#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol-Reference-Cited by-同舟云学术

#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol

Published:2022-10-02 Issue:1 Volume:37 Page:28-44
ISSN:1094-3420
Container-title:The International Journal of High Performance Computing Applications
language:en
Short-container-title:The International Journal of High Performance Computing Applications

Author:

Dommer Abigail¹,Casalino Lorenzo¹^ORCID,Kearns Fiona¹,Rosenfeld Mia¹^ORCID,Wauer Nicholas¹,Ahn Surl-Hee¹^ORCID,Russo John²^ORCID,Oliveira Sofia³^ORCID,Morris Clare¹^ORCID,Bogetti Anthony⁴,Trifan Anda⁵⁶,Brace Alexander⁵⁷^ORCID,Sztain Terra¹⁸,Clyde Austin⁵⁷,Ma Heng⁵,Chennubhotla Chakra⁴,Lee Hyungro⁹^ORCID,Turilli Matteo⁹,Khalid Syma¹⁰,Tamayo-Mendoza Teresa¹¹,Welborn Matthew¹¹,Christensen Anders¹¹,Smith Daniel GA¹¹,Qiao Zhuoran¹²^ORCID,Sirumalla Sai K¹¹,O’Connor Michael¹¹,Manby Frederick¹¹,Anandkumar Anima¹²¹³^ORCID,Hardy David⁶,Phillips James⁶^ORCID,Stern Abraham¹³,Romero Josh¹³,Clark David¹³,Dorrell Mitchell¹⁴,Maiden Tom¹⁴,Huang Lei¹⁵,McCalpin John¹⁵^ORCID,Woods Christopher³^ORCID,Gray Alan¹³,Williams Matt³^ORCID,Barker Bryan¹⁶,Rajapaksha Harinda¹⁶,Pitts Richard¹⁶^ORCID,Gibbs Tom¹³,Stone John⁶¹³,Zuckerman Daniel M.²^ORCID,Mulholland Adrian J.³^ORCID,Miller Thomas¹¹¹²,Jha Shantenu⁹,Ramanathan Arvind⁵^ORCID,Chong Lillian⁴^ORCID,Amaro Rommie E¹^ORCID

Affiliation:

1. UC San Diego, La Jolla, CA, USA

2. Oregon Health & Science University, Portland, OR, USA

3. University of Bristol, UK

4. University of Pittsburgh, Pittsburgh, PA, USA

5. Argonne National Laboratory, Lemont, IL, USA

6. University of Illinois at Urbana-Champaign, Urbana, IL, USA

7. University of Chicago, Chicago, IL, USA

8. Freie Universitat Berlin

9. Brookhaven National Lab and Rutgers University

10. University of Oxford, UK

11. Entos, Inc., San Diego, CA, USA

12. California Institute of Technology, Pasadena, CA, USA

13. NVIDIA Corp, Santa Clara, CA, USA

14. Pittsburgh Supercomputing Center, Pittsburgh, PA, USA

15. Texas Advanced Computing Center, Austin, TX, USA

16. Oracle for Research, Austin, TX, USA

Abstract

We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized.

Funder

National Science Foundation

U.S. Department of Energy

National Institutes of Health

Publisher

SAGE Publications

Subject

Hardware and Architecture,Theoretical Computer Science,Software

Link

http://journals.sagepub.com/doi/pdf/10.1177/10943420221128233

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1. GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers