COMMITTEE ON PROPOSAL EVALUATION FOR ALLOCATION OF SUPERCOMPUTING TIME FOR THE STUDY OF MOLECULAR DYNAMICS, ELEVENTH ROUND
IVET BAHAR (NAS), University of Pittsburgh
RAVINDER ABROL, California State University, Northridge
NATHAN BAKER, Pacific Northwest National Laboratory
JEROME BAUDRY, University of Alabama in Huntsville
CHIA-EN A. CHANG, University of California, Riverside
BRIAN DOMINY, Clemson University
ALEMAYEHU GORFE, The University of Texas Medical School at Houston
JAMES C. GUMBART, Georgia Institute of Technology
ELLINOR HAGLUND, University of Hawaii at Manoa
MARGARET JOHNSON, Johns Hopkins University
REBECCA K. LINDSEY, Lawrence Livermore National Laboratory
CLARE MCCABE, Vanderbilt University
YINGLONG MIAO, University of Kansas
SHIKHA NANGIA, Syracuse University
GIULIA PALERMO, University of California, Riverside
HEATHER W. PINKETT, Northwestern University
CAROL B. POST, Purdue University
LEONOR SAIZ, University of California, Davis
MARKUS SEELIGER, Stony Brook University
JEFFREY SKOLNICK, Georgia Institute of Technology
KAYLA G. SPRENGER, University of Colorado Boulder
JUAN M. VANEGAS, The University of Vermont
JOSH VERMAAS, Oak Ridge National Laboratory
YAROSLAVA G. YINGLING, North Carolina State University
STEVEN M. MOSS, Project Director, Board on Life Sciences
ANDREA HODGSON, Program Officer, Board on Life Sciences
JESSICA WOLFMAN, Research Associate, Board on Chemical Sciences and Technology
DARLENE GROS, Senior Program Assistant, Nuclear and Radiation Studies Board
BIOGRAPHICAL SKETCHES OF COMMITTEE MEMBERS
Ivet Bahar (NAS), Ph.D., is a Distinguished Professor and the John K. Vries Chair in the Department of Computational and Systems Biology at the University of Pittsburgh School of Medicine. She is also an Associate Director of the University of Pittsburgh Drug Discovery Institute and the 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 the 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 a member and the Chair of National Institutes of Health 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.
Ravinder “Ravi” Abrol, Ph.D., is an Assistant Professor of chemistry and biochemistry at California State University, Northridge. Dr. Abrol’s research lab is focused on developing and using computational methods to probe how protein structure and biochemical (protein–ligand and protein–protein) interactions of G protein-coupled receptors (GPCRs) determine cellular signaling and physiology, as well as how this knowledge can be used for the rational design of drugs targeting GPCR signaling pathways. GPCRs are integral membrane proteins that form the largest superfamily in the human genome. The activation of these receptors by a variety of bioactive molecules regulates key physiological processes (e.g., neurotransmission, cellular metabolism, secretion, cell growth, immunity, differentiation) through a balance of G protein-coupled and betaarrestin-coupled signaling pathways. This has made them targets for ~50% drugs in the clinic. A molecular and structural understanding of these GPCR signaling pathways will have a broad impact on understanding of cellular signaling and on drug discovery efforts targeting GPCRs. Research in the Abrol Lab lies at the interface of chemistry and biology, where they are using computational biophysics– and structural bioinformatics–based methods to gain mechanistic insights into the biochemistry of GPCR signaling. Dr. Abrol received a B.S. in 1994 from the University of Delhi, an M.S. in 1995 from the Indian Institute of Technology, and a Ph.D. in 2003 from the California Institute of Technology in Pasadena.
Nathan Baker, Ph.D., is the Director for the Advanced Computing, Mathematics, and Data Division at Pacific Northwest National Laboratory and a Visiting Faculty member in the Brown University Division of Applied Mathematics. His research focuses on developing new algorithms and mathematical methods in biophysics, nanotechnology, and informatics. His research projects include computational methods for modeling solvation in biomolecular systems, mathematical
methods for mesoscale materials modeling, and development of methods for signature discovery. Dr. Baker has served on review panels for various agencies, including as a member of the National Institutes of Health Macromolecular Structure and Function D study section. He currently is an editorial board member for the Biophysical Journal and serves on the editorial board for NPG Scientific Data. Dr. Baker is a Fellow of the American Association for the Advancement of Science and has been awarded the Hewlett-Packard Junior Faculty Excellence Award by the American Chemical Society, the National Cancer Institute caBIG Connecting Collaborators Award, and an Alfred P. Sloan Research Fellowship. He earned his doctorate in physical chemistry from the University of California, San Diego.
