Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Thirteenth Round

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This report evaluates submissions received in response to a Request for Proposals for Biomolecular Simulation Time on Anton 2, a supercomputer designed and built by D.E. Shaw Research (DESRES). Over the past 12 years, DERES has made an Anton or Anton 2 system housed at the Pittsburgh Supercomputing Center available to the non-commercial research community, based on the advice of previous committees of the National Academies of Sciences, Engineering, and Medicine. As in those prior rounds, the goal of the thirteenth Request for Proposals for simulation time on Anton 2 is to continue to facilitate breakthrough research in the study of biomolecular systems by providing a massively parallel system specially designed for molecular dynamics simulations. These capabilities allow multi-microsecond simulation timescales. The program seeks to continue to support research that addresses important and high impact questions demonstrating a clear need for the special capabilities of the Anton.

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22 pages · 8.5 x 11 ·
ISBN Ebook: 0-309-69479-5
DOI: https://doi.org/10.17226/26746

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National Academies of Sciences, Engineering, and Medicine. 2022. Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics: Thirteenth Round. Washington, DC: The National Academies Press.

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Carol B. Post

Carol B. Post, PhD, is Distinguished Professor of Medicinal Chemistry and Molecular Pharmacology at Purdue University. She specializes in Computational Chemistry and Biological NMR and is also an NIH 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. 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. 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 Fellow of the AAAS in 2020 and Fellow of the Biophysical Society in 2021. Dr. Post has served on previous molecular dynamics review committees convened by the National Academies.

Ravinder Abrol

Ravinder “Ravi” Abrol, PhD, is an Associate Professor of Chemistry and Biochemistry at California State
University, Northridge (CSUN). Abrol research lab is focused on developing and using enhanced
conformational sampling based on molecular dynamics (MD) 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 are
emerging as very complex biophysical machines whose signaling profiles are controlled by their
conformational ensembles. 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, as they are targets for ~50% of the drugs in the clinic. Research in the Abrol Lab is also
combining computational biophysics and structural bioinformatics methods to gain mechanistic insights
into the evolutionary as well as pathological biochemistry of membrane protein folding and functions.
Ravi received a B.Sc. (Honours) Chemistry degree in 1994 from the University of Delhi, a Chemistry
M.Sc. degree in 1995 from the Indian Institute of Technology Kanpur, and a Chemistry PhD in 2003
from the California Institute of Technology, Pasadena. He has served on several NIH study sections and a
couple of NASEM review panels for MD supercomputing time on Anton.

James Briggs

James Briggs, Ph.D., is a Professor within the Biology and Biochemistry Department 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. James Briggs’ 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 Committee Chair in 2019 for the 10th round of proposal evaluations.

Jianhan Chen

Jianhan Chen, Ph.D., is a Professor in the Department of Chemistry and Department Biochemistry and Molecular Biology at University of Massachusetts, Amherst. His research program focuses on the development of theoretical and computational methods and application of these methods to advance our understanding of biophysical, biochemical and biomedical problems. Key problems currently under study in Dr. Chen’s lab include intrinsically disordered proteins in biology and diseases, protein amyloid formation in neurogenerative diseases, self-assembling peptide vesicles for drug delivery, and transmembrane ion channel protein activation and regulation. Dr. Chen is a recipient of the NSF Career Award (2010), ACS Outstanding Junior Faculty Award (2011), and Outstanding Research Award in Research from UMass College of Natural Sciences (2022). He received his Ph.D. in Chemical and Material Physics from the University of California, Irvine in 2002.

Ryan Cheng

Ryan is currently a Research Scientist at the Center for Theoretical Biological Physics (Rice University); on August 1, 2022 he will start a position as an Assistant Professor of Chemistry at the University of Kentucky. Ryan specializes in theory and simulation of biomolecules. His early Ph.D. work focused on the loop closure of long disordered polymer chains and the role of internal friction. His early postdoctoral work focused on amino acid co-evolutionary information in the context of bacterial signaling networks. Currently he works on coarse-grained simulations of chromosomal organization. Relevant Honors/Awards: Full Member of Sigma Xi, the Scientific Research Honor Society (2021). Ryan received his Ph.D. in Theoretical Chemistry from the University of Texas at Austin on December 2012. He received his B.S. in Chemistry from Carnegie Mellon University in 2007.

