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Computer Simulation of a Single Polymer Chain Translocating through a Pore in an Asymmetric Particle Bath
- Acta Polymerica Sinica Vol. 50, Issue 12, Pages: 1331-1337(2019)
- 作者机构：
1.南京大学物理学院 南京 210093
2.苏州大学物理科学与技术学院 软凝聚态物理及交叉研究中心 苏州 215006
- 作者简介：
- 基金信息：
DOI：10.11777/j.issn1000-3304.2019.19107
CLC：Published：2019-12，
Published Online：27 August 2019，
Received：22 May 2019，
Revised：4 July 2019，
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Yan Wang, Wen-jie Wang, Yi-qi Xia, Hui-shu Li. Computer Simulation of a Single Polymer Chain Translocating through a Pore in an Asymmetric Particle Bath. [J]. Acta Polymerica Sinica 50(12):1331-1337(2019)
Yan Wang, Wen-jie Wang, Yi-qi Xia, Hui-shu Li. Computer Simulation of a Single Polymer Chain Translocating through a Pore in an Asymmetric Particle Bath. [J]. Acta Polymerica Sinica 50(12):1331-1337(2019) DOI： 10.11777/j.issn1000-3304.2019.19107.
摘要
采用分子动力学模拟方法研究高分子链在不对称粒子浴中的穿孔行为，重点分析高分子链的向左(活性粒子浴)穿孔概率和平均穿孔时间与粒子活性力之间的关系. 研究发现分子链进入活性粒子浴的概率随着活性粒子活性力的增大而迅速增加，并最终达到饱和(接近1)；而高分子链的平均穿孔时间会随着活性力的增大呈现先减小后增大的趋势. 这种穿孔时间变化的物理机制是：活性力的增大会导致分子链内应力增大，从而产生向左的拖拽力，但是当活性力增大到一定值后，活性粒子会贴边形成结晶态，抑制活性粒子的运动，增加分子链的穿孔时间. 此外，我们发现在小驱动力时，穿孔时间满足对数正态分布. 进一步探究了链长效应对高分子链穿孔行为的影响. 模拟结果表明：在小驱动力区间下，分子链越长，活性力越大，分子链中心点受向左的拖拽力越大，越容易左穿.
Abstract
Polymer translocation through a nanopore is of ubiquitous importance in many biological processes such as DNA and mRNA translocation through nuclear pores
protein transport across membrane channels. In real systems
polymer translocation process usually involves complex environments. One typical example is that there present different environments inside and outside the nanopore. It is interesting to study polymer translocation in an asymmetric environment. Here
Langevin dynamics simulation is performed to study polymer translocation through nanopore in an asymmetry bath of active particles and passive particles. The polymer is modeled by a bead-spring chain and the active particle is modeled by active Brownian particles with inherent orientation. We find that with the increase of the particle activity
the translocation probability of polymer chain toward active bath increases quickly
and finally reaches a saturation value. This may be because active particles exert a drag force on the polymer chain. Additionally
as the bath activity increases
the mean translocation time of polymer chain decreases fast and then increases slightly. The physical mechanism of the non-monotonic change is that the increase of the bath activity will induce the increase of tension in polymer chain
resulting in a drag force toward active region. However
when the bath activity is large enough
crystalline layers of active particles are formed near the boundary
which inhibits the motion of active particles and increases translocation time of the chain. Furthermore
it is found that the profile of translocation time at small active force can be fitted by log-normal distribution. Moreover
we also pay attention to the length effect of polymer chain on translocation mechanism at moderate active forces. The longer polymer chain and the higher activity of particles can lead to a larger value of drag force on the polymer chain. The results may provide an insight into the translocation behavior of polymer chain
and help understand the non-equilibrium processes in living organisms.
关键词
分子动力学方法高分子链活性粒子穿孔机理
Keywords
Langevin dynamicsPolymer chainActive particleTranslocation mechanism
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