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Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore

Maria G. Fyta·Simone Melchionna·Efthimios Kaxiras·Sauro Succi
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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.

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Maria G. Fyta, Simone Melchionna, Efthimios Kaxiras, Sauro Succi. 2007-01-02. Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore. https://doi.org/10.1137/060660576

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