Brownian dynamics is a powerful tool for performing large-scale molecular simulations. By averaging out the less important degrees of freedom, e.g. those of the solvent, with stochastic variables, specific mesoscopic level properties can be efficiently explored through brownian dynamics. Here brownian dynamics is further exploited to simulate protein dynamics with a coarse-grained protein force field developed by Kim and Hummer (2008). And a faster 'bead filling' hydrodynamics method with hydrodynamic shielding effect consideration is incorporated into the well-established brownian dynamics algorithm developed by Ermak and McCammon (1978). The success of brownian dynamics with coarse-grained protein model and a faster hydrodynamics method leads to low computational-cost simulations of diffusion processes of protein complexes in mesoscopic cellular environments, such as those in signaling transduction pathways.

Coarse-grained brownian dynamics with a better hydrodynamics method

243rd National Meeting (2012)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.