Capture of rod-like molecules by a nanopore: defining an "orientational capture radius"

Abstract

Both the translational diffusion coefficient $D$ and the electrophoretic mobility $\mu$ of a short rod-like molecule (such as dsDNA) that is being pulled towards a nanopore by an electric field should depend on its orientation. Since a charged rod-like molecule tends to orient in the presence of an inhomogeneous electric field, $D$ and $\mu$ will change as the molecule approaches the nanopore, and this will impact the capture process. We present a simplified study of this problem using theoretical arguments and Langevin Dynamics simulations. In particular, we introduce a new \textit{orientational capture radius} which we compare to the capture radius for the equivalent point-like particle, and we discuss the different physical regimes of orientation during capture and the impact of initial orientations on the capture time.