The necessary calculations were conducted for two years on the supercomputers Titan and Blue Waters.
Molecular biologists from the United States introduced a computer simulation that shows the interaction of the capsid (outer protein shell) of the human immunodeficiency virus with the environment.
The corresponding video published on the website of the University of Illinois at Urbana-Champaign.
It shows the yellow and blue particles coming in and out of the capsid ions inside the virus.
Negative ions, as shown by the modeling reported in the journal Nature Communications, accumulate on the positively charged surface on the inside of the capsid, whereas positive are outside. It is the latter attract the negatively charged nucleotides that comprise the DNA of a cell in which HIV is introduced.
At a certain value of potential difference possible rupture of the wall of the capsid. The vulnerability of HIV, scientists plan to use for the prevention and treatment of HIV infection.
A computer model of the capsid includes 64 million atoms. Simulation created using the methods of molecular dynamics. The necessary calculations were conducted for two years on the supercomputers Titan and Blue Waters.
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