APPENDIX D

COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS, SECOND ROUND

ROBERT L. JERNIGAN (Chair), Director, Laurence H. Baker Center for Bioinformatics and Biological Statistics and Professor, Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University

DAVID C. BAKER, Professor, Department of Chemistry, University of Tennessee

NILESH BANAVALI, Research Scientist, Wadsworth Center and Assistant Professor, School of Public Health, State University of New York, Albany

MICHAEL COLVIN, Interim Dean, Professor and Founding Faculty Member, School of Natural Sciences, University of California, Merced

RUXANDRA I. DIMA, Assistant Professor of Chemistry, University of Cincinnati

PHILLIP GEISSLER, Associate Professor, Department of Chemistry, University of California, Berkeley

WILLIAM A. GODDARD III, Ferkel Professor of Chemistry, Materials Science, and Applied Physics, California Institute of Technology

DAVID L. MOBLEY, Assistant Professor, Department of Chemistry, University of New Orleans

JOSE N. ONUCHIC, Professor of Physics and Co-Director Center for Theoretical Biological Physics, University of California, San Diego

CAROL PARISH, Professor, Department of Chemistry, University of Richmond

JERRY M. PARKS, Research Staff Scientist, Oak Ridge National Laboratory

STEVEN SCHWARTZ, Director, Seaver Foundation, Center for Bioinformatics and Professor of Physiology, Biophysics and Biochemistry, Albert Einstein College of Medicine

SADASIVAN SHANKAR, Senior Principal Engineer and Program Leader for Materials Design, Design and Technology Solutions, Technology and Manufacturing Group, Intel Corporation

TIMOTHY A. SPRINGER, Latham Family Professor of Pathology, Harvard Medical School

ROBERT STROUD, Professor, Biochemistry and Biophysics and Pharmaceutical Chemistry, University of California, San Francisco

ARIEH WARSHEL, Professor of Chemistry and Biochemistry, University of Southern California

HAREL WEINSTEIN, Chairman and Professor, Department of Physiology and Biophysics and Director, Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University

REVIEWERS

GERHARD HUMMER, Chief, Theoretical Biophysics Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health

DOUGLAS J. TOBIAS, Professor of Chemistry, University of California, Irvine

NATIONAL RESEARCH COUNCIL STAFF

KATHERINE BOWMAN, Senior Program Officer, Board on Life Sciences

DOUGLAS FRIEDMAN, Program Officer, Board on Chemical Sciences and Technology

KATHRYN HUGHES, Program Officer, Board on Chemical Sciences and Technology

ORIN LUKE, Senior Program Assistant, Board on Life Sciences



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APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS, SECOND ROUND ROBERT L. JERNIGAN (Chair), Director, Laurence H. Baker Center for Bioinformatics and Biological Statistics and Professor, Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University DAVID C. BAKER, Professor, Department of Chemistry, University of Tennessee NILESH BANAVALI, Research Scientist, Wadsworth Center and Assistant Professor, School of Public Health, State University of New York, Albany MICHAEL COLVIN, Interim Dean, Professor and Founding Faculty Member, School of Natural Sciences, University of California, Merced RUXANDRA I. DIMA, Assistant Professor of Chemistry, University of Cincinnati PHILLIP GEISSLER, Associate Professor, Department of Chemistry, University of California, Berkeley WILLIAM A. GODDARD III, Ferkel Professor of Chemistry, Materials Science, and Applied Physics, California Institute of Technology DAVID L. MOBLEY, Assistant Professor, Department of Chemistry, University of New Orleans JOSE N. ONUCHIC, Professor of Physics and Co-Director Center for Theoretical Biological Physics, University of California, San Diego CAROL PARISH, Professor, Department of Chemistry, University of Richmond JERRY M. PARKS, Research Staff Scientist, Oak Ridge National Laboratory STEVEN SCHWARTZ, Director, Seaver Foundation, Center for Bioinformatics and Professor of Physiology, Biophysics and Biochemistry, Albert Einstein College of Medicine SADASIVAN SHANKAR, Senior Principal Engineer and Program Leader for Materials Design, Design and Technology Solutions, Technology and Manufacturing Group, Intel Corporation TIMOTHY A. SPRINGER, Latham Family Professor of Pathology, Harvard Medical School ROBERT STROUD, Professor, Biochemistry and Biophysics and Pharmaceutical Chemistry, University of California, San Francisco ARIEH WARSHEL, Professor of Chemistry and Biochemistry, University of Southern California HAREL WEINSTEIN, Chairman and Professor, Department of Physiology and Biophysics and Director, Institute for Computational Biomedicine, Weill Cornell Medical College of Cornell University REVIEWERS GERHARD HUMMER, Chief, Theoretical Biophysics Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health DOUGLAS J. TOBIAS, Professor of Chemistry, University of California, Irvine NATIONAL RESEARCH COUNCIL STAFF KATHERINE BOWMAN, Senior Program Officer, Board on Life Sciences DOUGLAS FRIEDMAN, Program Officer, Board on Chemical Sciences and Technology KATHRYN HUGHES, Program Officer, Board on Chemical Sciences and Technology ORIN LUKE, Senior Program Assistant, Board on Life Sciences 13

