Open AccessMultiscale Coupling of Molecular Dynamics and Hydrodynamics: Application to DNA Translocation through a Nanopore
Author(s) -
Maria Fyta,
Simone Melchionna,
Efthimios Kaxiras,
Sauro Succi
Publication year - 2006
Publication title -
multiscale modeling and simulation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.037
H-Index - 70
eISSN - 1540-3467
pISSN - 1540-3459
DOI - 10.1137/060660576
Subject(s) - nanopore , mesoscopic physics , molecular dynamics , lattice boltzmann methods , langevin dynamics , multiscale modeling , dissipative particle dynamics , statistical physics , context (archaeology) , brownian dynamics , chemical physics , coupling (piping) , macromolecule , physics , polymer , materials science , chemistry , nanotechnology , computational chemistry , brownian motion , thermodynamics , paleontology , nuclear magnetic resonance , quantum mechanics , biology , metallurgy , biochemistry
We present a multiscale approach to the modeling of polymer dynamics in thepresence of a fluid solvent. The approach combines Langevin Molecular Dynamics(MD) techniques with a mesoscopic Lattice-Boltzmann (LB) method for the solventdynamics. A unique feature of the present approach is that hydrodynamicinteractions between the solute macromolecule and the aqueous solvent arehandled explicitly, and yet in a computationally tractable way due to the dualparticle-field nature of the LB solver. The suitability of the present LB-MDmultiscale approach is demonstrated for the problem of polymer fasttranslocation through a nanopore. We also provide an interpretation of ourresults in the context of DNA translocation through a nanopore, a problem thathas attracted much theoretical and experimental attention recently.Comment: 18 pages, 8 figure
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