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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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采用退火法模拟研究受外力F驱动的高分子链在吸引表面的吸附特性.通过高分子链的平均表面接触数〈M〉与温度T之间的关系计算临界吸附温度T_c,并发现T_c随着F的增加而减小;进而通过高分子链的均方回转半径分析外力驱动作用对高分子链构象的影响,并从回转半径极小值或者垂直外力方向的y和z分量的变化交叉校验临界吸附点T_c.模拟计算了处于吸附状态的高分子链随着外力F的增加是否会发生吸附状态到脱附状态的相变以及发生相变所需施加的外力是否由温度所决定.模拟结果表明:两种不同温度下高分子链的吸附性质和构象性质受外力驱动作用而产生不同现象,在温度区间T*_cTT_c时会发生脱附现象,而在TT*_c时不会发生脱附现象. 相似文献
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随着单分子操纵技术的发明与发展,人们已经可以对单个生物大分子施以力或力矩,并测量它们的物理性质,DNA单分子的力学实验表明,在分子尺度上理解生物大分子的生化过程,力与能量是同等重要的结构与功能参数。一个梯子模型被用来描述双链DNA的外力拉伸曲线,在这个模型中,DNA是由许多碱基对(梯子的横杆,横杆之间存在吸引势)连接两条聚核苷酸虫链(梯子的两侧)形成的高分子,利用路径积分法得出的理论曲线与实验曲线吻合得很好,对于单链DNA,用分立的杂化高分子链统计理论的母函数方法来计算其弹性行为,得出与实验相符合的外力引起的解链相变结果。此外,对于抑瘤蛋白p53识别序列DNA微环弹性进行分析,发现其弹性模量只是通常随机序列的三分之一。 相似文献
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本文讨论了分数阶对数耦合系统在非周期外力作用情况下, 耦合粒子链的定向输运现象. 由于粒子在黏性介质中的运动具有“记忆性”, 所以本文通过将系统建模为分数阶对数耦合模型来研究各个系统参数对粒子链运动状态的影响. 数值仿真表明: 1)对于此类系统, 只有在存在外力作用的情况下粒子链才能够产生定向输运现象, 并且粒子链平均流速随着外力的增大而增大. 2)对于分数阶阶数较小的系统, 阻尼记忆性对粒子链的运动状态有显著的影响, 具体表现为: 粒子链的平均流速存在上界(这个上界非常小), 无论外力、耦合力以及噪声强度如何变化, 粒子链的平均流速都不会超过这个上界. 当系统的阻尼力很大且外力为零时, 粒子链不会产生定向输运现象. 3) 当系统的阶数与外力较大时, 虽然粒子链能够产生定向流, 但是此时系统对耦合力与噪声具有免疫性. 4) 耦合力与噪声强度对粒子链运动的影响只在外力较小的情况下有所表现. 在这种情况下, 当系统阶数充分大时, 粒子链的平均流速随着耦合力与噪声强度的变化而变化, 并且伴随着定向流的产生. 相似文献
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单链DNA在受限环境中伸展的Monte Carlo模拟 总被引:1,自引:0,他引:1
将MonteCarlo方法和键长涨落算法相结合,模拟了受限于两平行平面间的单链DNA分子在外力作用下的伸展以及撤除外力以后弛豫的动力学过程,研究了受限程度对DNA分子的伸展长度及弛豫过程的影响.结果表明,随着受限程度的增加,DNA分子链的构象更加伸展,这主要是由于随着平面间距的减少,DNA分子不同链段之间流体力学相互作用将会被平面屏蔽所致,受限程度不同时DNA分子的弛豫过程进一步证实了这一点.DNA分子的伸展长度(即末端距)随着流速的变化关系与文献给出的实验结果及其对此所做的理论分析是基本一致的. 相似文献
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采用粗粒化模型,应用分子动力学方法研究了单个纳米粒子对聚合物结晶行为的影响.通过改变纳米粒子与聚合物单体之间作用方式(吸引作用或排斥作用)、纳米粒子与聚合物单体之间作用强度和聚合物分子链的长度,计算整个系统和局部区域的有序参数,研究了三个不同因素下纳米粒子对聚合物结晶行为的不同影响.研究表明,在聚合物基体中添加单个纳米粒子,纳米粒子对整个系统的结晶影响不明显,但是纳米粒子对其周围聚合物单体的结晶存在局部强化作用.当纳米粒子与聚合物单体之间为吸引作用且作用强度较大时,纳米粒子对聚合物结晶表现出明显的局部强化作用,聚合物分子链长度也有着一定的影响,在较大吸引作用强度下,长链样本比短链样本有着更为显著的局部强化作用. 相似文献
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《Physics letters. A》2006,359(4):261-264
Molecular Dynamics simulations of polymer translocation are hereby reported. No external force was applied to the polymer during translocation, and the dynamics was dominated by polymer–pore interactions. It was found that hydrodynamic interactions play an important role in the relaxation of the polymer on each side of the membrane but have a negligible impact on the translocation process itself. Also, the scaling laws obtained for the relaxation and translocation times indicate that long translocating polymers may be considered to be following a quasi-equilibrium anomalous diffusion process in the absence of external forces. 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
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We present a study of the dynamics of single polymers colliding with molecular obstacles using Molecular-dynamics simulations.
In concert with these simulations we present a generalized polymer-obstacle collision model which is applicable to a number
of collision scenarios. The work focusses on three specific problems: i) a polymer driven by an external force colliding with
