Supercomputer Simulation of HIV Virus may Provide New Treatment Options

Graphic by Juan Perilla

After two years of work on the Department of Energy’s Titan supercomputer, researchers successfully simulated 1.2 microseconds of an HIV capsid navigating through a human cell. The findings, which are published in Nature Communications, gives new details about how the virus infects its host.


Juan R. Perilla, the study’s leader and a research scientist from the University of Illinois, is optimistic that these insights will help scientists looking for HIV treatments. He said, “We are learning the details of the HIV capsid system, not just the structure but also how it changes its environment and responds to its environment.”


After the simulation of the 64 million atoms involved was performed on Titan, another supercomputer, this time Blue Waters at the National Center for Supercomputing Applications at the University of Illinois, was used to analyze the data produced. Physics professor Klaus Schulten, who co-led the study, was the pioneer of the molecular dynamics simulation used to examine the biological system, a method he called ‘computational microscopy’.

The simulation study revealed the HIV capsid structure to be a protein cage composed of hexagon and pentagon shaped structures in a complex network. Each capsid has a small pore in the center and contains the RNA of the HIV virus protected inside, safe from the human body’s defenses.


Never before have scientists seen the full scope of what the HIV shuttle can do. Now they know of its ability to transmit information through oscillating frequencies and its delicate ion charge, which has presented a puzzle as to how to defeat the infection cycle of HIV. However, as the simulation has also shown areas of stress on the capsid that can be exploited, researchers can use the vulnerabilities to create new treatments against HIV.

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