熵驱动下柱状高分子刷螺旋结构的研究

自然界中广泛存在螺旋结构,在特定情形下熵能驱动高分子链形成螺旋结构.本文采用分子动力学方法研究柱状高分子刷吸附在无限长圆柱表面时的构象行为.发现其构象与嫁接支链条数、柱状高分子刷与圆柱表面之间的吸附能密切相关.在较弱的吸附能下,具有较多支链条数的柱状高分子刷能形成完整的螺旋结构,其本质就是熵驱动下形成的螺旋结构.该研究有助于加深对生物大分子螺旋结构的理解.     

Modulation of intra- and inter-sheet interactions in short peptide self-assembly by acetonitrile in aqueous solution

Besides our previous experimental discovery(Zhao Y R, et al. 2015 Langmuir, 31, 12975) that acetonitrile(ACN)can tune the morphological features of nanostructures self-assembled by short peptides KIIIIK(KI4K) in aqueous solution,further experiments reported in this work demonstrate that ACN can also tune the mass of the self-assembled nanostructures.To understand the microscopic mechanism how ACN molecules interfere peptide self-assembly process, we conducted a series of molecular dynamics simulations on a monomer, a cross-β sheet structure, and a proto-fibril of KI4 K in pure water, pure ACN, and ACN-water mixtures, respectively. The simulation results indicate that ACN enhances the intra-sheet interaction dominated by the hydrogen bonding(H-bonding) interactions between peptide backbones, but weakens the inter-sheet interaction dominated by the interactions between hydrophobic side chains. Through analyzing the correlations between different groups of solvent and peptides and the solvent behaviors around the proto-fibril, we have found that both the polar and nonpolar groups of ACN play significant roles in causing the opposite effects on intermolecular interactions among peptides. The weaker correlation of the polar group of ACN than water molecule with the peptide backbone enhances H-bonding interactions between peptides in the proto-fibril. The stronger correlation of the nonpolar group of ACN than water molecule with the peptide side chain leads to the accumulation of ACN molecules around the proto-fibril with their hydrophilic groups exposed to water, which in turn allows more water molecules close to the proto-fibril surface and weakens the inter-sheet interactions. The two opposite effects caused by ACN form a microscopic mechanism clearly explaining our experimental observations.     

表面黏附导致的接触行为转变

应用大规模分子动力学方法, 模拟了具有不同原子级粗糙形貌的两种刚性球形探头与弹性平面基体的黏附接触行为. 研究了载荷与真实接触面积、接触界面排斥力与真实接触面积, 以及黏附力与真实接触面积之间的关系. 分子模拟得到的载荷与真实接触面积的关系, 与连续力学接触理论预测很好地定性一致. 无论是原子级光滑探头还是粗糙探头, 黏附接触下的排斥力与真实接触面积的关系, 都与无黏附接触时的规律相一致, 即黏附力对接触行为的影响作用, 可以等效为附加在真实外载荷基础上的虚拟载荷, 将对黏附接触行为的分析转变为无黏附接触分析. 两种探头的黏附力随真实接触面积都呈幂函数形式的增长, 但是, 原子级光滑探头的幂指数大于1, 而原子级粗糙探头的幂指数小于1. 关键词： 接触行为 表面黏附 分子动力学模拟     

Asymmetry of the water flux induced by the deformation of a nanotube

The behavior of nano-confined water is expected to be fundamentally different from the behavior of bulk water.At the nanoscale,it is still unclear whether water flows more easily along the convergent direction or the divergent one,and whether a hourglass shape is more convenient than a funnel shape for water molecules to pass through a nanotube.Here,we present an approach to explore these questions by changing the deformation position of a carbon nanotube.The results of our molecular dynamics simulation indicate that the water flux through the nanotube changes significantly when the deformation position moves away from the middle region of the tube.Different from the macroscopic level,we find water flux asymmetry(water flows more easily along the convergent direction than along the divergent one),which plays a key role in a nano water pump driven by a ratchet-like mechanism.We explore the mechanism and calculate the water flux by means of the Fokker-Planck equation and find that our theoretical results are well consistent with the simulation results.Furthermore,the simulation results demonstrate that the effect of deformation location on the water flux will be reduced when the diameter of the nanochannel increases.These findings are helpful for devising water transporters or filters based on carbon nanotubes and understanding the molecular mechanism of biological channels.     