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BIOGRAPHICAL SKETCHES OF COMMITTEE MEMBERS AND REVIEWERS CHAIR Robert L. Jernigan is the Director of the Laurence H. Baker Center for Bioinformatics and Biological Sciences as well as a Professor in the Department of Biochemistry, Biophysics, and Molecular Biology at Iowa State University. He received his B.S. in Chemistry from the California Institute of Technology in 1963 and completed his Ph.D. in 1968 at Stanford University. He has previously served as Deputy Chief of the Laboratory of Experimental and Computational Biology and Chief of the Section on Molecular Structure in the National Cancer Institute of the National Institutes of Health. He is also a former Chair of the NIH Advisory Committee on Computer Usage and has served on many committees on computing resources. Dr. Jernigan is currently on the editorial boards for the journals Biochemistry and Bioinformatics and Biological Insights. He is a Fellow of the Biophysical Society and a Fellow of the AAAS. His recent research focuses on mechanics of proteins and RNA and the role of mechanics in the mechanisms of molecular machines. MEMBERS David C. Baker is Professor of Organic Chemistry at the University of Tennessee. He is active in the Carbohydrate, Medicinal, and Organic Divisions of the American Chemical Society. Prior to his academic career he worked at the Parke-Davis Pharmaceutical Research, following a postdoctoral at Syntex Research. He is a frequent reviewer for the National Institutes of Health and serves as an editor of Carbohydrate Research, an international journal in the field. Dr. Baker received a Ph.D. in chemistry from The Ohio State University. Nilesh Banavali received his Ph.D. from the University of Maryland in 2001 for studies on nucleic acid force fields and base flipping with Alexander MacKerell Jr. He pursued postdoctoral training at Weill Medical College of Cornell University and the University of Chicago with Benoît Roux on implicit and implicit/explicit solvent models and free energy characterization of conformational change and allostery in macromolecules. He currently serves as a Research Scientist at the Wadsworth Center and as Assistant Professor in the School of Public Health at the State University of New York, Albany. The primary goal of his research is to use computational calculations and refined analysis techniques to optimally extract free energy landscapes describing biologically relevant macromolecular conformational change. Dr. Banavali also develops techniques to facilitate validation of computational predictions with structural and biochemical data. Michael Colvin is Interim Dean, Professor and Founding Faculty Member in the School of Natural Sciences at the University of California, Merced. Dr. Colvin's research uses a wide range of simulation methods to model biological systems at different levels. Much of his research uses molecular modeling to study biochemical problems, with a particular emphasis on modeling the activity of DNA-binding food mutagens and anticancer drugs. These methods involve computing the structures and energetics of biomolecules using either quantum or classical mechanics, and often require the use of supercomputers. Dr. Colvin received his Ph.D. from the University of California, Berkeley. Ruxandra I. Dima has an interdisciplinary training in theoretical and computational physics and physical chemistry and her current research focuses on the area of computational biophysical chemistry with special emphasis on single molecule experiments and aggregation. After 14

