Eur. Phys. J. Special Topics 227, 1639-1655 (2019)
https://doi.org/10.1140/epjst/e2019-800189-3

Regular Article

Modeling the current modulation of dsDNA in nanopores – from mean-field to atomistic and back

Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany

^a e-mail: fweik@icp.uni-stuttgart.de
^b e-mail: holm@icp.uni-stuttgart.de

Received: 21 October 2018
Received in final form: 19 November 2018
Published online: 8 March 2019

Abstract

All-atom molecular dynamics (MD) simulations of double stranded DNA (dsDNA) translocating through a cylindrical nanopore by Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] have revealed that ions close to the surface of the DNA experience an additional friction contribution when compared to their bulk value. This friction is a key ingredient in reproducing the 2006 experimentally observed current modifications by Smeets and coworkers. While these findings were already incorporated into a coarse-grained model by Weik et al. [J. Chem. Phys. 145, 194106 (2016)], we now present an extended mean-field model for solving the electrokinetic equations of a dsDNA confined to a structureless cylindrical pore. This is done by incorporating a suitably constructed friction term into the Nernst-Planck equation. Solving the modified electrokinetic equations using a finite element method, we demonstrate that this model is able to reproduce experimental and atomistic MD results for dsDNA current modulations. The advantage of our model is that it allows a fast evaluation of new geometric arrangements of the DNA within the cylinder.