APPENDIX E

ROSTER AND BIOGRAPHICAL SKETCHES OF COMMITTEE MEMBERS

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

Chair

JAMES C. “J.C.” GUMBART, Georgia Institute of Technology

Members

RAVINDER “RAVI” ABROL, California State University, Northridge

JEROME BAUDRY, University of Alabama in Huntsville

JAMES BRIGGS, University of Houston

DAVID CASE, Rutgers University

XIAOLIN CHENG, The Ohio State University

BRIAN DOMINY, Clemson University

ELLINOR HAGLUND, University of Hawaii at Mānoa

Y. MINDY HUANG, Wayne State University

MARGARET JOHNSON, Johns Hopkins University

VIVEK NARSIMHAN, Purdue University

CAROL B. POST, Purdue University

PENGYU REN, The University of Texas at Austin

STEVEN W. RICK, University of New Orleans

LEONOR SAIZ, University of California, Davis

JANANI SAMPATH, University of Florida

JEFFREY SKOLNICK, Georgia Institute of Technology

KAYLA G. SPRENGER, University of Colorado Boulder

JUAN M. VANEGAS, The University of Vermont

JOSH V. VERMAAS, Michigan State University

Project Staff

ANDREW BREMER, Project Director, Board on Life Sciences

NANCY CONNELL, Senior Scientist, Board on Life Sciences

JESSICA DE MOUY, Research Associate, Board on Life Sciences

TAYLOR JONES, Program Assistant, Board on Life Sciences

STEVEN MOSS, Program Officer, Board on Life Sciences

BIOGRAPHICAL SKETCHES OF COMMITTEE MEMBERS

Chair

James C. “J.C.” Gumbart, Ph.D., is an Associate 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 in 2009 under the mentorship of Klaus Schulten, focusing on the area of computational biophysics. After 2 years as a postdoctoral fellow at the 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. Dr. Gumbart has served on previous molecular dynamics review committees convened by the National Academies.

Members

Ravinder “Ravi” Abrol, Ph.D., is an Associate Professor of biochemistry at California State University, Northridge (CSUN). 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% of clinically-approved drugs. A molecular and structural understanding of these GPCR signaling pathways will have a broad impact on our 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 also combining computational biophysics and structural bioinformatics based methods to gain mechanistic insights into the biochemistry of GPCR signaling along with membrane protein folding mechanisms. Dr. Abrol received a B.S. in 1994 from the University of Delhi, an M.S. in 1995 from Indian Institute of Technology, and a Ph.D. in 2003 from the California Institute of Technology.

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 University of Tennessee and Oak Ridge National Laboratory 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.

James Briggs, Ph.D., is a Professor within the Department of Biology and Biochemistry at the University of Houston. Dr. Briggs received his Ph.D. in chemistry from Purdue University in 1990. His research focuses on computational studies of protein structure and function, inhibitor design, investigations of possible inhibitor resistance pathways, and development of methods for the above areas. Targets for these studies include those important in the treatment of AIDS, cancer, bacterial infections, and other disease states. In addition, Dr. Briggs has worked on inhibitors to aid in biowarfare defense (botulinum neurotoxins, anthrax toxin, cholera toxin). Dr. Briggs’s research is focused in the highly interdisciplinary and collaborative area of computational chemistry/biochemistry. He develops and applies computational methods to problems of chemical and biochemical interest. His research falls into two general categories: computer-aided inhibitor design/discovery and computational biophysics. His main target areas in the inhibitor/ligand area are Rho kinase 1 (heart disease), PTEN (cancer), PTEN/5HTC2C (addiction control), BCL2 (cancer), gluconeogenesis and glucose uptake (cancer); those for the computational biophysics area include cholera toxin, biofilm control, RNA structure prediction, protein electrostatics and pKa predictions, and identification of protein/enzyme function from structure only. Dr. Briggs has served on previous molecular dynamics review committees convened by the National Academies, including serving as the committee Chair in 2019 for the tenth round of proposal evaluations.

