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Report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics Twelfth Round (2021) / Chapter Skim
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Letter Report
Pages 2-8

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From page 2...
... 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 twelfth 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 (MD)
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From page 3...
... 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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From page 4...
... . In alphabetical and numerical order by proposal submission number, the proposals judged by the committee as best meeting the selection criteria of the RFP are: CHE100024P Kendall Houk, University of California, Los Angeles; Mechanistic Study and Catalytic Site Redesign of Pyr Family of Enzymes to Access Potent Antibiotics [Returning user identified for 443,808 MDUs]
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From page 5...
... MCB160087P Mahmoud Moradi, University of Arkansas at Little Rock; Characterizing pHTriggered Activation of Influenza Hemagglutinin Protein [Returning user identified for 420,000 MDUs] MCB160089P Igor Vorobyov; University of California, Davis; Elucidating Molecular Determinants of Pro-Arrhythmic Proclivities of Beta Blocking Drugs for a Multi-Scale Modeling Pipeline [Returning user identified for 230,000 MDUs]
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From page 6...
... MCB200087P Paul Robustelli, Dartmouth College; Characterizing the Binding Mechanisms of Castration-Resistant Prostate Cancer Therapeutics to the Intrinsically Disordered N-Terminal Domain of the Androgen Receptor [Returning user identified for 460,000 MDUs] MCB200095P Taras Pogorelov, University of Illinois at Urbana-Champaign; Signaling Protein Dynamics in Mammalian Cytoplasm [Returning user identified for 230,000 MDUs]
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From page 7...
... MCB210020P Michael Regnier, University of Washington; Dynamics of Super Relaxed Myosin and Modulation by 2′-Deoxy-ATP [New user identified for 230,000 MDUs] MCB210021P Sandhya Kortagere, Drexel University; Distinct Conformational States Induced by Agonists Promote Biased Signaling at the Dopamine D3 Receptors [New user identified for 100,000 MDUs]
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From page 8...
... Philip Blood, Pittsburgh Supercomputing Center Dr. Elizabeth Eide, National Academies of Sciences, Engineering, and Medicine Dr.
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Key Terms

  • simulation time
  • selection criteria
  • time allocations
  • conformational dynamics
  • molecular dynamics

  • molecular mechanisms
  • biomolecular simulation
  • intrinsically disordered
  • hemagglutinin protein
  • protein machinery

  • distinct conformational
  • protein targeting
  • elucidating molecular
  • required simulation
  • protein binding

  • time provided
  • spike protein
  • inactivated state
  • signaling protein
  • protein dynamics

  • molecular dynamic
  • protein core
  • molecular determinants
  • conformational states
  • androgen receptor

  • biased signaling
  • agonists promote
  • nebraska medical
  • mechanotransduction channel
  • influenza fusion


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