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, THIRD ROUND L. MARIO AMZEL, (Chair), Professor and Director, Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine IOAN ANDRICIOAEI, Associate Professor, Chemistry, School of Physical Sciences, University of California, Irvine 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 RICCARDO BARON, Assistant Professor, Department of Medicinal Chemistry, College of Pharmacy, The University of Utah ANGEL E. GARCIA, Professor of Physics and Senior Constellation Chaired Professor in Biocomputation and Bioinformatics, Rensselaer Polytechnic Institute TOSHIKO ICHIYE, Professor and William G. McGowan Chair in Chemistry, Department of Chemistry, Georgetown University TERRY P. LYBRAND, Professor, Department of Chemistry, Pharmacology, & Center for Structural Biology, Vanderbilt University GLENN MARTYNA, Research Staff Member, Physical Sciences Division, IBM T. J. Watson Lab DAVID L. MOBLEY, Assistant Professor, Department of Pharmaceutical Sciences, University of California, Irvine RICHARD W. PASTOR, Chief, Membrane Biophysics Section, National Heart Lung Blood Institute, National Institutes of Health LOUKAS PETRIDIS, Research Staff Scientist, Center for Molecular Biophysics, Oak Ridge National Laboratory B. MONTGOMERY PETTITT, Robert A. Welch Distinguished Chair in Chemistry, Professor in the Departments of Pharmacology and Toxicology and of Biochemistry and Molecular Biology, and Director of the Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch. SCOTT A. SHOWALTER, Assistant Professor, Department of Chemistry, Pennsylvania State University FENG WANG, Associate Professor, Department of Chemistry and Biochemistry, University of Arkansas ARIEH WARSHEL, Distinguished Professor of Chemistry, Department of Chemistry, University of Southern California NATIONAL RESEARCH COUNCIL STAFF KATHERINE BOWMAN, Senior Program Officer, Board on Life Sciences KATHRYN HUGHES, Senior Program Officer, Board on Chemical Sciences and Technology ORIN LUKE, Senior Program Assistant, Board on Life Sciences SAYYEDA AYESHA AHMED, Senior Program Assistant, Board on Life Sciences 12
OCR for page 13
BIOGRAPHICAL SKETCHES OF COMMITTEE MEMBERS CHAIR 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. MEMBERS Ioan Andricioaei, Ph.D., is Associate Professor of Chemistry in the School of Physical Sciences at the University of California, Irvine. His research focuses on exploring theoretical and computational topics at the interface between molecular biophysics and physical chemistry, with the central themes of (1) developing novel theoretical techniques, and (2) applying computer and modeling methods to describe, in terms of dynamics and thermodynamics, biologically important molecular processes, with the aim to complement, enhance, or predict experimental findings. Research directions include enhanced sampling in trajectory space, computer simulations of DNA-binding machines, and dynamics-function relationships. Dr. Andricioaei received his Ph.D. from Boston University in 1999. 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. Riccardo Baron, Ph.D., is Assistant Professor of Medicinal Chemistry and Adjunct Assistant Professor of Bioengineering at the University of Utah. His research develops chemical theory and computational approaches to address problems of relevance for public health. Following his education at the Università degli Studi di Milano (Italy) and University of Cambridge (U.K.), he carried out his doctoral research at the Department of Chemistry and Applied Biosciences of the Swiss Federal Institute of Technology, ETH Zurich (Switzerland). During his Ph.D. with Prof. Wilfred F. van Gunsteren, he designed a wide range of methods for biomolecular simulation, including entropy and free energy calculation, force field and software development. His postdoctoral research with J. Andrew McCammon, Investigator, Howard Hughes Medical Institute at the University of California, San Diego, led to a paradigm shift on the understanding of the physicochemical forces driving molecular recognition, approaches to efficiently introduce protein dynamics ensemble models in drug discovery and design, and models to understand the reactants transport in biocatalysts. He has published more than forty publications in the field of biomolecular simulation and actively serves as a member of the American Chemical Society and as a reviewer for numerous international journals, scientific societies, and computational centers 13
OCR for page 14
in the areas of chemistry, biology, physics, medicine, and engineering. He was recently awarded the "Alfredo di Braccio" Prize for Chemistry from the Accademia Nazionale dei Lincei (Italy) and the Postdoctoral Research Award from the American Chemical Society (U.S.). His current research integrates computational approaches with experiments through collaborations with world leading groups in enzymology and drug discovery. Angel E. García, Ph.D., is the Senior Constellation Professor of Biocomputation and Bioinformatics at Rensselaer Polytechnic University. His research focuses on the use of theoretical and computational methods to study biomolecular dynamics and statistical mechanics, with the objectives of understanding the folding, dynamics and stability of biomolecules. Particular interests include the hydrophobic effect, enzyme catalysis, nucleic acid structure and dynamics, RNA folding, electrostatics, protein hydration, and peptide interactions with membranes. Before joining Rensselaer he was Group Leader at the Theoretical Biology and Biophysics Group at Los Alamos National Laboratory. Dr. García is a Fellow of the American Physical Society. He received the Edward Bouchet Award from the American Physical Society in 2006. Dr. García is the Associate Editor of Proteins, Structure, Function and Bioinformatics and belongs to the editorial board of Biophysical Journal and Molecular Simulations. He is a member of the American Physical Society, Biophysical Society, American Chemical Society, Protein Society and the American Association for the Advancement of Science. 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. Terry P. Lybrand, Ph.D., is a Professor in the Department of Chemistry at Vanderbilt University. Dr. Lybrand's research focuses on molecular modeling and bioinformatics techniques. His laboratory utilizes computational methods to study the properties and behavior of biomacromolecules and ligand-biomacromolecule complexes, and to aid in the design of small molecule ligands with desired binding properties for targeted receptors. Techniques used include quantum mechanical calculations, molecular dynamics and Monte Carlo simulation, and free energy perturbation methods. Dr. Lybrand received his Ph.D. in Pharmaceutical Chemistry from the University of California, San Francisco in 1984. 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 sciences 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. David L. Mobley, Ph.D., is an Assistant Professor in the Department of Pharmaceutical Sciences at the University of California, Irvine. His research focuses on applying computational and theoretical methods to understand and quantitatively predict fundamental biological processes 14
