Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics Eighth Round (2017) / Chapter Skim
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Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics: Eighth Round
Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics: Eighth Round
Pages 1-23
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Repor of th Committ on Proposal rt he tee n Evaluatio for Alloca on ation o Sup of percommputin ng Tim for the Study of Mo me r S o olecula Dyn ar namicss, Eight Rou th und Commi ittee on Pro oposal Evaaluation for Allocatio of Super r on rcomputin Time for the ng r Study of Molecular Dynamics Eighth R r s, Round Board on Life Scie n ences Board on Chemical Sciences and Techn n l nology vision on Earth and L Studies Div Life s A Consensus Study R Report of
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available to the non-commercial research community, based on the advice of previous National Research Council committees. As in prior rounds, the goal of the eighth RFP 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.
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The committee was further asked to allocate at least 25% of the time to principal investigators who had not previously received an Anton allocation. The judgments of the committee are based on which proposals best met the selection criteria described above and on the estimates of required simulation time provided by the applicants.
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* PSCA17012P Sharon Loverde, CUNY College of Staten Island; Molecular Dynamics Simulations of the Interaction of Drug Amphiphiles with a Model Phospholipid Membrane [Returning user identified for 196,085 MDUs]
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* PSCA17028P Peter Searson, Johns Hopkins University; Quantifying the Binding Affinity of the P-Glycoprotein Multidrug Efflux Pump Using Unbiased Long-Timescale Molecular Dynamics Simulations [New user identified for 230,000 MDUs]
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Hoogerheide, National Institute of Standards and Technology; Molecular Mechanisms of the Voltage-Dependent Anion Channel Regulation by Tubulin Isotypes [Returning user identified for 360,000 MDUs] PSCA17052P Wenwei Zheng, Arizona State University; Investigating the Molecular Interactions Controlling the Liquid Droplet Formation by Intrinsically Disordered Proteins [New user identified for 50,549 MDUs]
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* PSCA17069P Peter Freddolino, University of Michigan Medical School; Accurate Modeling of Transcription Factor-DNA Interactions Enabled by Extreme Molecular Dynamics Simulations [New user identified for 246,588 MDUs]
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* PSCA17077P Graham Fleming, University of California, Berkeley; Microsecond Molecular Dynamics Simulations of the Transmembrane Proton Gradient Sensor Protein PsbS Required for Rapid Induction of Non-Photochemical Quenching of Chlorophyll in Light Harvesting Plants [New user identified for 100,000 MDUs]
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E Shaw Research, the Pittsburgh Supercomputing Center, and all of the 2017 Anton 2 applicants for the opportunity to assist in identifying the proposals best meeting the selection criteria for time allocations on the Anton machine.
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Roster and Biographical Sketches of Committee Members E Board on Life Sciences, Board on Chemical Sciences and Technology, and the National Academies F
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Impact that successful completion of the proposed research would have on the knowledge, methods, and current barriers in the field 3. Project is scientifically and technologically feasible with clear, well-developed, and appropriate goals, objectives, and approach to the proposed studies Justification for requested time allocation.
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GUMBART, Georgia Institute of Technology MARGARET JOHNSON, Johns Hopkins University IVAYLO IVANOV, Georgia State University ANDRZEJ KLOCZKOWSKI, Research Institute at Nationwide Children's Hospital JIANING LI, University of Vermont DIANE LYNCH, University of North Carolina CHRISTOPHER ROWLEY, Memorial University MARKUS SEELIGER, Stony Brook University Medical School LEI SHI, National Institutes of Health CHUNG WONG, University of Missouri-St. Louis Project Staff ANDREA HODGSON, Project Director, Board on Life Sciences ELIZABETH BOYLE, Program Officer, Board on Chemical Sciences and Technology ANGELA KOLESNIKOVA, Senior Program Assistant, Board on Life Sciences KEEGAN SAWYER, Senior Program Officer KATIE BOWMAN, Senior Program Officer 12
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MEMBERS Nilesh Banavali, PhD, is a Research Scientist at the Wadsworth Center of the New York State Department of Health and an Assistant Professor in the School of Public Health at the University at Albany, SUNY. 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.
