Volume 26, Number 3 Supercomputing Institute for Advanced Computational Research a unit of the Office of the Vice President for Research

Fall 2010 Research Bulletin Medical Devices Medical Device Invention and Evaluation Through Simulation, Visualization, and Interactive Design apid advances in high-per - growing interest on the part of signer could have access to early, formance (supercomput - both industry and the Food and accurate feedback on device per - Ring) simulations are revo - Drug Administration (FDA) in formance and be able to exhaus - lutionizing biomedicine in both the using computer modeling and sim - tively explore many design itera - research and industrial context. ulation to support medical device tions. In this way, simulation could Scientists and engineers now run innovation and validation. As new reduce the time it takes to reach patient-specific computational capabilities to better incorporate bench tests and animal trials, make fluid dynamics (CFD) and finite simulation into engineering prac - these trials more efficient and ef - element analysis (FEA) simula - tice emerge, these can have a fective, and, in time, overtake tions at unprecedented levels of transformative impact on medical these methods as the primary eval - resolution and accuracy. A driving device engineering and medicine. uative approach in device design. force behind these advances is For example, a medical device de - To realize this potential will re - quire tackling several difficult re - search challenges. A group of University of Min - nesota researchers have begun a collaboration to work toward a vi - sion of an immersive design envi - ronment composed of coupled components for running simula -

Also in This Issue

2010 MSI Intern Program . . . .5 GPU Computing Conference . .8 2011 Research Exhibition . . . .8 New Supercomputer, Koronis .9 Figure 1. A new data-intensive medical device design workflow is made possible Viñals Welcome ...... 9 by rapidly advances in high-performance supercomputing. The system design Outreach Activities ...... 10 shown here couples simulation, visualization, and interaction with the goal of im - Research Reports ...... 12 proving early design feedback and evaluation and, eventually, leading to im - Email notification sign-up . . .18 proved design of safe and effective medical devices. Medical Devices

Figure 2. Groundbreaking fluid-solid interaction (FSI) models now make simulating accurate time-varying blood flow in pa - tient specific geometries possible. The simulation describes flow through a synthetic heart valve as it opens and closes with the beat of the heart inside of a patient-specific model of the left ventricle and aorta.

tions, visualizing and comparing ronment vision: the Interactive Vi - framework has been developed to massive numbers of results, and sualization Lab in the Department couple computational fluid dynam - interacting directly with the pa - of Computer Science and Engi - ics (CFD) simulations with ad - rameter space to explore new de - neering, the St. Anthony Falls vanced fluid-solid interaction vice designs. A schematic of this Laboratory (SAFL), and the Med - (FSI) models in order to simulate a immersive simulation-based virtu - ical Devices Center. Members of heartbeat and the resulting opening al design environment can be seen the team include: Dane Coffey and closing of mechanical valves in Figure 1. In this vision, all of (Computer Science), Trung Le implanted in the heart. Results the components are backed by (SAFL), Vamsi Konchada (Com - from this work have established a databases composed of pre-exist - puter Science), Nicholas Malbraat - new standard in physiologically ing device models, patient-specific en (Computer Science), Chi-Lun accurate cardiovascular simulation. anatomies, and tissue properties. Lin (Mechanical Engineering), Yi Figure 2 shows a visualization of This design environment would Sun (Mechanical Engineering), simulated blood flow through a enable a fundamentally new data- Molly Staker (Mechanical Engi - patient-specific model of the left intensive workflow for device en - neering), Iman Borazjani (SAFL), ventricle and aorta extracted from gineers to create initial designs Victoria Interante (Computer Sci - CT imaging data. The researchers and interactively refine them with ence), Daniel Keefe (Computer envision that the new power pro - the informed context provided by Science), Fotis Sotiropoulos (Di - vided by simulations such as these accurate simulation results. In rector, SAFL), and Arthur Erdman can form the backbone of the in - partnership with the Minnesota (Mechanical Engineering; Direc - teractive design environment out - Supercomputing Institute, three tor, Medical Devices Center). MSI lined in Figure 1. In this vision of groups across campus have started staff who have contributed to this the future, where fast, accurate to explore the research challenges research include Nancy Rowe and simulation is coupled with engi - associated with this new biomed - H. Birali Runesha. neering design tools, the results of ical workflow and immersive envi - A high-performance simulation multiple simulations could be

2 Supercomputing Institute Research Bulletin Fall 2010 Medical Devices

compared using visualization to techniques for visualizing data environment. In addition to room- understand the impact of different using immersive virtual reality sized VR environments, the team design parameters on valve func - (VR) provide new opportunities is also investigating the potential tion and the three-dimensional for insights and discoveries that of smaller scale, more affordable geometry of the valve could be ed - may have otherwise been missed. VR environments constructed ited interactively by engineers. Using visualization environments, using commercially available To employ this style of simula - such as the MSI PowerWall shown three-dimensional televisions, tion-based design workflow, new in Figure 3 (located in the which may provide the engineer - techniques for visualizing large, LCSE/MSI Visualization Labora - ing workbench of the future. complex datasets are needed. tory), scientists and engineers can In addition to the challenge of Rapid increases in complexity and view simulation results from the visualizing complex datasets, the resolution of CFD simulation data perspective of a blood cell, investi - new data-intensive workflow envi - parallel the exponential advances gating small-scale data features in sioned by the team also raises sig - in supercomputing resources. detail. Interactive VR environ - nificant challenges for human- However, a major bottleneck ex - ments, such as this one, combine computer interaction, as the suc - ists in conveying the information stereoscopic vision with three-di - cess of these visualizations de - that results from these visualiza - mensional head tracking to pro - pends heavily on the ability of en - tions to users. Traditional desktop- duce three-dimensional views of gineers to explore their data, test - based data visualizations struggle the data that update, recalculating ing hypotheses and forming new to convey the complex spatial rela - the correct perspective projection hypotheses as they work. To better tionships and other complexities in of the three-dimensional scene, as support visualization at the work - the data. In contrast, emerging scientists walk through the virtual bench scale, the team is new data

Figure 3. Immersive virtual reality (VR) visualizations provide scientists and engineers with new detailed views of complex anatomical geometries and data. Using the MSI PowerWall, results of a blood flow simulation through an aorta and synthet - ic heart valve can be explored interactively.