低温下Cu13团簇负载于Cu(001)表面上结构变化的分子动力学研究

应用分子动力学方法研究温度为10和50 K时具有二十面体结构的Cu13团簇以不同接触条件与Cu(001)表面结合后的结构变化,原子间的相互作用势采用Johnson的嵌入原子方法模型.通过基于原子密度分布函数的分析表明,负载团簇与表面的结合能主要受团簇与载体相接触的最低层原子数及这些原子所具有的不同几何构型影响,同时更高层的原子呈现出不同的几何结构.温度为10 K时,负载团簇的初始位置对团簇几何结构和结合能影响较大.     

低温下Cu13团簇负载于Cu(001)表面上结构变化的分子动力学研究

应用分子动力学方法研究温度为10和50 K时具有二十面体结构的Cu₁₃团簇以不同接触条件与Cu（001）表面结合后的结构变化,原子间的相互作用势采用Johnson的嵌入原子方法模型.通过基于原子密度分布函数的分析表明,负载团簇与表面的结合能主要受团簇与载体相接触的最低层原子数及这些原子所具有的不同几何构型影响,同时更高层的原子呈现出不同的几何结构.温度为10 K时,负载团簇的初始位置对团簇几何结构和结合能影响较大. 关键词： 分子动力学 团簇 表面 计算机模拟     

摩擦导致的聚合物表层微观结构改变

应用大规模分子动力学方法, 模拟了锥形探头在非晶态聚合物薄膜表面的滑动摩擦过程, 研究了摩擦导致的聚合物薄膜表层微观结构改变, 以及探头与基体间黏着作用、滑动速度和分子链长度对基体表层微观结构改变的影响. 当探头与基体之间为黏着作用时, 摩擦导致基体表面滑痕区域的键取向沿滑动方向重新取向, 导致表层分子链回转半径沿滑动方向伸长, 并且这些表层微观结构的改变程度随滑动速度的减小而增大. 在摩擦导致结构改变的过程中, 链端单体和链中单体的贡献作用不同, 形成了不同的分子链拉伸变形机制. 当样本缠结度较大或探头滑动速度较小时, 相比于链中单体, 探头对链端单体的拖曳作用使更多分子链发生拉伸变形. 研究还发现, 在探头与聚合物薄膜系统中, 使薄膜表层微观结构发生改变是摩擦能量耗散的重要途径.     

表面能梯度驱动下纳米水滴在不同微结构表面上的运动

近年来, 微观尺度下水滴在能量梯度表面上的运动情况受到了广泛关注, 然而通过实验进行研究尚存在困难. 本文利用分子动力学方法研究了不同微结构表面上纳米水滴在表面能梯度驱动下的运动情况. 结果表明: 槽状和柱状微结构可以明显提升纳米水滴在微结构表面上的运动效率, 钉状微结构会降低纳米水滴的运动效率, 尽管它具有稳定的疏水性; 结合槽状和钉状结构的混合状微结构兼具二者的优点, 不但可以有效地提高纳米水滴在粗糙表面上的运动效率, 而且具有比较高的疏水稳定性. 此外, 表面能的微小改变会明显影响水滴的运动效率.     

Structure and Dynamics of Ethanol Adsorbed on a Mica Surface

The structural and dynamic properties of nanoscale ethanol film on a mica surface are investigated via molecular dynamics simulations.We observe a dense,almost flat ethanol bilayer formed in the vicinity of the mica surface,with the hydrophobic alkyl groups pointing outward from the surface.Remarkably,such ethanol bilayer is laterally well-ordered with patterned adsorption sites.Each ethanol molecule in the first layer donates one hydrogen bond to the surface basal oxygen atoms and accepts one hydrogen bond from that in the second layer.The ethanol molecules within the bilayer exhibit constrained lateral mobility and delayed dynamics as compared with bulk ethanol,whereas those on top of the bilayer have bulk-like characteristics.     

Coalescence between Cu57 and Cu58 clusters at a room temperature: molecular dynamics simulations

Three coalescence processes of Cu57-Cu57,Cu57-Cu58,and Cu58-Cu58 clusters at 300 K are investigated by employing molecular dynamics simulations.According to the evolutions of mean square displacement and local atom packing,the coalescence process can be separated into three stages including an approaching stage,a coalescing stage,and a coalesced stage.The simulations show that the coalescence processes and the formed products are sensitive to the respective initial structures of,and the relative configuration between,the two coalescing icosahedron-based clusters.     

