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Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics (2010)

Chapter: APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS

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Suggested Citation:"APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS." National Research Council. 2010. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. Washington, DC: The National Academies Press. doi: 10.17226/13003.
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APPENDIX D
COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS

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

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

DAVID L. BEVERIDGE, Professor of Theoretical Chemistry and Molecular Biophysics, Wesleyan University

CHARLES L. BROOKS III, Warner-Lambert/Parke-Davis Professor of Chemistry and Professor of Biophysics, University of Michigan

XIAOLIN CHENG, Staff Scientist, Oak Ridge National Laboratory and Adjunct Professor, University of Tennessee, Knoxville

RUXANDRA DIMA, Assistant Professor of Chemistry, University of Cincinnati

BARRY H. HONIG, Director, Center for Computational Biology and Bioinformatics and Professor of Biochemistry and Molecular Biophysics, Columbia University

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

RONALD M. LEVY, Board of Governors Professor of Chemistry & Chemical Biology and Director, BioMaPS Institute for Quantitative Biology, Rutgers University

GLENN J. MARTYNA, Researcher, IBM

GREGORY PETSKO, Gyula and Katica Tauber Professor of Biochemistry and Chemistry, Brandeis University

CAROL B. POST, Professor of Medicinal Chemistry and Molecular Pharmacology, Purdue University

KLAUS J. SCHULTEN, Swanlund Professor of Physics, University of Illinois, Urbana-Champaign

JEFFREY SKOLNICK, Professor and Director of the Center for the Study of Systems Biology, Georgia Research Alliance Eminent Scholar in Computation Systems Biology, Georgia Institute of Technology

FENG WANG, Assistant Professor, Department of Chemistry, Boston University

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

STAFF

KATHERINE BOWMAN, Senior Program Officer, Board on Life Sciences

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

CARL-GUSTAV ANDERSON, Senior Program Assistant, Board on Life Sciences

JAMES MULLER, Intern, Board on Life Sciences

Suggested Citation:"APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS." National Research Council. 2010. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. Washington, DC: The National Academies Press. doi: 10.17226/13003.
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BIOGRAPHICAL SKETCHES OF COMMITTEE MEMBERS

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 multiple committees on computing resources. Dr. Jernigan is currently on the editorial boards for the journals Biochemistry, the Journal of Data Mining in Genomics and Proteomics, and Bioinformatics and Biological Insights.

MEMBERS

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.


David L. Beveridge attended the College of Wooster, Wooster Ohio graduating in 1959, with a major in chemistry. After two years at Monsanto Research Laboratory, he went for graduate studies at the University of Cincinnati. Based on his studies and research under the mentorship of the eminent physical chemist, Hans H. Jaffe, he was awarded a Ph.D. in Physical Chemistry in 1965. He was granted an NIH Postdoctoral Fellowship to study molecular quantum mechanics at the Centre de Mecanique Ondulatoire Appliquee in Paris, France with Dr. Odilon Chalvet. Dr. Beveridge continued his postdoctoral studies at Carnegie Mellon University with Prof. J.A. Pople, where he worked on the development of INDO molecular orbital theory. In 1968, Dr. Beveridge joined faculty of the City University of New York, at first in a joint appointment with Hunter College Chemistry Department and The Mount Sinai School of Medicine and subsequently full time at Hunter College. In 1986, Dr. Beveridge moved from New York City to become Professor of Chemistry at Wesleyan University. In 1988, he was granted a Merit Award by the NIH and named University Professor of the Natural Sciences and Mathematics. His current research involves theoretical and computational modeling studies of the structure, motions, salvation, and ligand binding properties of DNA and RNA using molecular dynamics simulation. He served as Dean of Natural Sciences and Mathematics (1992-1999) and has authored or co-authored over 200 papers in the scientific literature. In addition to research and teaching, he now serves Wesleyan as Director of the NIH supported Program in Molecular Biophysics and Biological Chemistry.


Charles L. Brooks received a B.S. from Alma College in 1978. Dr. Brooks pursued graduate studies at Purdue University under the direction of Professor Stephen A. Adelman. His graduate

Suggested Citation:"APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS." National Research Council. 2010. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. Washington, DC: The National Academies Press. doi: 10.17226/13003.
×

work focused on the development of non-equilibrium statistical mechanical theories for reactions on surfaces, in solids and in liquids using molecular timescale generalized Langevin (MTGLE) theory. In 1982, he received his Ph.D. in Physical Chemistry from Purdue University. Dr. Brooks was engaged in postgraduate work at Harvard University with Professor Martin Karplus between the years of 1982 and 1985, focusing on theoretical and computational biophysics. Dr Brooks was also the recipient of an NIH Postdoctoral Fellowship between 1983 and 1985. In 1985, Professor Brooks joined the Chemistry Faculty of Carnegie Mellon University and was promoted to Professor of Chemistry in 1992. He received an Alfred P. Sloan Research Fellowship in 1992 and during this period, 1992-1993, spent a sabbatical year working at the Karolinska Institute in Stockholm Sweden and The Scripps Research Institute in La Jolla California. Dr. Brooks has recently moved to the University of Michigan, where he holds the positions of Warner-Lambert/Parke-Davis Professor of Chemistry and Professor of Biophysics. Dr. Brooks’ research includes multi-scale modeling of the dynamics and assembly of complex biological assemblies, protein folding, unfolding and aggregation, and free energy approximations.


