共查询到20条相似文献,搜索用时 15 毫秒
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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. 相似文献
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Muthukumar M 《Physical review letters》2001,86(14):3188-3191
Based on an analogy between polymer translocation across a free energy barrier associated with polymer worming through a hole and classical nucleation and growth process, the escape time tau is predicted asymptotically to be N(N/rho)(1/3nu). N is the polymer length, rho is the monomer density prior to escape, and nu is the radius of gyration exponent. Monte Carlo simulation data collected in the high salt limit (nu approximately 3/5) are in agreement with the asymptotic law and provide vivid details of the escape. 相似文献
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Rouhollah Haji Abdolvahab 《Physics letters. A》2018,382(4):162-167
Chaperone-assisted biopolymer translocation is the main model proposed for translocation in vivo. A dynamical Monte Carlo method is used to simulate the translocation of a stiff homopolymer through a nanopore driven by chaperones. Chaperones are proteins that bind to the polymer near the wall and prevent its backsliding through Cis side. The important parameters include binding energy, size and the local concentration of the chaperones. The profile of these local concentrations, build up the chaperones distribution. Here we investigate the effects of binding energy, size and the exponential distribution of chaperones in their equilibration in each step of the polymer translocation needed for stable translocation time. The simulation results show that in case of chaperones with the size of a monomer () and/or positive effective binding energy and/or uniform distribution, the chaperones binding equilibration rate/frequency is less than 5 times per monomer. However, in some special cases in the exponential distribution of chaperones with size and negative effective binding energy the equilibration rate will diverge to more than 20 times per monomer. We show that this non-equilibrium effect results in supper diffusion, seen before. Moreover, we confirm the equilibration process theoretically. 相似文献
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Davide Valenti Giovanni Denaro Dominique Persano Adorno Nicola Pizzolato Salvatore Zammito Bernardo Spagnolo 《Central European Journal of Physics》2012,10(3):560-567
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. 相似文献
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Viorel P. Paun 《Central European Journal of Physics》2009,7(3):607-613
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.
相似文献
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S. T. T. Ollila K. F. Luo T. Ala-Nissila S. -C. Ying 《The European physical journal. E, Soft matter》2009,28(4):385-393
Using Langevin dynamics simulations, we investigate the translocation dynamics of an externally driven polymer chain through
a nanopore, where a pulling force F is exerted on the first monomer whilst there is an opposing force F
E < F within the pore. Such a double-force arrangement has been proposed recently to allow better dynamical control of the translocation
process in order to sequence biopolymers. We find that in the double-force arrangement translocation becomes slower as compared
to the case under a single monomer pulling force of magnitude F - F
E , but scaling of the translocation time as a function of the chain length ∼ N
2 does not change. The waiting time (m) for monomer m to exit the pore is found to be a monotonically increasing function of the bead number almost until m
N , which indicates relatively well-defined slowing down and control of the chain velocity during translocation. We also study
the waiting time distributions for the beads in the chain, and characterize in detail fluctuations in the bead positions and
their transverse position coordinates during translocation. These data should be useful in estimating position-dependent sequencing
errors in double-force experiments. 相似文献
9.
利用Langevin动力学方法模拟了脱氧核糖核酸(DNA)单链在电场力作用下穿越纳米孔道的动力学过程.研究表明,不同种类的单体对应着不同的居留时间,相邻单体的居留时间随着孔道长度的增大而减小.在简化模型的基础上,可以从居留时间图中一次性地推测出一条DNA链的嘌呤和嘧啶的分布.应用该方法对17条不同序列的DNA链进行了预测,平均准确率为951%.在此方法的基础上做一些改进,可以为DNA链的测序提供一种高效的低成本方法.
关键词:
Langevin动力学
脱氧核糖核酸单链
序列预测 相似文献
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《Physica A》2005,350(1):95-107
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. 相似文献
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We investigate the translocation of single polymer chain through a nanopore located on a membrane with different solvents in the two sides of the membrane. For the case under study, the effect of solvents on the translocation dynamics is significant, and as a result, the mean first passage time shortens remarkably compared with that calculated in the case of good solvents on both the sides of the membrane. In addition, we also discuss the condition such that the present result holds true. 相似文献
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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. 相似文献
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采用nPERMis (new pruned-enriched rosenbluth method with importance sampling) 算法,研究了高分子链在通道中穿行的力学行为. 在管道穿行的过程中,计算了其作用力,发现进入中间通道的过程其对应的作用力f和第一个单体在x轴方向的位置关系曲线有一个平台(f>0). 由于高分子链的受限减少了高分子链的构象数目和熵,从而增加了其自由能, 因此只有在外力的作用下,高分子链才可以进入中间管道. 当高分子运动到某一位置后,第二个平台开始形成(f<0),这时高分子链自发进入右通道. 这是因为在右通道中高分子链的自由能降低的比左通道中高分子链的自由能升高的快. 右通道中的高分子链自发地拉动左通道中的高分子链. 研究了链长、左、右通道宽度对穿孔有很大影响. 通过这些研究可以详细解释各部分穿行时间不同的原因. 相似文献
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We consider the escape of a flexible, self-avoiding polymer chain out of a confined geometry. By means of simulations, we demonstrate that the translocation time can be described by a simple scaling law that exhibits a nonlinear dependence on the degree of polymerization and that is sensitive to the nature of the confining geometry. These results contradict earlier predictions but are in agreement with recently confirmed geometry-dependent expressions for the free energy of confinement. 相似文献
