Bulletin of the American Physical Society
APS March Meeting 2011
Volume 56, Number 1
Monday–Friday, March 21–25, 2011; Dallas, Texas
Abstract: S1.00070 : Simulation of DNA Electrophoresis by Coarse-Grained Hybrid Molecular Dynamics Approach
Author:
Simulation of DNA electrophoresis facilitates the design of DNA separation
devices. Various methods have been explored for simulating DNA
electrophoresis and other processes using implicit and explicit solvent
models. Explicit solvent models are highly desired but their applications
may be limited by high computing cost in simulating large number of solvent
particles. In this work, a coarse-grained hybrid molecular dynamics (CGH-MD)
approach was introduced for simulating DNA electrophoresis in explicit
solvent of large number of solvent particles. CGH-MD was further applied to
the simulation of DNA electrophoresis in polymer solution and in a
well-studied nanofluidic device. Simulation results are consistent with
observations and reported simulation results, suggesting that CGH-MD is
potentially useful for studying electrophoresis of macromolecules and
assemblies in nano-fluidic, micro-fluidic, and microstructure array systems
that involve extremely large number of solvent particles, non-uniformly
distributed electrostatic interactions, bound and sequestered water
molecules.
To cite this abstract, use the following reference: http://meetings.aps.org/link/BAPS.2011.MAR.S1.70
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