TCBG Seminar

A First-Passage Algorithm for Brownian Dynamics

James A. Given
Center for Advanced Research in Biotechnology and Biotechnology Division, NIST
Gaithersburg, MD

Monday, October 14, 1996
3:00 pm (CT)
3269 Beckman Institute


First-passage algorithms were previously employed to treat random diffusion in a complex, two-phase environment. These algorithms utilize an efficient diffusion propagator selected from a library of Laplacian Green's functions in order to traverse, in a single propagation event, a large portion of the diffusing particle's environment which is known to be free of interaction sites. This approach was shown to provide the most accurate calculations currently available of translational hydrodynamic friction of an irregularly shaped object, e.g. a macromolecule. In this paper, we introduce a powerful extension of this class of algorithms: we show how to solve a general, stationary Smoluchowski equation by shifting the force-field terms, i.e., all the terms other than the Laplacian term, to the RHS and treating them as source terms to be determined self-consistently. These field- induced source terms then prescribe the rate at which diffusing particles subsequently undergo force-free diffusion in the environment. We then accelerate treatment of this diffusion process by using the original high-speed first-passage algorithm. In particular, we provide a detailed algorithm for Brownian dynamics of a small, charged ligand in the vicinity of a macromolecule.

Tea and coffee will be served in R3151 Beckman Institute at 2:15pm.

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