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receiving her undergraduate degree from the University of Bucharest, Romania in 1994, she studied at the Pennsylvania State University where she obtained her Ph.D. in 1999. Her thesis was concerned with the determination of mean field free-energy potentials between amino acids in proteins. She then took a postdoctoral appointment (2000-2005) at the Institute for Physical Science and Technology, University of Maryland where she worked on problems related to protein aggregation, allostery, RNA folding, and single-molecule biophysics. In 2005 she took a faculty position at the University of Massachusetts, Lowell. She joined the faculty at the University of Cincinnati in 2006. Dr. Dima’s research focuses on the micromechanics of large protein assemblies from cytoskeletal filaments to fibrin fibers, using multi-scale models that are continuously developed in her group to access experimental length and timescales. Phillip Geissler is an Associate Professor in the Department of Chemistry at the University of California, Berkeley. Dr. Geissler is also a faculty member of the Biophysics Graduate Group at the University of California, Berkeley, a faculty scientist in the Chemical Sciences, Physical Biosciences, and Materials Sciences Divisions of the Lawrence Berkeley National Laboratory, and a faculty affiliate at the California Institute for Quantitative Biosciences (QB3). His research focuses on the microscopic behavior of complex biological and material systems, particularly theories and simplified models for chemical phenomena in condensed phases, for biomolecular structure and dynamics, and for the role of fluctuations in nanoscale materials. Among his current interests are the polymeric framework of living cells and the dynamics of nanometer-sized solutes in a liquid undergoing phase change. In 2006, Dr. Geissler was named a Kavli Frontiers Fellow. He received his bachelor’s degree in chemistry from Cornell University and Ph.D. in chemistry from the University of California, Berkeley. William A. Goddard III is the Charles and Mary Ferkel Professor of Chemistry and Applied Physics, and Director, Materials and Process Simulation Center at the California Institute of Technology. He has made many contributions to theoretical chemistry, such as the generalized valence bond (GVB) method for ab initio electronic structure calculations and the ReaxFF force field for classical molecular dynamics simulations. He is a member of the International Academy of Quantum Molecular Science. His research interests include quantum mechanics for the electronic wave functions of large molecules and crystals, including the many-body effects needed to describe reactions, force fields to describe the dynamics of atomic motions, molecular dynamics of large molecules and solids to determine the structure, vibrations, and dynamical processes of materials and statistical mechanics to describe phase diagrams (mixtures of molecules and polymers; metallic alloys). Dr. Goddard received his Ph.D. from the California Institute of Technology. He is an elected member of the National Academy of Sciences. David L. Mobley is an Assistant Professor in the Department of Chemistry at the University of New Orleans. His research focuses on applying computational and theoretical methods to understand and quantitatively predict fundamental biological processes such as protein-ligand binding, solvation, and solubility. His research interests include the binding of small-molecule ligands to proteins and the interactions of small molecules with water and other solvents. Current computational methods have limited accuracy for pharmaceutical drug discovery applications, and his laboratory seeks to develop and apply more accurate methods for computing and even predicting binding affinities. Recent work has also examined solute geometry and the role of entropy in small molecule solvation. Dr. Mobley received the Hewlett-Packard Outstanding Junior Faculty Award in Computational Chemistry from the American Chemical Society (2009). He received his B.S. and Ph.D. degrees in physics from the University of California, Davis. Jose N. Onuchic is the co-Director of the Center for Theoretical Biological Physics and Professor of Physics at the University of California, San Diego. His research group introduced the concept of protein-folding funnels to show the types of amino acid sequences that can fold into a 15

