Simulating vesicle fusion on Blue Waters

Vijay Pande, Stanford University

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Robert Brunner, Vijay Pande, Gert Kiss, Joseph Gomes, Morgan Lawrenz, Kyle Beauchamp, Lili Peng, Carlos Hernandez, Lee-Ping Wang, Kalli Kappel, Amir Barati Farimani

Membrane fusion, the process by which neuronal exocytosis and infection by enveloped viruses occur, has been notoriously difficult to characterize at a molecular level. Part of the problem is that the underlying reaction that fusion proteins catalyze is not fully understood. The development of robust predictive models for the mechanism of lipid membrane fusion and its catalysis by viral fusion proteins will greatly aid in the understanding of the underlying physical process and how to effectively target it with antiviral agents. Simulations with the Gromacs software package will be used to generate high-fidelity models of fusion in experimental model systems, and predict the catalytic mechanism of influenza fusion proteins.

http://pande.stanford.edu/