Fall 2010 Supercomputing Institute Research Bulletin 3 Medical Devices

Figure 4. New human-computer interfaces are needed to support data exploration. Here a multi-touch table display is cou - pled with a VR display to provide new possibilities for interacting with data, such as manipulating three-dimensional data that appears (through stereoscopic projection) to float above the table by manipulating its shadow.

exploration interfaces that leverage al data from a blood flow simula - serve as the a medical device de - emerging technologies, such as tion using rich multi-touch ges - signer’s workbench, enabling new multi-touch input. Figure 4 shows tures made on top of an interactive modes of refining design itera - a semi-immersive VR environment shadow of the data displayed on tions, spinning off high-resolution that is coupled with a large multi- the table. In addition to supporting simulations, and organizing mas - touch table display. This environ - rich input, the table display surface sive amounts of data, and, ulti - ment makes it possible to explore also provides a large visual surface mately, leading to improved inno - complex three-dimensional data- capable of organizing and display - vation and design of safe and ef - sets in using a variety of new in - ing additional information. In the fective medical devices. teraction metaphors. For example, future, the researchers expect that in the figure, the user navigates interactive visual data exploration through complex three-dimension - environments such as this one will

4 Supercomputing Institute Research Bulletin Fall 2010 Supercomputing Institute Programs

2010 Undergraduate Internship Program he Supercomputing Insti - other researchers and also prepare University of Minnesota chem - tute’s Undergraduate Intern - a written report. istry major Erik M. Fritz worked Tship Program, now in its The Summer 2010 program in - with Professor Steven A. Kass, 20th year, gives undergraduates cluded 11 interns who worked on Department of Chemistry and Su - the opportunity to experience projects in a wide variety of fields. percomputing Institute Fellow. Mr. working in a research environ - They were selected from over 100 Fritz, who was also in the 2009 in - ment. The interns get to participate applicants at colleges and universi - tern program in the Kass group, in a challenging and enriching ed - ties in the United States and Puer - worked on a project called “Ener - ucational experience that helps to Rico. Eight of the interns gy Barriers and Relative Basicity.” them decide whether they want to worked on projects sponsored by Timothy M. Hecht was in the pursue graduate or professional the Supercomputing Institute’s Re - research group of Professor J. education and research. The pro - search Experiences for Undergrad - Woods Halley, Department of gram encompasses digital simula - uates (REU) grant from the Na - Physics and Supercomputing Insti - tion and advanced computation tional Science Foundation (NSF), tute Fellow. Mr. Hecht is a physics and all aspects of high-perform - two were sponsored by internal major with mathematics and busi - ance computing and scientific MSI funds, and one was sponsored ness minors at Brigham Young modeling and simulation, as well by his faculty mentor’s NSF grant. University in Provo, Utah. His as graphics, visualization, infor - Bjorn K. Berntson , a Universi - project was entitled “Electronic matics, and high-performance net - ty of Minnesota physics and math - Spin Structures of Pt, O, and H work communications. Interns ematics double major, worked With Possible Catalysis Applica - work with Principal Investigators with Professor Christopher J. tions.” at the Supercomputing Institute Cramer, Department of Chemistry Michelle S. Lenz , from Bethel and their research groups on their and MSI Fellow. Mr. Berntson’s University in St. Paul, Minnesota, projects. They give a presentation project was titled “Electronic worked with the research group of about their research to the intern Structure Characterization of the Regents Professor Donald G. group as well as the faculty and (bpy) 2MO 2 Catalyst.” Truhlar, Department of Chemistry

Michelle Lenz, Tim Hecht, Erik Fritz, and Bjorn Berntson at the intern program Welcome Luncheon.

Fall 2010 Supercomputing Institute Research Bulletin 5 Supercomputing Institute Programs

Adam M. Novak , who attends Harvey Mudd College in Clare - mont, California, worked with Professor Victor Barocas, Depart - ment of Biomedical Engineering and Supercomputing Institute Fel - low. Mr. Novak is a double major in computer science and biology, and his project was “Multi-scale Modeling on the GPU.” University of Minnesota mathe - matics major David A. Sanchez worked with Professor David A. Yuen, Department of Geology and Geophysics and Supercomputing Institute Fellow. His project was “2D and 3D Mantle Convection on Andrew Wesson gives his presentation. the GPU.” Ashwin P. Srikrishna , who at - tends North Carolina State Univer - and Supercomputing Institute Fel - computing Institute Associate Fel - sity in Raleigh, North Carolina, low. Ms. Lenz is an engineering low. His project was “Anthrax worked with Assistant Professor science major with an emphasis in Toxin Lethal Factor Inhibitors: In Kevin Dorfman, Department of biomedical engineering, and her Silico Design Approaches.” Chemical Engineering and Materi - project was “Electrochemical Brendan A. Murphy , a Univer - als Science and Supercomputing Properties of Ruthenium Catalysts sity of Minnesota biomedical engi - Institute Associate Fellow. Mr. in Solution.” neering major, worked with Assis - Srikrishna majors in chemical en - University of Minnesota neuro - tant Professor Tay I. Netoff, De - gineering with a minor in nuclear science major Aatif Mansoor partment of Biomedical Engineer - engineering. Mr. Srikrishna’s proj - worked with Assistant Professor ing. His project was “Deep Brain ect was entitled “Parallelization of Elizabeth A. Amin, Department of Stimulation and Neuronal Syn - a Brownian Dynamics Simulation Medicinal Chemistry and Super - chrony.”

Left to right: Andrew Wesson, Bjorn Berntson, Erik Fritz, Aatif Mansoor, Adam Novak, Michelle Lenz, Alexandra Zudova, Tim Hecht, Aaron Erdman, and Ashwin Shrikrishna.