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unique protein structure. Dr. Onuchic and his collaborators also created the concept of tunneling pathways and the methodology for reducing proteins into a combination of relevant tubes of pathways that provides a new way of designing electron transfer proteins. His research interests include exploring theoretical and computational methods for molecular biophysics, chemical reactions in condensed matter and gene networks. Dr. Onuchic received his Ph.D. in chemistry from the California Institute of Technology and M.S. degree in applied physics from the University of California, San Diego. He is an elected member of the National Academy of Sciences. Carol Parish is Professor of Chemistry, Computational and Theoretical Physical Chemistry at the University of Richmond. Her research focuses on understanding the dynamical behavior of molecular systems using the tools of quantum mechanics, conformational searching and free energy simulation to answer questions about the structure, energy and dynamics of HIV-1 protease inhibitor drugs, Bergman cyclization in enediyne anti-cancer warhead drugs, homology modeling of membrane-bound desaturase enzymes, investigations of the flexibility of polyoligomeric silsesquioxane cages (POSS), the role of O-to-N acyl migration in insect defense secretions, and oligomeric models for synthetic enzymes that display enzyme-like acyltransferase activity. Dr. Parish is a member of the American Chemical Society. She received her Ph.D. in physical chemistry from Purdue University. Jerry M. Parks is a Research Staff Scientist for the Center for Molecular Biophysics in the Biosciences Division at Oak Ridge National Laboratory. His research involves molecular simulations and free energy calculations to solve chemical problems. Dr. Parks received his Ph.D. in Chemistry from Duke University and his M.S. in Chemistry from Southern Methodist University. Steven Schwartz is Director of the Seaver Foundation, Center for Bioinformatics and Professor of Physiology, Biophysics and Biochemistry at the Albert Einstein College of Medicine. He was elected as a Fellow of the American Physical Society and a Fellow of the American Association for the Advancement of Science. Dr. Schwartz's selection recognizes his development of the theory of the coupling of protein vibrations to catalytic function in enzymes. Dr. Schwartz is the executive editor of the Journal of Theoretical and Computational Chemistry. He also serves on the editorial boards of the Biophysical Journal and Progress in Theoretical Chemistry. His research interests include theoretical studies of biophysical systems and theoretical condensed phase chemistry. Dr. Schwartz received his Ph.D. in theoretical chemical physics from the University of California, Berkeley. Timothy A. Springer majored in Biochemistry at the University of California, and graduated Phi Beta Kappa with Distinction and the Departmental Citation. He received his Ph.D. in biochemistry working with Jack Strominger on the isolation, protein chemistry, and organization in the membrane of major histocompatibility complex antigens. Realizing the power of monoclonal antibodies for the characterization of proteins on the cell surface, Springer did postdoctoral work with César Milstein. He started as an Assistant Professor at Harvard Medical School in 1977 where he has been ever since, moving a few blocks down the street to the Dana- Farber Cancer Institute in 1981 and to the CBR Institute for Biomedical Research in 1988. He is an elected member of the National Academy of Sciences. Robert Stroud is Professor of Biochemistry and Biophysics and Pharmaceutical Chemistry and Principal Investigator of the Stroud laboratory at the University of California, San Francisco. At the Stroud laboratory, scientists seek to understand molecular mechanisms of certain key biological processes, as well as signal transduction between processes at the level of protein structure, dynamics, and mechanism. Three-dimensional molecular structures are defined 16

