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Pioneering Simulations Focus on HIV-1 Virus

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Full-scale model of a realistic HIV-1 lipid vesicle at united atom resolution (MARTINI force-field) has been developed using supercomputer resources.

The key finding shows that the complex, asymmetric membrane composition of the HIV-1 virus can lead to macroscopic properties such as the differential displacement between leaflets and lipid microdomain formation.

Credit: Bryer et al.

Researchers used supercomputers to generate the first biologically authentic computer simulations of the HIV-1 virus liposome and genome capsid.

The University of Delaware's Alex Bryer and colleagues employed the Texas Advanced Computing Center (TACC)'s Stampede2 and Frontera systems; the Pittsburgh Supercomputing Center's Bridges-2 supercomputer; Grizzly at the U.S. Department of Energy's Los Alamos National Laboratory, and Blue Waters at the National Center for Supercomputing Applications.

"I was able to perform calculations, and without needing to transfer data, I could set up a visualization session through the TACC portal and analyze and work with my data directly on Stampede2," Bryer said.

He also highlighted analysis made on Frontera, which processed in minutes data that might have otherwise taken serial naive implementation three weeks to process.

The project is focused on how the HIV-1 viral envelope responds during infection.

From Texas Advanced Computing Center
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Abstracts Copyright © 2022 SmithBucklin, Washington, DC, USA


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