熔融Cu57团簇在急冷过程中弛豫和局域结构转变的分子动力学研究

采用基于嵌入原子方法的正则系综分子动力学研究熔融Cu₅₇团簇在急冷过程中的弛豫及其局域结构变化.通过对弛豫过程中均方位移、非相干中间散射函数和非Gauss参数三种函数和原子键对随急冷温度不同所发生变化的分析表明,在经过短时间的原子剧烈运动后,急冷温度极大地影响着团簇内原子结构弛豫过程.急冷温度较高时,原子在经历短时间剧烈运动的β弛豫后,进入α弛豫区后以扩散运动为主,随后原子运动表现为非扩散性的原子局域结构重排,团簇内没有出现明显的成核结构.随着温度的降低,原子局域结构的变化在经过短时间原子剧烈运动的β弛豫后,在α弛豫区原子运动表现为扩散性运动,并出现一定数量的不稳定二十面体结构.当急冷温度很低时,在进入α弛豫区后,团簇结构变化逐渐表现为非扩散性原子局域结构重排,形成相当数量的稳定成核二十面体结构. 关键词： 团簇 分子动力学 计算机模拟 表面     

低温下Au959团簇负载于MgO(100)表面后结构变化的分子动力学研究

采用基于Chen-Mbius反演方法,从金属/金属氧化物界面第一性原理计算的粘结能结果中推导出的Au/MgO原子间相互作用势的正则系综(NVT)分子动力学,模拟了在10 K条件下,Au959团簇负载于MgO(100)表面后团簇结构的变化.根据原子对分析技术和对分布函数的分析表明,由于团簇界面处原子间距与载体原子间距相匹配,置于载体上的Au团簇经过一个变形过程后,较其孤立自由表面时的团簇体积变大.     

低温下Au959团簇负载于MgO(100)表面后结构变化的分子动力学研究

采用基于Chen-Mbius反演方法,从金属/金属氧化物界面第一性原理计算的粘结能结果中推导出的Au/MgO原子间相互作用势的正则系综（NVT）分子动力学,模拟了在10 K条件下,Au₉₅₉团簇负载于MgO（100）表面后团簇结构的变化.根据原子对分析技术和对分布函数的分析表明,由于团簇界面处原子间距与载体原子间距相匹配,置于载体上的Au团簇经过一个变形过程后,较其孤立自由表面时的团簇体积变大. 关键词： 团簇 分子动力学 计算机模拟 表面     

Structure and dynamics of ordered water in a thick nanofilm on ionic surfaces

The structure and dynamics of water in a thick film on an ionic surface are studied by molecular dynamic simulations. We find that there is a dense monolayer of water molecules in the vicinity of the surface. Water molecules within this layer not only show an upright hydrogen-down orientation, but also an upright hydrogen-up orientation. Thus, water molecules in this layer can form hydrogen bonds with water molecules in the next layer. Therefore, the two-dimensional hydrogen bond network of the first layer is disrupted, mainly due to the O atoms in this layer, which are affected by the next layer and are unstable. Moreover, these water molecules exhibit delayed dynamic behavior with relatively long residence time compared with those bulk-like molecules in the other layers. Our study should be helpful to further understand the influence of water film thickness on the interfacial water at the solid-liquid interface.     

小尺寸铜团簇冷却与并合过程中结构变化的原子尺度研究

研究Cu_N（N=57,58,59）熔融铜团簇在冷却过程以及300 K时两个具有二十面体结构Cu₅₅团簇在并合过程中的结构变化.对这些小尺寸团簇的结构变化采用基于嵌入原子方法的正则系综分子动力学进行计算机模拟.通过对模拟结果的分析表明,小团簇的冷却和并合过程存在阶段变化的特点.降温过程中Cu_N（N=57,58,59）团簇的原子运动及其微观结构变化表现出较大差异,由此导致这三类团簇内原子排布的不同,其中Cu₅₉团簇结构的有序程度最低.在两个Cu₅₅团簇并合早期阶段,这两个团簇相接触后发生变形导致原子位置出现较大改变,在随后的并合过程中,原子扩散引起原子局部位置调整导致所并合体系的结构发生变化.远离两个团簇接触区的原子仍保持其并合前的结构. 关键词： 团簇 分子动力学 计算机模拟 表面     

Nano-sized local magnetic field induced by circular motion of ions and molecules in a nanotorus under gigahertz rotating electric fields

