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: Contribution to journalArticlepeer-review

Abstract

Enveloped viruses, such as SARS-CoV-2, infect cells via fusion of their envelope with the host membrane. By employing molecular simulations to characterize viral envelopes, researchers can gain insights into key determinants of infection. Here, the Frontera supercomputer is leveraged for large-scale modeling and analysis of authentic viral envelopes, whose lipid compositions are complex and realistic. Visual Molecular Dynamics (VMD) with support for MPI is employed, overcoming previous computational limitations and enabling investigation into virus biology at an unprecedented scale. The techniques applied here to an authentic HIV-1 envelope at two levels of spatial resolution (29 million particles and 280 million atoms) are broadly applicable to the study of other viruses. The authors are actively employing these techniques to develop and characterize an authentic SARS-CoV-2 envelope. A general framework for carrying out scalable analysis of simulation trajectories on Frontera is presented, expanding the utility of the machine in humanity's ongoing fight against infectious diseases.
Original languageEnglish (US)
Article number9181446
Pages (from-to)11-20
Number of pages10
JournalComputing in Science and Engineering
Volume22
Issue number6
DOIs
StatePublished - Nov 2020

Keywords

  • Coronavirus
  • COVID-19
  • severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
  • Novel coronavirus
  • 2019-nCoV
  • Pandemic
  • Computational modeling
  • Viruses (medical)
  • Lipidomics
  • Biological system modeling
  • Biomembranes
  • Analytical models
  • Trajectory

ASJC Scopus subject areas

  • Engineering(all)
  • Computer Science(all)

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