6 Supercomputing Institute Research Bulletin Fall 2010 Supercomputing Institute Programs

of DNA Electrophoresis in a Non - homogeneous Electric Field.” Summer 2011 Andrew J. Wesson attends Undergraduate Internship Program Carnegie Mellon University in Pittsburgh, Pennsylvania, where he The Supercomputing Institute is pleased to announce its Under - is a physics major. He worked in graduate Internship Program for Summer 2011. Appointments are for the research group of Professor full-time, 10-week internships, and will run from June 6 through Au - Thomas W. Jones, Department of gust 12, 2011. A student interested in becoming an intern must still Astronomy, Supercomputing Insti - be an undergraduate in August 2011 and must be a citizen or perma - tute Fellow, and Interim Director nent resident of the United States or its possessions. Interns will be of the Institute until August 1, paid a stipend of $5,000. Room and board at the University resi - 2010. His project was “Radiative dence hall are free to the interns. If interns wish to live elsewhere, Cooling in Astrophysical Magne - they will receive a per-diem food allowance and can request reim - to-Hydrodynamic Simulations.” bursement for housing costs. Alexandra M. Zudova , a Uni - versity of Minnesota chemical en - All applications are evaluated competitively based on the qualifi - gineering major with a chemistry cations of the applicant and the availability of a suitable project. minor, worked with Professor Projects are available in the following disciplines: David D. Thomas, Department of Biochemistry, Molecular Biology, Aerospace Engineering and Mechanics and Biophysics and MSI Fellow. Astronomy Her project was “Molecular Dy - Biochemistry namics Simulation of a Spin-la - Biomedical Engineering beled Membrane Protein.” Chemistry While not a member of the for - Computer Science mal program, Aaron Erdman , a Geology and Geophysics student at Century College in Medicinal Chemistry White Bear Lake, Minnesota, par - Physics ticipated in many of the intern pro - gram’s activities during the sum - Complete application information, application forms, and project mer. Mr. Erdman is a student in lists are available on the Supercomputing Institute website at: the Telecommunication Technolo - www.msi.umn.edu/programs/undergraduateinternship.html gy program at Century. He worked with MSI Scientific Computing Applications, transcripts, and letters of recommendation can be Consultant Nancy Rowe on sever - emailed, faxed, or mailed as shown below. al projects at the LCSE-MSI Visu - Email: [email protected] alization Laboratory during the Fax: 612-624-8861 summer. Mail: Undergraduate Internship Coordinator See the sidebar on this page for University of Minnesota the announcement about next Supercomputing Institute year’s intern program. 599 Walter 117 Pleasant Street SE Minneapolis, MN 55455 Phone: (612) 624-2330

All applications and letters of recommendation must be received by February 28, 2011.

Fall 2010 Supercomputing Institute Research Bulletin 7 Events

International Workshop on GPU Computing avid A. Yuen (Geology and Geophysics and MSI DFellow) was on the organ - izing committee for the 2010 In - ternational Workshop of GPU So - lutions to Multiscale Problems in Science and Engineering, which was held in Harbin, China during Summer 2010. The two-day work - shop included over 100 attendees from colleges, universities, and re - search centers from around the world. The attendees discussed such topics as GPU solutions to multi-scale problems, focusing on high-performance computing trends. Besides Professor Yuen, at - presentation), MSI Summer 2010 methods and algorithms, efficient tendees from the University of Undergraduate Intern David A. software implementation tech - Minnesota included MSI Scientific Sanchez (see article, page 5), and nique, the construction of the sci - Computing Consultant Dr. Shuxia MSI Summer 2009 Undergraduate entific computing environment, Zhang (shown above, giving a Intern Robin Weiss. and mainstream development

MSI Research Exhibition 2011

MSI will host a Research Exhibition poster session on April 29, 2011. All MSI researchers will be invited to present posters of their work using MSI re - sources. Prizes will be awarded to the outstanding posters.

The Call for Posters will be sent out in early February. We will post more in - formation as it becomes available on the Research Exhibition 2011 website (www.msi.umn.edu/events/researchexhibition2011.html ).

8 Supercomputing Institute Research Bulletin Fall 2010 Supercomputing Institute News

New Supercomputer, “Koronis” SI was recently awarded major users of Koronis an NIH grant that is al - will include Jiali Gao Mlowing us to purchase a (Chemistry, MSI Fel - new supercomputing system, low), Donald Truhlar which has been named “Koronis” (Chemistry, MSI Fel - after a lake in central Minnesota. low), George Karypis Koronis features an SGI Altix UV (Computer Science and 1000 supercomputer that has a Engineering, MSI Asso - shared-memory architecture in ciate Fellow), David which each core can access all 3.1 Largaespada (Genetics, terabytes of memory directly. Ko - Cell Biology, and De - ronis also includes high-perform - velopment), Kelvin Lim ance visualization workstations (Psychiatry), and Bin and high-performance and -fidelity He (Biomedical Engi - data storage. This system will be neering). Koronis will used by MSI researchers working also be available to on a number of NIH-funded proj - other MSI researchers ects in the areas of multi-scale who have NIH funding. modeling, chemical dynamics, Koronis was deliv - bioinformatics and computational ered in early October and is under - site as it becomes available: biology, and biomedical imaging. going acceptance testing. It should www.msi.umn.edu/hardware/ The Principal Investigator on the be available for full-scale use in grant is Professor Darrin York January 2011. Up-to-date informa - (Chemistry, MSI Fellow). Other tion can be found on the MSI web - Welcome Reception for MSI Director n September 14, MSI held a reception to formally welcome Jorge Viñals as the new Director of the Su - percomputing Institute. Attendees included MSI researchers and staff, members of the staff of the Office Oof the Vice President for Re - search, supercomputing vendors, and other members of the MSI extended community. In the picture at right, Vice President for Research Tim Mulcahey makes a few welcoming re - marks. Left to right: Jorge Viñals, H. Birali Runesha (MSI Assistant Direc - tor of Scientific Computing), Tim Mulcahey, Mike Balak (IT Director, CFANS), and Brian Ropers-Huilman (MSI Assistant Director of HPC Oper - ations). At far right, back to camera, Mark Nelson (MSI HPC Systems Ad - ministrator).

Fall 2010 Supercomputing Institute Research Bulletin 9 Supercomputing Institute Outreach

Outreach Activities

MSI at the Minnesota State Fair On September 2, 2010, MSI was at the Minnesota State Fair with the Medical Devices Cen - ter. Visitors to the University of Minnesota’s building that day got to “fly through” a three-di - mensional visualization of a heart. In the picture at right, MSI Visualization Specialist Mike Knox (right, in yellow shirt) talks to a fair visitor about what she’s seeing on- screen. The visitor is wearing 3D glasses to view the image.

