Simulating the inner life of an HIV virus
It took two years and two supercomputers to simulate 1.2 microseconds in the life of an HIV capsid from the atoms up.
In the inner realm of the HIV virus, beneath its lipid bilayer membrane barrier festooned with glycoproteins, lies the capsid, a cloaking cage of proteins that protect the HIV genome, composed of two strands of RNA, and deliver it to the nucleus of the cells it infects.
The above cut-away model of the HIV virus, created by Juan Perilla of the University of Illinois, shows the capsid cage in blue. Perilla and physics professor Klaus Schulten spent two years using a supercomputer to simulate just 1.2 microseconds of a capsid’s life.
The 64-million-atom simulation was performed by the Titan supercomputer at Oak Ridge National Laboratory in Tennessee. Data analysis was performed by a second supercomputer, Blue Waters, at the National Center for Supercomputing Applications in Illinois.
The findings, reported in the journal Nature Communications, indicate several properties that enhance the capsid’s adeptness at finding a path to the nucleus of a target cells, but also potential vulnerabilities that could be exploited to defeat the HIV virus.