半刚性聚电解质链与带相反电荷颗粒复合体系的动力学模拟

用Langevin动力学研究了半刚性聚电解质链与带相反电荷球状颗粒在溶液中的复合体系，并研究了链的拉伸性质.具体考察了带电颗粒的电量以及溶液中盐离子浓度对复合体系的影响.链两端没有施加外力的情况下，当溶液中盐离子浓度较低时，复合体系呈现一种串珠状结构；当溶液中盐离子浓度较高时，复合体系转变为一种聚集态结构.链的两端施加外力的情况下，带电颗粒从链上脱落的过程可以分为两步. 关键词： 聚电解质链 Langevin动力学 Debye-Hückel长度     

DNA及基于DNA链替换反应的分子计算

DNA是生物遗传信息的载体,同时也是一种理想的生物相容材料.单链黏性末端(toehold)协助的链替换反应是DNA常温纳米技术的基础.利用DNA的碱基互补特性和碱基序列的可编程性,人们可以基于DNA链替换反应构建分子机器并对其运转进行精确调控,实现各种复杂分子计算.本文回顾了近年来DNA结构和力学性质方面的研究进展,探讨DNA链替换反应的微观理解,介绍DNA分子计算领域的最新成果,以及它在DNA恒温自组装等方面的应用.     

单个人类端粒重复序列d(TTAGGG)对长链端粒DNA-d[AGGG(TTAGGG)_6]结构影响的研究（英文）

本文使用超速离心沉降速度法、聚丙烯酰胺凝胶电泳和圆二色光谱和紫外吸收检测熔融实验研究了长序列端粒DNA-d[AGGG(TTAGGG)_6](G_6-DNA)的结构以及单个重复序列DNA-d(TTAGGG)(G_(01)-DNA)对G_6-DNA结构的影响.结果表明G_6-DNA可以在水溶液中形成二聚体,并且G_(01)-DNA可以通过与G_6-DNA结合形成额外的G-四链体结构,从而改变单体与二聚体的平衡.然而,G_(01)-DNA对序列为d[AGGG(TTAGGG)_3](G_3-DNA)的结构没有影响.该研究为长序列单链端粒DNA的结构多样性提供了新的见解.     

单分子技术研究T7解旋酶的解旋与换链

单分子荧光共振能量转移(smFRET)和磁镊(MT)技术目前广泛应用于研究分子马达.相较于常规技术,其具有高精度及动态观测的优点.本文研究对象为T7解旋酶,是六聚体解旋酶的典型代表.研究表明,这种解旋酶主要消耗脱氧胸苷三磷酸(dTTP)提供能量,且仅能沿着5′-3′单向进行行走和解旋工作.目前对于六聚体解旋酶的解旋和换链机制的认知仍然存在着诸多问题,因此本文主要以此作为切入点开展研究.首先通过运用smFRET技术研究T7解旋酶在不同DNA底物上的解旋现象,发现其需要3′-尾链参与到解旋工作中,但其为单链或双链结构并无明显区别;通过改变脱氧核糖核酸(DNA)序列中的GC含量,发现T7解旋酶随着序列中GC含量的升高会更容易在解旋过程中发生回退现象,导致解旋长度明显缩短;通过进一步分析发生回退先的实验数据,发现T7解旋酶除了可以瞬时回退到叉形DNA岔口或脱落外,还可以缓慢回退到叉形DNA岔口;运用MT技术研究该解旋酶,同样发现这种缓慢回退现象的存在.根据T7解旋酶解旋DNA遵循的单向性和极性,其只能沿着5′到3′方向进行行走和解旋.因此,本文推测这种缓慢回退的现象可能是解旋酶从5′-链转移至3′-链上,即发生换链过程;最后,本文提出了T7解旋酶在解旋过程中进行换链的模型,将有助于进一步理解环状六聚体解旋酶行使其功能的分子机制.     

