2005 - 2006 2005 2005 - 2006 DEIXIS - 2006 THE DOE CSGF ANNUAL DEIXIS DEIXIS – – THE THE DOE CSGF ANNUAL DOE CSGF ANNUAL DEPARTMENT OF ENERGY COMPUTATIONAL SCIENCE GRADUATE FELLOWSHIP Funded by: The Krell Institute Office of Science and 1609 Golden Aspen Drive, Suite 101 National Nuclear Security Ames, IA 50010 Administration’s Office of (515) 956-3696 Defense Programs www.krellinst.org/csgf THE DOE CSGF ANNUAL Department of Energy DEIXIS Computational Science Graduate Fellowship TABLE OF CONTENTS 2005 - 2006 PAGE 13 DEIXIS Editor (∆ΕΙΞΙΣ) transliterated Shelly Olsan from classical Greek into the Roman alphabet, (pronounced da¯ksis) means Copy Editor a display, mode or process of proof; Ron Winther PAGE 23 the process of showing, proving or Design demonstrating. DEIXIS can also Juls Design, Inc. PAGE 15 refer to the workings of an individual’s 46 keen intellect, or to the means by which Contributors 4 Alumni Profiles such individuals, e.g. DOE CSGF Jacob Berkowitz Practicum fellows, are identified. Alan S. Brown Experiences 46 Chris Oehmen PAGE 19 Victor D. Chase 14 Pacific Northwest DEIXIS is an annual publication Karen Hede 4 The Reasearcher’s Roadtrip Department of Energy National Laboratory of the Department of Energy Michael Szpir Lab Research Computational Science Graduate 4 Bree Aldridge 30 Fusion and Ice 47 Joel Parriott Fellowship (DOE CSGF) program. DEIXIS, The DOE CSGF Annual Measuring the Stroke of 14 Inside a Flame Brookhaven National Laboratory Office of Management and Budget DEIXIS illustrates work done at is published by the Krell Institute. The Krell Institute administers the Department a Butterfly’s Wing Lawrence Berkeley eight multi-program DOE laboratories of Energy Computational Science Graduate National Laboratory 34 Of Tsunamis, Thermonuclear 48 Mayya Tokman and highlights the DOE CSGF fellows Fellowship program for the DOE under contract DE-FG02-97ER25308. The Krell Institute is a 8 Sam Stechmann Explosions, & Asteroids University of California and alumni. The DOE CSGF is non-profit company that works in partnership Modeling the Ocean’s 18 Radioactive Retention Los Alamos National Laboratory funded by the Office of Science and with national science and technology Invisible Waves Sandia National Laboratories the National Nuclear Security research and education communities to help them achieve national priorities. 38 Heavy Metal Blues 49 Administration’s Office of 10 Teresa Bailey 22 Facilitating Warp Pacific Northwest Howes Scholars Defense Programs. Faster Math Ignites Speed Computing National Laboratory For additional information about the Department of Energy Computational Fusion Experiments Oak Ridge National Laboratory Science Graduate Fellowship program, 42 PETSc Engines 50 the Krell Institute, or topics covered in 12 Mary Biddy 26 Simulating an Urban Disaster Alumni Directory this publication, please contact: Argonne National Laboratory Salad Days for Lawrence Livermore Editor, DEIXIS The Krell Institute Plant-based Lubricants National Laboratory 1609 Golden Aspen Drive, Suite 101 56 Ames, IA 50010 Fellows Directory (515) 956-3696 www.krellinst.org/csgf PAGE 29 Copyright 2005 by the Krell Institute. All rights reserved. PAGE 39 PAGE 31 FEATURE PRACTICUM EXPERIENCES 5 The Researcher’s Roadtrip THE DEPARTMENT OF ENERGY Computational Science Graduate Fellowship (DOE CSGF) program supports the brightest science and engineering students as they prepare for a future in their respective fields. Nearly 15 years old, the DOE CSGF has grown to over sixty active fellows and over 200 alumni. Aldridge and her graduate advisors, Measuring the Douglas Lauffenburger and Peter Sorger of Massachusetts Institute of Stroke of a Technology, Cambridge, Massachusetts, have teamed with Steve Wiley of Butterfly’s Pacific Northwest National Laboratory (PNNL), Richland, Washington, to Wing craft a large-scale mathematical representation of interacting cell signaling pathways. BREE ALDRIDGE “The general goal of studying these Massachusetts Institute of Technology signaling networks is so that we can | Pacific Northwest National understand how cells process so many Laboratory | Story by Karyn Hede signals and always make the correct decision,” says Aldridge. “Or another More than 30 years ago, way of looking at this is for cancer meteorologist Edward therapy. Today, drug companies see Lorenz poetically protein A is allowing the cancer cell described how small to survive when it should die, so they Left to right: events can have large try to inhibit protein A. But maybe in New imaging technologies can reveal the Teresa Bailey, consequences when he some cells protein A doesn’t matter location of oncogenic proteins in living Mary Biddy, posed the question: or the cell can alter its pathway a bit cells. Shown are human epithelial cells Sam Stechmann can a butterfly flapping its wings in to go around protein A. It may be expressing the oncogene HER2 that emit and Bree Aldridge Brazil cause a tornado in Texas two that protein A or protein C or protein green fluorescence. Lysosomes