputing Institute Research Report 2005/83, May 2005. 2005/91 “Under-Knotted and Over-Knotted Polymers: 1. Unrestricted Loops,” N. T. Moore, R. C. Lua, and A. Y. Grosberg, University of Minnesota Supercomputing Institute Research Report UMSI 2005/91, June 2005, and CB 2005-25. Publication in press, Physical and Numerical Models in Knot Theory Including Applications to the Life Sciences. 2005/92 “Under-Knotted and Over-Knotted Polymers: 2. Compact Self-Avoiding Loops,” R. C. Lua, N. T. Moore, and A. Y. Grosberg, University of Minnesota Supercomputing Institute Research Report UMSI 2005/92, June 2005, and CB 2005-26. Publication in press, Physical and Numerical Models in Knot Theory Including Applications to the Life Sciences. 2005/101 “Phonon Mediated Helium Atom Transmission Through Superfluid Helium Four,” K. A. Lidke, A. Wynveen, N. Baisch, C. Koay, C. F. Giese, and J. W. Halley, University of Minnesota Supercomputing Institute Research Report UMSI 2005/101, June 2005. 2005/102 “Mechanisms of Lithium Transport in Amorphous Polyethylene Oxide,” Y. Duan, J. W. Halley, L. Curtiss, and P. Redfern, University of Minnesota Supercomputing Institute Research Report UMSI 2005/102, June 2005. 2005/103 “Self Consistent Tight Binding Study of Low-Index Titanium Surfaces,” S. Erdin and J. W. Halley, University of Minnesota Supercomputing Institute Research Report UMSI 2005/103, June 2005. 2005/104 “Application of Self Consistent Tight Binding Method to the Study of Anatase Nanocrystals,” J. W. Halley, S. Erdin, Y. Lin, and P. Zapol, University of Minnesota Supercomputing Institute Research Report UMSI 2005/104, June 2005. 2005/105 “Helium-Vapor Dynamics: Can BEC Be Produced in a Moving Frame Without Confinement,” J. W. Halley, Y. Lutyshyn, and A. Wynveen, Laser Physics, 15, p. 636 (2005). 2005/119 “Nanoscale Ferromagnet-Superconductor-Ferromagnet Switches Controlled by Magnetization Orientation,” K. Halterman and O. T. Valls, University of Minnesota Supercomputing Institute Research Report 2005/119, August 2005. 2005/120 “Direct Evidence for the Maldacena Conjecture for N = (8,8) Super Yang-Mills Theory in 1+1 Dimensions,” J. R. Hiller, S. Pinsky, N. Salwen, and U. Trittmann, University of Minnesota Supercomputing Institute Research Report UMSI 2005/120, August 2005. 2005/142 “Two-Boson Truncation of Pauli-Villars-Regulated Yukawa Theory,” S. J. Brodsky, J. R. Hiller, and G. McCartor, University of Minnesota Supercomputing Institute Research Report UMSI 2005/142, August 2005.

320 2006 Annual Research Report of the Supercomputing Institute Index and Bibliography

