Brownian dynamics (BD) is a stochastic simulation method that can quantitatively describe the non-equilibrium behavior of long polymers (∼1 micron contour length) over long time scales (∼1 s). With the increasing use of nanofluidic and microfluidic devices for the handling of biopolymers such as DNA, BD has the potential to be a powerful design tool for the separation and transport processes carried out in these devices. As a coarse-grained simulation method, BD also serves as a natural bridge between atomistic and continuum modeling. In this talk, an introduction to the Brownian dynamics simulation method will be given along with simulation results for some applications of current interest. The introduction will review basic molecular models for polymers (bead-rod, bead-spring) and the stochastic differential equations used to describe their dynamics. The applications will focus on polyelectrolyte adsorption and electrophoresis.

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