多孔介质中流体输运的孔尺度MD模拟

本文采用分子动力学(MD)方法对流体流过单个纳米尺度孔的过程进行数值模拟。纳米尺度孔是由两块平行的三氧化二铝平板构成的。通过对孔内每个水分子施加均匀的外力来驱动流体流动。分子之间的相互作用都采用12-6 L-J势能模型来描述。本文数值模拟了流体输运的孔尺度效应,分析了孔尺度对壁面速度是否存在滑移的影响,讨论了驱动力和通道尺度对滑移速度和壁面动力黏性系数的影响,模拟发现存在一临界尺度,它决定了是否存在滑移,还发现特定尺度下存在一临界驱动力,它决定了等效黏度的非牛顿流体特征。     

纳米通道内液体流动的分子动力学研究

本文采用分子动力学方法模拟液体在定截面及变截面纳米通道内的三维Poiseuille流动,研究液体浸润性及通道截面变化对纳米通道内液体流动的影响.研究结果表明:液体对壁面不湿润时,壁面处有速度滑移存在,并且随接触角的增大而增大,液体对壁面湿润则不存在速度滑移;同时,摩擦阻力系数随接触角的减小而增大.通道截面形状的变化对流场的影响随着远离变截面位置而迅速减弱,对流体通道平直处的流体速度相对值分布影响不大,对摩擦阻力系数影响较大.     

纳米通道内液态微流动密度分布特性数值模拟研究

微通道内流动因表面积/体积比值极大, 造成许多微尺度效应, 进而使微通道内出现完全不同于宏观流动的流体密度分布特性. 本文以纳米通道内液态Poiseuille流为对象, 采用非平衡分子动力学模拟方法研究了流体原子间相互作用强度ε_LL, 流体原子间平衡距离σ_LL以及壁面原子与流体原子间平衡距离σ_LS对通道内流体密度分布的影响规律. 数值模拟中, 统计系综取微正则系综, 势能函数选用LJ/126模型, 壁面设为Rigid-atom壁面, 温度校正使用速度定标法, 牛顿运动方程的求解则采用Verlet算法. 模拟结果表明, 随ε_LL的减弱, 近壁面区密度分布的振荡幅度则逐渐增大; 而σ_LL 则同时影响流体原子的存在形态和密度分布, 较大的σ_LL 会造成流体原子在整个通道内呈现面心立方结构的类似固体排列, 较小的σ_LL会使得流体原子呈现不断变化的 "团簇" 结构; 随σ_LS的变大, 近壁面区流体密度振荡幅度增大, 且流体密度分布起点离壁面越远. 另外, 本文还从近壁面区流体原子的 "俘获-逃逸" 行为角度, 初步解释了原子间相互作用强度对密度分布的影响规律. 关键词： 纳米通道 微流动 密度分布 分子动力学     

纳米尺度下气泡核化生长的分子动力学研究

采用分子动力学方法模拟纳米尺度下液体在固体壁面上发生核化沸腾的过程,主要研究壁面浸润性对气泡初始核化过程和气泡生长速率的影响以及固-液界面效应在液体核化沸腾的能量传递过程中所起到的作用.研究结果发现：壁面浸润性越强,气泡在固壁处越容易核化.该结果与经典核化理论中“疏水壁面易于产生气泡”的现象产生了明显的区别.其根本原因是在纳米尺度下,固-液界面热阻效应不能被忽略.一方面,在相同的壁温下,通过增强固-液相互作用,可以显著降低界面热阻,使得热量传递效率提高,导致靠近壁面处的流体温度升高,气泡核化等待时间缩短,有利于液体沸腾核化.另一方面,气泡的生长速率随着壁面浸润性的增强而明显升高.当气泡体积生长到一定程度时,会在壁面处形成气膜,从而导致壁面传热性能恶化.因此,通过壁面的热流密度呈现出先增大后减小的规律.     

壁面粗糙度对油-水-固三相接触线的影响

本文建立了十二烷-水-石墨壁面系统的分子动力学模型,通过分析微观接触角、油水分子在壁面的吸附特性及水分子吸附能研究了壁面粗糙度对油-水固三相接触线的影响。模拟结果表明,壁面凸起的存在会减弱其对油水分子的吸附强度,因此水侧壁面有凸起时水侧接触角增大,而油侧壁面有凸起时水侧接触角减小;壁面吸附油分子平行于壁面排列,壁面凸起结构对其影响不大;凸起结构的存在使壁面吸附水分子的定向排布趋势减弱,吸附强度和稳定性降低。     

纳米通道内高分子稀溶液的分子动力学模拟

运用分子动力学方法对纳米通道内的高分子稀溶液进行了模拟,分析了通道宽度、壁面性质和链长对高分子链构象参数和质心密度分布的影响。模拟结果表明:随着通道宽度和壁面接触角的增大,回转半径逐渐减小,高分子链实现了从二维构象向三维构象的转变;通道宽度的减小和壁而接触角的增大,均导致高分子链远离壁面;在通道宽度一定时,长链高分子易呈伸展状且远离壁面,而短链易呈团聚状且移向壁面.     