Jerome Baudry, Ph.D., is the Pei-Ling Chan Professor of Biological Sciences in the Department of Biological Sciences at the University of Alabama in Huntsville (UAH). Dr. Baudry obtained his Ph.D. in molecular biophysics from the University of Paris, UPMC/Sorbonne Universities, France. He subsequently joined the group of Klaus Schulten at the University of Illinois at Urbana-Champaign as a postdoc. After his postdoctoral work, Dr. Baudry worked in the pharmaceutical industry as a Research Scientist, and then accepted a Senior Research Scientist position back in Illinois on a non-tenure track research faculty position. Dr. Baudry joined the University of Tennessee, Knoxville, and the UT/ORNL Center for Molecular Biophysics as a tenure track Assistant Professor in 2008. In 2014, he was promoted to Associate Professor with tenure. In August 2017, Dr. Baudry joined UAH as the Pei-Ling Chan Professor. At UAH, Dr. Baudry’s group develops and applies methods and protocols for computational drug discovery, both on small molecules and biologicals, within academic, national laboratories and industrial collaborations.
Chia-en A. Chang, Ph.D., is an Associate Professor of chemistry and bioinformatics at the University of California, Riverside. The central goal of her research is to understand the fundamental mechanism of biomolecular recognition and binding kinetics using theory and classical mechanical models. Her research involves the development and application of computational methods and theoretical models to address medically and chemically important problems. These methods are of practical importance in studying biomolecular function and in the design of new molecules that bind strongly to their receptors. Systems of particular interest include existing or potential drug targets, cell signaling complexes, and chemical host–guest systems.
Brian Dominy, Ph.D., is an Associate Professor in the Department of Chemistry at Clemson University. Dr. Dominy earned his B.S. from Carnegie Mellon University in the biological sciences and computer science tracks with a minor in chemistry. He then joined The Scripps Research Institute as a Ralph M. Parsons Foundation predoctoral fellow, earning his Ph.D. under the direction of Dr. Charles L. Brooks III. Following this, he worked as a National Institutes of Health postdoctoral fellow at Harvard University with Dr. Eugene Shakhnovich in the Department of Chemistry and Chemical Biology. During this time, his research dealt with improving statistical mechanical models, primarily inverse Boltzmann knowledge-based potentials, designed for rapid binding free energy prediction and automated drug design. His current research involves the development and application of molecular mechanics and bioinformatics techniques to explore the physical chemical basis of biological phenomena at the molecular level. Specifically, his group focuses on applications relevant to medicine, including drug design and biomolecular evolution of drug targets (i.e., drug resistance).
Alemayehu Gorfe, Ph.D., is an Associate Professor in the Department of Integrative Biology and Pharmacology at The University of Texas Medical School at Houston. He has a Ph.D. in biochemistry from the University of Zurich in Switzerland. Dr. Gorfe and his research team use computer simulations to study the organization of cell signaling components, interfacial interactions, and allostery to aid in the development of treatments for unsolved health challenges. Their special focus is on the Ras family of lipid-modified enzymes that regulate a variety of cell signaling pathways and whose malfunction leads to many forms of cancer. There is an urgent need for an ongoing effort to find drugs that abrogate signaling through defective Ras. Aiming at contributing to this effort, Dr. Gorfe and his team study Ras at the atomic, molecular, and supramolecular levels of detail using multiscale simulations and collaborative cell-biological and biophysical experiments. They are particularly interested in understanding how dynamics and lateral distribution of Ras and related G proteins on membrane surfaces may affect their ability to functionally interact with other proteins. Other interests of the group include modeling transient signaling complexes and interaction between specific drugs and phospholipids.
