Melnikov Dmitriy V, Nikolaev Alexey, Leburton Jean-Pierre, Gracheva Maria E
Department of Physics, Clarkson University, Potsdam, NY, USA.
Methods Mol Biol. 2012;870:187-207. doi: 10.1007/978-1-61779-773-6_11.
We have developed a two-level computational model that enables us to calculate electrostatic fields created by a semiconductor membrane submerged in electrolytic solution and investigate the effects of these fields on the dynamics of a polymer translocating through a nanopore in the membrane. In order to calculate the electrostatic potentials and the ionic concentrations in a solid-state nanopore, we have self-consistently solved Poisson equation within the semiclassical approximation for charge carrier statistics in the membrane and electrolyte. The electrostatic potentials obtained from these simulations are then used in conjunction with Langevin (Brownian) dynamics to model polymer translocation through the nanopore. In this work, we consider single-stranded DNA (ssDNA) translocation through semiconductor membranes consisting of heavily doped p- and n-layers of silicon forming a pn-junction which is capable of creating strong electric fields. We show that the membrane electric field controls dynamics of a biomolecule inside the channel, to either momentarily trap it, slow it down, or allow it to translocate at will.
我们开发了一种两级计算模型，该模型使我们能够计算浸没在电解液中的半导体膜所产生的静电场，并研究这些场对聚合物通过膜中纳米孔转运动力学的影响。为了计算固态纳米孔中的静电势和离子浓度，我们在膜和电解质中电荷载流子统计的半经典近似范围内自洽地求解了泊松方程。然后，将这些模拟得到的静电势与朗之万（布朗）动力学结合使用，以模拟聚合物通过纳米孔的转运。在这项工作中，我们考虑单链DNA（ssDNA）通过由重掺杂的p型和n型硅层组成的半导体膜的转运，这些硅层形成了能够产生强电场的pn结。我们表明，膜电场控制通道内生物分子的动力学，使其要么瞬间捕获、减慢速度，要么随意转运。
