dorsal/arxiv
View SchemaMultiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore
| Authors | Maria G. Fyta, Simone Melchionna, Efthimios Kaxiras, Sauro Succi |
|---|---|
| Categories | |
| ArXiv ID | physics/0701029 |
| URL | https://arxiv.org/abs/physics/0701029 |
| DOI | 10.1137/060660576 |
| Journal | Multiscale Modeling and Simulation, 5 (2006) 1156 |
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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"abstract": "We present a multiscale approach to the modeling of polymer dynamics in the\npresence of a fluid solvent. The approach combines Langevin Molecular Dynamics\n(MD) techniques with a mesoscopic Lattice-Boltzmann (LB) method for the solvent\ndynamics. A unique feature of the present approach is that hydrodynamic\ninteractions between the solute macromolecule and the aqueous solvent are\nhandled explicitly, and yet in a computationally tractable way due to the dual\nparticle-field nature of the LB solver. The suitability of the present LB-MD\nmultiscale approach is demonstrated for the problem of polymer fast\ntranslocation through a nanopore. We also provide an interpretation of our\nresults in the context of DNA translocation through a nanopore, a problem that\nhas attracted much theoretical and experimental attention recently.",
"arxiv_id": "physics/0701029",
"authors": [
"Maria G. Fyta",
"Simone Melchionna",
"Efthimios Kaxiras",
"Sauro Succi"
],
"categories": [
"physics.bio-ph",
"physics.comp-ph"
],
"doi": "10.1137/060660576",
"journal_ref": "Multiscale Modeling and Simulation, 5 (2006) 1156",
"title": "Multiscale coupling of molecular dynamics and hydrodynamics: application to DNA translocation through a nanopore",
"url": "https://arxiv.org/abs/physics/0701029"
},
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