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Giacomo Fiorin, PhD, is an Associate Professor of Research at the Institute for Computational Molecular Science at Temple University. He is a computational scientist with experience in the fields of molecular biophysics, soft matter systems, molecular dynamics, free-energy calculations, and highperformance computing.
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His lab carries out molecular dynamics simulations aimed primarily at understanding the composition, construction, and function of the Gram-negative bacterial cell envelope. Margaret Johnson, PhD, joined the Biophysics faculty at Johns Hopkins University in 2013.
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Dr. Kloczkowski's National Institutes of Health–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.
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He has performed molecular dynamics simulations on numerous proteins since the 1980s using various computer architectures. He was among the first group of scientists to use explicit-solvent models with periodic boundary conditions, rather than simple distance-dependent dielectric functions, to simulate proteins with molecular dynamics simulations.
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POWER, University of California, Berkeley LANA SKIRBOLL, Sanofi JANIS WEEKS, University of Oregon Staff FRANCES SHARPLES, Director JO HUSBANDS, Senior Scholar JAY LABOV, Senior Scholar LIDA ANESTIDOU, Senior Program Officer KATIE BOWMAN, Senior Program Officer KEEGAN SAWYER, Senior Program Officer AUDREY THEVENON, Program Officer ANDREA HODGSON, Associate Program Officer BETHELHEM MEKASHA, Financial Associate JENNA OGILVIE, Research Associate ANGELA KOLESNIKOVA, Senior Program Assistant AANIKA SENN, Senior Program Assistant 18
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POWELL, Shell PETER J ROSSKY, NAS, Rice University TIMOTHY SWAGER, NAS, Massachusetts Institute of Technology Staff TERESA FRYBERGER, Director MARILEE SHELTON-DAVENPORT, Senior Program Officer CAMLY TRAN, Program Officer ANNA SBEREGAEVA, Associate Program Officer JESSICA WOLFRAM, Senior Program Assistant JARRETT NGUYEN, Program Assistant SHUBHA BANSKOTA, Financial Associate SUZANNE THILENIUS, Administrative Assistant 19
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Dzau is president. The three Academies work together as the National Academies of Sciences, Engineering, and Medicine to provide independent, objective analysis and advice to the nation and conduct other activities to solve complex problems and inform public policy decisions.
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Consensus Study Reports published by the National Academies of Sciences, Engineering, and Medicine document the evidence-based consensus on the study's statement of task by an authoring committee of experts. Reports typically include findings, conclusions, and recommendations based on information gathered by the committee and the committee's deliberations.
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APPENDIX F ACKNOWLEDGEMENT OF REPORT REVIEWER This Consensus Study Report was reviewed in draft form by an individual chosen for his diverse perspective and technical expertise. The purpose of this independent review is to provide candid and critical comments that will assist the National Academies of Sciences, Engineering, and Medicine in making each published report as sound as possible and to ensure that it meets the institutional standards for quality, objectivity, evidence, and responsiveness to the study charge. The review comments and draft manuscript remain confidential to protect the integrity of the deliberative process. We thank the following individual for his review of this report: Robert L. Jernigan, Iowa State University Although the reviewer listed above provided many constructive comments and suggestions, he was not asked to endorse the conclusions or recommendations of this report. In addition, he was responsible for making certain that an independent examination of this report was carried out in accordance with the standards of the National Academies and that all review comments were carefully considered. Responsibility for the final content rests entirely with the authoring committee and the National Academies. 22
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Recused 17007P Lei Shi 17008P Nilesh Banavali 17009P Giacomo Fiorin 17010P Lei Shi 17021P Giacomo Fiorin 17023P Nilesh Banavali, Giacomo Fiorin, Christopher Rowley 17025P Vincenzo Carnevale 17027P Lei Shi 17028P Margaret Johnson 17030P Giacomo Fiorin, Lei Shi 17043P Christopher Rowley 17046P Jianing Li 17054P Margaret Johnson, Jianing Li 17055P Margaret Johnson 17062P Vincenzo Carnevale, Lei Shi 17069P William A Goddard 17071P Markus Seeliger 17072P William A
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