Formation of gold nanowires with impurities: a first-principles molecular dynamics simulation

We present first-principles molecular dynamics simulations of the formation of monatomic gold nanowires with different impurities (H, C, O, S). Special care was taken not to bias the probability that the impurity atoms participate in the monatomic wire, which is the main focus of this work. Hydrogen always evaporated before the formation of the monatomic chains. Carbon and oxygen were found in the final chains with low probability ( approximately 10%), while sulfur almost always participated in it (probabability approximately 90%). The mean distances between gold atoms bridged by carbon, oxygen, and sulfur were 3.3, 4.4, and 5.0 A, respectively, in good agreement with experimental observations. The contributions of carbon, oxygen, and sulfur to the density of electronic states at the Fermi level are neglegible, moderate, and large, respectively.     

Determination of ion quantity by using low-temperature ion density theory and molecular dynamics simulation

In this paper, we report a method by which the ion quantity is estimated rapidly with an accuracy of 4%. This finding is based on the low-temperature ion density theory and combined with the ion crystal size obtained from experiment with the precision of a micrometer. The method is objective, straightforward, and independent of the molecular dynamics(MD)simulation. The result can be used as the reference for the MD simulation, and the method can improve the reliability and precision of MD simulation. This method is very helpful for intensively studying ion crystal, such as phase transition,spatial configuration, temporal evolution, dynamic character, cooling efficiency, and the temperature limit of the ions.     

Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons.     

Conformational properties of cyclooctane: a molecular dynamics simulation study

Atomistic molecular dynamics simulations have been used to elucidate the conformational properties of cyclooctane in the gas and bulk liquid phases. Accurate reproduction of the gas phase structure, and of the liquid phase densities and solubility parameters have been used as prerequisites to the prediction of conformational properties. The gas phase results clearly indicate the presence of a conformational mixture consisting of the crown, boat-chair, twist-boat-chair and boat-boat conformers at all temperatures (161, 313 and 400 K) studied. The fraction of the crown family of conformers was found to be relatively insensitive to temperature. However, the relative concentrations of the twist-boat-chair and boat-chair conformations was found to be highly temperature dependent with the boat-chair being favoured at low temperatures. Bulk packing was found to have a profound effect on the conformational properties in the liquid phase. At the temperatures studied (313 and 400 K) the boat-chair family was predominant, with the crown and boat families being essentially absent. The twist-boat-chair conformation was detected in the liquid phase at both temperatures. The pseudorotation pathway for the twist-boat-chair to boat-chair interconversion was prevalent in both gas and liquid phases establishing the conformational flexibility and the relative importance of the twist-boat-chair conformer in comparison to the crown family. The study successfully explains the separate experimental findings in both the gas and liquid phases of cyclooctane.     

Relaxation dynamics and power spectra of liquid water: a molecular dynamics simulation study

We present molecular dynamics simulations of liquid water at normal and supercooled conditions. Autocorrelation functions (ACFs) of several structural quantities and their fourier transforms are obtained and analysed. Structural correlations and relaxation times increase linearly with degree of supercooling. Power spectra of ACFs show increase in librational motion of liquid water with cooling. These modes intensify with supercooling because of structuring and ordering of water molecules. Overall, liquid water structure is homogenous over the temperatures and pressures studied and undergoes fluctuation–dissipation in its local-density variations [English and Tse, Phys. Rev. Lett. 106, 037801 (2011)].     

Study of mechanical properties of amorphous copper with molecular dynamics simulation

The formation and mechanical properties of amorphous copper are studied using molecular dynamics simulation. The simulations of tension and shearing show that more pronounced plasticity is found under shearing, compared to tension. Apparent strain hardening and strain rate effect are observed. Interestingly, the variations of number density of atoms during deformation indicate free volume creation, especially under higher strain rate. In particular, it is found that shear induced dilatation does appear in the amorphous metal.     

Study of mechanical properties of amorphous copper with molecular dynamics simulation

The formation and mechanical properties of amorphous copper are studied using molecular dynamics simulation. The simulations of tension and shearing show that more pronounced plasticity is found under shearing, compared to tension. Apparent strain hardening and strain rate effect are observed. Interestingly, the variations of number density of atoms during deformation indicate free volume creation, especially under higher strain rate. In particular, it is found that shear induced dilatation does appear in the amorphous metal.     

