Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics Tenth Round (2019) / Chapter Skim
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Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Tenth Round
Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Tenth Round
Pages 1-21
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Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Tenth Round Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Tenth Round Board on Life Sciences Division on Earth and Life Studies A Consensus Study 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 those prior rounds, the goal of the tenth 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 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. The committee was permitted to consider a modified time allocation if it concluded that the proposed research required a greater or smaller number of node-hours than initially requested by an applicant, up to the 460,000 MDUs maximum.
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Klauda, University of Maryland, College Park; Modeling the Intracellular and Transmembrane Structure of the Active Dimer of PlexinA1 [Returning user identified for 460,000 MDUs] MCB110023P Matthias Buck, Case Western Reserve University; Computational Modeling of Ras: Effector Protein Complex at the Membrane with Signaling Lipids PIP2 [Returning user identified for 230,632 MDUs]
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MCB130045P Albert Lau, Johns Hopkins University; Ligand-Binding Mechanisms in the NMDA Receptor [Returning user identified for 460,000 MDUs] MCB130048P David Cowburn, Yeshiva University; FG Repeats Domain Interactions of the Nuclear Pore by Simulation and Experiment [Returning user identified for 460,000 MDUs]
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* MCB180081P Liqun Zhang, Tennessee Technological University; Anton Simulation on Human Beta Defensins Binding with and Disruption Inside Lipid Membranes [Returning user identified for 230,000 MDUs]
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MCB190068P Tongye Shen, The University of Tennessee, Knoxville; Long-time Simulation of Nuclear Hormone Receptor: DNA Binding Modulates Protein Domain Interactions [New user identified for 140,000 MDUs] MCB190070P Alexey Ladokhin, University of Kansas, All Campuses; Atomistic Modeling of Membrane-Induced Conformational Changes in Anti-Apoptotic Bcl-xL [New user identified for 230,000 MDUs]
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Sincerely, James Briggs Chair, Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Tenth Round cc: Dr. Philip Blood, Pittsburgh Supercomputing Center Dr.
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C Proposal Evaluation Criteria D
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Project is scientifically and technologically feasible with clear, well-developed, and appropriate goals, objectives, and approaches to the proposed studies; a plan for analyzing the data was presented or indicated via specific publication Justification for requested time allocation. This should be evaluated by considering: 1.
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(JC) GUMBART, Georgia Institute of Technology ELLINOR HAGLUND, University of Hawaii at Manoa FATEMEH KHALILI-ARAGHI, University of Illinois at Chicago ANDRZEJ KLOCZKOWSKI, Nationwide Children's Hospital THEMIS LAZARIDIS, City College of New York ERIC MAY, University of Connecticut CLARE MCCABE, Vanderbilt University YINGLONG MIAO, The University of Kansas VIVEK NARSIMHAN, Purdue University STEVEN W
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Dr. Columbus's lab focuses on using biophysical chemistry to study membrane biophysics and membrane protein structure, function, and dynamics.
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from the University of Illinois at Urbana-Champaign. She was a postdoctoral scholar at The University of Chicago, where she continued studies of membrane proteins with a focus on the Na/K ATPase using computational modeling techniques, as well as molecular dynamics simulations.
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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.
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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, the lab's work has provided new avenues to integrate the molecular properties of cellular components directly into the dynamics of cellular networks.
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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.
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WALT, Harvard Medical School Staff FRANCES SHARPLES, Director KATHERINE BOWMAN, Senior Program Officer JESSICA DE MOUY, Senior Program Assistant ANDREA HODGSON, Program Officer JO HUSBANDS, Senior Scholar STEVEN MOSS, Associate Program Officer KEEGAN SAWYER, Senior Program Officer AUDREY THEVENON, Program Officer KOSSANA YOUNG, Senior Program Assistant 17
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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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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: Nathan Baker, Pacific Northwest National Laboratory Although the reviewer listed above provided many constructive comments and suggestions, he was not asked to endorse the conclusions or recommendations of this report.
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Recused CHE120043P Yaroslava Yingling CHE190026P Juan Vanegas CHE190029P Yaroslava Yingling MCB100017P Jerome Baudry, James Gumbart, Fatemeh Khalili-Araghi, Juan Vanegas MCB100018P James Gumbart, Fatemeh Khalili-Araghi, Christopher Rowley MCB110023P Themis Lazaridis MCB110059P Linda Columbus MCB110066P Juan Vanegas MCB120079P James Gumbart, Yinglong Miao MCB130061P James Gumbart, Fatemeh Khalili-Araghi, Christopher Rowley MCB140062P Leonor Saiz MCB160079P Themis Lazaridis MCB170103P Eric May MCB180087P Linda Columbus, Yinglong Miao MCB190041P Yinglong Miao MCB190044P James Gumbart MCB190049P Yinglong Miao MCB190053P Linda Columbus MCB190064P Ellinor Haglund MCB190067P Markus Seeliger MCB190068P Jerome Baudry MCB190070P Themis Lazaridis MCB190084P James Gumbart 21
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