Members
ANGEL GARCIA (Chair), Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York
ORLANDO ACEVEDO, Department of Chemistry and Biochemistry, Auburn University, Alabama
IVET BAHAR, Department of Computational and Systems Biology, University of Pittsburgh, Pennsylvania
DAVID BERATAN, Department of Chemistry, Duke University, North Carolina
BERNARD BROOKS, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
THOMAS CHEATHAM III, Department of Medicinal Chemistry, University of Utah, Salt Lake City
DONALD HAMELBERG, Department of Chemistry, Georgia State University
ANDRZEJ KLOCZKOWSKI, Battelle Center for Mathematical Medicine, Nationwide Children’s Hospital, Columbus, Ohio
MARIA KURNIKOVA, Department Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania
EDWARD LYMAN, Department of Physics and Astronomy, University of Delaware, Newark
ALEXANDER MACKERELL, School of Pharmacy, University of Maryland, Baltimore
SERGEI NOSKOV, Department of Biological Sciences, University of Calgary, Alberta, Canada
JED PITERA, IBM Almaden Research Center, San Jose, California
SCOTT SHOWALTER, Department of Chemistry, Pennsylvania State University, University Park
CHUNG WONG, Department of Chemistry and Biochemistry, University of Missouri-St. Louis
TROY WYMORE, Center for Molecular Biophysics, University of Tennessee-Knoxville and Oak Ridge National Laboratory
National Research Council Staff
KATHERINE BOWMAN, Senior Program Officer, Board on Life Sciences
CAMLY TRAN, Postdoctoral Fellow, Board on Chemical Sciences and Technology
LAUREN SONI, Senior Program Assistant, Board on Life Sciences
BIOGRAPHICAL SKETCHES OF COMMITTEE MEMBERS
Chair
Angel Garcia, Ph.D., is Department Head of the Physics, Applied Physics and Astronomy Department at Rensselaer Polytechnic Institute. He is also Professor of Physics and Senior Constellation Chaired Professor of Biocomputation and Bioinformatics. The Garcia Research Group focuses on the use of theoretical and computational methods to study aspects related to biomolecular dynamics and statistical mechanics. Their main research objectives are to understand the folding, dynamics and stability of biomolecules. Research interests include the hydrophobic effect, enzyme catalysis, nucleic acid structure and dynamics, RNA folding, electrostatics, protein hydration, and peptide interactions with membranes. Dr. García received a Ph.D. in Theoretical Physics from Cornell University. He is a fellow of the American Physical Society and a member of the Biophysical Society, The Protein Society, the AAAS, and the American Chemical Society. He received the Edward Bouchard prize of the American Physical Society in 2006. Dr. García is an Associate Editor of Proteins, Structure, Function and Bioinformatics, a member of the editorial board of the Biophysical Journal, Molecular Simulations, and a member of the Faculty of 1000 for BioMed Central.
Members
Orlando Acevedo, Ph.D., is an S. D. and Karen H. Worley Associate Professor of Chemistry and Biochemistry at Auburn University. Dr. Acevedo's research program focuses upon the application and development of new computational tools that target organic and enzymatic catalyst design, alternative environmentally friendly solvent design, and drug discovery. Fundamental problems in organic and medicinal chemistry are probed, such as elucidation of enzymatic reactions, controlling enantioselectivity for chiral compounds, transition structure prediction, de novo design of high-affinity inhibitors, and origins of drug resistance. Obtaining quantitative success with large-scale quantum and molecular mechanical calculations involves the development of improved force fields, software, and methodology. Dr. Acevedo received his B.S. from Florida International University, his Ph.D. from Duquesne University and completed postdoctoral work at Yale University.
Ivet Bahar, Ph.D., is Distinguished Professor and JK Vries Chair in the Department of Computational and Systems Biology at the University of Pittsburgh School Of Medicine. She is also Associate Director of the University of Pittsburgh Drug Discovery Institute and Co-Director of the Molecular and Systems Modeling Core of the Clinical and Translational Science Institute. Dr. Bahar was the Founding Chair of the University of Pittsburgh School of Medicine’s Department of Computational Biology and Founding Director of the joint University of Pittsburgh and Carnegie Mellon University Ph.D. program in computational biology. Her research focuses on biomolecular systems dynamics at multiple scales, the evolution of protein sequence, structure, dynamics and function, computer-aided drug discovery and polypharmacology, network models for protein-protein interactions, modeling and simulation of membrane proteins dynamics, and mechanisms of membrane protein interactions. Dr. Bahar has served on the Council and the Executive Board of the Biophysical Society and as member and chair of NIH study sections including Modeling and Analysis of Biological Systems, National Technology Centers for Networks and Pathways, and Computational Biology, Image Processing, and Data Mining. She received her Ph.D. in Chemistry from Istanbul Technical University, Turkey.
