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The European Physical Journal Special Topics

, Volume 227, Issue 14, pp 1639–1655 | Cite as

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

  • Florian WeikEmail author
  • Kai Szuttor
  • Jonas Landsgesell
  • Christian HolmEmail author
Regular Article
  • 17 Downloads
Part of the following topical collections:
  1. Particle Methods in Natural Science and Engineering

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.

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Copyright information

© EDP Sciences, Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Institute for Computational Physics, University of StuttgartStuttgartGermany

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