Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse-grained hybrid molecular dynamics approach.
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 tested in the simulation of a polymer solution and computation of nonuniform charge distribution in a cylindrical nanotube, which shows good agreement with observations and those of more rigorous computational methods at a significantly lower computing cost than other explicit-solvent methods. CGH-MD was further applied to the simulation of DNA electrophoresis in a 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 nanofluidic, microfluidic, and microstructure array systems that involve extremely large number of solvent particles, nonuniformly distributed electrostatic interactions, bound and sequestered water molecules.
Wang
Rong
R
Department of Polymer Science and Engineering, Nanjing National Laboratory of Microstructures, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China. rong_wang73@hotmail.com
Wang
Jian-Sheng
JS
Liu
Gui-Rong
GR
Han
Jongyoon
J
Chen
Yu-Zong
YZ
D003198:Computer Simulation; D004247:DNA / Q000302:isolation & purification*; D004586:Electrophoresis / Q000295:instrumentation / Q000379:methods*; D004867:Equipment Design; D008956:Models, Chemical; D012997:Solvents
D012997:Solvents; D004247:DNA