Scalable Analysis of Authentic Viral Envelopes on FRONTERA

Fabio González-Arias, Tyler Reddy, John E. Stone, Jodi A Hadden-Perilla, Juan R Perilla

Research output: Working paper

Abstract

Enveloped viruses infect host cells via fusion of their viral envelope with the plasma membrane. Upon cell entry, viruses gain access to all the macromolecular machinery necessary to replicate, assemble, and bud their progeny from the infected cell. By employing molecular dynamics simulations to characterize the dynamical and chemical-physical properties of viral envelopes, researchers can gain insights into key determinants of viral infection and propagation. Here, the Frontera supercomputer is leveraged for large-scale analysis of authentic viral envelopes, whose lipid compositions are complex and realistic. VMD with support for MPI is employed on the massive parallel computer to overcome previous computational limitations and enable investigation into virus biology at an unprecedented scale. The modeling and analysis techniques applied to authentic viral envelopes at two levels of particle resolution are broadly applicable to the study of other viruses, including the novel coronavirus that causes COVID-19. A framework for carrying out scalable analysis of multi-million particle MD simulation trajectories on Frontera is presented, expanding the the utility of the machine in humanity’s ongoing fight against infectious disease.
Original languageEnglish (US)
PublisherCold Spring Harbor Laboratory Press
Number of pages7
DOIs
StateIn preparation - Jul 6 2020

Publication series

NamebioRxiv

Keywords

  • Coronavirus
  • COVID-19
  • severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
  • Novel coronavirus
  • 2019-nCoV
  • Pandemic

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    González-Arias, F., Reddy, T., Stone, J. E., Hadden-Perilla, J. A., & Perilla, J. R. (2020). Scalable Analysis of Authentic Viral Envelopes on FRONTERA. (bioRxiv). Cold Spring Harbor Laboratory Press. https://doi.org/10.1101/2020.07.05.188367