Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse‐grained hybrid molecular dynamics approach
Simulation of DNA electrophoresis in systems of large number of solvent particles by coarse‐grained hybrid molecular dynamics approach
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DOI：
10.1002/jcc.21081
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发表时间：
2009-03
影响因子：
3
通讯作者：
Rong Wang;Jian-Sheng Wang;Gui-rong Liu;Jongyoon Han;Yu Zong Chen
中科院分区：
文献类型：
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作者：
Rong Wang;Jian-Sheng Wang;Gui-rong Liu;Jongyoon Han;Yu Zong Chen
DNA电泳的模拟为DNA分离设备的设计提供了便利。已经探索了各种方法来使用隐式和显式溶剂模型来模拟DNA电泳和其他过程。显式溶剂模型是非常理想的模型，但其在模拟大量溶剂颗粒时的高计算量可能会限制其应用。本文采用粗粒杂化分子动力学(CGH-MD)方法模拟了大量溶剂颗粒在显性溶剂中的DNA电泳图。CGH-MD在聚合物溶液的模拟和柱状纳米管中电荷非均匀分布的计算中得到了验证，与观测结果和更严格的计算方法符合得很好，而且计算量明显低于其他显式溶剂方法。CGH-MD被进一步应用于模拟DNA在聚合物溶液中的电泳和在一个研究得很好的纳米流体装置中。模拟结果与观察结果和已报道的模拟结果相一致，表明CGH-MD可用于研究纳米流体、微流体和微结构阵列体系中的大分子和组件的电泳性，这些体系涉及大量的溶剂颗粒、非均匀分布的静电相互作用、结合和隔离的水分子。©2008威利期刊公司J Comput Chem 2009
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. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009