are stained weeks later? Lorenz’ musing was no F is important. So inhibiting each red and the cell nucleus is stained blue mere philosophical question. He of these pathways a little bit might for reference. proceeded to show mathematically how be more effective than completely small changes in starting conditions shutting down just one of them. can cause large effects in complex, That’s the sort of information we interdependent systems. hope to get someday out of these quantitative models.” Today biologists are teaming with TO A COLLEGE STUDENT, summer typically means warm mathematicians to apply quantitative beaches, lazy weekends, and no classes, but the DOE CSGF fellows live out a approaches to complex biological different kind of dream for the warmest three months of the year. During systems that have much in common the summer, fellows take a practicum in one of the Department of Energy’s with Lorenz’ meteorological laboratories — an experience that may impact the future of their research. conundrum. Department of Energy Computational Science Graduate The idea is to eavesdrop on the cell’s communication channels The opportunity for hands-on experience with world-class researchers and Fellowship (DOE CSGF) Fellow the latest technology is more than just a chance to hone analytical skills; it Bree Aldridge has set her sights on and discern, from seemingly indecipherable “chatter,” patterns is the quintessential road trip of one’s career (and maybe even self) measuring the molecular equivalent discovery. This trip is an opportunity to see what you have of Lorenz’ butterfly effect in the of signaling that cells use to make crucial decisions, become, and, perhaps, decide where you are going. complex milieu of the living cell. such as when to divide or when it’s time to die. 4 We simulate models of the signaling pathways to gain insight into the complex 7 signaling resulting from extracellular cues (graphic: Suzanne Gaudet, adapted by Bree Aldridge) 90 80 80 70 60 60 PROGRAM 50 40 REQUIREMENTS 40 leaved casp-3 20 30 Students selected for fellowships 0 agree to undertake study and %C 20 research in computational science. 2000 The program of study must provide 5 10 Tim 1000 2 ) background in a scientific or e 1 (x10 engineering discipline, computer 0 0 science, and applied mathematics. IAP molec./cell In order to be considered for the DOE CSGF, students must be U.S. A schematic of the signaling networks induced by cytokine activation. citizens or permanent resident Cells use this complicated and intertwined protein pathway to process aliens and working toward a Ph.D. extracellular cues into a life-or-death decision. (Drawn by Peter Sorger and “There is no consistent language in “We are using gene expression and at a United States university. Douglas Lauffenburger, MIT). systems biology,” says Aldridge. “This proteomic data to filter the diagram and makes sharing models difficult. One cull out what are the real connections Students applying for fellowships must of my goals was to merge our two and interactions,” says Wiley. “One of be undergraduate seniors or in their models together so we can continue the things Bree was involved in was first or second year of graduate study. and expand our collaboration.” taking a look at the wiring diagram and Maintaining larger ODE-based as a list of Prior to the third year of the fellowship, The idea is to eavesdrop on the Wiley’s laboratory studies the epidermal equations is increasingly difficult as the looking at our list of genes that we had fellows must complete a practicum cell’s communication channels growth factor (EGF) receptor pathway, network models are expanded. In order to Another problem was that the identified as actually being involved assignment at a Department of Energy and discern, from seemingly which is implicated in many types begin merging model together, we needed models were built based on data and then, experimentally, looking to laboratory. Currently, approximately indecipherable “chatter,” patterns of cancer. Lauffenburger’s group to represent each model in the same format from two different kinds of cells. see if we knock out a particular piece, 15% of fellows who graduate from the of signaling that cells use to make studies tumor necrosis factor alpha (SBML) and annotate it using a graphical The Lauffenberger group studies a does it have the predicted effect on DOE CSGF program work or have worked in a Department of Energy laboratory. crucial decisions, such as when to (TNFalpha), another pathway that modeling tool (Teranode VLX Design Suite). colon cancer cell line, while Wiley’s the wiring diagram?” divide or when it’s time to die. often gets activated in cancers. EGF This screen shot shows how complicated group studies mammary cancer cells. and TNFalpha are signaling molecules just a part of the model is! (graphic: Bree Aldridge) The models the two labs developed When the practicum was over, Aldridge “Every cell in your body sees information called cytokines that communicate were different, but complementary.