Brownian Dynamics Simulations of Biological Molecules

Brownian dynamics (BD) is a technique for carrying out computer simulations of physical systems that are driven by thermal fluctuations. Biological systems at the macromolecular and cellular level, while falling in the gap between well-established atomic-level models and continuum models, are especially suitable for such simulations. We present a brief history, examples of important biological processes that are driven by thermalmotion, and those that have been profitably studied by BD. We also present some of the challenges facing developers of algorithms and software, especially in the attempt to simulate larger systems more accurately and for longer times.