Driven translocation of a semi-flexible chain through a nanopore: A Brownian dynamics simulation study in two dimensions
Driven translocation of a semi-flexible chain through a nanopore: A Brownian dynamics simulation study in two dimensions
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DOI：
10.1063/1.4807002
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发表时间：
2013-05-28
影响因子：
4.4
通讯作者：
Bhattacharya, Aniket
中科院分区：
文献类型：
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作者：
Adhikari, Ramesh;Bhattacharya, Aniket
我们使用 Langevin 动力学模拟在孔内存在外部偏置 F 的情况下研究半柔性聚合物链通过二维纳米级孔的易位动力学。对于本文考虑的链长度 N 和刚度参数 kappa(b)，我们观察到平均首次通过时间与 l(p)(aN) 类似，其中 kappa(b) 和 l(p) 分别是刚度参数和持久长度，a(N) 是一个具有弱 N 依赖性的常数。我们监测顺式室中最后一个单体 x(N)(t) 的时间依赖性，并直接从类似于最近非平衡 TP 理论 [T.坂上，物理学家。 Rev. E 76, 021803 (2007)] 及其对布朗动力学张力传播理论的修改 [T. Ikonen、A. Bhattacharya、T. Ala-Nissila 和 W. Sung，物理学家。修订版 E 85, 051803 (2012)； J.化学。物理。 137, 085101 (2012)]最初是为了研究完全柔性链的易位而开发的。我们还从易位坐标 s（即孔内的单体）的等待时间分布 W(s) 的峰值位置测量 t(tp)，并明确证明沿着易位链的链主链的潜在 TP 图片对于半柔性链也有效。根据模拟数据，我们确定了 t(tp) 对链持久长度 l(p) 的依赖性，并表明比率 t(tp)/ 与偏差 F 无关。(C) 2013 AIP Publishing LLC。
We study translocation dynamics of a semi-flexible polymer chain through a nanoscopic pore in two dimensions using Langevin dynamics simulation in presence of an external bias F inside the pore. For chain length N and stiffness parameter kappa(b) considered in this paper, we observe that the mean first passage time increases as similar to l(p)(aN), where kappa(b) and l(p) are the stiffness parameter and persistence length, respectively, and a(N) is a constant that has a weak N dependence. We monitor the time dependence of the last monomer x(N)(t) at the cis compartment and calculate the tension propagation time (TP) t(tp) directly from simulation data for < x(N)(t)> similar to t as alluded in recent nonequlibrium TP theory [T. Sakaue, Phys. Rev. E 76, 021803 (2007)] and its modifications to Brownian dynamics tension propagation theory [T. Ikonen, A. Bhattacharya, T. Ala-Nissila, and W. Sung, Phys. Rev. E 85, 051803 (2012); J. Chem. Phys. 137, 085101 (2012)] originally developed to study translocation of a fully flexible chain. We also measure t(tp) from peak position of the waiting time distribution W(s) of the translocation coordinate s (i.e., the monomer inside the pore), and explicitly demonstrate the underlying TP picture along the chain backbone of a translocating chain to be valid for semi-flexible chains as well. From the simulation data, we determine the dependence of t(tp) on chain persistence length l(p) and show that the ratio t(tp)/ is independent of the bias F. (C) 2013 AIP Publishing LLC.