APPENDIX D

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

MICHAEL LEVITT (Chair), Professor and Chair, Department of Structural Biology, Stanford University School of Medicine

L. MARIO AMZEL, Professor and Director, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine

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

JAMES BRIGGS, Associate Professor and Interim Chair, Department of Biology and Biochemistry, University of Houston

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

THOMAS CHEATHAM III, Associate Professor, Department of Medicinal Chemistry, University of Utah

SCOTT FELLER, Howell Professor of Chemistry and Chair, Division of Natural Sciences and Mathematics, Wabash College

TOSHIKO ICHIYE, Professor and William G. McGowan Chair in Chemistry, Department of Chemistry, Georgetown University

JEFFRY D. MADURA, Professor, Department of Chemistry and Biochemistry, Duquesne University

GLENN MARTYNA, Research Staff Member, Physical Sciences Division, IBM T. J. Watson Lab

RUTH NUSSINOV, Senior Investigator, Center for Cancer Research, National Cancer Institute, National Institutes of Health

LOUKAS PETRIDIS, Research Staff Scientist, Center for Molecular Biophysics, Oak Ridge National Laboratory

JEFFERY SKOLNICK, Georgia Research Alliance Eminent Scholar in Computational Systems Biology, Center for the Study of Systems Biology, Georgia Institute of Technology

CHUNG WONG, Professor, Department of Chemistry and Biochemistry, University of Missouri-St. Louis

NATIONAL RESEARCH COUNCIL STAFF

KATHERINE BOWMAN, Senior Program Officer, Board on Life Sciences

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

CARL G. ANDERSON, Program Associate, Board on Life Sciences



The National Academies | 500 Fifth St. N.W. | Washington, D.C. 20001
Copyright © National Academy of Sciences. All rights reserved.
Terms of Use and Privacy Statement



Below are the first 10 and last 10 pages of uncorrected machine-read text (when available) of this chapter, followed by the top 30 algorithmically extracted key phrases from the chapter as a whole.
Intended to provide our own search engines and external engines with highly rich, chapter-representative searchable text on the opening pages of each chapter. Because it is UNCORRECTED material, please consider the following text as a useful but insufficient proxy for the authoritative book pages.

Do not use for reproduction, copying, pasting, or reading; exclusively for search engines.

OCR for page 12
APPENDIX D COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS, FOURTH ROUND MICHAEL LEVITT (Chair), Professor and Chair, Department of Structural Biology, Stanford University School of Medicine L. MARIO AMZEL, Professor and Director, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine NILESH BANAVALI, Research Scientist, Wadsworth Center, New York State Department of Health, and Assistant Professor, School of Public Health, State University of New York, Albany JAMES BRIGGS, Associate Professor and Interim Chair, Department of Biology and Biochemistry, University of Houston CHARLES L. BROOKS III, Warner-Lambert/Parke-Davis Professor of Chemistry and Professor of Biophysics, Department of Chemistry and Biophysics, University of Michigan THOMAS CHEATHAM III, Associate Professor, Department of Medicinal Chemistry, University of Utah SCOTT FELLER, Howell Professor of Chemistry and Chair, Division of Natural Sciences and Mathematics, Wabash College TOSHIKO ICHIYE, Professor and William G. McGowan Chair in Chemistry, Department of Chemistry, Georgetown University JEFFRY D. MADURA, Professor, Department of Chemistry and Biochemistry, Duquesne University GLENN MARTYNA, Research Staff Member, Physical Sciences Division, IBM T. J. Watson Lab RUTH NUSSINOV, Senior Investigator, Center for Cancer Research, National Cancer Institute, National Institutes of Health LOUKAS PETRIDIS, Research Staff Scientist, Center for Molecular Biophysics, Oak Ridge National Laboratory JEFFERY SKOLNICK, Georgia Research Alliance Eminent Scholar in Computational Systems Biology, Center for the Study of Systems Biology, Georgia Institute of Technology CHUNG WONG, Professor, Department of Chemistry and Biochemistry, University of Missouri-St. Louis NATIONAL RESEARCH COUNCIL STAFF KATHERINE BOWMAN, Senior Program Officer, Board on Life Sciences KATHRYN HUGHES, Senior Program Officer, Board on Chemical Sciences and Technology CARL G. ANDERSON, Program Associate, Board on Life Sciences 12

