Scalable Analysis of Authentic Viral Envelopes on FRONTERA
| Autor: | Juan R. Perilla, Jodi A. Hadden-Perilla, Tyler Reddy, John E. Stone, Fabio González-Arias |
|---|---|
| Rok vydání: | 2020 |
| Předmět: |
2019-20 coronavirus outbreak
General Computer Science Coronavirus disease 2019 (COVID-19) Computer science viruses Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Computational biology medicine.disease_cause Viral infection 01 natural sciences Article Virus 03 medical and health sciences Viral envelope 0103 physical sciences medicine Coronavirus 030304 developmental biology Cellular biophysics Cell entry 0303 health sciences 010304 chemical physics General Engineering Supercomputer Scalability Envelope (motion) |
| Zdroj: | Computing in Science & Engineering Computing in science & engineering |
| ISSN: | 1558-366X 1521-9615 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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