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 closed polymers through a nanopore under an applied external field

The dynamic behaviours of the translocations of closed circular polymers and closed knotted polymers through a nanopore, under the driving of an applied field, are studied by three-dimensional Langevin dynamics sinmlations. The power-law scaling of the translocation time T with the chain length N and the distribution of translocation time are investigated separately. For closed circular polymers, a crossover scaling of translocation time with chain length is found to be T - N^a with the exponent a varying from a = 0.71 for relatively short chains to a = 1.29 for longer chains under driving force F = 5. The scaling behaviour for longer chains is in good agreement with experimental results, in which the exponent α= 1.27 for the transloeation of double-strand DNA. The distribution of translocation time D（τ） is close to a Gaussian function for duration time τ 〈 τp and follows a falling exponential function for duration time T 〉 wp. For closed knotted polymers, the scaling exponent a is 1.27 for small field force （F = 5） and 1.38 for large field force （F = 10）. The distribution of translocation time D（τ） remarkably features two peaks appearing in the case of large driving force. The interesting result of multiple peaks can conduce to the understanding of the influence of the number of strands of polymers in the pore at the same time on translocation dynamic process and scaling property.

Single long-polymer translocation through a long pore

This paper theoretically studies the free energy and conformational entropy of a long polymer threading a long nanopore （no/N ≥0.1） on external electric field. The polymer expanded model is built in this paper, that is, a single long polymer chain with N monomers （each of size a） threading a pore with no monomers can be regarded as polymer with N ＋ no monomers translocating a 2-dimension hole embedded in membrane. A theoretical approach is presented which explicitly takes into account the nucleation theory. Our calculations imply that, the structure of polymer changes more acutely than other situation, while its leading monomer reaches the second vacuum and its end monomer escapes the first vacuum. And it is also shown that the length scale of polymer and pore play a very important role for polymer translocation dynamics. The present model predicts that the translocation time depends on the chemical potential gradient and the property of the solvent on sides of pore to some extent.

Translocation of Polymer Through a Nanopore Studied by Langevin Dynamics:Effect of the Friction Coefficient

The driven polymer translocation through a nanopore with unbiased initial configuration has been studied by using Langevin dynamics(LD) simulations.It is found that the scaling relationship between translocation time and the polymer chain length is strongly affected by the friction coefficient in LD and the driving force.However,there is no scaling relationship between the translocation time and the friction coefficient.The translocation time is almost inversely proportional to the driving force,which is in agreement with those obtained in biased translocation.The scaling relationship between gyration radius(R g) of subchain at the trans side with the subchain length(L) is R g ～L 0.33 that is in good agreement with the limiting value for molten globule state,while the curve of R g of subchain at the cis side has two distinct stages.During translocation,the subchain at the cis side is being stretched gradually,and the structure of the subchain transforms from sphere-like to rod-like.When the effect of stretching reaches the tail end,the subchain is at the most stretched state.Finally the subchain will rapidly restore to coil structure.According to the results of force analysis,the retarding force at the trans side is more crucial during the practical translocation.

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.

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.

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.

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.

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.

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.

Translocation of polymer through nanopore:dissipative particle dynamics simulation

Dissipative particle dynamics simulations are performed to study the forced translocation of polymer through a nanopore inside which the polymer experiences a driving force F.Hydrodynamic interaction(HI) is taken into account for the polymer in good solvent.We find that the mean translocation time<τ>scales with the polymer length N as<τ>～Nx with a = 1.26 ± 0.03 close to a theoretical prediction,and the probability distribution of s can be described by a Gaussian function.Our results show that the dynamics of polymer translocation with the HI is different from that without the HI.However,the exponent d in the scaling<τ>～δ F-dis found not to be affected by the HI effect.

Translocation of a Self-propelled Polymer through a Narrow Pore

Recent studies indicate that active polymers often show curious conformational and dynamical properties.Specially,rigid polymers with self-propelled tangential forces can move directionally and even push a cargo.Motivated by this,the tran slocation of an active bead-spring polymer through a narrow pore is studied simulationly in this work.Each bead of the polymer is propelled by a tangential active force(f) along the contour of the polymer.Simulation results show that the active polymer translocates through the pore in a railway-motion manner.The tran slocation velocity v of the polymer is determined only by f,resulting that the translocation time(r) as a function of the polymer length(N)and the active force fcan be expressed as τ∝ Nf,which is independent of the rigidity of the polymer.Our results indicate that the tran slocation dynamics of active polymers is quite different from that of passive polymers.

Effect of Solvent Viscosity on the Driven Translocation of Charged Polymers through Nanopores

The effect of viscosity of non-translocated(cis)side,ηcis,on the driven translocation of charged polymers through nanopores is investigated using Langevin dynamics simulation.Results show that the translocation of polymer chains can be regulated by changingηcis.Asηcis decreases,the translocation timeτdecreases,and the exponentδin the scaling relation with driving force f,τ~f-δ,increases whereasαin the scaling relation with chain length N,τ~Nα,decreases.Simultaneously,the conformation of the polymer chain at the cis side gravitates towards an equilibrium state.The results imply a relationship between the translocation and the conformation of polymer chains.To verify this hypothesis,we change the conformation of polymer by artificially relaxing the translocating polymer via adding an additional relaxation time in the simulation.A sufficient large additional relaxation time for the translocating polymer chain at the cis side only or at both cis and trans sides results in exponentsαandδboth close to 1,in contrast toα=1.36 andδ=0.8 for the translocation without the additional relaxation.The additional relaxation for the polymer chain at the cis side accelerates the translocation and plays a more important role than that for polymer chain at the trans side.

