Molecular Chaperone-Dependent Polymer Translocation through Nanopores: The Effects of Chaperone Concentration and Chaperone-Polymer Interaction

The polymer translocation through a nanopore from a donor space(or named cis side) to a receiver space(trans side) in the chaperone-induced crowded environment has attracted increasing attention in recent years due to its significance in biological systems and technological applications. In this work, we mainly focus on the effects of chaperone concentration and chaperone-polymer interaction on the polymer translocation. By assuming the polymer translocation to be a quasi-equilibrium process, the free energy F of the polymer can be estimated by Rosenbluth-Rosenbluth method and then the translocation time τ can be calculated by Fokker-Plank equation based on the obtained free energy landscape. Our calculation results show that the translocation time can be controlled by independently tuning the chaperone concentration and chaperone-polymer interaction at the cis side or the trans side. There exists a critical chaperone-polymer attraction ε~*=-0.2 at which the volume exclusion and interaction effects of the chaperone can balance each other. Additionally, we also find that at large chaperone-polymer attraction, the translocation time is mainly governed by the diffusion coefficient of the polymer.

Polymer Translocation

The translocation of a polymer through a pore that is much smaller than its size is a fundamental and actively researched topic in polymer physics.An understanding of the principles governing polymer translocation provides important guidance for various practical applications,such as the separation and purification of polymers,nanopore-based single-molecule deoxyribonucleic acid/ribonucleic acid(DNA/RNA)sequencing,transmembrane transport of DNA or RNA,and infection of bacterial cells by bacteriophages.The past several decades have seen great progresses on the study of polymer translocation.Here we present an overview of theoretical,experimental,and simulational stduies on polymer translocation,focusing on the roles played by several important factors,including initial polymer conformations,external fields,polymer topology and architectures,and confinement degree.We highlight the physical mechanisms of different types of polymer translocations,and the main controversies about the basic rules of translocation dynamics.We compare and contrast the behaviors of force-induced versus flow-induced translocations and the effects of unknotted versus knotted polymers.Finally,we mention several opportunities and challenges in the study of polymer translocation.

Effect of Interaction upon Translocation of Confined Polymer Chain Through Nanopore

The effect of the interaction between nanopore and chain monomer on the translocation of a single polymer chain confined in a finite size square through an interacting nanopore to a large space has been studied by two-dimensional bond fluctuation model with Monte Carlo simulation. Results indicate that the free energy barrier before the successful translocation of the chain depends linearly on the chain length as well as the nanopore length for different pore-polymer interaction, and the attractive interaction reduces the free energy barrier, leading to the reduction of the average trapping time.

Translocation of Polymer Chains Through a Channel with Complex Geometries

The elastic behavior of a single chain transporting through complex channel which can be seen as the combination of three different channels （left channel, middle channel, and right channel, respectively） is investigated using the new pruned-enriched Rosenbluth method with importance sampling. The elastic force during the translocation process is calculated. At the entrance into the middle channel, there is the first plateau in the curve of the elastic force f （f〉0） versus x, here x represents the position of the first monomer along the x-axis direction. When the first monomer moves to a certain position, a second plateau is observed with the elastic force f〈0, which represents spontaneous translocation. The free energy difference between the subchain in the right channel and the subchain in the left channel may drive the transloeation. The influence of chain length and width of the left and right channels on the translocation process are also investigated. From the simulation results, more detailed explanations for the reason why the component translocation time is not the same for different channels can be presented.

Simulation Study on Translocation of Confined Chain Through Interacting Nanopore

The translocation of a confined polymer chain through an interacting nanopore has been studied using two-dimensional bond fluctuation model with Monte Carlo dynamics. For different pore-polymer interaction, the average escaping time （Tesc） of the polymer chain through the nanopore, increases roughly linearly with the chain length and the nanopore length~ respectively. However~ the large repulsive and attractive pore-polymer interaction adds the difficulty of the monomers of the chain entering and leaving the nanopore, respectively, leading to the nonmonotonical dependence of （Tesc） on the pore-polymer interaction. The detailed translocation dynamics of the chain through the interacting nanopore is inves- tigated too.

Translocation of Heterogeneous Flexible Polymers Assisted by Binding Particles

A polymer chain usually contains two or more types of monomeric species from the perspective of polymer chemistry,which poses achallenge to the understanding of structure-property relationships.It is of course true in the field of polymer translocation.In the present work,Iinvestigate the translocation dynamics of heterogeneous flexible polymers composed of two types of monomers labeled A and B through ananopore assisted by binding particles(BPs)by using the coarse-grained Langevin dynamics simulations in two-dimensional domains.Specifically,multiblock copolymers with different block lengths and monomeric components are considered.I critically examine how thetranslocation dynamics responds to the variations in the block length and the monomeric content.Interestingly,it is found that the periodicstructure of a multiblock copolymer causes an obvious fingerprint feature in the residence time of individual monomers in which the number ofpeaks is exactly equal to the number of blocks.These findings provide a basic understanding about the sequence-dynamics relationship for theBPs-assisted translocation of heterogeneous flexible polymers.

Effect of Hydrodynamic Interaction on Flow-induced Polymer Translocation Through a Nanotube

We investigated the effect of hydrodynamic interaction（HI） on flow-induced polymer translocation through a nanotube by Brownian dynamics simulations. Whether there is HI in the simulation system is separately controlled by using different diffusion tensors. It is found that HI has no effect on critical velocity flux for long po- lymer chains due to the competition between more drag force and the hindrance of chain stretching from HI, however, HI broadens the transition interval. In addition, for flow-induced polymer translocation with HI, the critical velocity flux firstly slowly decreases with the increase of chain length and then becomes identical to that of it without HI, that is, the critical velocity flux is independent of chain length. At the same time, HI also accelerates the translocation process and makes the relative variation amplitude of single bead translocation time smaller. In fact, HI can enhance the intrachain cooperativity to make the whole chain obtain more drag force from fluid field and hinder chain stret- ching, both of which play an important role in translocation process.