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

• Published in: The Journal of chemical physics Vol. 152; no. 14; p. 144902
• Main Authors: Qiao, Le, Slater, Gary W
• Format: Journal Article
• Language: English
• Published: United States 14.04.2020
• ISSN: 1089-7690
• DOI: 10.1063/5.0002044

Both the translational diffusion coefficient D and the electrophoretic mobility μ of a short rod-like molecule (such as dsDNA) that is being pulled toward 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 μ 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 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.