Translocation time of a polymer chain through an energy gradient nanopore

The translocation time of a polymer chain through an interaction energy gradient nanopore was studied by Monte Carlo simulations and the Fokker-Planck equation with double-absorbing boundary condi- tions. Both the simulation and calculation revealed three different behaviors for polymer translocation. These behaviors can be explained qualitatively from free-energy landscapes obtained for polymer translocation at different parameters. Results show that the translocation time of a polymer chain through a nanopore can be tuned by suitably designing the interaction energy gradient.

受限高分子链的静态与动态性质

受限条件下高分子链的静态与动态性质是高分子物理学研究的重要组成部分,也是生物物理学关注的焦点问题之一。相对于自由高分子链,受限高分子链往往随受限程度和受限区域的不同而表现出一系列独特的规律性。本文首先回顾了自由空间中高分子链的基本性质,然后重点介绍了在不同受限程度下高分子链的静态性质和动力学行为,对比了不同受限区域下这些性质的差异性,并且系统总结了流场诱导下高分子链过孔的经典理论及其详细推导过程。最后,展望了受限高分子链今后的发展方向。

半柔性大分子链穿越微孔行为的研究

采用动态蒙特卡罗模拟方法,模拟半柔性大分子链在电场作用下穿越纳米孔道进入球腔的输运过程.主要研究电场强度及半柔性大分子链的刚性强度对穿孔过程的影响.发现：平均穿孔时间τ随电场强度的增大而减小,τ与链的长度N满足标度关系τ~N~α,并且电场强度E和弯曲能b对标度指数有显著影响.研究结果表明,当电场强度为中等时,刚性弱和刚性强的大分子的穿孔过程是完全不同的.研究半柔性大分子链穿越微孔的行为,有助于更深入认识生物大分子在生命体内的输运过程.

支化高分子链穿孔行为的研究

采用Langevin dynamics方法对支化高分子链的穿孔行为进行了研究.通过研究一条高分子链上各个单体的进孔时间来判断支点的位置,从而预测出支化高分子链的支链位置.模拟研究发现:支化高分子链的平均穿孔时间τ与主链的长度N满足标度关系τ～Nα,其中标度系数α随着外场力F的增大而增大.同时还研究了支链数n对穿孔时间的影响,发现标度系数α的值随着n的增大有减小的趋势.通过对支化高分子链穿孔行为的研究从而加深对生物大分子穿孔行为的了解.

高分子链移位动力学的理论和模拟研究

高分子链通过纳米管道或纳米孔的移位,存在于各种生命过程中,是物理、化学和生物领域的重要课题,在实验、理论和计算机模拟等领域已经被广泛研究,并应用于科技的不同领域。本文总结了高分子链移位的理论和模拟方面的最新研究成果,讨论了自由能形貌对高分子链移位动力学过程的影响。结合理论计算和模拟研究,分析了链与管道的相互作用、链的组分、链节电荷分布、管道的性质等因素对自由能形貌和高分子链移位时间的影响,并结合自由能形貌对研究结果进行了解释。研究结果有助于理解高分子链的移位机制,从而进一步调控高分子链的移位时间。

Elucidating the dynamics of polymer transport through nanopores using asymmetric salt concentrations

While notable progress has been made in recent years both experimentally and theoretically in understanding the highly complex dynamics of polymer capture and transport through nanopores,there remains significant disagreement between experimental observation and theoretical prediction that needs to be resolved.Asymmetric salt concentrations,where the concentrations of ions on each side of the membrane are different,can be used to enhance capture rates and prolong translocation times of electrophoretically driven polymers translocating through a nanopore from the low salt concentration reservoir,which are both attractive features for single-molecule analysis.However,since asymmetric salt concentrations affect the electrophoretic pull inside and outside the pore differently,it also offers a useful control parameter to elucidate the otherwise inseparable physics of the capture and translocation process.In this work,we attempt to paint a complete picture of the dynamics of polymer capture and translocation in both symmetric and asymmetric salt concentration conditions by reporting the dependence of multiple translocation metrics on voltage,polymer length,and salt concentration gradient.Using asymmetric salt concentration conditions,we experimentally observe the predictions of tension propagation theory,and infer the significant impact of the electric field outside the pore in capturing polymers and in altering polymer conformations prior to translocation.

流场中单链高分子过孔输运的动力学行为

采用布朗动力学方法,通过模拟不同温度和流速下,不同链长的单链高分子穿过纳米孔洞的动力学行为,证实了临界流速的存在,并验证了理论预测的结果,即临界流量随体系温度线性增大,且与链长无关.还对高分子链过孔输运时间以及输运过程中链构象的变化进行了研究.模拟结果为明晰在剪切流场中高分子穿过纳米孔洞的动力学行为提供了有益参考.