OCR for page 12
BIOGRAPHICAL SKETCHES OF COMMITTEE MEMBERS CHAIR Michael Levitt, Ph.D. (NAS), is Professor and Chair of the Department of Structural Biology at Stanford University School of Medicine. He is known for his pioneering work in computational biology, especially protein folding. He co-discovered the four protein-fold classes and explained how these segments pack. He was also the first to automate secondary structure identification and pioneered simulation of protein unfolding in solution, emphasizing qualitative aspects and using film to show protein motion. His early use of restraints and annealing in folding forms the basis for current methods of NMR structure determination. Primarily focused on proteins, he has also contributed to the computational structural biology of DNA and RNA. Starting with his model for tRNA, which captured many features of the subsequently determined x-ray structure, he went on to correctly predict that DNA would have 10.5 not 10 base-pairs per turn in solution. He also ran the first molecular dynamics simulations of DNA in vacuo and in solution and has developed methods to combine distant homology searches of genomic sequences with automated modeling. These results have been combined in the BioSpace database. Dr. Levitt received his Ph.D. in Biophysics from the University of Cambridge in 1971. MEMBERS L. Mario Amzel, Ph.D., is Professor and Director of the Department of Biophysics and Biophysical Chemistry at the Johns Hopkins University School of Medicine. Dr. Amzel’s research interests include structural enzymology of redox and phosphoryl-transfer enzymes, particularly the enzymes MICAL, VP14, PI3K, and Nudix hydrolases, and selected areas of structural thermodynamics. He received his Ph.D. in Physical Chemistry in 1968 from the Universidad de Buenos Aires, Argentina and completed his postdoctoral research in the structure of proteins from 1969-1970 at the Johns Hopkins University School of Medicine. Nilesh Banavali, Ph.D, is a Research Scientist at the Wadsworth Center of the New York State Department of Public Health and an 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. He 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. James Briggs, Ph.D., is Associate Professor and Interim Chair of Biology and Biochemistry at the University of Houston. He studies the kinetic and thermodynamic properties of enzymes and receptors utilizing molecular mechanics, molecular and Brownian dynamics, electrostatics, quantum mechanics, and quantitative structure-activity relationship methods. Application areas include the search for inhibitors of e.g., HIV-1 integrase (anti-AIDS), Rho Kinase 1, PTen, STAT3, identification of the function of proteins of known structure but unknown function, inhibition of biofilm formation, and more. Dr. Briggs received his Ph.D. in Theoretical Organic Chemistry from Purdue University in 1990. 13