Xiaolin Cheng

Xiaolin Cheng received his B.S. from Nanjing University in China, his M.S. from Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, and his Ph.D. from the Stony Brook University. After a postdoctoral fellowship at University of California, San Diego, he joined the Center for Molecular Biophysics (CMB) at 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 College of Pharmacy, at The Ohio State University (OSU) in 2017. He is also core faculty of OSU’s Translation Data Analytics Institute (TDAI). At OSU, his research is focused on employing a myriad of computational and data analytics methods to elucidate molecular basis of drug action and to rationally design new drug molecules. Additionally, he is engaged in developing and applying advanced molecular simulation techniques to study the structure, dynamics and function of membranes and membrane-associated proteins.

David Cowburn

Dr. Cowburn is currently a Professor at Albert Einstein College of Medicine. He was previously faculty at Rockefeller University, and was the startup President and CEO of the New York Structural Biology Center. He has extensive experience in structural biology, principally using NMR, and computational approaches to understanding the role of dynamics in protein function. He is a member of the Editorial Board of the Journal of Biological Chemistry, a Fellow of the New York Academy of Sciences, and of the Royal Society of Chemistry. He trained in Biophysics at King’s College, London, and did postdoctoral research in neurochemistry at Columbia University.

Brian Dominy

Brian Dominy, PhD, is an Associate Professor in the Department of Chemistry and Associate Dean of the
Graduate School at Clemson University. Dr. Dominy earned his B.S. degree with honors 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 an NIH Ruth L. Kirschstein
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 an NSF 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.

Alemayehu Gorfe

Dr. Gorfe is a professor of integrative biology and pharmacology at the McGovern Medical School of the University of Texas Health Science Center in Houston (UTHealth). He joined UTHealth in 2009 as a tenure-track assistant professor, and promoted to associate professor with tenure in 2014 and full professor in 2021. His laboratory strives to discover therapies for unmet health challenges through a detailed study of bio-molecular dynamics and interactions using molecular simulations and experiments. Among his major contributions is the finding that oncogenic Ras proteins adopt multiple membrane orientations whose relative population is modulated by the bound nucleotide, mutation, or lipid composition. Disproving a decades-old dogma on the undruggability of Ras proteins, Dr. Gorfe developed the earliest proof-of-concept for inhibiting Ras via allosteric mechanisms, and subsequently discovered several high-affinity Ras inhibitors. His laboratory is also interested in developing new methods for ligand binding site identification in membrane-bound targets.

James C. Gumbart

James C. “J.C.” Gumbart, PhD, 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 PhD in Physics from the University of Illinois, Urbana-Champaign in 2009 under the mentorship of Klaus Schulten, focusing on the area of computational biophysics. After two years as a postdoctoral fellow at Argonne National Lab 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.

Ellinor Haglund

Ellinor Haglund, PhD, is currently an Assistant Professor in the Department of Chemistry at the University of Hawaii in Manoa. Dr. Haglund received her Masters in Molecular Biology and Chemistry from Umeå University, her Ph.D. at Stockholm University in 2010, and completed her post-doctoral 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 and function of proteins with complex topologies, 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.

Yu-ming M. Huang

Dr. Huang received her Ph.D. 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 23 published articles, including 13 first-author papers and 9 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 Wiley Computers in Chemistry Outstanding Postdoc Award. She has also been awarded computational time on the specialized architecture ANTON machine for hundreds of µs MD and also received the computational allocation award of CPU and GPU hours on the XSEDE supercomputer.

Andrzej Kloczkowski

2011-present, Professor, Department of Pediatrics (tenured since April 1, 2011) The Ohio State University, College of Medicine
2010-present, Principal Investigator II, Battelle Center for Mathematical Medicine The Research Institute at Nationwide Children's Hospital
Primary professional/research expertise: Computational Biology, Computational Medicine
Ph.D. 1980 (Statistical Thermodynamics), Institute of Physical Chemistry of the Polish Academy of Sciences
Postdoctoral training Stanford University 1981-1983
NRC Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics 2014, 2015, 2017, 2019

