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Eradicating Emerging Viruses

Published on September 3, 2019 by Faith Singer-Villalobos



This scientific image shows influenza viral proteins (green) beginning the process of merging the viral envelope with a model of the cell membrane, a key step in viral infection. [Credit: Peter Kasson, University of Virginia]

Emerging viruses have been with us for hundreds of years and will be with us for hundreds more. If you follow the news, we are continually concerned about whether there will be another outbreak of influenza or increasing incidence of Ebola or other viruses that threaten our health.

An emerging virus is a term applied to a newly discovered virus, one that is increasing in incidence or has the potential to spread. HIV is the clearest example of a previously unknown virus that has now produced one of the largest pandemics in history.

Peter Kasson, associate professor of Molecular Physiology and Biomedical Engineering at the University of Virginia and an early user on Frontera.

Peter Kasson, an associate professor of Molecular Physiology and Biomedical Engineering at the University of Virginia, has combined computer science and biology throughout his educational and professional career.

"We work to understand viral infections such as influenza and Zika," Kasson said. "What we do guides the development of new antiviral therapies, and also helps us assess how well vaccines work and how well people's immunity can prevent new viral threats from causing widespread disease in the United States."

Kasson and his team observe viruses experimentally by tagging them with fluorescent proteins and using microscopy to understand how they affect cells.

However, the experiments provide them with a very limited level of detail. "To be able to really study the mechanisms of viral infection, we have to combine experiments with computer models where we build a model of the virus, one atom at a time, and then simulate the mechanics of how the atoms interact," Kasson said. "It's a challenge that requires the fastest supercomputers in the world."

"To be able to really study the mechanisms of viral infection, we have to combine experiments with computer models where we build a model of the virus, one atom at a time, and then simulate the mechanics of how the atoms interact. It's a challenge that requires the fastest supercomputers in the world."
Peter Kasson, University of Virginia

The new Frontera supercomputer at the Texas Advanced Computing Center (TACC) is the fastest academic supercomputer in the world. Its hundreds of thousands of closely linked computational cores are well-suited for the kinds of simulations Kasson's team needs to run. Their research uses experimental data to refine their simulations, and has the potential to serve as a test case for and also develop large-scale adaptive ensemble methods — programs that run many simulations, examine the results, and decide what to run next so that the process of deciding what simulations to do is automated as well as the simulations themselves.

Kasson leads one of the 34 research groups selected to participate in the Frontera early user period. "The initial experience has been extremely smooth. We've been able to get some exciting preliminary results that we're very eager to run further," Kasson said. "In the time we've been using Frontera, our simulations are proceeding two or three times faster than on the prior supercomputers we've had access to."

Stopping viruses in their tracks in Kasson's ultimate goal. "Viruses are these really tiny packages that encode a lot of complexity. We can observe the function experimentally, but taking them apart and achieving a mechanistic understanding is something that we need the simulations to help with — that really gets me excited."

In addition to enabling simulations on a massive scale, Frontera offers the opportunity to train young scientists on a cutting-edge system. "They learn best practices, advance science, and do this on the best supercomputer the country has to offer to prepare us for the future," Kasson said.


This award by the NSF Office of Advanced Cyberinfrastructure is jointly supported by the Division of Chemistry within the NSF Directorate for Mathematical and Physical Sciences and the Division of Chemical, Bioengineering, Environmental, and Transport Systems within the NSF Directorate for Engineering. Award Abstract #1835780: Collaborative Research: NSCI Framework. Software: SCALE-MS - Scalable Adaptive Large Ensembles of Molecular Simulations.


Contact

Faith Singer-Villalobos

Communications Manager
faith@tacc.utexas.edu | 512-232-5771

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Science And Technology Writer
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