Femtosecond laser ablation of metals:a molecular dynamics simulation study

Using molecular dynamics (MD) methods combining with two-step radiation heating model, the mechanisms of ablation and the thermodynamic states at Ni surface under femtosecond laser irradiation are investigated. Simulation results show that the main mechanisms of ablation are evaporation and tensile stresses generated inside the target. The velocity of stress wave is predicted to be nearly equal to sound velocity. The rates of ablation at different fluences obtained from simulations are in good agreement with experimental data. Superheating phenomenon is also discovered.     

非绝热分子动力学的量子路径模拟

基于近期发展的经典-量子混合模拟非绝热分子动力学的量子路径方案,本文对5个典型势能面模型进行了模拟,包括单交叉模型、双交叉模型、拓展耦合模型、哑铃模型以及双弓模型.由于难以在严格意义上得到退相干速率,数值模拟中,我们比较了三个不同的退相干速率公式,包括冻结高斯波包近似退相干速率、能量分辨速率以及力分辨速率.在模拟过程中,我们恰当地处理了势能面跳跃时的能量守恒和力的反向问题.通过与全量子动力学模拟的精确结果进行对比发现,对于结构较简单的势能面模型,三种退相干速率都能得到较好的结果;然而对于较复杂的势能面模型,由于复杂量子干涉的原因,与其他混合经典-量子动力学方案类似,量子路径方案仍然难以得到较准确的结果.如何发展更加有效的混合经典-量子模拟方案,是未来研究的重要课题.     

分子动力学模拟方法在非线性光学中的应用

有机分子非线性光学材料在频率转换、电光调制和双光子吸收等方面具有重要的应用.介绍了近年来分子动力学模拟方法在有机分子非线性光学性质理论研究中的主要应用,包括电场极化效应、局域场因子、非线性极化率和双光子吸收等.此外,结合最新的科研工作,介绍了分子动力学模拟方法在溶剂效应和聚集效应研究中发挥的重要作用. 关键词： 分子动力学模拟 溶剂效应 聚集效应 双光子吸收     

非晶态石英的变电荷分子动力学模拟

基于迭代变电荷方法,用分子动力学模拟了非晶态石英的结构与振动特征.首先利用熔化-猝火方法得到了非晶石英的平衡结构.在此基础上获得了体系不同原子对之间的对关联函数、键角分布函数和振动频谱等,结果与实验数据均符合较好.变电荷方法的计算结果表明,非晶石英体系内粒子的电荷与石英晶体内粒子电荷显著不同,并且出现了较大的涨落. 关键词： 分子动力学 变电荷 非晶石英     

Electrostatic interactions in molecular dynamics simulation of a three-dimensional system with periodicity in one direction

The Mellin transform and Poisson summation formula are used to derive an expression for the Coulomb interaction energy of a three-dimensional system with periodicity in one direction. Initially, calculations are performed for interactions characterized by any inverse power and, using the analytical continuation of the energy function, one obtains the final expression for the interaction energy of charges. We consider also a special case when two different charges are located on a line parallel to the periodicity direction. The energy and force expressions are identical to those obtained from the Lekner summation which is simply a sum over reciprocal lattice terms. The convergence behaviour of the Lekner summation is compared with that based on the Ewald type approach.     

碳纳米管从硅基板上剥离的拉伸分子动力学模拟研究

采用拉伸分子动力学方法研究了单壁碳纳米管(8, 8)在室温下从硅基板上被剥离的过程.当碳纳米管(CNT)在硅基底上被剥离时, 剥离距离和理想弹簧所测平均剥离力之间呈现一定规律的关系曲线,并出现了较大的正、负峰值. 比较了不同剥离速度下的平均剥离力,并拟合了其峰值与速度的关系. 拉伸分子动力学模拟结果显示,所需剥离力的最大值与速度之间呈现一定的线性关系, 模拟结果同生物物理学上类似的剥离实验结果符合较好,但相比于高分子, CNT和硅(Si)组成的界面吸附性能更强.讨论了碳纳米管长度、 半径及缺陷对剥离过程的影响,研究表明:所需最大的剥离力与CNT的长度无关, 但随CNT半径的增加,需要的最大剥离力线性增加; 5-7-7-5缺陷对剥离力最大值影响较小,而半径变化缺陷会削减最大剥离力. 在原子尺度对未来的试验进行了理论预测,为碳纳米管在硅微电子工业中的应用提供了理论基础.     

