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     

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.     

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.     

Translocation of polymers in a lattice model

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.     

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 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.     

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.     

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.     

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.     

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.     

A steered molecular dynamics study on the elastic behaviour of knotted polymer chains

In this paper the influence of a knot on the structure of a polymethylene （PM） strand in the tensile process is investigated by using the steered molecular dynamics （SMD） method. The gradual increasing of end-to-end distance, R, results in a tighter knot and a more stretched contour. That the break in a knotted rope almost invariably occurs at a point just outside the ＇entrance＇ to the knot, which has been shown in a good many experiments, is further theoretically verified in this paper through the calculation of some structural and thermodynamic parameters. Moreover, it is found that the analyses on bond length, torsion angle and strain energy can facilitate to the study of the localization and the size of a knot in the tensile process. The symmetries of torsion angles, bond lengths and bond angles in the knot result in the whole symmetry of the knot in microstructure, thereby adapting itself to the strain applied. Additionally, the statistical property of the force-dependent average knot size illuminates in detail the change in size of a knot with force f, and therefore the minimum size of the knot in the restriction of the potentials considered in this work for a PM chain is deduced. At the same time, the difference in response to uniaxial strain, between a knotted PM strand and an unknotted one is also investigated. The force-extension profile is easily obtained from the simulation. As expected, for a given f, the knotted chain has an R significantly smaller than that of an unknotted polymer. However, the scaled difference becomes less pronounced for larger values of N, and the results for longer chains approach those of the unknotted chains.     

离散颗粒层被横向推移过程中的力学行为研究

研究发现,颗粒物质层被匀速推移挤压过程中,所需推移力先以线性规律增加,在某一确定点后,则会以指数规律增加.而颗粒物质是由众多离散颗粒组成的软凝聚态物质,其宏观上反映的是离散颗粒的个体性质和凝聚态物质的集体效应.颗粒与颗粒之间以及颗粒与边界之间的细观尺度接触力链的构成以及演变规律将会直接影响各种宏观受力情况,其摩擦力与挤压力便是力链的主要构成形式.围绕着定量描述细观力链特征,从而揭示力的变化规律这一目标,采用计算机模拟的方法,依照球形颗粒Hertz法向接触理论和Mindlin-Deresiewicz切向接触理论,对重力作用下不同数目的三维等径球体颗粒层的推移情况进行了离散元仿真模拟,量化分析了推移力变化规律、各摩擦力变化规律以及力链分布规律,发现摩擦力与挤压力在颗粒堆积的不同阶段对力链的构成起到了不同的主次作用,使得力链发生强弱演变,从而发现了推移颗粒物质层时推移力的变化规律及原因.这些结果有利于从力链角度揭示颗粒内部和颗粒与各边界之间的受力情况.     

Translocation of Polymer Chains Through a Channel with Complex Geometries

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.     

Polymer translocation in a double-force arrangement

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.     

静态堆积颗粒中的力链分布

颗粒物质是由众多离散颗粒组成的软凝聚态物质,涉及多个物理层次结构和机制,是多尺度问题. 首先阐述了颗粒物质多尺度力学的研究框架,指出颗粒间接触力链构成的细观尺度是核心,颗粒物质显示出的独特静态堆积特性和动态流变特性都与细观尺度力链的复杂演变规律直接相关. 围绕着定量描述力链特征这一目标,采用严格的球形颗粒Hertz法向接触理论和Mindlin-Deresiewicz切向接触理论,对重力作用下12000个球心共面的二维等径颗粒静态堆积进行了离散动力学模拟,对力链分布特征、接触力规律等做了量化分析,考察了颗粒 关键词： 颗粒物质 力链 离散模型 多尺度力学     

Predicting Optimal Lengths of Random Knots

In a thermally fluctuating long linear polymeric chain in a solution, the ends, from time to time, approach each other. At such an instance, the chain can be regarded as closed and thus will form a knot or rather a virtual knot. Several earlier studies of random knotting demonstrated that simpler knots show a higher occurrence for shorter random walks than do more complex knots. However, up to now there have been no rules that could be used to predict the optimal length of a random walk, i.e. the length for which a given knot reaches its highest occurrence. Using numerical simulations, we show here that a power law accurately describes the relation between the optimal lengths of random walks leading to the formation of different knots and the previously characterized lengths of ideal knots of a corresponding type.     

Free energy and scalings for polymer translocation through a nanopore: A molecular dynamics simulation study combined with milestoning

Coarse-grained molecular dynamics simulations combined with milestoning method are used to study the stochastic process of polymer chain translocation though a nanopore. We find that the scalings for polymer translocation process (the chain is initialized with the first monomer in the nanopore) and for polymer escape process (the chain is initialized with the middle monomer in the nanopore) are different. The translocation process is mainly controlled by the entropic barrier, while the polymer escape process is driven by the effective force due to free energy difference.     

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.     

Influences of flexible defect on the interplay of supercoiling and knotting of circular DNA

Knots are discovered in biophysical systems, such as DNA and proteins. Knotted portions in knotted DNA are significantly bent and their corresponding bending angles are comparable with or larger than the sharp bending angle resulting in flexible defects. The role of flexible defects in the interplay of supercoiling and knotting of circular DNA were predicted by a Monte Carlo simulation. In knotted DNA with a particular knot type, a flexible defect noticeably enhances the supercoiling of the knotted DNA and the decreasing excitation energy makes the knotted portion more compact. A reduction in twist rigidity and unwinding of flexible defects are incorporated into the numerical simulations, so that interplay of supercoiling and knotting of circular DNA is studied under torsional conditions. Increasing unwinding not only results in a wider linking number distribution, but also leads to a drift of the distribution to lower values. A flexible defect has obvious effects on knotting probability. The summation of equilibrium distribution probability for nontrivial knotted DNA with different contour length does not change with excitation energy monotonically and has a maximum at an intermediate value of excitation energy around 5 kBT. In the phase space of knot length and gyration radius of knotted DNA, knot length does not anticorrelate with its gyration radius, which is attributed to the flexible defect in the knotted portion, which leads to the release of bending energy and inhibited the competition between entropy and bending energy.     

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.     

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.