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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 simulations. The power-law scaling of the translocation time τ 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 τ~ N α , with the exponent α varying from α = 0.71 for relatively short chains to α = 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 translocation of double-strand DNA. The distribution of translocation time D(τ) is close to a Gaussian function for duration time τ < τ p and follows a falling exponential function for duration time τ > τ p . For closed knotted polymers, the scaling exponent α 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. 相似文献
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XiaoHui Lin ChiBin Zhang Jun Gu ShuYun Jiang JueKuan Yang 《中国科学:物理学 力学 天文学(英文版)》2014,57(11):2104-2113
A non-continuous electroosmotic flow model (PFP model) is built based on Poisson equation, Fokker-Planck equation and Navier-Stokse equation, and used to predict the DNA molecule translocation through nanopore. PFP model discards the continuum assumption of ion translocation and considers ions as discrete particles. In addition, this model includes the contributions of Coulomb electrostatic potential between ions, Brownian motion of ions and viscous friction to ion transportation. No ionic diffusion coefficient and other phenomenological parameters are needed in the PFP model. It is worth noting that the PFP model can describe non-equilibrium electroosmotic transportation of ions in a channel of a size comparable with the mean free path of ion. A modified clustering method is proposed for the numerical solution of PFP model, and ion current translocation through nanopore with a radius of 1 nm is simulated using the modified clustering method. The external electric field, wall charge density of nanopore, surface charge density of DNA, as well as ion average number density, influence the electroosmotic velocity profile of electrolyte solution, the velocity of DNA translocation through nanopore and ion current blockade. Results show that the ion average number density of electrolyte and surface charge density of nanopore have a significant effect on the translocation velocity of DNA and the ion current blockade. The translocation velocity of DNA is proportional to the surface charge density of nanopore, and is inversely proportional to ion average number density of electrolyte solution. Thus, the translocation velocity of DNAs can be controlled to improve the accuracy of sequencing by adjusting the external electric field, ion average number density of electrolyte and surface charge density of nanopore. Ion current decreases when the ion average number density is larger than the critical value and increases when the ion average number density is lower than the critical value. Our numerical simulation shows that the translocation velocity of DNA given by the PFP model agrees with the experimental, results better than that given by PNP model or PB model. 相似文献
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基于粗粒化分子动力学方法模拟电驱动蛋白质过孔过程,研究纳米孔-水/纳米孔-蛋白质相互作用对电泳迁移率的影响;用操控式分子动力学模拟分析蛋白质在不同相互作用下过孔摩擦系数和摩擦阻力.研究发现:蛋白质黏附纳米孔壁面对其过孔特性影响并不明显,而纳米孔-水相互作用对蛋白质过孔电泳迁移率和摩擦系数影响较大.随纳米孔-水相互作用增强,纳米孔壁面与蛋白质附近水分子运动差异显现,蛋白质过孔摩擦阻力显著增大,过孔摩擦系数随之增大,进而影响蛋白质过孔电泳迁移率.所得结果可为纳米孔材料设计提供理论指导. 相似文献
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M. G. Kucherenko A. P. Rusinov T. M. Chmereva A. A. Ignat’ev D. A. Kislov N. Yu. Kruchinin 《Optics and Spectroscopy》2009,107(3):480-485
The kinetics of a two-stage laser-induced reaction between electronically excited molecules of two sorts (an organic luminophore
and oxygen) in a regular porous nanostructure whose cells are filled with linear macromolecules is studied. A mathematical
model of the process is proposed that takes into account an inhomogeneous distribution of polymer chain links in a nanopore,
with this distribution determining the radial profile of reagents. One version of the theory considers a radial diffusion
flux of activated oxygen molecules, while the other version considers a thermodiffusion flux of unexcited molecules. The numerical
results of the model are compared to the data of molecular dynamic calculations and experiment. 相似文献
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Zurek S Kośmider M Drzewiński A van Leeuwen JM 《The European physical journal. E, Soft matter》2012,35(6):47-7
Voltage-driven polymer translocation is studied by means of a stochastic lattice model. The model incorporates voltage drop over the membrane as a bias in the hopping rate through the pore and exhibits the two main ingredients of the translocation process: driven motion through the pore and diffusive supply of chain length towards the pore on the cis-side and the drift away from the pore on the trans-side. The translocation time is either bias limited or diffusion limited. In the bias-limited regime the translocation time is inversely proportional to the voltage drop over the membrane. In the diffusion-limited regime the translocation time is independent of the applied voltage, but it is rather sensitive to the motion rules of the model. We find that the whole regime is well described by a single curve determined by the initial slope and the saturation value. The dependence of these parameters on the length of the chain, the motion rules and the repton statistics are established. Repulsion of reptons as well as the increase of chain length decrease the throughput of the polymer through the pore. As for free polymers, the inclusion of a mechanism for hernia creations/annihilations leads to the cross-over from Rouse-like behaviour to reptation. For the experimentally most relevant case (Rouse dynamics) the bimodal power law dependence of the translocation time on the chain length is found. 相似文献
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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. 相似文献