Boëder PDF Brownian simulations for macromolecular rod-like particles near uneven solid surfaces

A molecular dynamics simulation is presented to calculate the Probability Distribution Functions (PDF) for the spatial positions and angular orientations of macromolecular rod-like particles in dilute solutions, under hydrodynamic flow, in the vicinity of uneven solid boundaries. The Brownian and hydrodynamic restitution model for ideally flat surfaces is generalized to simulate the diffusive collisions between the macromolecular particles and an uneven solid surface. Two types of uneven surfaces are particularly considered: the periodic grating and the random rough, with characteristic profiles of heights and lateral variations. Different from ideally flat surfaces, the simulation results demonstrate that uneven surfaces have characteristic depletion layers, and characteristic and variable PDF. This is the case under varying conditions of hydrodynamic flow, Brownian movement and diffusive collisions. These characteristics uniquely identify Boeder PDF signatures for the uneven surface topography.