David Case, Ph.D., is a Professor of chemistry and chemical biology at Rutgers University. His research involves simulations of proteins and nucleic acids and analysis of results from biomolecule nuclear magnetic resonance (NMR) and crystallography. He is the lead developer for the Amber suite of biomolecular simulation software. He received a Ph.D. from Harvard University in 1977 in chemical physics. He received the President’s Award from the International Society of Quantum Biology and Pharmacology in 2014 and the American Chemical Society Award for Computers in Chemical and Pharmaceutical Research in 2015.

Xiaolin Cheng, Ph.D., received his B.S. from Nanjing University in China and his Ph.D. from Stony Brook University. After a postdoctoral fellowship at the University of California, San Diego, he joined the Center for Molecular Biophysics (CMB) at the Oak Ridge National Laboratory (ORNL) as an Associate R&D Staff Scientist. After leaving his position as a Senior R&D Staff Scientist at ORNL, he became an Associate Professor in the College of Pharmacy at The Ohio State University (OSU) in 2017. He is also a core faculty of OSU’s Translation Data Analytics Institute. His research is focused on employing a myriad of computational and data analytics methods to elucidate the molecular basis of drug action and to rationally design new drug molecules. Additionally, he is engaged in developing and applying advanced molecular modeling and simulation techniques to integrate experimental data, specifically from cryo-electron microscopy, into structural models of dynamic biological assemblies. His research has been continuously funded by the National Institutes of Health, the National Science Foundation, and the U.S. Department of Energy.

Brian Dominy, Ph.D., is an Associate Professor in the Department of Chemistry and the Associate Dean of the Graduate School 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 National Research Service Award postdoctoral fellow at Harvard University with Dr. Eugene Shakhnovich in the Department of Chemistry and Chemical Biology. Dr. Dominy joined the faculty of the Department of Chemistry at Clemson in 2005 and received a National Science Foundation CAREER award in 2010 for his research in the development and application of computational models to study the physical chemistry driving biomolecular evolution. His service responsibilities over the years have focused significantly on the development and assessment of academic programs at the departmental, college, and university levels at Clemson. Dr. Dominy served as the interim Associate Dean of academic affairs for the newly formed College of Science from 2016–2018, and since 2018 has served as the Associate Dean of the Graduate School at Clemson University. This is Dr. Dominy’s third year serving on this recurring molecular dynamics review committee.

Ellinor Haglund, Ph.D., is currently an Assistant Professor in the Department of Chemistry at the University of Hawaii in Mānoa. 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.

Y. Mindy Huang, Ph.D., received her doctorate degree in computational chemistry from the University of California, Riverside, in 2014. She is currently an Assistant Professor in the Department of Physics and Astronomy at Wayne State University (WSU). Since joining WSU, she has established a vibrant Computational Biophysics Group. The central goal of her research work is to understand the fundamental mechanism of biomolecular recognition and diffusion processes by using theoretical and classical mechanical models. Her research involves the development and application of computational methods to address biologically and medically important problems. Dr. Huang has established an excellent track record of 22 published articles, including 12 first-author papers and 8 corresponding or co-corresponding author papers. Her pioneering work on the diffusion study has been honored with the NVIDIA GPU award, Best Paper Award from Protein Science publications, and the Wiley Computers in Chemistry Outstanding Postdoc Award. She has also been awarded computational time on the specialized architecture Anton machine for hundreds of microseconds of molecular dynamics simulations and also received a computational allocation award on the Extreme Science and Engineering Discovery Environment supercomputer.

Margaret Johnson, Ph.D., joined the biophysics faculty at Johns Hopkins University in 2013. She received her B.S. in applied mathematics 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.