James C. “J. C.” Gumbart, Ph.D., is an Assistant Professor of physics at the Georgia Institute of Technology in Atlanta, Georgia. He obtained his B.S. from Western Illinois University and his Ph.D. in physics from the University of Illinois at Urbana-Champaign under the mentorship of Klaus Schulten, focusing on the area of computational biophysics. After 2 years as a postdoctoral fellow at Argonne National Laboratory working with Benoit Roux, he started his lab at Georgia Tech in early 2013. His lab carries out molecular dynamics simulations aimed primarily at understanding the composition, construction, and function of the Gram-negative bacterial cell envelope.
Ellinor Haglund, Ph.D., is currently an Assistant Professor in the Department of Chemistry at the University of Hawaii at Manoa. Dr. Haglund received her master’s degree in molecular biology and chemistry from Umeå University, her Ph.D. at Stockholm University, and completed her postdoctoral work at Rice University and the University of California, San Diego, with the Center for Theoretical Biological Physics. Her research is focused on the folding event in proteins, utilizing both computational and experimental techniques to understand the molecular details of how proteins fold into biologically active molecules. She is inspired by how nature works and utilizes her multidisciplinary training to answer questions at the interface of chemistry, biology, and physics.
Margaret Johnson, Ph.D., joined the Department of Biophysics faculty at Johns Hopkins University in 2013. She received her B.S. in applied math from Columbia University and her Ph.D. in bioengineering from the University of California, Berkeley. She completed postdoctoral training in the Laboratory of Chemical Physics at the National Institutes of Health in Bethesda, Maryland. Her research focuses on understanding how the individual interactions between thousands of diverse components in the cell generate order and collective function at the right time and the right place. She develops theoretical and computational approaches to study the evolution and mechanics of dynamic systems of interacting and assembling proteins.
Rebecca K. Lindsey, Ph.D., is a Computational Chemist at the Lawrence Livermore National Laboratory. Dr. Lindsey’s primary research interest is in development and application of quantum-accurate machine-learned models for reactive materials under extreme conditions. Dr. Lindsey
currently has under development “ChIMES,” which models have proven capable of up to 100,000× increase in efficiency over DFT-MD based methods while retaining accuracy. Other interests include (1) development of methods for atomistic simulations, (2) understanding microscopic phenomena governing reaction-driven nucleation, (3) understanding dynamic response in soft materials, and (4) investigation of structure, sorption, and thermodynamics at material interfaces. Dr. Lindsey has a B.S. from Wayne State University (2010), an M.S. from the University of Minnesota (2012), and a Ph.D. in chemical physics from the University of Minnesota (2016).
Clare McCabe, Ph.D., received her bachelor’s degree and Ph.D. in chemistry from The University of Sheffield. After postdoctoral and research faculty appointments at the University of Tennessee, she joined the Colorado School of Mines faculty as an Assistant Professor of chemical engineering. She is currently a Faculty member at Vanderbilt University, where she is the Cornelius Vanderbilt Chair of Engineering and Professor of Chemical and Biomolecular Engineering. Dr. McCabe is also the Associate Dean of the Graduate School and the Director of the Office of Postdoctoral Affairs. Her research interests focus on the use of molecular modeling techniques to understand and predict the thermodynamic and transport properties of complex fluids and materials. She is a Fellow of the Royal Society of Chemistry and recently received the American Institute of Chemical Engineers Computational Molecular Science and Engineering Forum Impact Award.
Yinglong Miao, Ph.D., is an Assistant Professor in the Department of Molecular Biosciences and Center for Computational Biology at The University of Kansas. Dr. Miao obtained his Ph.D. in computational chemistry in the lab of Peter Ortoleva at Indiana University. His graduate work was focused on all-atom multiscale modeling of infectious viruses and other bionanosystems. He subsequently began his postdoctoral research with Jeremy Smith and Jerome Baudry at the University of Tennessee and Oak Ridge National Laboratory. There he combined the world-class experimental and supercomputing resources to investigate the structural dynamics and function of protein enzymes that are responsible for drug metabolism. Dr. Miao then moved to Andy McCammon’s lab at the Howard Hughes Medical Institute and the University of California, San Diego, where he worked on both method developments and cutting-edge applications in accelerated biomolecular simulations and drug discovery of the G protein-coupled receptors. Dr. Miao develops novel theoretical and computational methods, with applications in protein folding, molecular recognition, cellular signaling, and computer-aided drug design.
