Title: A fluctuating hydrodynamics based approach for Brownian dynamics

Abstract:
A numerical scheme, named Fluctuating Immersed MATerial (FIMAT) dynamics, for the Brownian motion of rigid particles will be presented. This approach relies on two key ideas. First, we assume that the entire fluid-particle domain is a fluid and then constrain the particle domain to move with a rigid motion. Second, the thermal fluctuations are included in the fluid equations via random stress terms. Solving the fluctuating hydrodynamic equations coupled with the rigid motion constraint results in the Brownian motion of the particles. Our approach can easily address irregularly shaped objects, and can simultaneously resolve their translational and rotational diffusion. The viscous interactions are resolved more accurately in this approach compared to the conventional Brownian dynamics approach. FIMAT can also be extended to accommodate flexible bodies. Thus, this tool could be very convenient to set up mesoscale simulations of complex biomolecules and study its dynamics in variety of scenarios. Some potential applications of interest include studying binding pathways of ligands and dynamics of motor proteins.