Parallel multiscale modeling of biopolymer dynamics with hydrodynamic correlations

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dc.creatorFyta, Maria
dc.creatorSircar, Jayanta
dc.creatorKaxiras, Efthimios
dc.creatorMelchionna, Simone
dc.creatorBernaschi, Massimo
dc.creatorSucci, Sauro
dc.date2007-11-16
dc.date.accessioned2026-07-07T09:23:11Z
dc.date.available2026-07-07T09:23:11Z
dc.descriptionWe employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic 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. We describe an efficient parallel implementation of the method which exhibits excellent scalability on the Blue Gene platform. We investigate both dynamical and statistical aspects of the translocation process 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.
dc.description10 pages, 5 figures, 3 tables. to appear in International Journal for Multiscale Computational Engineering
dc.identifierhttps://arxiv.org/abs/0711.2665
dc.identifierhttp://arxiv.org/abs/0711.2665
dc.identifiervol. 6, issue 1 (2008)
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/155643
dc.subjectComputational Physics
dc.subjectBiological Physics
dc.titleParallel multiscale modeling of biopolymer dynamics with hydrodynamic correlations
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