Molecular dynamics simulation of ss-DNA translocation between copper nanoelectrodes incorporating electrode charge dynamics
Molecular dynamics simulation of ss-DNA translocation between copper nanoelectrodes incorporating electrode charge dynamics
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DOI：
10.1021/jp077483e
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发表时间：
2008-02-14
影响因子：
3.3
通讯作者：
Cummings, Peter T.
中科院分区：
文献类型：
--
作者：
Payne, Christina M.;Zhao, Xiongce;Cummings, Peter T.
分子动力学模拟已经被执行，研究单链(ss)-DNA的易位通过纳米级电极之间的纳米级间隙提出的基因组测序装置。在这个项目中，以电极和一小段ss-DNA样本之间的固定间隙宽度作为初始起点，研究了外加电场对易位速度的影响。为了描述水、离子和ss-DNA与纳米级电极之间的静电相互作用，我们应用了电极电荷动力学（ECD）方法。通过密度分布和移位速度与外推实验数据的比较，我们发现与常用的通用力场（UFF）相比，ECD势可以更好地描述金属/非金属静电相互作用。利用ECD电位获得的易位速度与模拟的整体数据一致。
Molecular dynamics simulations have been performed to, study the translocation of single-stranded (ss)-DNA through the nanoscale gap between the nanoscale electrodes of a proposed genomic sequencing device. Using a fixed gap width between the electrodes and a small sample segment of ss-DNA as initial starting points in this project, the effect of applied electric fields on translocation velocity was studied. To describe the electrostatic interactions of the water, ions, and ss-DNA with the nanoscale electrodes, we applied the electrode charge dynamics (ECD) method. Through the density profile and comparison of translocation velocities to extrapolated experimental data, we found the ECD potential to be a better descriptor of the metal/nonmetal electrostatic interactions compared to the commonly used universal force field (UFF). Translocation velocities obtained using the ECD potential were consistent with simulated bulk data.