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#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

View ORCID ProfileAbigail Dommer, View ORCID ProfileLorenzo Casalino, View ORCID ProfileFiona Kearns, View ORCID ProfileMia Rosenfeld, View ORCID ProfileNicholas Wauer, Surl-Hee Ahn, View ORCID ProfileJohn Russo, Sofia Oliveira, Clare Morris, View ORCID ProfileAnthony Bogetti, View ORCID ProfileAnda Trifan, Alexander Brace, View ORCID ProfileTerra Sztain, View ORCID ProfileAustin Clyde, View ORCID ProfileHeng Ma, View ORCID ProfileChakra Chennubhotla, View ORCID ProfileHyungro Lee, View ORCID ProfileMatteo Turilli, View ORCID ProfileSyma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel G. A. Smith, Zhuoran Qiao, Sai Krishna Sirumalla, Michael O’Connor, View ORCID ProfileFrederick Manby, View ORCID ProfileAnima Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, View ORCID ProfileJohn Stone, View ORCID ProfileDaniel Zuckerman, Adrian Mulholland, Thomas Miller III, Shantenu Jha, View ORCID ProfileArvind Ramanathan, View ORCID ProfileLillian Chong, View ORCID ProfileRommie Amaro
doi: https://doi.org/10.1101/2021.11.12.468428
Abigail Dommer
1UC San Diego
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Lorenzo Casalino
1UC San Diego
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Fiona Kearns
1UC San Diego
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Mia Rosenfeld
1UC San Diego
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Nicholas Wauer
1UC San Diego
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Surl-Hee Ahn
1UC San Diego
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John Russo
2Oregon Health & Science University
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Sofia Oliveira
3University of Bristol
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Clare Morris
1UC San Diego
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Anthony Bogetti
4University of Pittsburgh
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Anda Trifan
5Argonne National Laboratory
6University of Illinois at Urbana-Champaign
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Alexander Brace
5Argonne National Laboratory
7University of Chicago
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Terra Sztain
1UC San Diego
8Freie Universität Berlin
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Austin Clyde
5Argonne National Laboratory
7University of Chicago
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Heng Ma
5Argonne National Laboratory
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Chakra Chennubhotla
4University of Pittsburgh
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Hyungro Lee
9Brookhaven National Lab & Rutgers University
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Matteo Turilli
9Brookhaven National Lab & Rutgers University
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Syma Khalid
10University of Oxford
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Teresa Tamayo-Mendoza
11Entos, Inc.
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Matthew Welborn
11Entos, Inc.
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Anders Christensen
11Entos, Inc.
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Daniel G. A. Smith
11Entos, Inc.
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Zhuoran Qiao
12California Institute of Technology
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Sai Krishna Sirumalla
11Entos, Inc.
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Michael O’Connor
11Entos, Inc.
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Frederick Manby
11Entos, Inc.
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Anima Anandkumar
12California Institute of Technology
13NVIDIA Corporation
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David Hardy
6University of Illinois at Urbana-Champaign
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James Phillips
6University of Illinois at Urbana-Champaign
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Abraham Stern
13NVIDIA Corporation
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Josh Romero
13NVIDIA Corporation
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David Clark
13NVIDIA Corporation
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Mitchell Dorrell
14Pittsburgh Supercomputing Center
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Tom Maiden
14Pittsburgh Supercomputing Center
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Lei Huang
15Texas Advanced Computing Center
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John McCalpin
15Texas Advanced Computing Center
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Christopher Woods
3University of Bristol
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Alan Gray
13NVIDIA Corporation
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Matt Williams
3University of Bristol
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Bryan Barker
16Oracle for Research
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Harinda Rajapaksha
16Oracle for Research
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Richard Pitts
16Oracle for Research
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Tom Gibbs
13NVIDIA Corporation
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John Stone
6University of Illinois at Urbana-Champaign
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Daniel Zuckerman
2Oregon Health & Science University
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Adrian Mulholland
3University of Bristol
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Thomas Miller III
11Entos, Inc.
12California Institute of Technology
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Shantenu Jha
9Brookhaven National Lab & Rutgers University
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Arvind Ramanathan
5Argonne National Laboratory
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Lillian Chong
4University of Pittsburgh
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Rommie Amaro
1UC San Diego
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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 ob-scure 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.

ACM Reference Format Abigail Dommer1†, Lorenzo Casalino1†, Fiona Kearns1†, Mia Rosenfeld1, Nicholas Wauer1, Surl-Hee Ahn1, John Russo,2 Sofia Oliveira3, Clare Morris1, AnthonyBogetti4, AndaTrifan5,6, Alexander Brace5,7, TerraSztain1,8, Austin Clyde5,7, Heng Ma5, Chakra Chennubhotla4, Hyungro Lee9, Matteo Turilli9, Syma Khalid10, Teresa Tamayo-Mendoza11, Matthew Welborn11, Anders Christensen11, Daniel G. A. Smith11, Zhuoran Qiao12, Sai Krishna Sirumalla11, Michael O’Connor11, Frederick Manby11, Anima Anandkumar12,13, David Hardy6, James Phillips6, Abraham Stern13, Josh Romero13, David Clark13, Mitchell Dorrell14, Tom Maiden14, Lei Huang15, John McCalpin15, Christo- pherWoods3, Alan Gray13, MattWilliams3, Bryan Barker16, HarindaRajapaksha16, Richard Pitts16, Tom Gibbs13, John Stone6, Daniel Zuckerman2*, Adrian Mulholland3*, Thomas MillerIII11,12*, ShantenuJha9*, Arvind Ramanathan5*, Lillian Chong4*, Rommie Amaro1*. 2021. #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy ofDeltaSARS-CoV-2 in a Respiratory Aerosol. In Supercomputing ‘21: International Conference for High Perfor-mance Computing, Networking, Storage, and Analysis. ACM, New York, NY, USA, 14 pages. https://doi.org/finalDOI

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵† Joint first authors

  • ↵* Contact authors.

  • Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from permissions{at}acm.org.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 15, 2021.
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#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, Sofia Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel G. A. Smith, Zhuoran Qiao, Sai Krishna Sirumalla, Michael O’Connor, Frederick Manby, Anima Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel Zuckerman, Adrian Mulholland, Thomas Miller III, Shantenu Jha, Arvind Ramanathan, Lillian Chong, Rommie Amaro
bioRxiv 2021.11.12.468428; doi: https://doi.org/10.1101/2021.11.12.468428
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#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol
Abigail Dommer, Lorenzo Casalino, Fiona Kearns, Mia Rosenfeld, Nicholas Wauer, Surl-Hee Ahn, John Russo, Sofia Oliveira, Clare Morris, Anthony Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel G. A. Smith, Zhuoran Qiao, Sai Krishna Sirumalla, Michael O’Connor, Frederick Manby, Anima Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John Stone, Daniel Zuckerman, Adrian Mulholland, Thomas Miller III, Shantenu Jha, Arvind Ramanathan, Lillian Chong, Rommie Amaro
bioRxiv 2021.11.12.468428; doi: https://doi.org/10.1101/2021.11.12.468428

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