OCR for page 15
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 was previously an Assistant Professor in Chemistry at the University of New Orleans (2008 to 2012) and 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. Richard W. Pastor, Ph.D., is Chief of the Membrane Biophysics Section at the National Heart Lung and Blood Institute of the National Institutes of Health. He received a B.A. in philosophy from Hamilton College (1973), a M.S. in chemistry from Syracuse University (1977), and Ph.D. in Biophysics from Harvard University (1984). He did research and review at the Food and Drug Administration from 1984 to 2007, and moved to the National Institutes of Health in 2007. His research focuses on computer simulations of membranes, including method development (all- atom and coarse grained lipid force fields); fundamental theory (treatment of diffusion in two dimensions, and spontaneous curvature in membranes); biological applications (conformations of peptides in bilayers; fencing of PIP2); and technological applications (polymer transport through ion channels). Dr. Pastor is also a CHARMM developer (algorithms involving pressure anisotropy and long range forces). 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. B. Montgomery Pettitt, Ph.D., is the Robert A. Welch Distinguished Chair in Chemistry and Professor in the Departments of Pharmacology and Toxicology and of Biochemistry and Molecular Biology at the University of Texas Medical Branch. He also directs the Sealy Center for Structural Biology and Molecular Biophysics, a research center serving the greater Houston- Galveston area with facilities for structural biology (x-ray, NMR and cryoEM) and scientific computing for use in the areas of simulation and modeling. His research focuses on understanding molecular recognition and folding of biopolymers in solution. His theoretical research interests have led to the development of novel methods for calculating the behavior of biopolymers in solution and near surfaces. He earned his B.S. and Ph.D. from the University of Houston, was a postdoctoral fellow at the University of Texas at Austin, and was an NIH Fellow at Harvard University. Scott A. Showalter, Ph.D., is an Assistant Professor in the Department of Chemistry at the Pennsylvania State University. Dr. Showalter's research aims to understand structure-function relationships in biomolecular systems that display extensive conformational dynamics. His group has developed solution NMR spectroscopy methods based on direct carbon detection that enable high resolution structural and dynamic studies of intrinsically disordered proteins and the conformational changes they undergo in folding-upon-binding reaction mechanisms. Combining 15
OCR for page 16
NMR data with isothermal titration calorimetry assays and conformational modeling using ultra- long molecular mechanics calculations performed on the ANTON platform provides atomistic ensembles with high spatial and temporal resolution, as well as mechanistic insight into disordered protein function. The Showalter laboratory also applies similar biophysical techniques to study non-specific double-stranded RNA binding by double-stranded RNA binding proteins involved in microRNA maturation. Dr. Showalter received his Ph.D. from Washington University School of Medicine in St. Louis, MO, where he was an NSF predoctoral fellow. He was an NIH- NRSA postdoctoral fellow at the National High Magnetic Field Laboratory in Tallahassee, FL. Feng Wang, Ph.D., is an Associate Professor in the Department of Chemistry and Biochemistry at the University of Arkansas. He was formerly an Assistant Professor in the Department of Chemistry at Boston University from 2005 to 2012. Dr. Wang's research focuses on developing high quality force fields, free energy calculations, and enhanced sampling. He received his B.S. in Chemistry from Peking University (1998) and Ph.D. in Theoretical Chemistry from the University of Pittsburgh (2003) with Prof. Kenneth D. Jordan. He did post-doctoral research in computational physical chemistry at the University of Utah with Professor Gregory A. Voth. While at the University of Pittsburgh, Dr. Wang received an IBM graduate student award in 2001 and a Mellon Fellowship in 2002. He received a NSF CAREER Award in 2007 and an HP outstanding Junior Faculty Award in 2010. Arieh Warshel, Ph.D., is a Distinguished Professor of Chemistry and Biochemistry at the University of Southern California. Dr. Warshel is known for his work on computational biochemistry and biophysics, in particular for pioneering computer simulations of the functions of biological systems, and for developing what is known today as Computational Enzymology. Dr. Warshel made major contributions in introducing computational methods for structure function correlation of biological molecules, pioneering and co-pioneering programs, methods and key concepts for microscopic studies of functional properties of biological molecules including Cartezian based force field programs, the QM/MM method for simulating enzymatic reactions, the first molecular dynamic simulation of a biological process, microscopic electrostatic models for proteins, and free energy perturbation in proteins and other key advances. He 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. He is an elected member of the United States National Academy of Sciences (2009), a fellow of the Royal Society of Chemistry (2008), a fellow of the Biophysical Society (2000), and an Alfred P. Sloan fellow (1978). He has received awards including the Annual Award of the International Society of Quantum Biology and Pharmacology (1993); Tolman Medal (2003); President's award for computational biology from the ISQBP (2006); and RSC Soft Matter and Biophysical Chemistry Award (2012). 16