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

TL;DR

This paper investigates how the orientation of rod-like molecules affects their capture by nanopores, introducing an 'orientational capture radius' to better understand the physical regimes and initial orientation effects during the process.

Contribution

The study introduces the concept of an 'orientational capture radius' and compares it to the point-like particle capture radius, providing new insights into orientation-dependent capture dynamics.

Findings

The orientational capture radius differs from the point-like particle radius.

Molecular orientation significantly influences capture time.

Different physical regimes of orientation during capture are identified.

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.