Math and Science Family Fun Fair MSI participated in the College of Sci - ence and Engineering’s Math and Sci - ence Family Fun Fair on Saturday, No - vember 13. MSI staff members Yectli Huerta and Samantha Thomas and MSI PI Carlos Sosa and his son Daniel showed the visiting kids and their par - ents how supercomputers help re - searchers. The children were able to build model molecules and see how scientists use computers to make ani - mated molecule simulations.

10 Supercomputing Institute Research Bulletin Fall 2010 Supercomputing Institute Outreach

Visitors to the LCSE-MSI Visualization Laboratory

On October 14, two groups of middle-school students from the Washington Technology Magnet school in St. Paul, Minnesota vis - ited the lab. These students are part of the BioSMART (Biologi - cally focused Science, Math, Aca - demic Rigor, and Technology) Program. The students watched three-dimensional visualizations on the LMVL’s large screen and learned how doctors and scientists use these visualizations.

On October 21, students participating in “Body Forward,” the 2010 Minnesota FIRST LEGO League robotics competition, visited the LMVL as part of the University of Minnesota Research Workshop. At left, Assistant Pro - fessor Matt Johnson (Biomedical En - gineering, MSI Principal Investigator) shows the students how doctors can look at CAT scans in three dimen - sions. The students also got to partici - pate in some hands-on virtual reality brain surgery. The University of Min - nesota Research Workshop is hosted by the College of Science and Engi - neering. More information about FIRST LEGO League can be found at www.firstlegoleague.org .

On November 12, Dave Plescia, a repre - sentative from Johnson & Johnson, visit - ed the University of Minnesota to discuss collaboration possibilities with University researchers involved in medical-device development. Professors Dan Keefe (Computer Science and Engineering), Fotis Sotiropoulos (Director, SAFL), and Art Erdman (Mechanical Engineering; Director, Medical Devices Center) and some of their students attended the pres - entation about Johnson & Johnson’s med - ical devices. Mr. Plescia (pictured at right) also watched some of the visualiza - tions currently being created using MSI resources.

Fall 2010 Supercomputing Institute Research Bulletin 11 Research Reports

Aerospace Engineering 2010/147 and CB 2010-50 Biochemistry, Molecular The Genetics of Barley Low-Tiller - and Mechanics ing Mutants: Low number of Biology, and Biophysics Tillers-1 (lnt1) 2010/137 T. Dabbert, R.J. Okagaki, S. Cho, 2010/89 and CB 2010-34 Dynamic k-Equation Model for S. Heinen, J. Boddu, and G.J. Structural Insight Into Methyl- Large Eddy Simulation of Com - Muehlbauer Coenzyme M Reductase Chemistry pressible Flows 2010/148 and CB 2010-51 Using Coenzyme B Analogues X. Chai and K. Mahesh Structural and Functional Charac - P.E. Cedervall, M. Dey, A.R. Pear - 2010/138 terization of a Winter Malting Bar - son, S.W. Ragsdale, and C.M. Euler-Lagrangian Simulation of ley Wilmot Bubble Migration in a Turbulent M. Munoz-Amatriain, L. Cistue, Y. 2010/90 and CB 2010-35 Boundary Layer Xiong, H. Bilgic, A.D. Budde, Structural Features Promoting M. Mattson and K. Mahesh M.R. Schmitt, K.P. Smith , P.M. Dioxygen Production by 2010/139 Hayes, and G.J. Muehlbauer Dechloromonas aromatica Chlorite Simulations of High Speed Turbu - 2010/172 and CB 2010-63 Dismutase lent Jets in Crossflow Transcript Profiling of Common B.R. Goblirsch, B.R. Streit, J.L. X. Chai and K. Mahesh Bean ( Phaseolus vulgaris L .) Using DuBois, and C.M. Wilmot 2010/140 the GeneChip Soybean Genome 2010/91 and CB 2010-36 Transition of Hypersonic Flow Array: Optimizing Analysis by Kinetic and Structural Analysis of Past Flat Plate With Roughness El - Masking Biased Probes Substrate Specificity in Two Cop - ements S.S. Yang, O. Valdes-Lopez, W.W. per Amine Oxidases From P.S. Iyer, S. Muppidi, and K. Ma - Xu, B. Bucciarelli, J.W. Gron - Hansenula polymorpha hesh wald , G. Hernandez, and C.P. C.M. Chang, V.J. Klema, B.J. Vance Johnson, M. Mure, J.P. Klinman, 2010/191 and C.M. Wilmot DNS of Transition in Supersonic 2010/173 and CB 2010-64 Boundary Layers Transcript Profiling of Two Alfalfa 2010/92 and CB 2010-37 S. Muppidi and K. Mahesh Genotypes With Contrasting Cell In Crystallo Posttranslational Wall Composition in Stems Using a Modification Within a MauG/Pre- Agronomy and Cross-Species Platform: Optimiz - Methylamine Dehydrogenase Com - ing Analysis by Masking Biased plex Plant Genetics Probes L.M.R. Jensen, R. Sanishvili, V.L. S.S. Yang, W.W. Xu, M. Tesfaye, Davidson, and C.M. Wilmot 2010/131 and CB 2010-44 J.F.S. Lamb, H.J.G. Jung, K.A. An Integrative Approach to Ge - 2010/149 and CB 2010-52 VandenBosch, C.P. Vance , and Phosphorylation-Induced Structur - nomic Introgression Mapping J.W. Gronwald A.J. Severin, G.A. Peiffer, W.W. al Changes in Smooth Muscle Xu, D.L. Hyten, B. Bucciarelli, Animal Science Myosin Regulatory Light Chain J.A. O’Rourke, Y.-T. Bolon, D. D. Kast, L.M. Espinoza-Fonseca, Grant, A.D. Farmer, G.D. May, 2010/134 and CB 2010-45 C. Yi, and D.D. Thomas C.P. Vance , R.C. Shoemaker, and Genome-Wide Association Analysis R.M. Stupar of Total Cholesterol and High-Den - 2010/146 and CB 2010-49 sity Lipoprotein Cholesterol Levels Transcriptome Analysis of the Bar - Using the Framingham Heart ley –Deoxynivalenol Interaction: Study Data Evidence for a Role of Glutathione L. Ma, J. Yang, H. B. Runesha, T. in Deoxynivalenol Detoxification Tanaka, L. Ferrucci, S. Bandinelli, S.A. Gardiner, J. Boddu, F. and Y. Da Berthiller, C. Hametner, R.M. Stu - par , G. Adam, and G.J. Muehlbauer

Names of Supercomputing Institute principal investigators appear in bold type. This list contains reports entered into the reports database during August –November 2010.