C. Denise Okafor

Dr. Denise Okafor received her B.S. in biomedical chemistry from Oral Roberts University. She earned an M.S. in chemistry and a Ph.D. in biochemistry at Georgia Institute of Technology. She performed postdoctoral research at Emory University working on nuclear receptors, a family of ligand-regulated transcription factors. Awards: Burroughs Wellcome Fund Career award at the scientific interface, Ford foundation postdoctoral fellowship (declined). Since January 2020, Dr. Okafor has been an assistant professor in the Department of Biochemistry and Molecular biology at Pennsylvania State University. Her lab uses molecular dynamics simulations and biochemical experiments to understand how structural properties of nuclear receptor ligands dictate transcriptional outcomes. Awards: NSF CAREER award.

Priyanka Prakash

Dr. Priyanka Prakash is an Institute Research Investigator at the Institute of Applied Cancer Science at the University of Texas MD Anderson Cancer Center in Houston, Texas. Prior to this role, she worked as a Scientist at the National Cancer Institute in Frederick, Maryland and prior to NCI she held research and teaching roles at the University of Texas Health Science Center at Houston. Her work and expertise in molecular dynamics simulations includes modeling of the pharmaceutically-relevant drug target K-Ras and Raf kinase-membrane interaction. Her work spans protein-protein interactions and protein-lipid membrane interactions. She completed her PhD in Biological Science and Bioengineering at the Indian Institute of Technology, Kanpur. She holds a MSc and BSc in Chemistry from the University of Delhi.

Leonor Saiz

Leonor Saiz, PhD, 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

Janani Sampath 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 Pacific Northwest National Lab. She obtained her Ph.D. in chemical engineering from the Ohio State University in 2018.

Kayla G. Sprenger

Kayla G. Sprenger, PhD, 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 for the Institute for Medical Engineering & Science and the Chakraborty Laboratory for Computational Immunology. Her research interests include molecular simulation, the adaptive immune response, and the in silico design of optimal immunization protocols against highly mutable pathogens like HIV and influenza. She has a BS and an MS in chemical engineering and earned her PhD from the University of Washington in 2017. Dr. Sprenger has served on a previous molecular dynamics review committee convened by the National Academies.

Rui Sun

Rui Sun is an Assistant Professor of Chemistry at the University of Hawaii, Manoa. Rui got his Ph.D. in Computational Chemistry from Texas Tech University in 2014 under the supervision of Prof. William L. Hase; and then worked as a postdoctoral scholar at the University of Chicago with Prof. Gregory Voth on Biophysical simulations. He received NSF Career Award and Board of Region (University of Hawaii) Research Award in 2022, and he is a member of American Chemistry Society. His research is currently supported by Army Research Office, Air Force Office of Research, National Institutes of Health, National Science Foundation, and Eli Lilly.

Troy Wymore

Troy Wymore is currently a Research Associate Professor at the Laufer Center for Physical and Quantitative Biology within Stony Brook University in NY. Prior to this, he was a research scientist at the University of Michigan, Oak Ridge National Laboratory and the Pittsburgh Supercomputing Center (PSC). After obtaining his Ph.D. in Physical Chemistry from the University of Missouri in 1999, he began investigating enzyme mechanisms and evolutionary relationships at PSC using atomistic simulations and molecular phylogenetics. He was awarded a fellowship in 2001 to study at the Institute of Structural Biology in Grenoble, France with Martin J. Field. In the past, he has help support Anton users as well as serving on the NRC “Study of Molecular Dynamics” panel three previous times and was a coordinator of the overall report in 2020.

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Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Thirteenth Round

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Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Thirteenth Round

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Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics: Thirteenth Round

Description

Collaborators

Committee

Sponsors

Staff

Parent projects

Board on Life Sciences

Major units and sub-units

Contact

Contact us

Provide feedback

Request materials

More like this

Modernizing Mathematics Education for Grades 9-14

Health Care Financing to Improve Availability of Affordable Contraception: Identifying Promising Practices

Review of Methods in the Report on Carcinogens Handbook

Computing Research, Technologies, and Systems Program Area

Science and Technology Policy and Law Program Area

Center for Health, People, and Places

Life Sciences and Biotechnology Program Area

State of Human H5N1 Therapeutics: A Rapid Expert Consultation

Review of Methods in the Report on Carcinogens Handbook