Citation: 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, ;2019, 50(12): 1331-1337. doi: 10.11777/j.issn1000-3304.2019.19107 shu

Computer Simulation of a Single Polymer Chain Translocating through a Pore in an Asymmetric Particle Bath

Yan Wang ¹ ,
Wen-jie Wang ² ,
Yi-qi Xia ² ,
Hui-shu Li ^2,,

1.
School of Physics, Nanjing University, Nanjing 210093
2.
Center for Soft Condensed Matter Physics & Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006

Corresponding author: Hui-shu Li, hsli@suda.edu.cn
Received Date: 22 May 2019
Revised Date: 4 July 2019

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.
- Langevin dynamics,
- Polymer chain,
- Active particle,
- Translocation mechanism
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