12 Supercomputing Institute Research Bulletin Fall 2010 Research Reports

2010/169 and CB 2010-60 Chemical Engineering 2010/192 Synthesis, Properties, and Applica - Quasiharmonic Thermal Elasticity tions of Diazotrifluropropanoyl- and Materials Science of Crystals: An Efficient Analytical Containing Photoactive Analogs of Approach Farnesyl Diphosphate Containing 2010/104 Z. Wu and R.M. Wentzcovitch Modified Linkages for Enhanced Koopmans’ Condition for Density- 2010/193 Stability functional Theory The Hubbard U Correction for M.L. Hovlid, R.L. Edelstein, O. I. Dabo, A. Ferretti, N. Poilvert, Y. Iron-Bearing Minerals: A Discus - Henry, J. Ochocki, A. DeGraw, S. Li, N. Marzari, and M. Cococcioni sion Based on (Mg,Fe)SiO 3 Per - Lenevich, T. Talbot, V.G. Young, 2010/113 ovskite A.W. Hruza, F. Lopez-Gallego, Dynamics of Surface Structure H. Hsu, K. Umemoto, M. Cococ - N.P. Labello, C.L. Strickland, C. Evolution in Colloidal Adsorption: cioni , and R.M. Wentzcovitch Schmidt-Dannert , and M.D. Dis - Charge Patterning and Polydisper - tefano 2010/194 sity Thermodynamic Properties of 2010/200 and CB 2010-80 D.D. Brewer, M. Tsapatsis , and S. MgSiO 3 Majorite and Phase Tran - LTQ-iQuant: A Freely Available Kumar sitions Near 660-km Depth in Software Pipeline for Automated 2010/133 MgSiO 3 and Mg 2SiO 4: A First and Accurate Protein Quantifica - Accurate and Efficient Calcula - Principles Study tion of Isobaric Tagged Peptide tions on Strongly Correlated Min - Y.G. Yu, R.M. Wentzcovitch , V.L. Data From LTQ Instruments erals With the LDA+U Method: Vinograd, and R.J. Angel G. Onsongo, M.D. Stone, S.K. Van Review and Perspectives 2010/195 Riper, J. Chilton, B. Wu, L. Hig - M. Cococcioni gins, T.C. Lund, J.V. Carlis , and Effect of the d Electrons on Phase 2010/136 T.J. Griffin Transitions in Transition-Metal Tuning the Charge-Transport Pa - Sesquioxides BioTechnology Institute rameters of Perylene Diimide Sin - K. Umemoto and R.M. Wentzcov - gle Crystals via End and/or Core itch 2010/145 and CB 2010-48 Functionalization: A Density Func - Switching From an Esterase to a tional Theory Investigation Chemical Engineering, Hydroxynitrile Lyase Mechanism M.C. Ruiz Delgado, E.-G. Kim, UMD Requires Only Two Amino Acid D.A. da Silva Filho, and J.-L. Substitutions Bredas 2010/197 S.K. Padhi, R. Fujii, G.A. Legatt, 2010/174 Combined Gravitational and Ther - S.L. Fossum, R. Berchtold, and Existence, Stability, and Nonlinear mocapillary Interactions of Spheri - R.J. Kazlauskas Dynamics of Detached Bridgman cal Drops With Incompressible Growth States Under Zero Gravity Surfactant Center for Drug Design A. Yeckel and J.J. Derby M.A. Rother 2010/93 and CB 2010-38 2010/176 and CB 2010-67 Dual Inhibitors of Inosine Free Energy Profile of the Interac - Chemistry Monophosphate Dehydrogenase tion Between a Monomer or a and Histone Deacetylase Based on Dimer of Protegrin-1 in a Specific 2010/95 and CB 2010-41 a Cinnamic Hydroxamic Acid Core Binding Orientation and a Model Equilibrium Mercury Isotope Frac - Structure Lipid Bilayer tionation Between Dissolved Hg(II) L. Chen, R. Petrelli, G. Gao, D.J. V. Vivcharuk and Y. Kaznessis Species and Thiol-Bound Hg J.G. Wiederhold, C.J. Cramer , K. Wilson, G.T. McLean, H.N. Ja - 2010/177 and CB 2010-66 Daniel, I. Infante, B. Bourdon, and yaram, Y.Y. Sham , and K.W. Antimicrobial Mechanism of Pore- R. Kretzschmar Pankiewicz forming Protegrin Peptides: 100 2010/168 and CB 2010-59 Pores to Kill E. coli 2010/96 and CB 2010-40 N-3 Hydroxylation of Pyrimidine- D. Bolintineanu, E. Hazrati, H.T. High Tg Aliphatic Polyesters by 2,4-diones Yields Dual Inhibitors of Davis, R.I. Lehrer, and Y.N. Kaz - the Polymerization of Spirolactide HIV Reverse Transcriptase and In - nessis Derivatives tegrase G.L. Fiore, F. Jing, V.G. Young, Jr., J. Tang, K. Maddali, C.D. Dreis, C.J. Cramer , and M.A. Hillmyer Y.Y. Sham , R. Vince, Y. Pommier, and Z. Wang

