Dynamics of polymer translocation through nanopores: theory meets experiment

The dynamics of translocation of polymer molecules through nanopores is investigated via molecular dynamics. We find that an off-lattice minimalist model of the system is sufficient to reproduce quantitatively all the experimentally observed trends and scaling behavior. Specifically, simulations show (i) two translocation regimes depending on the ratio of pore and polymer length, (ii) two different regimes for the probability of translocation depending on applied voltage, (iii) an exponential dependence of translocation velocity upon applied voltage, and (iv) an exponential decrease of the translocation time with temperature. We also propose a simple theoretical explanation of each of the observed trends within a free energy landscape framework.     

Effects of an attractive wall on the translocation of polymer under driving

The effects of an attractive wall at the trans side on the translocation of an eight-site bond-fluctuation model (BFM) polymer through a pore in a membrane under driving are simulated by the dynamic Monte Carlo method. The attractive wall shows two contrary effects: its excluded volume effect reduces configuration entropy and thus hinders the translocation of the polymer, while its attraction decreases the energy and thus accelerates the translocation. At a critical polymer-wall interaction ε*?≈-?1, we find that the two effects compensate each other and the translocation time τ is roughly independent of the separation distance between the wall and the pore. The value ε*?≈-?1 is roughly equal to the critical adsorption point for the BFM polymer. Moreover, the value of the critical attraction is roughly independent of chain length N and chemical potential difference Δμ. At last, a scaling relation τ?～?N(α) is observed for polymer translocation at a high value of NΔμ. Though the translocation time is highly dependent on the polymer-wall interaction and pore-wall separation distance, the exponent α is always about 1.30?±?0.05 so long as NΔμ is large enough.     

Dynamics of polyelectrolyte transport through a protein channel as a function of applied voltage

We study the transport of dextran sulfate through a protein channel as a function of applied voltage. Below 60 mV, the chain's entrance to the pore is hindered by an entropic barrier; above 60 mV, the strong local electric field forces the chain entrance. The effective charge of the polyelectrolyte inside the pore is reduced. We observe two types of blockades which have durations that decrease when the applied voltage increases. The shortest is a straddling time between the polyelectrolyte and the pore; the longest is the translocation time. The translocation time obeys an exponential dependence upon applied voltage.     

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 (n₀/N \ge 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 n₀ monomers can be regarded as polymer with N+n_{0} 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.     

Polymer translocation in crowded environments

We study the effect of the crowded environments on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are significantly altered, leading to novel scaling behaviors of the translocation time. We also observe new and qualitatively different translocation regimes depending upon the extent of crowding, transmembrane chemical potential asymmetry, and polymer length.     

Monte Carlo analysis of polymer translocation with deterministic and noisy electric fields

Polymer translocation through the nanochannel is studied by means of a Monte Carlo approach, in the presence of a static or oscillating external electric voltage. The polymer is described as a chain molecule according to the two-dimensional “bond fluctuation model”. It moves through a piecewise linear channel, which mimics a nanopore in a biological membrane. The monomers of the chain interact with the walls of the channel, modelled as a reflecting barrier. We analyze the polymer dynamics, concentrating on the translocation time through the channel, when an external electric field is applied. By introducing a source of coloured noise, we analyze the effect of correlated random fluctuations on the polymer translocation dynamics.     

Passage times for unbiased polymer translocation through a narrow pore

We study the translocation process of a polymer in the absence of external fields for various pore diameters b and membrane thickness L. The polymer performs Rouse and reptation dynamics. The mean translocation time (tau(t)) that the polymer needs to escape from a cell and the mean dwell time (tau(d)) that the polymer spends in the pore during the translocation process obey scaling relations in terms of the polymer length N, L, and b/R(g), where R(g) is the radius of gyration for the polymer. We explain these relations using simple arguments based on polymer dynamics and the equilibrium properties of polymers.     

Two-dimensional diffusion model for the biopolymers dynamics at nanometer scale

In this paper the driven transport of linear polymers through a nanopore is presented. Biopolymer physical behavior in an external electric field is modeled and its motion is simulated using the Langevin impulse integrator method. Within fairly large limits, the polymer translocation time is inversely proportional with the electric field intensity and directly proportional with the polymer chain length.      

Influence of polymer-pore interactions on translocation

We investigate the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. An attractive interaction can greatly improve the translocation probability. At the same time, it also increases the translocation time slowly for a weak attraction while an exponential dependence is observed for a strong attraction. For fixed driving force and chain length the histogram of translocation time has a transition from Gaussian distribution to long-tailed distribution with increasing attraction. Under a weak driving force and a strong attractive force, both the translocation time and the residence time in the pore show a nonmonotonic behavior as a function of the chain length. Our simulations results are in good agreement with recent experimental data.     

Driven translocation dynamics of polynucleotides through a nanopore: off-lattice Monte-Carlo simulations

The driven translocation dynamics of a polynucleotide chain through a nanopore is studied using off-lattice Monte-Carlo simulations, which plays an important role in the nanopore sequencing of polynucleotides. We report a detailed study on the dependence of translocation dynamics on the chain length and the local geometry near the nanopore. In particular, we find that the length dependence of the infection time of the chain could exhibit very different behaviors for different geometries.     

Hard Sphere Diffusion Behaviour of Polymer Translocating through Interacting Pores

The translocation of polymer chain through a small pore from a high concentration side (cis side) to a low concentration side (trans side) is simulated by using Monte Carlo technique. The effect of the polymer--pore interaction on the translocation is studied. We find a special interaction at which the decay of the number of polymer chain, N, at the cis side obeys Fick's law, i.e. N decreases exponentially with time. The behaviour is analogous to the diffusion of hard sphere.     