Shikha Nangia, Ph.D., is an Associate Professor in the Department of Biomedical and Chemical Engineering at Syracuse University. Dr. Nangia received her Ph.D. in chemistry from the University of Minnesota, Twin Cities, in 2006, and completed her postdoctoral training at The Pennsylvania State University. Dr. Nangia’s research focuses on using computational approaches to overcome biological barriers and to enhance drug delivery. Her research projects include exploring treatments for Alzheimer’s and Parkinson’s diseases, cancer, and diabetes. Her recent focus has been to examine the architecture of the blood–brain barrier with the aim to identify novel strategies to facilitate the transport of drug molecules into the brain. Using innovative computational approaches, Dr. Nangia’s research has received substantial funding to date. Dr. Nangia has also received numerous honors and awards for her research and teaching throughout her career, and she was most recently awarded for her outstanding contribution to the student experience and university initiatives at Syracuse University.
Giulia Palermo, Ph.D., is a computational biophysicist with expertise in molecular simulations. She is an Assistant Professor in the Department of Bioengineering at the University of California, Riverside, and a cooperating Faculty in the Department of Chemistry. Her research uses computational biophysics to clarify the mechanism of action of biological systems of key importance for genome editing and regulation. She is a native of Italy where she earned her Ph.D. in 2013 from the Italian Institute of Technology, working in the group of Dr. Marco De Vivo. She has been a postdoc in the group of Professor Ursula Rothlisberger at the Swiss Federal Institute of Technology, where she worked on ab-initio methods. In 2016, she was awarded a Swiss National Science Foundation postdoctoral fellowship to join the group of Professor J. Andrew McCammon at the University of California, San Diego, where she earned experience in novel multiscale methods enabling the study of increasingly realistic biological systems.
Heather W. Pinkett, Ph.D., is an Associate Professor at Northwestern University in the Department of Molecular Biosciences. Dr. Pinkett studies the structure and function of membrane proteins, which are located within a cell membrane and act as pumps to actively transport metabolites and compounds. The specific transporters she studies are medically relevant; they are responsible for the development of multidrug resistance and have been implicated in numerous diseases. Her lab uses a combination of structural biology, biochemistry, and molecular genetics to determine how these transporter proteins relate to their selective function. She received a 2016 Hartwell Individual Biomedical Research Award for her work advancing children’s health. Dr. Pinkett received her B.A. from Connecticut College in 1997 and a Ph.D. at the University of Pennsylvania Perelman School of Medicine in 2004. From 2004 through 2008 she was a postdoctorate fellow at the California Institute of Technology.
Carol B. Post, Ph.D., is a Professor of medicinal chemistry and molecular pharmacology and a Professor of biomedical engineering at Purdue University. She specializes in computational chemistry and biological NMR and is also a National Institutes of Health principal investigator. Since 1990, she has directed a research program toward understanding protein structure and molecular mechanisms that regulates molecular interactions and enzymatic activity. Her research program utilizes primarily computer simulation methods and NMR spectroscopy to study the structure and function of proteins and protein complexes associated with signaling, with current efforts being focused on Src and Syk tyrosine kinase. Molecular dynamics simulation methods and NMR spectroscopy are the approaches taken to study proteins and protein complexes associated with cancer and human viruses. Dr. Post is an internationally recognized leader in the regulation and function of protein–protein interactions associated with cell signaling and viruses. She has an exceptional record of scientific research and impact in such critical areas as cancer biology, therapeutics, and infectious and immune diseases. Dr. Post was recognized in 2009 with the Lions Club Award for Outstanding Achievements in Cancer Research, the Chaney Faculty Scholar Award from the College of Pharmacy in 2013, and the Provost’s Award for Outstanding Graduate Mentor in 2016.