Fall 2010 Supercomputing Institute Research Bulletin 13 Research Reports

2010/97 2010/156 2010/164 and CB 2010-57 Prediction of SAMPL2 Aqueous Binding Energy of d 10 Transition Direct Dynamics Implementation of Solvation Free Energies and Tau - Metals to Alkenes by Wave Func - the Least-Action Tunneling Trans - tomeric Ratios Using the SM8, tion Theory and Density Function - mission Coefficient. Application to SM8AD, and SMD Solvation Mod - al Theory the CH 4/CD 3H/CD 4 + CF 3 Ab - els B.B. Averkiev, Y. Zhao, and D.G. straction Reactions R.F. Ribeiro, A.V. Marenich, C.J. Truhlar R. Meana-Paneda, D.G. Truhlar , Cramer , and D.G. Truhlar 2010/157 and CB 2010-55 and A. Fernandez-Ramos 2010/126 Density Functional Calculations of 2010/167 and CB 2010-58 Enolates in 3-D: An Experimental E2 and S N2 Reactions: Effects of Density-Functional Expansion and Computational Study of De - the Choice of Density Functional, Methods: Evaluation of LDA, GGA protonated 2-Adamantanone Basis Set, and Self-Consistent Iter - and Meta-GGA Functionals and M.M. Meyer and S.R. Kass ations Different Integral Approximations 2010/127 and CB 2010-43 Y. Zhao and D.G. Truhlar T.J. Giese and D.M. York An Infrared Multiphoton Dissocia - 2010/158 2010/169 and CB 2010-60 tion Spectroscopy Study of Proto - On the Performances of the M06 Synthesis, Properties, and Applica - nated p-Aminobenzoic Acid: Does Family of Density Functionals for tions of Diazotrifluropropanoyl- Electrospray Ionization Afford the Electronic Excitation Energies Containing Photoactive Analogs of Amino- or Carboxy-Protonated D. Jacquemin, E.A. Perpete, I. Farnesyl Diphosphate Containing Ion? Ciofini, C. Adamo, R. Valero, Y. Modified Linkages for Enhanced J. Schmidt, I. Spector, M.M. Zhao, and D.G. Truhlar Stability Meyer, and S.R. Kass 2010/159 and CB 2010-56 M.L. Hovlid, R.L. Edelstein, O. 2010/135 and CB 2010-46 Communication: Energetics of Re - Henry, J. Ochocki, A. DeGraw, S. Internal Proton Transfer in the Ex - action Pathways for Reactions of Lenevich, T. Talbot, V.G. Young, ternal Pyridoxal 5’-Phosphate Ethenol With the Hydroxyl Radical: A.W. Hruza, F. Lopez-Gallego, Schiff Base in Dopa Decarboxylase The Importance of Internal Hydro - N.P. Labello, C.L. Strickland, C. Y. Lin and J. Gao gen Bonding at the Transition State Schmidt-Dannert , and M.D. Dis - tefano 2010/152 and CB 2010-54 O. Tishchenko, S. Ilieva, and D.G. Tunneling in Enzymatic and Truhlar 2010/170 and CB 2010-61 Nonenzymatic Hydrogen Transfer 2010/161 Selective Labeling of Polypeptides Reactions Density Functional Approximations Using Protein Farnesyltransferase D.G. Truhlar for Charge Transfer Excitations via Rapid Oxime Ligation With Intermediate Spatial Overlap M. Rashidian, J.K. Dozier, S. 2010/153 Lenevich, and M.D. Distefano Tests of the RPBE, revPBE, τ-HC - R. Li, J. Zheng, and D.G. Truhlar THhyb, wB97X-D, and MOHLYP 2010/162 2010/171 and CB 2010-62 Density Functional Approximations Sorting Out the Relative Contribu - Evaluation of Alkyne-Modified Iso - and 29 Others Against Representa - tions of Electrostatic Polarization, prenoids as Chemical Reporters of tive Databases for Diverse Bond Dispersion, and Hydrogen Bonding Protein Prenylation Energies and Barrier Heights in to Solvatochromic Shifts on Verti - A.J. DeGraw, C. Palsuledesai, J.D. Catalysis cal Electronic Excitation Energies Ochocki, J.K. Dozier, S. Lenevich, K. Yang, J. Zheng, Y. Zhao, and A.V. Marenich, C.J. Cramer , and M. Rashidian, and M.D. Distefano D.G. Truhlar D.G. Truhlar 2010/160 2010/154 2010/163 Free-Energy Surfaces for Liquid- Density Functional Study of CO Computational Thermochemistry: Phase Reactions and Their Use To and NO Adsorption on Ni-doped Scale Factor Databases and Scale Study the Border Between Concert - MgO(100) Factors for Vibrational Frequen - ed and Nonconcerted α, b-Elimina - R. Valero, J.R.B. Gomes, D.G. cies Obtained From Electronic tion Reactions of Esters and Truhlar , and F. Illas Model Chemistries Thioesters I.M. Alecu, J. Zheng, Y. Zhao, and Y. Kim, J.R. Mohrig, and D.G. 2010/155 and CB 2010-53 Truhlar Kinetics of Hydrogen-Transfer Iso - D.G. Truhlar merizations of Butoxyl Radicals J. Zheng and D.G. Truhlar

