Hydrodynamic effects in the capture of rod-like molecules by a nanopore

Abstract

In the approach of biomolecules to a nanopore, it is essential to capture the effects of hydrodynamic anisotropy of the molecules and the near-wall hydrodynamic interactions which hinder their diffusion. We present a detailed theoretical analysis of the behaviour of a rod-like molecule attracted electrostatically by a charged nanopore. We first estimate the time scales corresponding to Brownian and electrostatic translations and reorientation. We find that Brownian motion becomes negligible at distances within the pore capture radius, and numerically determine the trajectories of the nano-rod in this region to explore the effects of anisotropic mobility. This allows us to determine the range of directions from the pore in which hydrodynamic interactions with the boundary shape the approach dynamics and need to be accounted for in detailed modelling.