title: A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments.
abstract: We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.
authors.affiliation: Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany.
authors.forename: Florian
authors.initials: F
authors.lastname: Weik
authors.affiliation: Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Kesselheim
authors.affiliation: Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Holm
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D009068:Movement / Q000187:drug effects; D011189:Potassium Chloride / Q000494:pharmacology; D015203:Reproducibility of Results; D012997:Solvents / Q000737:chemistry
chemical_list: D012997:Solvents; D011189:Potassium Chloride; D004247:DNA