Xiaolin Cheng is a staff scientist at the Center for Molecular Biophysics of the Oak Ridge National Laboratory. He is also an adjunct professor in the Department of Biochemistry and Cellular and Molecular Biology at the University of Tennessee, Knoxville. Dr. Cheng received his B.S. from Nanjing University, China, and his Ph.D. in Computational Chemistry from the State University of New York at Stony Brook, where he worked with Professor Carlos Simmerling on application of enhanced sampling approaches to biomolecular simulations. He subsequently joined Professor Andy McCammon's group at University of California, San Diego as a postdoctoral research associate, mainly working on nicotinic acetylcholine receptor simulation, and methodological development for fast and scalable continuum electrostatic calculation. Dr. Cheng moved to Oak Ridge National Laboratory in early 2008.


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 receiving her undergraduate degree from the University of Bucharest, Romania in 1994, she studied at the Pennsylvania State University where she obtained her PhD 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.


Barry H. Honig is a biophysicist who specializes in bioinformatics and in developing theoretical methods for analyzing the physical chemical properties of macromolecules. He received a B.A. from the Polytechnic Institute of Brooklyn in 1963, an M.A. from Johns Hopkins University in 1964, and completed a Ph.D. in chemistry at the Weismann Institute of Sciences. He is particularly noted for innovating methods to compute and display the electrostatic potentials of macromolecules based on their 3D structures. The computer programs DelPhi and GRASP were developed in his laboratory and are widely used by the academic and industrial communities. Since 1981, Dr. Honig has been a Professor of Biochemistry and Molecular Biophysics at Columbia University. In 1990, Dr. Honig was elected President of the Biophysical Society, he received an NIH Merit Award in 1995, and he is a recipient of the 2002 Founders Award of the Biophysical Society. Dr. Honig is a Howard Hughes Medical Institute (HHMI) Investigator. He serves on the editorial boards of several journals and has published over 190 scientific papers

Suggested Citation:"APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS." National Research Council. 2010. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. Washington, DC: The National Academies Press. doi: 10.17226/13003.
×

throughout his distinguished career. He was elected to membership in the National Academy of Sciences in 2004.


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.


Ronald M. Levy is a Board of Governors Professor of Chemistry at Rutgers University. He received his B.A. from Reed College in 1970 and completed his Ph.D. in 1976 at Harvard University. His research is primarily in the areas of protein simulation and modeling and molecular solvation. He has been awarded a Sloan Foundation Fellowship, a Johnson and Johnson Discovery Research Award, an NIH Research Career Development Award, and a Guggenheim Fellowship. Over the past two decades he has developed the IMPACT molecular modeling code. Current interests include the exploration of energy landscapes for protein binding and folding, new molecular simulation methods and multi-scale models, and the determination of solvation free energies.


Glenn J Martyna received a Ph.D. in chemical from Columbia University in 1989. He was then a NSF postdoctoral fellow in computational science and engineering at the University of Pennsylvania. Dr. Martyna was appointed to faculty of Indiana University, Bloomington, in 1993 and was awarded tenure in 2000. In 2001, he joined IBM's TJ Watson Research Lab in Yorktown Heights, NY. Dr. Martyna was awarded an honorary Professorship of Physics at the University of Edinburgh, UK in 2008. His research focuses on the use of novel methodology, parallel algorithms, and computer simulation to probe biophysical, materials and chemical systems including studies of aqueous solutions, complex heterogeneous interfaces, phase change materials, and nanomaterials.


Gregory A. Petsko is the Gyula and Katica Tauber Professor of Biochemistry and Molecular Pharmacodynamics and the director of the Rosenstiel Basic Medical Sciences Research Center at Brandeis University. He was elected to membership in the National Academy of Sciences in 1995 and to the Institute of Medicine in 2001. He has developed low-temperature methods in protein crystallography and their use to study enzymatic mechanisms and has pioneered the study of protein dynamics in enzymatic reactions. For over 25 years, he has worked to understand how enzymes achieve their extraordinary catalytic power, developing crystallographic methods for direct observation of productive enzyme-substrate and enzyme-intermediate complexes that led to techniques for studying protein crystal structures at very low temperatures. Dr. Petsko is also a founding scientist of the combinatorial-chemistry company ArQule, Inc.


