Department of Mechanical Engineering, Dong-A University, Saha-gu, Busan, South Korea.
J Chem Phys. 2011 Aug 7;135(5):055103. doi: 10.1063/1.3622490.
We conducted a numerical study on the translocation of a biopolymer from the cis side to the trans side of a membrane through a synthetic nano-pore driven by an external electric field in the presence of hydrodynamic interactions (HIs). The motion of the polymer is simulated by 3D Langevin dynamics technique using a worm-like chain model of N identical beads, while HI between the polymer and fluid are incorporated by the lattice Boltzmann equation. The translocation process is induced by electrophoretic force, which sequentially straightens out the folds of the initial random configuration of the polymer chain on the cis side. Our simulation results on translocation time and velocity are in good quantitative agreement with the corresponding experimental ones when the surface charge on the nano-pore and the HI effect are considered explicitly. We found that the translocation velocity of each bead inside the nano-pore mainly depends upon the length of the straightened portion of the polymer in forced motion near the pore. We confirmed this by a theoretical formula. After performing simulations with different pore lengths, we observed that translocation velocity mainly depends upon the applied potential difference rather than upon the electric field inside the nano-pore.
我们通过 3D Langevin 动力学技术模拟了聚合物的运动，使用 N 个相同珠子的蠕虫链模型，同时通过格子玻尔兹曼方程将聚合物和流体之间的流体动力学相互作用（HIs）纳入考虑。聚合物的迁移过程是由电泳力引起的，该力依次将聚合物链在 cis 侧的初始随机构型的折叠拉直。当考虑纳米孔表面电荷和 HIs 效应时，我们的迁移时间和速度的模拟结果与相应的实验结果非常吻合。我们发现，纳米孔内每个珠子的迁移速度主要取决于聚合物在强制运动中靠近孔的拉直部分的长度。我们通过一个理论公式证实了这一点。在进行不同孔径的模拟后，我们观察到迁移速度主要取决于施加的电势差，而不是纳米孔内的电场。