Vivek Narsimhan, Ph.D., is an Assistant Professor of chemical engineering at Purdue University. Dr. Narsimhan received his bachelor’s degree in chemical engineering from the California Institute of Technology, his Master in Advanced Study in mathematics from the University of Cambridge, his Ph.D. in chemical engineering from Stanford University, and completed his postdoctoral research at the Massachusetts Institutes of Technology. His research uses a mixture of theory, simulations, and experiments to examine problems in the areas of suspensions, complex interfaces, fluid mechanics, and polymers. He has developed mathematical models, performed simulations, and conducted experiments to describe the mechanics of droplets, red blood cells, and vesicles under various flow types and microfluidic geometries. These investigations provide insight into how complex membranes alter the mechanical stability and motion of fluid-filled particles, both individually and as a suspension.

Carol B. Post, Ph.D., is a Distinguished Professor of Medicinal Chemistry and Molecular Pharmacology 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 regulate 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, the Provost’s Award for Outstanding Graduate Mentor in 2016, and appointment as a Fellow of the American Association for the Advancement of Science in 2020 and a Fellow of the Biophysical Society in 2021. Dr. Post has served on previous molecular dynamics review committees convened by the National Academies.

Pengyu Ren, Ph.D., has the E.C.H. Bantel Professorship for Professional Practice at The University of Texas at Austin. He studies the structure and function of biomolecules, with pharmaceutical and biomedical applications. Dr. Ren’s research team uses a range of computational tools to study the structure, dynamics, and interactions of proteins, nucleic acids, and other macromolecules, and to search for compounds mimicking and interfering with biomolecules for diagnostic and therapeutic purposes. His lab is developing a multi-scale modeling technique that allows scientists to efficiently study bimolecular assemblies. Dr. Ren is an elected Fellow of the American Institute for Medical and Biological Engineering. He has published about 80 journal articles and 5 book chapters. He received a Ph.D. in chemical engineering from the University of Cincinnati.

Steven W. Rick, Ph.D., is a Professor in the Department of Chemistry at the University of New Orleans. Dr. Rick received his bachelor’s degree from the University of California, Los Angeles, his Ph.D. from the University of California, Berkeley, in 1989, and completed his postdoctoral research at Columbia University. His research applies theoretical and computational approaches to a variety of chemically interesting systems. His work involves the development of more efficient computer simulation methods and better models for molecular interactions. Dr. Rick’s group is applying these methods to the study of liquid water, interfaces, aqueous solutions, proteins, and ion transport through various materials. Dr. Rick has served on a previous molecular dynamics review committee convened by the National Academies.

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.

Janani Sampath, Ph.D., is an Assistant Professor of chemical engineering at the University of Florida. She joined the department in January 2021. Her expertise lies in using molecular dynamics simulations to understand the behavior of polymers, proteins, and their hybrids. Her group uses a combination of coarse grained and atomistic models to study systems ranging from synthetic polymer membranes, polymer-protein bioconjugate self-assembly, and polymers for therapeutic applications. Prior to this, she was a postdoctoral researcher at the University of Washington and the Pacific Northwest National Laboratory. She obtained her Ph.D. in chemical engineering from The Ohio State University in 2018.

Jeffrey Skolnick, Ph.D., is a Professor and the Mary and Maisie Gibson Chair and GRA Eminent Scholar in Computational Systems Biology at 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., is an Assistant Professor 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 at the Institute for Medical Engineering

and Science in the Chakraborty Laboratory for Computational Immunology. Her research interests include using molecular dynamics simulations, mathematical modeling, and machine learning to investigate host immune responses to infectious disease pathogens and neurological disease pathways. She has a B.S. and an M.S. in chemical engineering and earned her Ph.D. from the University of Washington in 2017. Dr. Sprenger has served on a previous molecular dynamics review committee convened by the National Academies.

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 coarse-grained, 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 V. Vermaas, Ph.D., is a computational biophysicist working within the Plant Research Laboratory and the Department of Biochemistry and Molecular Biology at Michigan State University. 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, the Oak Ridge National Laboratory, and the 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. The Vermaas lab uses atomic simulation tools to create accurate molecular-scale models for plant processes and materials at the nanoscale.