道路交通流状态的多参数融合预测方法

针对道路交通流普遍存在的混沌特性以及单交通参数不足 以全面反映交通流状态的实际情况,考虑交通动力学系统中多个 交通参数之间的关联关系,提出一种新的多参数混沌时间序列预 测算法.该算法在相空间重构理论的基础上,借助Bayes估计将多个参数在 同一高维相空间中进行相点最优融合,从而增加重构相空间的系统信息量, 使得相空间的相点轨迹更加逼近原交通系统的动力学行为.同时借鉴单 参数混沌时间序列预测方法,从不同角度对动力学系统的运动状态进行描 述,以实现多参数时间序列的混沌预测.实验结果表明,通过融合多交通参数时 间序列,获得了更加完整的交通流状态变化特征.与单交通参数时间序列的预测 结果相比,其预测误差显著降低,均衡系数相应增大,提高了交通流状态预测的准确率.     

单链DNA在受限环境中伸展的Monte Carlo模拟

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.     

DNA在熵受限管道中穿越过程的计算机模拟

利用Metropolis Monte-Carlo动力学方法结合键长涨落算法，模拟了单链DNA分子在电场作用下穿越熵受限管道的动力学过程.结果表明，DNA分子穿越管道时将经历无规迁移、受限迁移及快速迁移等几个显著不同的阶段.平均迁移率随外场增加而增大并最终达到饱和值μ0，受限时间的对数与所加场强的倒数之间基本满足线性关系.模拟结果不仅与文献所给的实验结果基本一致，而且还可以提供实验不能直接观察到的DNA分子较为详细的穿越过程.     

基于Bernstein多项式的自适应混沌时间序列预测算法

提出了利用Bernstein多项式对混沌时间序列的动力学方程进行建模的方法,并将该方法与递推最小二乘(RLS)算法相结合,从而可以自适应地逼近混沌时间序列的动力学特性,以达到预测的目的.理论分析和仿真实验表明该方法对一些常见的混沌时间序列具有较高的预测精度和较理想的准确预测率.由于RLS算法的收敛速度较快,因此该方法比较适合于对短混沌时间序列进行实时预测. 关键词： 混沌 预测 Bernstein多项式 RLS算法     

紧密高分子链从无规线团到球形相变的蒙特卡洛模拟：链单体的相互作用

本文采用蒙特卡洛模拟研究紧密高分子单链的无规线团到球形转变过程. 首先,研究某一固定链单体的相互作用下的有效尺寸效应,并发现短链表现出一次的坍塌相变,而长链则出现两次,这从热熔曲线上可以明显看出. 随着链单体相互作用的减小,热熔曲线上峰值对应的转变温度朝着低温转移. 从体系的能量、均方回转半径和形状因子可以进一步看出,高分子相变发生在更低的温度区间. 这些结果有助于加深理解高分子坍塌相变过程中链单体相互作用的影响.     

紧密高分子链从无规线团到球形相变的蒙特卡洛模拟:链单体的相互作用（英文）

本文采用蒙特卡洛模拟研究紧密高分子单链的无规线团到球形转变过程.首先,研究某一固定链单体的相互作用下的有效尺寸效应,并发现短链表现出一次的坍塌相变,而长链则出现两次,这从热熔曲线上可以明显看出.随着链单体相互作用的减小,热熔曲线上峰值对应的转变温度朝着低温转移.从体系的能量、均方回转半径和形状因子可以进一步看出,高分子相变发生在更低的温度区间.这些结果有助于加深理解高分子坍塌相变过程中链单体相互作用的影响.     

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.     

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.     

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     

纳米孔壁面作用对蛋白质过孔影响的粗粒化分子动力学模拟

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.     

Poisson-Fokker-Planck model for biomolecules translocation through nanopore driven by electroosmotic flow

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.     

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.     

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.     

Concentration polarization in translocation of DNA through nanopores and nanochannels

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.     

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.     

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.