AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics
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- Lorenzo Casalino
- University of California San Diego, La Jolla, CA, USA
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- Abigail C Dommer
- University of California San Diego, La Jolla, CA, USA
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- Zied Gaieb
- University of California San Diego, La Jolla, CA, USA
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- Emilia P Barros
- University of California San Diego, La Jolla, CA, USA
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- Terra Sztain
- University of California San Diego, La Jolla, CA, USA
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- Surl-Hee Ahn
- University of California San Diego, La Jolla, CA, USA
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- Anda Trifan
- Argonne National Lab, Lemont, IL, USA
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- Alexander Brace
- Argonne National Lab, Lemont, IL, USA
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- Anthony T Bogetti
- University of Pittsburgh, Pittsburgh, PA, USA
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- Austin Clyde
- Argonne National Lab, Lemont, IL, USA
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- Heng Ma
- Argonne National Lab, Lemont, IL, USA
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- Hyungro Lee
- Rutgers University, Piscataway, NJ, USA
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- Matteo Turilli
- Rutgers University, Piscataway, NJ, USA
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- Syma Khalid
- University of Southampton, Southampton, UK
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- Lillian T Chong
- University of Pittsburgh, Pittsburgh, PA, USA
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- Carlos Simmerling
- Stony Brook University, Stony Brook, NY, USA
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- David J Hardy
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
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- Julio DC Maia
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
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- James C Phillips
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
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- Thorsten Kurth
- NVIDIA Corporation, Santa Clara, CA, USA
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- Abraham C Stern
- NVIDIA Corporation, Santa Clara, CA, USA
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- Lei Huang
- Texas Advanced Computing Center, Austin, TX, USA
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- John D McCalpin
- Texas Advanced Computing Center, Austin, TX, USA
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- Mahidhar Tatineni
- San Diego Supercomputing Center, La Jolla, CA, USA
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- Tom Gibbs
- NVIDIA Corporation, Santa Clara, CA, USA
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- John E Stone
- University of Illinois at Urbana-Champaign, Urbana, IL, USA
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- Shantenu Jha
- Rutgers University, Piscataway, NJ, USA
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- Arvind Ramanathan
- Argonne National Lab, Lemont, IL, USA
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- Rommie E Amaro
- University of California San Diego, La Jolla, CA, USA
説明
<jats:p> We develop a generalizable AI-driven workflow that leverages heterogeneous HPC resources to explore the time-dependent dynamics of molecular systems. We use this workflow to investigate the mechanisms of infectivity of the SARS-CoV-2 spike protein, the main viral infection machinery. Our workflow enables more efficient investigation of spike dynamics in a variety of complex environments, including within a complete SARS-CoV-2 viral envelope simulation, which contains 305 million atoms and shows strong scaling on ORNL Summit using NAMD. We present several novel scientific discoveries, including the elucidation of the spike’s full glycan shield, the role of spike glycans in modulating the infectivity of the virus, and the characterization of the flexible interactions between the spike and the human ACE2 receptor. We also demonstrate how AI can accelerate conformational sampling across different systems and pave the way for the future application of such methods to additional studies in SARS-CoV-2 and other molecular systems. </jats:p>
収録刊行物
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- The International Journal of High Performance Computing Applications
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The International Journal of High Performance Computing Applications 35 (5), 432-451, 2021-04-20
SAGE Publications