OCR for page 12
Charles L. Brooks, Ph.D., is the Warner-Lambert/Parke-Davis Professor of Chemistry and Professor of Biophysics at the University of Michigan. His research includes multi-scale modeling of the dynamics and assembly of complex biological assemblies, protein folding, unfolding and aggregation, and free energy approximations. He received a B.S. from Alma College in 1978 and his Ph.D. in Physical Chemistry from Purdue University in 1982. Dr. Brooks was the recipient of an NIH Postdoctoral Fellowship and engaged in postgraduate work at Harvard University with Professor Martin Karplus, focusing on theoretical and computational biophysics. 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. Thomas E. Cheatham III, Ph.D., is an Associate Professor in the Department of Medicinal Chemistry and an Adjunct Associate Professor in the Department of Bioengineering at the University of Utah. He is also a member of the Henry Eyring Center for Theoretical Chemistry, a senior fellow of the Center for High Performance Computing, a member of the NSF Teragrid Scientific Advisory Board, and a member of the University of Utah Information Technology Council and the University of Utah Cyberinfrastructure Council. He serves as a member of the board of editors of the Journal of Biomolecular Structure & Dynamics. Dr. Cheatham’s research focuses on the development of molecular dynamics, free energy simulation, and trajectory analysis methodologies in applications aimed at better understanding biomolecular structure, dynamics and interactions including the representation of nucleic acid systems in solution. He received his Ph.D. in pharmaceutical chemistry from the University of California, San Francisco, and B.A. degrees in chemistry and in mathematics and computer science from Middlebury College. He was subsequently an NRC postdoctoral fellow in the Computational Biophysics Section of the Laboratory of Biophysical Chemistry at the National Heart, Lung and Blood Institute, National Institutes of Health. Scott Feller, Ph.D., is the Lloyd B. Howell Professor of Chemistry and Chair of the Division of Natural Sciences and Mathematics at Wabash College. His research focuses on simulations of lipid bilayers and on membrane biophysics. Dr. Feller was named the College’s McLain- McTurnan-Arnold Excellence in Teaching Award Winner for 2009 and often conducts his research with the students he teaches, many of who have gone on to pursue advanced degrees in the chemical sciences. Dr. Feller is a graduate of Willamette University in Oregon and holds his Ph.D. in Physical Chemistry from the University of California, Davis. Toshiko Ichiye, Ph.D., is Professor and William G. McGowan Chair in Chemistry at Georgetown University. She is a leader in the field of molecular dynamics simulations, an area of computational chemistry that enables pharmaceutical companies, biotechnology firms, and bioengineering firms to design and perfect their products. Dr. Ichiye’s research interests include theoretical biophysical and physical chemistry, structure and function of proteins, statistical mechanics of macromolecules and liquids, and molecular dynamics simulations of biological macromolecules. She received her B.A. in Physics from Rice University in 1978 and her Ph.D. in Biophysics in 1985 from Harvard University. Jeffry D. Madura, Ph.D., is a Professor in the Department of Chemistry and Biochemistry at Duquesne University. He served as Department Chair from 2000-2010. Dr. Madura earned a B.A. from Thiel College in 1980 and a Ph.D. in Physical Chemistry from Purdue University in 1985, followed by a postdoctoral fellowship in computational biophysics with Professor J. Andrew McCammon at the University of Houston. His research focuses on the computational biophysics of neurotransmitter transporters. He has published more than 100 papers in physical chemistry 14