Effect of Interaction upon Translocation of Confined Polymer Chain Through Nanopore

运用二维的键长涨落模型和蒙特卡洛方法研究高分子链从一个受限空间到自由空间穿孔过程中,链单体与纳米孔之间的相互作用.结果表明,在不同的链长和纳米孔交互作用下,高分子链成功穿越自由能能垒取决于链长和纳米孔长度,并且由于交互作用降低了自由能能垒,导致高分子链在纳米管的平均捕获时间缩短.     

非均匀外力对粗粒化DNA穿孔行为影响的模拟研究

通过建立DNA高分子的粗粒化模型,采用分子动力学方法模拟其穿孔行为,研究了不同的孔内非均匀外力对DNA高分子穿孔的影响.外力及高分子链内部势能在分子水平下对单体的综合作用很复杂,某些条件穿孔过程会产生后面粒子超过前面粒子而使高分子链堵塞在孔内的情况.研究还发现,穿孔行为是否成功与孔口力的大小有关,在成功穿孔的情况下,非均匀外力相比于恒力情况穿孔时间至少减少了1/2.这些结果对理解DNA复杂的穿孔机理提供了新的视角.     

金属/掺杂聚合物/金属结构中载流子的注入与输运

基于紧束缚的Su-Schrieffer-Heeger模型,利用非绝热的动力学方法,研究了金属/聚合物/金属三明治结构中载流子注入与输运的动力学过程,其中,聚合物中含有一个掺杂离子. 电子波函数随时间的演化满足含时Schrdinger方程,晶格运动满足经典的牛顿运动方程. 研究发现,掺杂离子对注入到聚合物中的载流子的作用类似一个控制阀门,阀门的状态与电场的强度和偏压的大小密切相关. 关键词： 载流子输运 波包 非绝热动力学     

Molecular Dynamics simulation of a polymer chain translocating through a nanoscopic pore

The detection of linear polymers translocating through a nanoscopic pore is a promising idea for the development of new DNA analysis techniques. However, the physics of constrained macromolecules and the fluid that surrounds them at the nanoscopic scale is still not well understood. In fact, many theoretical models of polymer translocation neglect both excluded-volume and hydrodynamic effects. We use Molecular Dynamics simulations with explicit solvent to study the impact of hydrodynamic interactions on the translocation time of a polymer. The translocation time τ that we examine is the unbiased (no charge on the chain and no driving force) escape time of a polymer that is initially placed halfway through a pore perforated in a monolayer wall. In particular, we look at the effect of increasing the pore radius when only a small number of fluid particles can be located in the pore as the polymer undergoes translocation, and we compare our results to the theoretical predictions of Chuang et al. (Phys. Rev. E 65, 011802 (2001)). We observe that the scaling of the translocation time varies from τ ∼ N ^11/5 to τ ∼ N ^9/5 as the pore size increases (N is the number of monomers that goes up to 31 monomers). However, the scaling of the polymer relaxation time remains consistent with the 9/5 power law for all pore radii.     

打结高分子链穿孔行为的研究

以三叶草型结(即3₁结)为例,采用分子动力学(MD)方法,研究打结高分子链在外场力作用下穿越微孔的动力学过程.模拟发现,在拉动打结高分子链的过程中,结的大小呈涨落变化,直至最后散结.定性讨论了结的存在对高分子链穿孔速率的影响.在外场力作用下,打结高分子链平均穿孔时间(τ)与链长(N)满足标度关系τ～N ^α,其中标度系数α随外场力f增大而增大.对于短链,外场力越大,平均穿孔时间越短     

Tunable magnetic relaxation mechanism in magnetic nanoparticles

We investigate theoretically the magnetization dynamics of a conducting magnetic nanoparticle weakly coupled to source and drain electrodes, under the assumption that all relaxation comes from exchange of electrons with the electrodes. In the regime of sequential tunneling, the magnetization dynamics is characterized by a relaxation time t(1), which strongly depends on temperature, bias voltage, and gate voltage. While a direct measure of a nanoparticle magnetization might be difficult, we find that t(1) can be determined through a time resolved transport measurement. For a suitable choice of gate voltage and bias voltage, the magnetization performs a bias-driven Brownian motion regardless of the presence of anisotropy.     

Sequence dependence of DNA translocation through a nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases A and C, which have been shown previously to have different interactions with the pore. We study DNA with repeating blocks A(n)C(n) for various values of n and find that the translocation time depends strongly on the block length 2n as well as on the orientation of which base enters the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through a nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences is contained in the periodicity of the residence time of the individual nucleotides inside the pore.     

Observation of the first-order transition in ultrafiltration of flexible linear polymer chains

Using a special double-layer membrane to avoid interaction among flow fields generated by different pores, we have, for the first time, observed the predicted discontinuous first-order transition in ultrafiltration of flexible linear polymer chains. Namely, the chain could pass through a pore much smaller than its unperturbed radius only when the flow rate is higher than a certain value. When only one chain and one pore are considered in theory, such a threshold is surprisingly independent of both the chain length and the pore size. Our results reveal that for a membrane with many pores and at a microscopic flow rate () lower than the threshold, the inevitable blocking of some pores by longer nonstretched coiled chains increases in those unblocked pores because the macroscopic flow rate () is a constant. Long chains have two populations, coiled and stretched, in a real ultrafiltration experiment when is lower than the threshold.     

Active polymer translocation through flickering pores

Single file translocation of a homopolymer through an active channel under the presence of a driving force is studied using Langevin dynamics simulation. It is shown that a channel with sticky walls and oscillating width could lead to significantly more efficient translocation as compared to a static channel that has a width equal to the mean width of the oscillating pore. The gain in translocation exhibits a strong dependence on the stickiness of the pore, which could allow the polymer translocation process to be highly selective.