Recently, we reported molecular dynamics simulations of stable cyclotron motions of ions and water molecules in a carbon nanotorus, induced by different rotating electric fields (EFs). This study is devoted to the calculation and characterisation of the magnetic field (MF) induced by these cyclotron motions. Results show that carbon nanotorus containing ions or water molecules acts as an EF-to-MF transducer. Components of the instantaneous induced MF show large-scale oscillations superimposed by strong fluctuations arising respectively from overall circular motion and random collisions of moving species. Analysis of the space-dependencies of the induced MF components shows that the induced MF is maximum at the centre of the nanotorus. The MF induced by cyclotron motion of ions follows the orders B(Ca²⁺)?>?B(Na⁺)?≈?B(K⁺) at E?=?1.0?V/nm and B(E?=?1.0?V/nm)?>?B(E?=?0.5?V/nm)?>?B(E?=?0.1?V/nm). The time-averaged induced MF of the cyclotron motion of 81 water molecules is almost 10² times stronger than that of ions. The induced MF strength is decreased with increasing distance from nanotorus and decays effectively at about 17.3–18.1 and 15.9–18.2?nm along the z-axis of the nanotorus for ions and water molecules, respectively. The magnitude of the MF induced by cyclotron motions of water molecules and ions, respectively, decreases and increases in the nanotorus with freed carbon atoms.     

Size-dependent surface tension of a cylindrical nanobubble in liquid Ar

In view of the continued disputes on the fundamental question of whether the surface tension of a vapour bubble in liquid argon increases,or decreases,or remains unchanged with the increase of curvature radius,a cylindrical vapour bubble of argon is studied by molecular dynamics simulation in this paper instead of spherical vapour bubble so as to reduce the statistical error.So far,the surface tension of the cylindrical vapour bubble has not been studied by molecular dynamics simulation in the literature.Our results show that the surface tension decreases with radius increasing.By fitting the Tolman equation with our data,the Tolman length δ = -0.6225 sigma is given under cut-off radius 2.5σ,where σ = 0.3405 nm is the diameter of an argon atom.The Tolman length of Ar being negative is affirmed and the Tolman length of Ar being approximately zero given in the literature is negated,and it is pointed out that this error is attributed to the application of the inapplicable empirical equation of state and the neglect of the difference between surface tension and an equimolar surface.     

About the influence of friction and polydispersity on the jamming behavior of bead assemblies

We study the jamming of bead assemblies placed in a cylindrical container whose bottom is pierced with a circular hole. Their jamming behavior is quantified here by the median jamming diameter, that is the diameter of the hole for which the jamming probability is 0.5. Median jamming diameters of monodisperse assemblies are obtained numerically using the Distinct Element Method and experimentally with steel beads. We obtain good agreement between numerical and experimental results. The influence of friction is then investigated. In particular, the formation of concentric bead rings is observed for low frictions. We identify this phenomenon as a boundary effect and study its influence on jamming. Relying on measures obtained from simulation runs, the median jamming diameter of bidisperse bead assemblies is finally found to depend only on the volume-average diameter of their constituting beads. We formulate this as a tentative law and validate it using bidisperse assemblies of steel beads.     

Effect of a monomeric sequence on the structure of hydrated Nafion in the sandwich model and solvent dynamics in nano-channels: a molecular dynamic study

Molecular dynamics simulations are performed to obtain insight into the structural properties of hydrated Nafion using the sandwich model of the polymer membrane. It is shown that a larger distance between the sulfonate groups of a chain leads to the polymer forming a better inverted micelles structure. Water– and hydronium–polymer interfaces are investigated. Comparing our results with others indicates that, from the perspective of distance, the formation of shells of water and hydronium ions is independent of the model and monomer type, but depends on both if the coordination number is considered. The behaviour of water molecules and hydronium ions is also studied dynamically. Our survey shows that there is an increasing jump in the diffusion coefficient of water at a certain distance between the sulfonate groups of a chain, which then tends to change slightly. Such behaviour is discussed on the basis of density, the available space, as well as the loss of one translational degree of freedom of the water molecules at larger distances. The diffusion coefficient for the hydronium ions was also determined to be much smaller than that for water (by 3.5–6.1 times). The diffusion coefficient of the hydronium ions shows a declining jump at a certain distance between the sulfonate groups of a chain, but the jump is not significant as that for the water molecules.     

Cu87团簇在升温与急冷过程中结构变化的原子尺度模拟

本文采用基于嵌入原子法的正则系综分子动力学方法在原子尺度上计算了包含87个原子的Cu87金属团簇在连续升温和急冷降温时的结构演化过程。根据原子平均势能、对分布函数、原子堆积结构和主要原子键对数目随温度的变化表明,温度的不同极大地影响团簇内的原子堆积结构。在升温过程中,随着温度的升高,团簇内原子堆积结构出现由密排六方、二十面体直到无序堆积的变化。在急冷降温过程中,随着急冷温度的降低,团簇内由出现的一定数量的二十面体和面心立方的局域结构、数量不一的HCP,FCC和二十面体局域结构,直到急冷温度较低时的一定数量的二十面体局域结构。