Brownian dynamics simulations of rigid rod-like macromolecular particles flowing in bounded channels

Brownian dynamics simulations have been carried out of the joint probability distribution functions (PDF), P(ξ,θ), for macromolecular rod-like particles in the limit of infinite dilution in a solution under hydrodynamic linear flow. These PDF are calculated as a function of the orientations of the rod-like particles, θ and of the positions, ξ, of their centres of mass measured from a solid surface boundary. These simulations are developed in the neighbourhood of a solid surface boundary and in a confined space bounded by two such boundaries. They are constructed for a wide range of key quantities depicting the ratio of the hydrodynamic shear rate to the rotational Brownian diffusion coefficient. The notion of restitution is introduced to develop an algorithm for the consequences of the Brownian and hydrodynamic collisions of these macromolecules with impenetrable solid surface boundaries, which approach applies to a wide range of surfaces and macromolecules. The simulation results for the PDF distributions are given for typically low and high hydrodynamic flow conditions, and their properties are discussed. We show, for example, for low shear rates that a phenomenon which we call Brownian restitution enables the macromolecular rods to pass through a channel that is narrower than the rod length.