OCR for page 12
and chemical physics and is co-author of the textbook General Chemistry: Principles and Modern Applications. He was the recipient of the 1997-1998 Dreyfus Teacher-Scholar Award, the Bayer School of Natural and Environmental Sciences Award for Excellence in Service in 2004, the Bayer School of Natural and Environmental Sciences and the Duquesne University Presidential Award for Excellence in Scholarship in 2007, was inducted into the Duquesne University Office of Research Hall of Fame in 2008, and was elected as an ACS Fellow in 2011. Glenn J Martyna, Ph.D., is a Research Scientist at IBM's T.J. Watson Research Lab in Yorktown Heights, NY. Dr. Martyna received his Ph.D. in chemical physics from Columbia University in 1989 and was an NSF postdoctoral fellow in computational science and engineering at the University of Pennsylvania. Dr. Martyna was appointed to the 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. Ruth Nussinov, Ph.D., is a Professor in the Department of Human Genetics, School of Medicine, Tel Aviv University and a Senior Principal Scientist and Principal Investigator at the National Cancer Institute (NCI) of the National Institutes of Health. She maintains a research group in Tel Aviv in collaboration with Prof. H. Wolfson from the School of Computer Science as well as a research group at NCI, and is the author of over 440 scientific papers. Dr. Nussinov was a pioneer in studying DNA sequence and structure and nucleic acid-protein interactions. Currently her research focuses on computational studies of protein folding, binding and protein function. She received her B.Sc. in Microbiology from the University of Washington and her Ph.D. in Biochemistry from Rutgers University. Dr. Nussinov serves as Editor-in-Chief of PLoS Computational Biology and as an Editor of the Journal of Biological Chemistry, Physical Biology, Proteins, Biophysical Journal, and BMC Bioinformatics. She also serves as a long term member on the NIH Study Section Macromolecular Structure and Function D. Loukas Petridis, Ph.D., is a Research Staff Scientist in the Center for Molecular Biophysics at Oak Ridge National Laboratory. His research focuses on high-performance computer simulation of biological macromolecules, neutron scattering in bioenergy research and polymer physics. In particular, he investigates the origins of biomass recalcitrance via the integration of computer simulation with neutron scattering experiments, undertakes computer simulations of lignocelluloses, and investigates molecular-scale mechanisms stabilizing soil organic carbon by application of molecular dynamics simulation and neutron reflectometry. He also studies scaling of molecular dynamics simulation on supercomputers and physics of biopolymers. He obtained his Ph.D. in theoretical physics from Cambridge University in 2006 and was a postdoctoral fellow at Oak Ridge National Laboratory from 2007 to 2009. Jeffrey Skolnick, Ph.D., is Professor and Director of the Center for the Study of Systems Biology and Georgia Research Alliance Eminent Scholar in Computation Systems Biology at Georgia Institute of Technology. He received his B.A. in Chemistry from Washington University, St. Louis in 1975, 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. His research focuses on computational systems biology and bioinformatics including the development of algorithms and their application to proteomes for the prediction of protein structure and function, the prediction of small molecule ligand-protein interactions with applications to drug discovery and the prediction of off-target uses of existing drugs, fundamental studies on the nature and completeness of protein structure space and the exploration of the interplay between protein 15

OCR for page 12
physics and evolution in determining protein structure and function, prediction of protein-protein and protein-DNA interactions, cancer metabolomics and molecular simulations of cellular processes. He is a member of the editorial boards of PeerJ, Journal of Metabonomics & Metabolites, Current Bioinformatics, Biology Direct, and Protein Science. Riina Tehver, Ph.D., is an Assistant Professor in the Department of Physics and Astronomy at Denison University. She received her Ph.D. in Physics from Pennsylvania State University and B.S. in Physics from Tartu University, Estonia. She was subsequently a postdoctoral research fellow at the Institute for Physical Science and Technology at the University of Maryland. Dr. Tehver’s research seeks to understand how biomolecules, particularly motor proteins, perform their cellular functions, using numerical analysis and computational modeling to connect protein structures to their operations. Dr. Tehver serves as a reviewer for the journals Bioinformatics and Physical Review Letters, and was the Chair of the Protein Folding Dynamics Gordon Research Seminar in 2010. Chung Wong, Ph.D., is an Associate Professor in the Department of Chemistry and Biochemistry at the University of Missouri-Saint Louis. He received his B.Sc. (Hons.) degree from the Chinese University of Hong Kong and his Ph.D. degree from the University of Chicago. He completed his postdoctoral work at the University of Houston. He has held academic and industrial positions at the University of Houston, Mount Sinai School of Medicine, SUGEN, Inc., University of California-San Diego, and the Howard Hughes Medical Institute before joining the faculty of University of Missouri, St. Louis in 2004. His research involves the development and applications of computational methods to study biomolecular structure, dynamics, and function and to aid the design of bioactive compounds. He has served on multiple grant review panels for the National Institutes of Health and the European Union and as a mentor for students in the Student Teacher as Research Scientist (STARS) program, a joint venture among University of Missouri-Saint Louis, Washington University, Saint Louis University, and several non-profit and for-profit institutions in Saint Louis to provide research opportunities to high-school students and teachers. 16