Leonor Saiz, Ph.D., is a Professor in the Biomedical Engineering Department at the University of California, Davis. Dr. Saiz received her Ph.D. in physics from the University of Barcelona. Her research involves the study of the dynamics of biological networks at the cellular and molecular level. Her lab combines computational and theoretical approaches together with experimental data to (1) understand how cellular behavior arises from the physical properties and interactions of the
cellular components; and to (2) infer detailed molecular properties, such as the in vivo DNA mechanics, from the cellular physiology. By developing novel methodologies that consider multiple spatial and temporal scales and multiple levels of biological organization, including atomic, molecular, and cellular, their work has provided new avenues to integrate the molecular properties of cellular components directly into the dynamics of cellular networks. The ultimate goal of her work is to understand and follow the impact of molecular perturbations in the cellular components, such as a mutation in a protein or interventions with small molecules or drugs, through the different cellular processes up to the cellular behavior; one of the major challenges of modern biomedical sciences.
Markus Seeliger, Ph.D., is an Associate Professor of pharmacological sciences and Associate Faculty of the Laufer Center for Computational and Physical Biology at Stony Brook University’s School of Medicine. Dr. Seeliger received his Ph.D. in biophysical chemistry from Cambridge University. The research in his group circles around the questions, how can we help small molecule inhibitors become clinically successful drugs, and what can we learn about the molecular regulation of drug targets through their interaction with small molecule drugs? He combines X-ray crystallography, NMR, and other biophysical methods with computational tools.
Jeffrey Skolnick, Ph.D., is a Professor and the Mary and Maisie Gibson Chair and GRA Eminent Scholar in Computational Systems Biology at the Georgia Institute of Technology. He received his B.A. in chemistry, from Washington University in 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. His research interests include using systems and computational biology approaches to solve health problems. He uses these tools to better understand important areas of study such as cancer metabolomics, drug design, and protein evolution. An additional area of research includes the prediction of protein structure from DNA sequences to better characterize human genes.
Kayla G. Sprenger, Ph.D., began her assistant professorship in August 2020 in the Department of Chemical and Biological Engineering at the University of Colorado Boulder. At the Massachusetts Institute of Technology, Dr. Sprenger was a postdoctoral associate for the Institute for Medical Engineering and Science and the Chakraborty Laboratory for Computational Immunology. Her research interests include molecular simulation, adaptive immune response, and the in silico design of optimal immunization protocols. She has a B.S. and an M.S. in chemical engineering and earned her Ph.D. from the University of Washington.
Juan M. Vanegas, Ph.D., is currently an Assistant Professor at The University of Vermont in the Department of Physics with appointments in the Materials Science and Cellular, Molecular, and Biomedical Sciences Graduate Programs. Dr. Vanegas received his master’s degree in biochemistry and biophysics from Oregon State University and his Ph.D. in biophysics from the University of California, Davis. His research uses coarsegrained, atomistic, and ab initio molecular simulation methods to understand how chemical structure determines mechanical properties of biomolecules and their response to mechanical stimuli. Some applications of this research include understanding elastic properties of lipid biomembranes and force transduction mechanisms in mechanosensitive channels. His lab leads the development of computational tools for local stress calculations from molecular dynamics simulations.
Josh Vermaas, Ph.D., is a computational biophysicist within the scientific computing group. During his Ph.D. training at the University of Illinois, Dr. Vermaas performed and analyzed molecular dynamics simulations at all scales. This time included graduate research opportunities throughout the national lab system at the National Renewable Energy Laboratory, Oak Ridge National Laboratory, and Sandia National Laboratory. This membrane-focused research was expanded during his postdoctoral tenure at the National Renewable Energy Laboratory to encompass biomass materials, with a particular focus on lignin. Dr. Vermaas is now applying this experience toward adapting molecular dynamics codes to trends in HPC architecture and enable advances at the bleeding edge of computational science.
Yaroslava G. Yingling, Ph.D., is a Professor of materials science and engineering at North Carolina State University. She received her University Diploma in computer science and engineering from St. Petersburg State Technical University of Russia and her Ph.D. in materials engineering and high performance computing from The Pennsylvania State University. She carried out postdoctoral research at Penn State’s Department of Chemistry and at the National Institutes of Health’s National Cancer Institute prior to joining North Carolina State University in 2007. Research interests in Professor Yingling’s group are focused on the development of soft materials informatics tools, advanced computational models, and algorithms for multiscale molecular modeling of soft and biological materials. These tools aim to provide a fundamental understanding of the structure–property relations of a variety of soft materials systems that are formed through the process of self-assembly.