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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
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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
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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
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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
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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).
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