a fixed microscopic post; ii) a polymer driven by a (plug-like) fluid flow colliding with a fixed microscopic post; and iii)
a polymer driven by an external force colliding with a free polymer. In all three cases, we present a study of the length-dependent
dynamics of the polymers involved. The simulation results are compared with calculations based on our generalized collision
model. The generalized model yields analytical results in the first two instances (cases i) and ii)), while in the polymer-polymer
collision example (case iii)) we obtain a series solution for the system dynamics. For the case of a polymer-polymer collision
we find that a distinct V-shaped state exists as seen in experimental systems, though normally associated with collisions
with multiple polymers. We suggest that this V-shaped state occurs due to an effective hydrodynamic counter flow generated
by a net translational motion of the two-chain system. 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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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. 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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Kraikivski P Lipowsky R Kierfeld J 《The European physical journal. E, Soft matter》2005,16(3):319-340
We study the thermally activated motion of semiflexible polymers in double-well potentials using field-theoretic methods. Shape, energy, and effective diffusion constant of kink excitations are calculated, and their dependence on the bending rigidity of the semiflexible polymer is determined. For symmetric potentials, the kink motion is purely diffusive whereas kink motion becomes directed in the presence of a driving force. We determine the average velocity of the semiflexible polymer based on the kink dynamics. The Kramers escape over the potential barriers proceeds by nucleation and diffusive motion of kink-antikink pairs, the relaxation to the straight configuration by annihilation of kink-antikink pairs. We consider both uniform and point-like driving forces. For the case of point-like forces the polymer crosses the potential barrier only if the force exceeds a critical value. Our results apply to the activated motion of biopolymers such as DNA and actin filaments or of synthetic polyelectrolytes on structured substrates. 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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In this Letter we provide a theory to show that high-field electrokinetic translocation of DNA through nanopores or nanochannels causes large transient variations of the ionic concentrations in front and at the back of the DNA due to concentration polarization (CP). The CP causes strong local conductivity variations, which can successfully explain the nontrivial current transients and ionic distributions observed in molecular dynamics simulations of nanopore DNA translocations as well as the transient current dips and spikes measured for translocating hairpin DNA. Most importantly, as the future of sequencing of DNA by nanopore translocation will be based on time-varying electrical conductance, CP, must be considered in experimental design and interpretation--currently these studies are mostly based on the incomplete pore conductance models that ignore CP and transients in the electrical conductance. 相似文献