Fabio González-Arias, Tyler Reddy, John E. Stone, Jodi A. Hadden-Perilla,
and Juan R. Perilla.
Scalable analysis of authentic viral envelopes on FRONTERA.
Computing in Science and Engineering, 22:11-20, 2020.
GONZ2020-JS
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.