Bibliography (continued) 2005/146 “Numerical Evidence for the Maldacena Conjecture in Two-Dimensional N = (8,8) Super Yang-Mills Theory,” J. R. Hiller, University of Minnesota Supercomputing Institute Research Report UMSI 2005/146, September 2005. 2005/158 “The Canonical Approach to Finite Density QCD,” S. Kratochvila and P. de Forcrand, University of Minnesota Supercomputing Institute Research Report UMSI 2005/158, October 2005. 2005/159 “Algorithm Shootout: R versus RHMC,” M. A. Clark, P. de Forcrand, and A. D. Kennedy, University of Minnesota Supercomputing Institute Research Report UMSI 2005/159, October 2005. 2005/178 “Interactions of Spin Waves With a Magnetic Vortex,” J. P. Park and P. A. Crowell, Physical Review Letters, 95, art. no. 167201 (2005). 2005/189 “New Isoreticular Metal-Organic Framework Materials for High Hydrogen Storage Capacity,” T. Sagara, J. Ortony, and E. Ganz, University of Minnesota Supercomputing Institute Research Report UMSI 2005/189, October 2005. Accepted for publication, Journal of Chemical Physics. 2005/223 “Finite Density QCD With a Canonical Approach,” P. de Forcrand and S. Kratochvila, University of Minnesota Supercomputing Institute Research Report UMSI 2005/223, December 2005. 2005/233 “Practical Applicability of the Jarzynski Relation in Statistical Mechanics: A Pedagogical Example,” R. C. Lua and A. Y. Grosberg, Journal of Physical Chemistry B, 109, p. 6805 (2005). 2005/234 “Limits of Analogy Between Self-Avoidance and Topology-Driven Swelling of Polymer Loops,” N. T. Moore and A. Y. Grosberg, Physical Review E, 72, art. no. 061803 (2005). 2005/237 “First Passage Times and Asymmetry of DNA Translocation,” R. C. Lua and A. Y. Grosberg, Physical Review E, 72, art. no. 061918 (2005) and CB 2005-66. 2006/34 “First Order Phase Transitions in Ferromagnet/Superconductor Layered Structures,” P. H. Barsic, O. T. Valls, and K. Halterman, University of Minnesota Supercomputing Institute Research Report 2006/34, April 2006. Physiology 2004/24 “Nerve Impulses and Their Encoding by Vertebrate Retinal Ganglion Cells: Temperature Effects and the Function of Membrane Capacitance,” J. F. Fohlmeister, University of Minnesota Supercomputing Institute Research Report UMSI 2004/24, February 2004 and CB 2004-4. 2004/25 “Nucleation and Accretion of Proto-Continents, and the Origin of Continental Drift; a Model Mechanism,” J. F. Fohlmeister, H.-C. Lin, and R. J. Renka, University of Minnesota Supercomputing Institute Research Report UMSI 2004/25, February 2004. 2004/26 “Plate-Kinematic Constraints From Mantle Bénard Convection,” J. F. Fohlmeister, Pure and Applied Geophysics, 161, p. 723 (2004). 2004/178 “Nerve Impulse Encoding Versus Axonal Propagation; Role of Membrane Capacitance and Temperature Q10 Restrictions,” J. F. Fohlmeister, University of Minnesota Supercomputing Institute Research Report UMSI 2004/178, October 2004 and CB 2004-48. Plant Biology 2004/83 “On the Origin of the Fig: Phylogenetic Relationships of Moraceae From ndhF Sequences,” S. L. Datwyler and G. D. Weiblen, American Journal of Botany, 91 p. 767 (2004) and CB 2004-27.

2006 Annual Research Report of the Supercomputing Institute 321 Index and Bibliography

Bibliography (continued) Plant Pathology 2006/25 “Insights Into Symbiotic Nitrogen Fixation in Medicago truncatula,” Mesfin Tesfaye, D. A. Samac, and C. P. Vance, Molecular Plant-Microbe Interactions, 19, p. 330 (2006) and CB 2006-2. 2006/41 “Towards Efficient Isolation of R Gene Orthologs From Multiple Genotypes: Optimization of Long Range-PCR,” M. J. Sanchez and J. M. Bradeen, Molecular Breeding, 17, p. 137 (2006) and CB 2006- 10. Soil, Water, and Climate 2004/284 “Concentration-Time Exposure Index for Modeling Soil Fumigation Under Various Management Scenarios,” D. Wang, J. M. He, and J. A. Knuteson, Journal of Environmental Quality, 33, p. 685 (2004). Surgery 2004/87 “Gene Expression Profiles in Esophageal Adenocarcinoma,” P. S. Dahlberg, L. F. Ferrin, S. M. Grindle, C. M. Nelson, C. D. Hoang, and B. Jacobson, The Annals of Thoracic Surgery, 77, p. 1008 (2004) and CB 2004-29. 2004/120 “Gene Expression Profiles in Matriptase Overexpression in Malignant Mesothelioma,” C. D. Hoang, J. D’Cunha, M. G. Kratzke, C. E. Casmey, S. P. Frizelle, M. A. Maddaus, and R. A. Kratzke, Chest, 125, p. 1843 (2004) and CB 2004-35. Veterinary and Biomedical Sciences 2005/90 “Regulation of Apoptotic Pathways in Bovine γ/δ T Cells,” M. Deng, J. Liu, C. N. Pelak, C. A. Lancto, and M. S. Abrahamsen, Veterinary Immunology and Immunopathology, 105, p. 15 (2005) and CB 2005- 24. 2005/108 “Gene Discovery and Expression Profiling in Porcine Peyer’s Patch,” C. M. T. Dvorak, K. A. Hyland, J. G. Machado, Y Zhang, S. C. Fahrenkrug, and M. P. Murtaugh, Veterinary Immunology and Immunopathology, 105, p. 301 (2005) and CB 2005-27. 2005/149 “Gene Expression Profiling of Jejunal Peyer’s Patches in Juvenile and Adult Pigs,” J. G. Machado, K. A. Hyland, C. M. T. Dvorak, and M. P. Murtaugh, Mammalian Genome, 16, p. 599 (2005) and CB 2005- 38.

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