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

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.

Automated summary

In this study, we conduct a detailed theoretical analysis of the behavior of rod-like molecules attracted by charged nanopores, estimating time scales for Brownian and electrostatic translations. We find that Brownian motion becomes negligible at certain distances, numerically determining trajectories of the nano-rod in the pore region to explore the effects of anisotropic mobility. This helps determine the range of directions from the pore where hydrodynamic interactions with the boundary shape approach dynamics, requiring consideration in detailed modeling.