TCB Members, NAMD, and VMD Part of 2021 ACM Gordon Bell Finalist for COVID-19 Research

Members of the Theoretical and Computational Biophysics Group were part of a multi-institutional interdisciplinary team awarded as finalists at Supercomputing 2021 with the internationally recognized ACM Gordon Bell Special Prize for COVID-19 Research, for 2021.

Announcement of the team's finalist paper at Supercomputing 2021.
All-atom molecular dynamics simulation of the SARS-CoV-2 virus in aersolized form presents tremendous challenges for researchers in terms of both computation and visualization, owing to the massive size (one billion atoms) of the aersolized virus model, the inclusion of irregular/sparse/empty regions of space in the simulation unit cell, and sampling required to observe key dynamics of the virion and the Delta variant of the SARS-CoV-2 spike protein, in particular.

Team members from U. Illinois provided performance and scalability advances in the NAMD molecular dynamics simulation software, and technological improvements to VMD, a key molecular modeling tool used to prepare, visualize, and analyze molecular dynamics simulations of the aersolized virus and spike protein. The NAMD and VMD software advances provided by U. Illinois team members enabled the science campaign to more efficiently utilize state-of-the-art supercomputers at national computing centers, including Summit, the most powerful supercomputer in the United States, operated by Oak Ridge National Laboratory.

These achievements required the unique skills of a diverse multi-institutional team to overcome both technical challenges and an extremely compressed research timeline. Every team member played a vital role in achieving the final outcome.

#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 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.

Team presentation at Supercomputing 2021:


Movie Trailer:


All-atom visualization of the aerosol droplet, and the proteins
that make up the virion and deep lung fluids. This billion-atom
visualization is the largest ever produced within VMD and the
built-in Tachyon CPU and GPU ray tracing engines.
Overview of the aerosolized Delta SARS-CoV-2 virion

Composition of the aerosol+virion model

NAMD scaling for the 1-Billion-atom aerosol+virion
running on ORNL Summit

Weighted ensemble methods, as implemented in WESTPA,
provided tremendous enhancement of molecular dynamics
sampling of rare events, yielding effective performance
levels orders of magnitude faster than can be achieved
through brute force parallel computation alone.

Research Team:

Research team members and supercomputer centers used for the research.

    California Institute of Technology
  • Zhuoran Qiao
    Oregon Health and Science University
  • John Russo
  • Daniel Zuckerman
    University of Bristol
  • Adrian Mullholland
  • Sofia Oliveira
  • Matt Williams
  • Christopher Woods
    Entos Corporation
  • Anders Christensen
  • Frederick Manby
  • Thomas Miller III
  • Michael O'Connor
  • Daniel G.A. Smith
  • Sai Krishna Sirumalla
  • Teresa Tamayo-Mendoza
  • Matthew Welborn
    NVIDIA Corporation
  • Anima Anandkumar
  • David Clark
  • Alan Gray
  • Abraham Stern
  • Josh Romero
  • Tom Gibbs
    Oracle Corporation
  • Bryan Barker
  • Richard Pitts
  • Harinda Rajapaksha