Ultra-Coarse-Grained Simulations of Biomolecular Processes at the Petascale

Gregory Voth, University of Chicago

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Gregory Voth, Robert Brunner, Anand Srivastava, Glen Hocky, Yuxing Peng, Amanda Jonsson, Anton Sinitskiy, John Grime, John Savage, Sang Yun Lee, Morris Cohen, Joseph Baker, Ruibin Liang, Jared Ostmeyer, Avisek Das, Aram Davtyan, Zachary Jarin, Anirban Polley, Rui Sun, Aleksander Durumeric, Tamara Bidone, Zhi Wang, Alexander Pak, Jesper Madsen, Dudu Tong, Alvin Yu, Paul Calio

The research team uses Blue Waters to study biomolecular systems. The three planned studies share a common simulation method, where simulations of coarse-grained models of molecules are used to understand the large-scale behavior of the molecular structures and to identify regions where full-resolution simulations of small parts of the structure are needed to understand detailed behavior. The NAMD, Gromacs, LAMMPS, and MSCGFM codes are employed. The three areas of investigation are:

• Key stages of the replication cycle of HIV
• The dynamic structural changes induced in cell membranes under the influence of remodeling of the ENTH (Epsin N-terminal homology) domain. This is significant in such processes as cell movement and fusion and vesicle budding.
• The early stage of the formation of clathrin-coated pits, areas of the cell’s plasma membrane that are made up of small protein-coated vesicles. This is an important stage in the process by which cells transfer nutrients, import signaling receptors, and to clean up the debris left by tissue inflammation.

http://vothgroup.uchicago.edu