June 15, 2020 — The Pittsburgh Supercomputing Center updated the community of the advances the center is making in the fight against COVID-19 in a news item posted below. In this week’s update, the center highlighted how the University of Arkansas and the University of California, Riverside are leveraging the Anton 2 supercomputer to develop simulations.
Anton 2 Simulates Coronavirus Binding to Human Cells
A team at the University of Arkansas is using the unparalleled ability of the Anton 2 supercomputer to simulate molecular systems for microseconds or longer to better understand how the Coronavirus that causes COVID-19 attaches to human cells. Anton was developed by D. E. Shaw Research (DESRES) to execute molecular dynamics simulations of biomolecules such as proteins, nucleic acids and lipids orders of magnitude faster than was previously possible. The Anton 2 at PSC is provided without cost by DESRES for non-commercial use by the U.S. research community. PSC supports that community’s use of this resource with operational funding from the National Institutes of Health.
In order to infect a human cell, a virus must first break into it. The “spike” glycoproteins of the SARS-CoV-2 (COVID-19) and SARS-CoV (2002-03 SARS epidemic) viruses begin this process by first attaching to the same human cell-surface protein, ACE2. The University of Arkansas group, led by Mahmoud Moradi, is using Anton 2 to study the activation and deactivation of these spike proteins. Understanding the spike-protein activation process, and particularly gaining a dynamic understanding of how the protein behaves rather than a static picture, is key to the development of vaccines and drugs against COVID-19. While these processes occur over a time period of only millionths of a second (microseconds), the requirements of simulating them exceed the reach of general-purpose supercomputers. Anton 2’s specialized software and hardware make it uniquely suited to such simulations.
Anton 2 Simulations Examine Experimental COVID-19 Test
Scientists at the University of California, Riverside, are using the Anton 2 supercomputer to study the interactions of the SARS-CoV-2 virus’s genetic material with the proteins behind the CRISPR gene-editing system. They hope to use this information to develop an experimental test for the virus, which causes COVID-19. Anton was developed by D. E. Shaw Research (DESRES) to execute molecular dynamics simulations of biomolecules such as proteins, nucleic acids and lipids orders of magnitude faster than was previously possible. The Anton 2 at PSC is provided without cost by DESRES for non-commercial use by the U.S. research community. PSC supports that community’s use of this resource with operational funding from the National Institutes of Health.
Doctors need better and faster tests for identifying SARS-CoV-2 in suspected patients. A new version of the CRISPR gene-editing system called CRISPR-Cas12a holds promise as the backbone for such a test. A University of California, Riverside, group led by Giulia Palermo will use Anton 2 to study how the CRISPR-Cas12a protein recognizes viral genetic material. The task requires microsecond-long simulations, which are beyond the reach of most supercomputers. Anton 2’s specialized software and hardware, though, enables such simulations, allowing researchers to observe the changes in emerging CRISPR-Cas proteins that are required for detection of viral genes.
COVID-19 HPC Consortium
Both sets of researchers obtained time on Anton 2 via the COVID-19 HPC Consortium, of which PSC is a leading member. The consortium also allocates COVID-19 research time on PSC’s large Bridges supercomputing platform as well as other consortium-members’ computers. You can find information on applying for COVID-19 research time on Anton 2 here.
About Pittsburgh Supercomputing Center
PSC is a joint effort of Carnegie Mellon University and the University of Pittsburgh. Established in 1986, PSC is supported by several federal agencies, the Commonwealth of Pennsylvania and private industry and is a leading partner in XSEDE (Extreme Science and Engineering Discovery Environment), the National Science Foundation cyber-infrastructure program.
Source: Pittsburgh Supercomputing Center