A Few Comments on the Calculation of the Diffusion Tensor Used in
Brownian Dynamics Simulations
Ms. Nuo Wang
Department of Chemistry and Biochemistry and
Center for Theoretical Biological Physics
UC San Diego
The diffusion tensor used in Brownian dynamics simulations is often calculated by the hydrodynamic bead models. The bead models are shown to reproduce the experimental diffusion coefficients (the diagonal tensor elements) of a single macromolecule, but the accuracy of the bead model calculation of the whole one-body or many-body diffusion tensor has not been closely investigated. Such investigation is important because Brownian dynamics simulations usually involve more than one molecule, and the whole diffusion tensor will be used instead of just the diagonal elements. As a first step, we investigated the accuracy of the bead model calculation of the diffusion tensor of two spheres. Our results show that bead models can produce fairly accurate diffusion tensors for two spheres. But its application in Brownian dynamics simulations needs extra caution, as its errors accumulate over time.