@article{644ae4527ec8483dba91f4532c90d979,
title = "#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol: 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 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.",
keywords = "aerosols, AI, computational virology, COVID-19, deep learning, Delta, GPU, HPC, molecular dynamics, multiscale simulation, SARS-CoV-2, weighted ensemble",
author = "Abigail Dommer and Lorenzo Casalino and Fiona Kearns and Mia Rosenfeld and Nicholas Wauer and Ahn, {Surl Hee} and John Russo and Sofia Oliveira and Clare Morris and Anthony Bogetti and Anda Trifan and Alexander Brace and Terra Sztain and Austin Clyde and Heng Ma and Chakra Chennubhotla and Hyungro Lee and Matteo Turilli and Syma Khalid and Teresa Tamayo-Mendoza and Matthew Welborn and Anders Christensen and Smith, {Daniel G.A.} and Zhuoran Qiao and Sirumalla, {Sai K.} and Michael O{\textquoteright}Connor and Frederick Manby and Anima Anandkumar and David Hardy and James Phillips and Abraham Stern and Josh Romero and David Clark and Mitchell Dorrell and Tom Maiden and Lei Huang and John McCalpin and Christopher Woods and Alan Gray and Matt Williams and Bryan Barker and Harinda Rajapaksha and Richard Pitts and Tom Gibbs and John Stone and Zuckerman, {Daniel M.} and Mulholland, {Adrian J.} and Thomas Miller and Shantenu Jha and Arvind Ramanathan and Lillian Chong and Amaro, {Rommie E.}",
note = "Funding Information: The author(s) disclosed receipt of the following financial support for the research, authorship, and/or publication of this article: This work was supported by National Science Foundation (CHE- 1801971); National Science Foundation (MCB- 2032054); National Science Foundation (OAC-1818253); National Science Foundation (TG-CHE060063); U.S. Department of Energy (DE-AC02-06CH11357); U.S. Department of Energy (DE-AC05- 00OR22725); National Institutes of Health (P41-GM104601); National Institutes of Health (R01-GM132826). Funding Information: We thank Prof. Kim Prather for inspiring and informative discussions about aerosols and for her commitment to convey the airborne nature of SARS-CoV-2. We thank D. Veesler for sharing the Delta spike NTD coordinates in advance of publication. We thank B. Messer, D. Maxwell, and the Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory supported by the DOE under Contract DE-AC05-00OR22725. We thank the Texas Advanced Computing Center Frontera team, especially D. Stanzione and T. Cockerill, and for compute time made available through a Director{\textquoteright}s Discretionary Allocation (NSF OAC-1818253). We thank the Argonne Leadership Computing Facility supported by the DOE under DE-AC02-06CH11357. We thank the Pittsburgh Supercomputer Center for providing priority queues on Bridges-2 through the XSEDE allocation NSF TG-CHE060063. We thank N. Kern and J. Lee of the CHARMM-GUI support team for help converting topologies between NAMD and GROMACS. We thank J. Copperman, G. Simpson, D. Aristoff, and J. Leung for valuable discussions and support from NIH grant GM115805. NAMD and VMD are funded by NIH P41-GM104601. This work was supported by the NSF Center for Aerosol Impacts on Chemistry of the Environment (CAICE), National Science Foundation Center for Chemical Innovation (NSF CHE-1801971), as well as NIH GM132826, NSF RAPID MCB-2032054, an award from the RCSA Research Corp., a UC San Diego Moore{\textquoteright}s Cancer Center 2020 SARS-CoV-2 seed grant, to R.E.A. This work was also supported by Oracle Cloud credits and related resources provided by the Oracle for Research program. AJM and ASFO receive funding from the European Research Council (ERC) under the European Union{\textquoteright}s Horizon 2020 research and innovation programme (PREDACTED Advanced Grant, Grant agreement No.: 101021207). Publisher Copyright: {\textcopyright} The Author(s) 2022.",
year = "2023",
month = jan,
doi = "10.1177/10943420221128233",
language = "English (US)",
volume = "37",
pages = "28--44",
journal = "International Journal of High Performance Computing Applications",
issn = "1094-3420",
publisher = "SAGE Publishing",
number = "1",
}