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primarily by x-ray crystallography and are often used to facilitate structure-based drug design, providing a quintessential test of our understanding of the relationship between structure and recognition. Currently the integration enzyme from HIV is subject to molecular biological, biochemical, and structural approaches. The molecular mechanisms of thymidylate synthase are derived from numerous structural studies in the laboratory. An important cancer target, these mechanisms pertain directly to our structure and mechanism based design of anticancer drugs. Dr. Stroud received his PhD in Biological Crystallography from Birkbeck College, London University, U.K. He is an elected member of the National Academy of Sciences. Arieh Warshel received his BS degree in Chemistry, Summa Cum Laude, from Technion Israel in 1966, and his M.S. and Ph.D. degrees in Chemical Physics in 1967 and 1969, respectively, from the Weizmann Institute of Science, Israel. After his PhD, he did postdoctoral work at Harvard University. From 1972 to 1976, he was at the Weizmann Institute and at the MRC Laboratory for Molecular Biology in Cambridge, England. In 1976 he joined the faculty of the Department of Chemistry at USC, where he now is Professor of Chemistry and Biochemistry and a Full Member of the USC Norris Cancer Center. Dr. Warshel has authored over 350 peer- reviewed research articles (H index 92) and book chapters, two books, and several key computer programs. Dr. Warshel’s research focuses on simulations of the functions of biological system and other challenging problems in modern computational biophysics and chemistry. He and his coworkers have pioneered the key approaches for simulating the functions of biological molecules, including introducing molecular dynamics (MD) in Biology, developing the quantum mechanical/molecular-mechanical (QM/MM) approach, introducing simulations of enzymatic reactions, developing simulations of electron transfer and proton transfer processes in proteins, pioneering microscopic modeling of electrostatic effects in macromolecules and introducing simulation of protein folding. Dr. Warshel received the Tolman Medal in 2003, has been elected a Fellow of the Biophysical Society in 2000, a Fellow of the Royal Society of Chemistry in 2008, and a Member of the National Academy of Sciences in 2009. Harel Weinstein is the Maxwell Upson Professor of Physiology and Biophysics and Chairman of the Department of Physiology and Biophysics, and the Director of the Institute for Computational Biomedicine at Weill Cornell Medical College (WCMC) of Cornell University in New York City. As a Tri-Institutional Professor, he holds professorial appointments at Rockefeller University, Sloan-Kettering Institute and Cornell University. He is the founding director of the Institute for Computational Biomedicine (ICB), which he developed it into an academic and research unit responsible for a novel approach to biomedicine that involves the mathematical, physical and computational sciences in combination with engineering and medical informatics. The ICB aims at fundamental study and practical use of the basic, quantitative understanding of physiological function and disease, in an integrative, multi-scale approach based on gene structure and defects responsible for properties and behaviors at all levels–from protein, to cell, tissue and organ. He has received numerous honors and awards, he was elected to the Executive Board of the International Society for Computational Biology in 2006, and President of the Biophysical Society in 2008. He has also served as President of the Association of Chairmen of Departments of Physiology, President of the International Society for Quantum Biology and Pharmacology, Chair of the Biophysics Section of the New York Academy of Sciences and Councilor of the Biophysical Society and of the New York Academy of Medicine. His research interests include studies in molecular and computational biophysics that address complex systems in physiology, and to the development and application of bioinformatics and engineering approaches to systems biology. 17

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REVIEWERS Gerhard Hummer received a doctoral degree in physics for work done jointly at the Max-Planck Institute for Biophysical Chemistry in Göttingen and the University of Vienna (1992). In 1996, he started his independent career in the Theoretical Division of Los Alamos National Laboratory after his postdoctoral work there. In 1999, Dr. Hummer joined the Laboratory of Chemical Physics in the National Institute of Diabetes and Digestive and Kidney Diseases at the National Institutes of Health where he is a Senior Investigator. His research focuses on areas including theory of single-molecule experiments; channel function; peptide and protein folding; complex formation and ligand binding; proton pumping and bioenergetics; reaction-rate calculations; and the development of new methods for biomolecular simulation and electrostatics. Douglas J. Tobias is a Professor in the Department of Chemistry at the University of California, Irvine. His research involves the use of atomic-scale computer simulation techniques to study the structure and dynamics of biological molecules and biomimetic materials and aqueous interfaces with air. A substantial portion of his work is devoted to the development, implementation, and optimization of novel simulation methodology and analysis tools. Current projects include interactions of peptides and proteins with lipids, molecular mechanisms of ion channel gating, and the dynamics of native and denatured proteins and their hydration water, among others. Dr. Tobias is an elected Fellow of the American Association for the Advancement of Science. He received his bachelors and masters degrees in chemistry from the University of California, Riverside and his Ph.D. in Chemistry and Biophysics from Carnegie Mellon University. 18