Modeling the current modulation of dsDNA in nanopores – from mean-field to atomistic and back
Institute for Computational Physics, University of Stuttgart, Stuttgart, Germany
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Received in final form: 19 November 2018
Published online: 8 March 2019
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.
© EDP Sciences, Springer-Verlag GmbH Germany, part of Springer Nature, 2019