David Beratan, Ph.D., is the R. J. Reynolds Professor of Chemistry, Biochemistry, and Physics at Duke University. Through his research, Dr. Beratan has established a molecular-level theory that
describes the rate of charge tunneling reactions in biomolecules, thus establishing the theoretical underpinnings for biological energy capture and conversion processes. He has also developed theoretical methods to assign the absolute chirality of complex natural products and is developing theoretical methods to navigate molecular space in order to discover promising new structures of use in biomedical, energy, and materials science. Dr. Beratan was a National Research Council Resident Research Associate at NASA’s Jet Propulsion Laboratory and later a member of the technical staff. In 1992, he moved to the University of Pittsburgh as Associate Professor of Chemistry; he was promoted to the rank of Professor in 1997. Dr. Beratan became the R. J. Reynolds Professor at Duke in 2001, where he served as Chair of Chemistry from 2004 to 2007. He has been a visiting Professor at All Souls College—University of Oxford, Conrad E. Ronneberg Visiting Scholar—University of Chicago, and Ralph and Lucy Hirschmann Visiting Professor—University of Pennsylvania. He has received the National Science Foundation National Young Investigator award, is a Fellow of the American Physical Society, and is a Fellow of the American Association for the Advancement of Science. He received a bachelor of science from Duke University and Ph.D. in chemistry from California Institute of Technology.
Bernard Brooks, Ph.D., is Chief of the Laboratory of Computational Biology at the National Heart, Lung, and Blood Institute of the National Institutes of Health. He also directs the Computational Biophysics Section of the Laboratory, which develops simulation and modeling techniques and applies them to the study of problems of biological significance. Techniques employed include molecular dynamics, quantum and molecular mechanics, ab initio analysis of small molecule structures, molecular modeling, and electron microscopy image analysis.
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.
Donald Hamelberg, Ph.D., is Associate Professor of Computational Biophysical Chemistry and Associate Graduate Director of Computational Chemistry and Biophysical Chemistry at Georgia State University. His research focuses on the application and development of theoretical and computational methods for understanding biological functions. Many interactions in cell signaling pathways are mediated by networks of interacting proteins and RNA molecules. Deregulation of these pathways could trigger cellular transformation, oncogenesis, and other diseases. The research in Dr. Hamelberg’s laboratory seeks to decipher the underlying principles governing cell signaling mechanisms and biomolecular interactions involving proteins and RNA. In these endeavors, he uses simulation based approaches, statistical mechanics, and classical and quantum mechanical methods as a complementary tool to experiments. Dr. Hamelberg received his Ph.D. from Georgia State University. He was a Postdoctoral Research Fellow at the University of Illinois, Chicago (2001-2003) and at Howard Hughes Medical Institute and the University of California, San Diego (2003-2005).
Andrzej Kloczkowski, M.D., is a Principal Investigator in the Battelle Center for Mathematical Medicine of The Research Institute at Nationwide Children’s Hospital. He is also a Professor of Pediatrics at The Ohio State University College of Medicine. Dr. Kloczkowski completed his graduate education at Warsaw University, received his MD from the Institute of Physical Chemistry of the Polish Academy of Sciences, and completed his postdoctoral work at Stanford University and Warsaw University. Dr. Kloczkowski’s NIH-funded research program focuses on computational structural biology and bioinformatics, including protein structure prediction from the amino acid sequence, prediction of biomacromolecular dynamics using elastic network models, development of coarse grained models and potentials for proteins and nucleic acids, and studies of protein-protein and protein-nucleic acid integrations. He is also interested in application of machine learning methods to various biomedical and clinical problems, and has ongoing collaboration with several experimental and clinical centers.
Maria Kurnikova, Ph.D., is an Associate Professor of Chemistry at Carnegie Mellon University. Her research focuses on the area of computational chemistry and biophysics. She is interested in understanding the work of membrane proteins, such as receptors, signal transduction proteins, toxins and ion channels. The goal is to model and predict structure-function relationships in these proteins associated with ligand binding, gating of channels and mechanisms of selectivity and mobility in the confined environment of the channel. The systems she is interested specifically include Glutamate Receptors (AMPA and NMDA types), alpha-Hemolysin, Diphteria Toxin t-domain, Gramicidin A, PDZ-domain — ligand interaction of the NHERF1 protein. The approach her research group is taking includes a combination of physics-based computational methodologies, such as molecular dynamics simulations, continuum electrostatics and quantum chemistry. Dr. Kurnikova received her Ph.D. in Theoretical Chemistry from the University of Pittsburgh.