14 Supercomputing Institute Research Bulletin Fall 2010 Research Reports

2010/181 and CB 2010-68 2010/188 and CB 2010-74 2010/112 A Non-Orthogonal Block-Localized Long-Range Electronic Communi - GPU-Accelerated Preconditioned Effective Hamiltonian Approach cation in Free-Base Meso- Iterative Linear Solvers for Chemical and Enzymatic Reac - Poly(Ferrocenyl)-Containing Por - R. Li and Y. Saad tions phyrins 2010/114 A. Cembran, A. Payaka, Y. Lin, V.N. Nemykin , G.T. Rohde, C.D. Domain-Decomposition-Type W. Xie, Y. Mo, L. Song, and Barrett, R.G. Hadt, J.R. Sabin, Methods for Computing the Diago - J. Gao G. Reina, P. Galloni, and B. Floris nal of a Matrix Inverse 2010/182 2010/189 and CB 2010-75 J.M. Tang and Y. Saad Generalized X-Pol Theory and Interpretation of the UV–vis Spec - 2010/115 Charge Delocalization States tra of the Meso(Ferrocenyl)-Con - Sparse Approximations of the J. Gao , A. Cembran, and Y. Mo taining Porphyrins Using a Schur Complement for Parallel Al - 2010/183 and CB 2010-69 TDDFT Approach: Is Gouterman’s gebraic Hybrid Solvers in 3D On the Interfragment Exchange in Classic Four-Orbital Model Still in L. Giraud, A. Haidar, and Y. Saad the X-Pol Method Play? V.N. Nemykin and R.G. Hadt 2010/200 and CB 2010-80 A. Cembran, P. Bao, Y. Wang, LTQ-iQuant: A Freely Available L. Song, D.G. Truhlar , and J. Gao Civil Engineering Software Pipeline for Automated 2010/184 and CB 2010-70 and Accurate Protein Quantifica - Internal Dynamics of an Analyti - 2010/124 tion of Isobaric Tagged Peptide cally Coarse-Grained Protein Reactivity of Alkyl Polyhalides to - Data From LTQ Instruments M.J.M. Mazack, A. Cembran, and ward Granular Iron: Development G. Onsongo, M.D. Stone, S.K. Van J. Gao of QSARs and Reactivity Cross Riper, J. Chilton, B. Wu, L. Hig - 2010/185 and CB 2010-71 Correlations for Reductive Dehalo - gins, T.C. Lund, J.V. Carlis , and The Opsin Shift and Mechanism of genation T.J. Griffin D.M. Cwiertny, W.A. Arnold , T. Spectral Tuning in Rhodopsin Computer Science, UMD R. Rajamani, Y. Lin, and J. Gao Kohn, L.A. Rodenburg, and A.L. Roberts 2010/186 and CB 2010-72 2010/118 Energy Decomposition Analysis 2010/178 Computational Approaches to Based on Block-Localized Wave - Large-Eddy Simulation of Stably- Measuring the Similarity of Short Function and Multistate Density Stratified Flow Over a Steep Hill Contexts: A Review of Applications Functional Theory F. Wan and F. Porté-Agel and Methods Y. Mo, P. Bao, and J. Gao 2010/179 T. Pedersen 2010/196 CB 2010-78 Large-Eddy Simulation of Wind- 2010/165 Active Participation of Mg 2+ Ion in turbine Wakes: Evaluation of Tur - Towards Improving Synonym Op - the Reaction Coordinate of RNA bine Parametrisations tions in a Text Modification Appli - Self-Cleavage Catalyzed by the Y.-T. Wu and F. Porté-Agel cation Hammerhead Ribozyme 2010/180 J. Burstein and T. Pedersen K. Wong, T.S. Lee , and D.M. York Large-Eddy Simulation of a Very Economics Chemistry and Large Wind Farm in a Stable At - mospheric Boundary Layer Biochemistry, UMD 2010/129 H. Lu and F. Porté-Agel Computing Dynamic Optimal Mechanisms When Hidden Types 2010/187 and CB 2010-73 Computer Science Are Markov Unexpected Fluorescence Proper - K. Fukushima and Y. Waki ties in an Axially σ-bonded Ferro - and Engineering cenyl-Containing Porphyrin 2010/130 P,V. Solntsev, J,R. Sabin, S,J. 2010/98 Quantifying the Welfare Gains Dammer, N,N. Gerasimchuk, and Content-Based Methods for Pre - From Flexible Dynamic Income V.N. Nemykin dicting Web-Site Demographic At - Tax Systems tributes K. Fukushima S. Kabbur, E.-H. Han, and G. Karypis

Fall 2010 Supercomputing Institute Research Bulletin 15 Research Reports

Electrical and Computer 2010/109 Mechanical Engineering The Impact of Variability in the Engineering Rheological Activation Parameters 2010/105 on Lower-Mantle Viscosity Stratifi - The Effects of Turbulence on 2010/100 cation and Its Dynamics Nanoparticle Growth in Turbulent Quantitative Analysis of Interac - C. Matyska, D.A. Yuen , and H. Reacting Jets tion Between Domain Walls and Cizkova S. Das and S.C. Garrick Magnetic Nanoparticles 2010/128 2010/106 T. Klein, D. Dorroh, Y. Li, and J.- Numerical Modeling of Protocore Modeling and Simulation of Titani - P. Wang Destabilization During Planetary um Dioxide Nanoparticle Synthesis 2010/141 Accretion: Feedbacks From Non- With Finite-Rate Sintering in Pla - Simulation of Erase After Write on Newtonian Rheology and Energy nar Jets 2.4T FeCo Solid Pole Writer Dissipation S.C. Garrick and G. Wang M. Patwari and R.H. Victora J.-R. Lin, T.V. Gerya, P.J. Tackley, D.A. Yuen , and G.J. Golabek 2010/107 2010/142 and CB 2010-47 On the Effect of Nanoparticle Size Optimization of Magnetic Laboratory Medicine in Homogeneous Metal Vapor Nu - Anisotropy and Applied Fields for cleation Hyperthermia Applications and Pathology J. Liu and S.C. Garrick H. Sohn and R.H. Victora 2010/108 2010/143 2010/119 and CB 2010-42 Large Eddy Simulation of Titanium Calculation of Spin Transfer S-MED: Sarcoma microRNA Ex - Dioxide Nanoparticle Formation Torque in Partially Polarized Spin pression Database and Growth in Turbulent Jets Valves Including Multiple Reflec - A.L. Sarver, R. Phalak, V. Thayan- J. Loffler, S. Das, and S.C. Gar - tions ithy, and S. Subramanian rick S. Hernandez and R.H. Victora Mathematics 2010/166 2010/144 Particle-in-Cell and Monte Carlo Extracting Intergranular Exchange 2010/125 Collision Simulation of Positive Coupling in Perpendicular Mag - The Zeta Function on the Critical and Negative Corona Plasmas netic Recording Media Line: Numerical Evidence for Mo - P. Wang, J. Chen, F.-G. Fan, and Y. Dong and R.H. Victora ments and Random Matrix Theory J.A. Swift Models Finance G.A. Hiary and A.M. Odlyzko Pharmaceutics 2010/203 Mathematics, 2010/94 and CB 2010-39 Effects of Real and Financial Fric - U of St. Thomas Understanding the Relationship tions on Corporate Capital Struc - Between Crystal Structure, Plastic - ture Variation Over Time ity and Compaction Behaviour of P. Nezafat 2010/201 Theophylline, Methyl Gallate, and Origins of the Granite Falls, MN Their 1:1 Co-crystal Geology and Geophysics Tornado, July 25, 2000 Revisited S. Chattoraj, L. Shi, and C.C. Sun D. Dokken , R. Naistat, B. Togstad, 2010/99 2010/190 and CB 2010-76 K. Scholz, K. Weise, J. Nelson, L. Influences of Lower-Mantle Prop - Cooperative Binding Isotherms for Edholm, and P. Shanahan erties on the Formation of As - Nearest Neighbor Interacting Lig - thenosphere in the Upper Mantle 2010/202 ands on Platonic Solids: A Simple D.A. Yuen , N. Tosi, and O. Cadek Investigations of Cai’s Power Law Model for Viral Capture Nanother - for Strong Tornados 2010/101 apy D. Dokken , K. Scholz, and M. Parallel Numerical Analysis on the R.A. Siegel and J.L. Linstad Shvartsman Rheology of the Martian Ice-rock Mixture H. Jing, H. Zhang, H. Li, D.A. Yuen , and Y. Shi

