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

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 Dommer ^1† , Lorenzo Casalino ^1† , Fiona Kearns ^1† , Mia Rosenfeld ¹ , Nicholas Wauer ¹ , Surl-Hee Ahn ¹ , John Russo, ² Sofia Oliveira ³ , Clare Morris ¹ , AnthonyBogetti ⁴ , AndaTrifan ^5,6 , Alexander Brace ^5,7 , TerraSztain ^1,8 , Austin Clyde ^5,7 , Heng Ma ⁵ , Chakra Chennubhotla ⁴ , Hyungro Lee ⁹ , Matteo Turilli ⁹ , Syma Khalid ¹⁰ , Teresa Tamayo-Mendoza ¹¹ , Matthew Welborn ¹¹ , Anders Christensen ¹¹ , Daniel G. A. Smith ¹¹ , Zhuoran Qiao ¹² , Sai Krishna Sirumalla ¹¹ , Michael O'Connor ¹¹ , Frederick Manby ¹¹ , Anima Anandkumar ^12,13 , David Hardy ⁶ , James Phillips ⁶ , Abraham Stern ¹³ , Josh Romero ¹³ , David Clark ¹³ , Mitchell Dorrell ¹⁴ , Tom Maiden ¹⁴ , Lei Huang ¹⁵ , John McCalpin ¹⁵ , Christo- pherWoods ³ , Alan Gray ¹³ , MattWilliams ³ , Bryan Barker ¹⁶ , HarindaRajapaksha ¹⁶ , Richard Pitts ¹⁶ , Tom Gibbs ¹³ , John Stone ⁶ , Daniel Zuckerman ² *, Adrian Mulholland ³ *, Thomas MillerIII ^11,12 *, ShantenuJha ⁹ *, Arvind Ramanathan ⁵ *, Lillian Chong ⁴ *, Rommie Amaro ¹ *. 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.