Edward Lyman, Ph.D., is an Assistant Professor within the Department of Physics and Astronomy at the University of Delaware. He received his Ph.D. in physics from Virginia Tech, where he studied nonequilibrium critical phenomena with Beate Schmittmann. He then did postdoctoral research in the Department of Computational Biology at the University of Pittsburgh with Dan Zuckerman. While in Pittsburgh he focused on methods development for biomolecular simulation, with an emphasis on statistically rigorous approaches for sampling protein conformation space. He then moved to Salt Lake City, Utah, where he joined the lab of Greg Voth. In Utah he worked on membrane protein simulation and multiscale simulation methods development.
Alexander MacKerell, Ph.D., is the Grollman-Glick Professor of Pharmaceutical Sciences at the University of Maryland School of Pharmacy. Research in Dr. MacKerell’s lab involves the development and application of computational methods to investigate the relationships of structure and dynamics to function in a range of biological and chemical systems. These efforts range from empirical force field development, implementation of novel sampling methodologies, understanding the physical forces driving the structure and dynamics of proteins, nucleic acids and carbohydrates and computer-aided drug design (CADD) studies. Dr. MacKerell received his B.S. in Chemistry from the University of Hawaii, Honolulu and completed his Ph.D. in Biochemistry at Rutgers University.
Sergei Noskov, Ph.D., is an Associate Professor at the Institute of Biocomplexity and Informatics at the University of Calgary. His research interests include molecular modeling, membrane proteins (ion channels and ion-coupled transporters), quantum chemistry of biologically relevant molecules, free energy profiles, and protein structure/function prediction. Dr. Noskov’s lab is comprised of a group of theoretical biologists and chemists interested in the understanding of molecular determinants of ligand transport across cellular membranes. Projects in his lab focus on studies of the family of fundamentally important ion-coupled neurotransmitter transporters implicated in diverse mechanisms of signal transduction in the brain. Their studies resulted in series of methods and software developed
in close collaboration with other theoretical groups across the world. Dr. Noskov received his Ph.D. from the Russian Academy of Sciences and completed his postdoctoral studies within the Department of Biochemistry and Structural Biology at Weill Medical College of Cornell University. Dr. Noskov is a recipient of AHFMR Scholar, CIHR New Investigator; and AIF New Faculty Awards (Canada); INTAS Young Scientist Award (European Union); and the Academia Sinica Research Fellowship and the American Epilepsy Foundation Post-Doctoral Fellowship (USA).
Jed Pitera, Ph.D., is a Research Staff Member in Science and Technology at the IBM Almaden Research Center. His research focuses on the use of computer simulation to address questions in biology and chemistry, particularly in the areas of protein folding, molecular recognition, self-assembly, and computer-aided materials design. His current research projects include simulations of polymeric materials for lithography, desalination, and drug delivery applications. Dr. Pitera received undergraduate training in Biology and Chemistry at the California Institute of Technology, where he worked in Prof. Pamela Bjorkman’s protein crystallography group. Subsequently, he pursued graduate studies in Biophysics at the University of California, San Francisco (UCSF) in the laboratory of Prof. Peter Kollman. In Dr. Kollman’s group, he developed an interest in the use of biomolecular simulation and free energy calculations in the rational design of proteins and pharmaceuticals. He pursued similar work in a postdoctoral position with Prof. Dr. Wilfred van Gunsteren at the ETH in Zurich, Switzerland, where his research focused on novel methods to calculate free energies for ligand design. Dr. Pitera is also an adjunct assistant professor in the UCSF Department of Pharmaceutical Chemistry, and maintains active collaborations with groups at UCSF and Stanford.
Scott Showalter, Ph.D., is an Associate Professor of Chemistry at Pennsylvania State University. He received his B.S. from Cornell University, his Ph.D. from Washington University School of Medicine, and completed his postdoctoral research at The National High Magnetic Field Laboratory in Tallahassee, Florida. Dr. Showalter's lab applies biophysical chemistry techniques to understand the function of partially disordered proteins and work to define the features of protein-RNA interactions.
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.
Troy Wymore, Ph.D., is a Research Assistant Professor in the Department of Biochemistry, Cellular and Molecular Biology at the University of Tennessee-Knoxville. He completed his B.S. and Ph.D. in Chemistry at the University of Missouri-Columbia. His research focuses on applying hybrid QC/MM simulations to investigate the enzymatic mechanisms of DFPase, Xylose Isomerase, and 5-epi-aristolocholene synthase. The results of these studies provide insight into strategies for redesigning these enzymes to more effectively degrade nerve agents (DFPase) and improve the process of biofuel and pharmaceutical agent production.
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