dorsal/arxiv
View SchemaMultiscale modeling of biopolymer translocation through a nanopore
| Authors | Maria Fyta, Simone Melchionna, Efthimios Kaxiras, Sauro Succi |
|---|---|
| Categories | |
| ArXiv ID | physics/0703086 |
| URL | https://arxiv.org/abs/physics/0703086 |
| Journal | Lecture Notes in Computer Science, 4487 786 (2007) |
Abstract
We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic Langevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB) method for the solvent dynamics, explicitly taking into account the interactions of the molecule with the surrounding fluid. Both dynamical and statistical aspects of the translocation process were investigated, by simulating polymers of various initial configurations and lengths. For a representative molecule size, we explore the effects of important parameters that enter in the simulation, paying particular attention to the strength of the molecule-solvent coupling and of the external electric field which drives the translocation process. Finally, we explore the connection between the generic polymers modeled in the simulation and DNA, for which interesting recent experimental results are available.
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"abstract": "We employ a multiscale approach to model the translocation of biopolymers\nthrough nanometer size pores. Our computational scheme combines microscopic\nLangevin molecular dynamics (MD) with a mesoscopic lattice Boltzmann (LB)\nmethod for the solvent dynamics, explicitly taking into account the\ninteractions of the molecule with the surrounding fluid. Both dynamical and\nstatistical aspects of the translocation process were investigated, by\nsimulating polymers of various initial configurations and lengths. For a\nrepresentative molecule size, we explore the effects of important parameters\nthat enter in the simulation, paying particular attention to the strength of\nthe molecule-solvent coupling and of the external electric field which drives\nthe translocation process. Finally, we explore the connection between the\ngeneric polymers modeled in the simulation and DNA, for which interesting\nrecent experimental results are available.",
"arxiv_id": "physics/0703086",
"authors": [
"Maria Fyta",
"Simone Melchionna",
"Efthimios Kaxiras",
"Sauro Succi"
],
"categories": [
"physics.bio-ph",
"physics.comp-ph"
],
"journal_ref": "Lecture Notes in Computer Science, 4487 786 (2007)",
"title": "Multiscale modeling of biopolymer translocation through a nanopore",
"url": "https://arxiv.org/abs/physics/0703086"
},
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