Correlated dynamics determining x-ray diffuse scattering from a crystalline protein revealed by molecular dynamics simulation

The dynamical origin of the x-ray diffuse scattering by crystals of a protein, Staphylococcal nuclease, is determined using molecular dynamics simulation. A smooth, nearly isotropic scattering shell at originates from equal contributions from correlations in nearest-neighbor water molecule dynamics and from internal protein motions, the latter consisting of -helix pitch and inter--strand fluctuations. Superposed on the shell are intense, three-dimensional scattering features that originate from a very small number of slowly varying (>10 ns) collective motions. The individual three-dimensional features are assigned to specific collective motions in the protein, and some of these explicitly involve potentially functional active-site deformations.     

Solvation dynamics in methanol: Experimental and molecular dynamics simulation studies

We have investigated the ultrafast dynamics of methanol by time dependent fluorescent shift experiments and molecular dynamic simulations. The experiments were performed with two different probe molecules, 1-aminonaphthalene and coumarin 153. The molecular dynamic simulations employed these probes as well as small atomic and diatomic solutes. We find a previously unobserved fast decay component in the solvation response of methanol. The molecular dynamics results are in good agreement with this experimental result. The origin of this fast response and the linearity of the solvent response are discussed.     

Methane in carbon nanotube: molecular dynamics simulation

The behaviour of methane molecules inside carbon nanotubes at room temperature is studied using classical molecular dynamics simulations. A methane molecule is represented either by a shapeless super-atom or by a rigid set of five interaction centres localized on atoms. Different loadings of methane molecules ranging from the dense gas density to the liquid density, and the influence of flexibility of the CNT on structural and dynamic properties of confined molecules are considered. The simulation results show the decreases of the diffusion coefficient of methane molecules with density. At higher densities diffusion coefficient values are almost independent of molecular shape, but at low densities one observes faster motion of the super-atom molecule than that for the tetrahedral model of the molecule. For loadings of methane considered here the nanotube flexibility, introduced by the reactive empirical bond order (REBO) potential for interactions between carbon atoms of nanotube, does not have an effect on diffusivity of methane molecules, and its impact on the molecular structure is weak. It is found that methane molecules in the vicinity of the nanotube wall show tripod orientation with respect to the nanotube surface.     

纳米多晶金属样本构建的分子动力学模拟研究

研究了分子动力学模拟中纳米多晶金属样本的构建过程.首先采用Voronoi几何方法生成初始的纳米多晶铝和铜样本,然后用快速冷凝(或共轭梯度)法得到样本的局域最低能态,最后在恒温零应力周围环境下(常温常压NPT系综)退火得到最低能态样本.使用样本的残余内应力来衡量纳米多晶样本是否与实验制备的一致.通过监测这两步弛豫过程中晶界结构的变化形态、体系平均内应力和能量下降过程及具体的局域分布和不同弛豫条件下最终样本的弹性常数,发现样本的能量和残余内应力都接近实验制备的纳米多晶金属.对Voronoi几何法生成的晶界而言     

纳米铜团簇凝结规律的分子动力学研究

采用分子动力学方法对包含147，309和561个原子数的液态纳米铜团簇凝结过程进行模拟研 究，结果表明降温速率及团簇原子数对凝结得到常温下的固态团簇结构有重要影响：在模拟 时间内，降温速度越慢，团簇原子数越少，凝结得到铜团簇越倾向生成二十面体结构，反之 则倾向生成面心立方结构.同时探讨了该现象的物理机理. 关键词： 铜团簇 凝结 结构 分子动力学