16 Supercomputing Institute Research Bulletin Fall 2010 Research Reports

Physics 2010/122 2010/103 Software Systems for Operation, Nonperturbative Calculations in 2010/110 Control, and Monitoring of the Light-Front QED (presented at Magnetic Order in a Spin-1/2 In - EBEX Instrument Light Cone 2010) terpolating Kagome/Square M. Milligan, P. Ade, F. Aubin, C. S. Chabysheva Heisenberg Antiferromagnet Baccigalupi, C. Bao, J. Borrill, C. 2010/198 R.F. Bishop, P. H.Y. Li, D.J.J. Far - Cantalupo, D. Chapman, J. Didier, Pauli-Villars Regularization of nell, and C.E. Campbell M. Dobbs, W. Grainger, S. Field Theories on the Light Front Hanany , S. Hillbrand, J. Hubmayr, 2010/111 (presented at QCD@Work 2010) P. Hyland, A. Jaffe, B. Johnson, T. J.R. Hiller Magnetic Order on a Frustrated Kisner, J. Klein, A. Korotkov, S. Spin-1/2 Heisenberg Antiferromag - Leach, A. Lee, L. Levinson, M. 2010/199 net on the Union Jack Lattice Limon, K. MacDermid, T. Mat - Nonperturbative Calculations in R.F. Bishop, P.H.Y. Li, D.J.J. Far - sumura, A. Miller, E. Pascale, D. Light-Front QED (presented at nell, and C.E. Campbell Polsgrove, N. Ponthieu, K. Raach, QCD@Work 2010) 2010/116 B. Reichborn-Kjennerud, I. Sagiv, S.S. Chabysheva Non-Classical Rotational Inertia in H. Tran, G. S. Tucker, Y. Vi - Plant Biology a Two-Dimensional Bosonic Solid nokurov, A. Yadav, M. Zaldarriaga, Containing Grain Boundaries and K. Zilic 2010/175 and CB 2010-65 C. Dasgupta and O.T. Valls 2010/123 Network Modeling Reveals Preva - 2010/117 The EBEX Cryostat and Support - lent Negative Regulatory Relation - Superconducting Proximity Effects ing Electronics ships Between Signaling Sectors in in Metals With a Repulsive Pairing I. Sagiv, A.M. Aboobaker, C. Bao, Arabidopsis Immune Signaling Interaction S. Hanany , T. Jones, J. Klein, M. M. Sato, K. Tsuda, L. Wang, O.T. Valls , M. Bryan, and I. Zutic Milligan, D.E. Polsgrove, K. J. Coller, Y. Watanabe, J. Glaze - 2010/120 Raach, K. Zilic, A. Korotkov, G.S. brook , and F. Katagiri Angular Dependence of the Super - Tucker, Y. Vinukurov, T. Matsumu - conducting Transition Temperature ra, P. Ade, W. Grainger, E. Pascale, Science and Mathematics, in Ferromagnet-Superconductor- D. Chapman, J. Didier, S. Hill - UMM Ferromagnet Trilayers brand, B. Reichborn-Kjennerud, M. J. Zhu, I.N. Krivorotov, K. Halter - Limon, A. Miller, A. Jaffe, A. 2010/150 man, and O.T. Valls Yadav, M. Zaldarriaga, N. Pon - Alternative Syntheses and Reactivi - thieu, M. Tristram, J. Borrill, C. 2010/121 ty of Platinum(II) Terpyridyl Ace - Cantalupo, T. Kisner, F. Aubin, M. tonitrile Complexes EBEX: A Balloon-Borne CMB Po - Dobbs, K. MacDermid, G. Hilton, larization Experiment T.M. Pappenfus , J.R. Burney, J. Hubmayr, K. Irwin, C. Reintse - K.A. McGee, G.G.W. Lee, Larissa B. Reichborn-Kjennerud, A.M. ma, C. Baccigalupi, S. Leach, B. Aboobaker, P. Ade, F. Aubin, C. R. Jarvis, D.P. Ekerholm, M. Johnson, A. Lee, H. Tran, and L. Farah, L.I. Smith, L.M. Hinkle, Baccigalupi, C. Bao, J. Borrill, C. Levinson Cantalupo, D. Chapman, J. Didier, and K.R. Mann M. Dobbs, J. Grain, W. Grainger, 2010/132 S. Hanany , S. Hillbrand, J. Hub - Observations of Large-Amplitude, mayr, A. Jaffe, B. Johnson, T. Narrowband Whistlers at Stream Jones, T. Kisner, J. Klein, A. Ko - Interaction Regions rotkov, S. Leach, A. Lee, L. Levin - A. Breneman, C. Cattell , S. son, M. Limon, K. MacDermid, T. Schreiner, K. Kersten, L.B. Wilson Matsumura, X. Meng, A. Miller, III, P. Kellogg, K. Goetz, and L.K. M. Milligan, E. Pascale, D. Pols - Jian grove, N. Ponthieu, K. Raach, I. Physics, UMD Sagiv, G. Smecher, F. Stivoli, R. Stompor, H. Tran, M. Tristram, G. 2010/102 S. Tucker, Y. Vinokurov, A. Yadav, Pauli-Villars Regularization of M. Zaldarriaga, and K. Zilic Field Theories on the Light Front (presented at Light Cone 2010) J. Hiller

Fall 2010 Supercomputing Institute Research Bulletin 17 Supercomputing Institute for Advanced Computational Research

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