纳米尺度下毛细流动的分子动力学模拟

采用分子动力学模拟研究纳米尺度下壁面润湿性对毛细流动的影响,主要考虑纳米通道两侧壁面润湿性相同与不同两种情况。研究表明：两侧壁面润湿性相同条件下,毛细流动随着壁面润湿性增强而加快, 毛细高度随时间的变化早期偏离Lucas-Washburn理论,但后期与其预测符合。在纳米通道两侧壁面润湿性不同的情况下,液面会发生振荡,两侧壁面毛细高度也不相等,且液面振荡的幅度和两侧壁面毛细高度差都随着两侧壁面润湿性差异的增大而增大。基于能量转化分析,提出两侧壁面湿润性不同情况下纳米通道中毛细流动发生的条件以及毛细流动快慢的判别依据。研究结果加深了对纳米尺度下毛细流动机理的认识,并为相关工程应用提供理论参考。     

非接触铜铝纳米薄膜侧向移动相互作用的分析

采用分子动力学方法模拟铜铝纳米薄膜相对侧向移动的相互作用能。研究了铜薄膜的侧向位移从0Å到50Å时温度、相互作用间距、表面形貌和表面粗糙度对作用能的影响。结果表明,相互作用强度随温度的增加而增大,随相互作用间距的减小而增大,随表面粗糙度的增大而减小。为研究薄膜在纳米尺度的相互作用提供了一个新的方法。     

非接触铜铝纳米薄膜侧向移动相互作用的分析

采用分子动力学方法模拟铜铝纳米薄膜相对侧向移动的相互作用能。研究了铜薄膜的侧向位移从0Å到50Å时温度、相互作用间距、表面形貌和表面粗糙度对作用能的影响。结果表明,相互作用强度随温度的增加而增大,随相互作用间距的减小而增大,随表面粗糙度的增大而减小。为研究薄膜在纳米尺度的相互作用提供了一个新的方法。     

壁面效应对纳米尺度气体流动的影响规律研究

采用分子动力学方法研究了过渡区纳米通道内的壁面力场对气体剪切流动的影响规律.在纳米尺度下,壁面力场对流场的主导作用更加显著,流动物理量对于壁面条件和系统温度的变化也更加敏感.壁面原子的运动采用Einstein模型模拟,结果表明随着壁面刚度的增加,气体在近壁面区域的速度峰值减小,气体分子与壁面的动量适应性变差.壁面粗糙度通过金字塔形模型来研究,发现无论是主流区域还是近壁区域,壁面粗糙度对流动的影响都非常明显.当粗糙单元高度增大时,气体分子在壁面处的聚集现象明显,与壁面完全动量适应.本文还研究了系统温度对纳米通道流动的影响,结果表明温度的影响是全局性的,温度的升高导致整个通道内流速降低,近壁区域气体密度减小,气-固动量适应性变差.     

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.     

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.     

Molecular Dynamics Simulation on Charge Transfer Relaxation between Myoglobin and Water

Dynamical processes of myoglobin after photon-excited charge transfer between Fe ion and surrounding water anion are simulated by a molecular dynamics model. The roles of Coulomb interaction effect and water effect in the relaxation process are discussed. It is found that the relaxations before and after charge transfer are similar. Strong Coulomb interactions and less water mobility decrease Coulomb energy fluctuations. An extra transferred charge of Fe ion has impact on water packing with a distance up to 0.86nm.     

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.     

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.     

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.     

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.     

脱氧核糖核酸单链序列的预测

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951%.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     

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.     

Water Transport through Multinanopores Membranes

We investigate the influence of correlation between water molecules transport through the neighbouring nanopores, whose centres are at a distance of only 6.2A, using the molecular dynamics simulations. Water molecule distribution in nanopore and average water flow are obtained. It is found that the average water molecule number and water flow are slightly different between a system made of the neighbouring nanopores and a system of a single pore. This indicates that transport of water chains in neighbouring pores do no show significant influence each other. These findings should be helpful in designing efficient artificial membrane made of nanopores and providing an insight into effects of the biological channel structure on the water permeation.