Carol Post received her B.S. from the University of Arizona in 1975, and received a Ph.D. from the University of California, San Diego in 1981. She pursued post-graduate research between 1982 and 1985 at Harvard University. She is currently a Professor of Medicinal Chemistry and Molecular Pharmacology at Purdue University, where she operates the Post Lab (Computational and Structural Biology Research Group). The research focus of the Post Lab is broadly described as investigations to understand the regulation and function of protein-protein interactions associated with cell signaling and viruses. Multi-dimensional, multinuclear NMR methods are used to determine 3-dimensional structure of protein complexes. Computational methods are

Suggested Citation:"APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS." National Research Council. 2010. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. Washington, DC: The National Academies Press. doi: 10.17226/13003.
×

used to study the mechanism of action of antiviral compounds, and the molecular mechanism for phosphotyrosine control of protein function in signal transduction.


Klaus Schulten received his Ph.D. from Harvard University in 1974. He is Swanlund Professor of Physics and is also affiliated with the Department of Chemistry as well as with the Center for Biophysics and Computational Biology at the University of Illinois, Urbana-Champaign. Professor Schulten is a full-time faculty member in the Beckman Institute and directs the Theoretical and Computational Biophysics Group. His professional interests are theoretical physics and theoretical biology. His current research focuses on the structure and function of supramolecular systems in the living cell, and on the development of non-equilibrium statistical mechanical descriptions and efficient computing tools for structural biology.


Jeffrey Skolnick received his B.A. in Chemistry, Summa Cum Laude, from Washington University, St. Louis in 1975. He received his M. Phil. in Chemistry from Yale University in 1977 and his Ph.D. in Chemistry from Yale University in 1978, with Professor Marshall Fixman. Dr. Skolnick is a Professor at Georgia Technical University and Director of the Center for the Study of Systems Biology. Dr. Skolnick has recently completed a very promising study in cancer metabolomics where he and his research group validated a predictive algorithm that can identify novel metabolites with anticancer properties. They have also developed a new, powerful algorithm that can predict protein function and binding sites, and which can be used for rapid screening ligand libraries. In addition, Dr. Skolnick has developed physics based, atomic potentials for protein structure refinement. He and his team demonstrated that the library of all protein folds is above the percolation threshhold, i.e., any protein structure can be related to any other by no more than eight intermediate structures.


Feng Wang received his B.S. in Chemistry from Peking University (1998) and Ph.D. in Theoretical Chemistry from the University of Pittsburgh (2003). He did post-doctoral research in computational physical chemistry at the University of Utah with Professor Gregory A. Voth. Since 2005, he has been an Assistant Professor in the Department of Chemistry at Boston University. Dr. Wang received a Mellon Fellowship at the University of Pittsburgh in 2002, an NSF CAREER Award in 2007, and an HP Outstanding Junior Faculty award in 2010. His research focuses on systematic development of high quality force fields, free energy determinations, and enhanced sampling.


Arieh Warshel received his BS degree in Chemistry, Summa Cum Laude, from Technion Israel in 1966, and his MS and PhD 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 Science in 2009.

Suggested Citation:"APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS." National Research Council. 2010. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. Washington, DC: The National Academies Press. doi: 10.17226/13003.
×
Page 13
Suggested Citation:"APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS." National Research Council. 2010. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. Washington, DC: The National Academies Press. doi: 10.17226/13003.
×
Page 14
Suggested Citation:"APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS." National Research Council. 2010. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. Washington, DC: The National Academies Press. doi: 10.17226/13003.
×
Page 15
Suggested Citation:"APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS." National Research Council. 2010. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. Washington, DC: The National Academies Press. doi: 10.17226/13003.
×
Page 16
Suggested Citation:"APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS." National Research Council. 2010. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. Washington, DC: The National Academies Press. doi: 10.17226/13003.
×
Page 17
Next: APPENDIX E THE BOARD ON LIFE SCIENCES AND THE NATIONAL ACADEMIES »
Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics Get This Book
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This letter details the work and transmits the final report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics. The committee evaluated submissions in response to a Request for Proposals (RFP) for Biomolecular Simulation Time on Anton, a specialized supercomputer designed and constructed by D.E. Shaw Research that allows for dramatically accelerated molecular dynamics simulations. D.E. Shaw is making time on a 512 node Anton machine available to the non-commercial research community without cost.

The goal of the RFP for Biomolecular Simulation Time on Anton is to facilitate breakthrough science in the study of biomolecular systems by providing access to a dedicated, massively parallel supercomputer that allows significantly faster simulations of biomolecular systems using periodic boundary conditions and explicit solvent models. Anton's capabilities allow questions to be addressed on multi-microsecond simulation timescales, so the program seeks to support projects addressing important and potentially high impact questions that would be most advanced by receiving time on this specialized machine.

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