Multiscale Coupling of Molecular Dynamics and Hydrodynamics: Application to DNA Translocation through a Nanopore

Abstract

We present a multiscale approach to the modeling of polymer dynamics in the presence of a fluid solvent. The approach combines Langevin molecular dynamics ( MD) techniques with a mesoscopic lattice Boltzmann (LB) method for the solvent dynamics. A unique feature of the present approach is that hydrodynamic interactions between the solute macromolecule and the aqueous solvent are handled explicitly, and yet in a computationally tractable way due to the dual particle-field nature of the LB solver. The suitability of the present LB-MD multiscale approach is demonstrated for the problem of polymer fast translocation through a nanopore. We also provide an interpretation of our results in the context of DNA translocation through a nanopore, a problem that has attracted much theoretical and experimental attention recently.