Pt(111)表面低能溅射现象的分子动力学模拟

利用嵌入原子方法的原子间相互作用势，通过分子动力学模拟，详细研究了贵金属原子在Pt (111)表面的低能溅射现象.模拟结果显示：对于垂直入射情况，入射原子的质量对Pt (11 1)表面的溅射阈值影响不大.当入射原子的能量小于溅射阈值时，入射原子基本以沉积为主 ；当入射原子的能量大于溅射阈值时，溅射产额随入射原子能量的增加而线性增大；当入射 原子能量达到200 eV时，各种入射原子的溅射产额都达到或接近1，此时入射原子主要起溅 射作用.溅射原子发射的角分布概率和溅射花样与高能溅射相类似.研究表明：与基于二体碰 撞近似的线性级联溅射理论不同，当入射原子能量大于溅射阈值时，低能入射原子的溅射产 额正比于入射原子的约化能量和入射原子与基体原子的质量比.通过对低能入射原子的钉扎 能力分析，提出了支配低能溅射的入射原子反射物理机理. 关键词： 分子动力学模拟、低能溅射     

金原子纳米团簇的负热容现象的分子动力学模拟研究

文中采用微正则分子动力学方法模拟研究了原子数N=60到675之间的6种金原子纳米团簇从固态到液态的熔解过程,得到了势能和热容量随温度的变化关系.其结果表明,所模拟的6种团簇在熔点附近出现负热容,通过对这些团簇熔解前后的势能以及结构变化的分析,探讨了产生负热容的微观机制.     

铜原子纳米团簇热力学性质的分子动力学模拟研究

利用分子动力学模拟方法,研究了CuN(N=80,140,216,312,408,500,628和736)纳米团簇在热化和冷凝过程中结构和热力学性质的变化,模型采用的是Johnson的EAM作用势.模拟结果表明:铜团簇的熔点和凝固点随其尺寸线性增加,并逐渐向大块晶体靠拢;所有团簇的凝固点都低于熔点,出现凝固过程中的滞后现象;在熔点和凝固点附近,团簇都具有负热容特性,负热容是由相变前后团簇内部结构突变引起的.     

Pressure effect of structural and vibrational properties of solid pentaerythritol by molecular dynamics simulations

The molecular dynamics simulations (MD) are used to calculate the structural, vibrational and thermodynamic properties of pentaerythritol (PE) crystal up to 4 GPa. The pressure effect for the cell volume, lattice constants, and molecular geometry of solid PE are presented and discussed. It is observed that the C–C bonds has maximum variation, followed by C–H and C–O bonds, which means decomposition of the initial explosion may begin with the C–C bonds. The vibrational frequencies at ambient conditions slightly more than experimental results, and the pressure-induced frequency shifts of these modes are discussed.     

温度对吡啶离子液体性质影响的分子动力学模拟研究

运用分子动力学模拟方法研究了温度对三种吡啶离子液体[BPy][BF_4]、[HPy][BF_4]、[OPy][BF_4]热力学性质的影响,得到了每个体系的密度、自扩散系数、电导率和黏度等.研究结果表明:随着温度升高,同一种离子液体的密度减小,阴阳离子的自扩散系数明显增大,电导率升高,而黏度降低.在同一温度下,随着阳离子上烷基链的增长,离子液体的密度减小,但热力学性质的变化规律并不完全同步.烷基链长最短的[BPy][BF_4]的自扩散系数和电导率在每个温度下均为最大,而黏度最小;但烷基碳链更长的[OPy][BF_4]和[HPy][BF_4]的各种性质相差不大,甚至当温度大于323 K时,烷基链较长的[OPy][BF_4]的自扩散系数比[HPy][BF_4]的大.     

温度对吡啶离子液体性质影响的分子动力学模拟研究

运用分子动力学模拟方法研究了温度对三种吡啶离子液体[BPy][BF4]、[HPy][BF4]、[OPy][BF4]热力学性质的影响, 得到了每个体系的密度、自扩散系数、电导率和黏度等. 研究结果表明: 随着温度升高, 同一种离子液体的密度减小, 阴阳离子的自扩散系数明显增大, 电导率升高, 而黏度降低. 在同一温度下, 随着阳离子上烷基链的增长, 离子液体的密度减小, 但热力学性质的变化规律并不完全同步. 烷基链长最短的[BPy][BF4]的自扩散系数和电导率在每个温度下均为最大, 而黏度最小; 但烷基碳链更长的[OPy][BF4]和[HPy][BF4]的各种性质相差不大,甚至当温度大于323K时, 烷基链较长的[OPy][BF4]的自扩散系数比[HPy][BF4]的大.     

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.     

GPU-accelerated molecular dynamics simulation for study of liquid crystalline flows

We have developed a GPU-based molecular dynamics simulation for the study of flows of fluids with anisotropic molecules such as liquid crystals. An application of the simulation to the study of macroscopic flow (backflow) generation by molecular reorientation in a nematic liquid crystal under the application of an electric field is presented. The computations of intermolecular force and torque are parallelized on the GPU using the cell-list method, and an efficient algorithm to update the cell lists was proposed. Some important issues in the implementation of computations that involve a large number of arithmetic operations and data on the GPU that has limited high-speed memory resources are addressed extensively. Despite the relatively low GPU occupancy in the calculation of intermolecular force and torque, the computation on a recent GPU is about 50 times faster than that on a single core of a recent CPU, thus simulations involving a large number of molecules using a personal computer are possible. The GPU-based simulation should allow an extensive investigation of the molecular-level mechanisms underlying various macroscopic flow phenomena in fluids with anisotropic molecules.     

碳纳米锥力学特性的分子动力学研究

结合原子间短程作用势(Brenner势)和长程作用势(Lennard-Jones势),利用分子动力学方法对各种锥角的碳纳米锥进行拉伸和压缩实验,获得其载荷-应变关系曲线、受拉/压载荷极限、应变极限和构形演变等力学特性,并与等量原子组成的碳纳米管进行比较研究.研究结果表明,等量碳原子组成的碳纳米锥的受拉/压载荷极限随着锥角的增大先是增大后减小,受拉/压应变极限则随着锥角的增大而增大.与碳纳米锥相比,等量碳原子组成的碳纳米管的受拉/压载荷极限和应变极限显得既不突出也不逊色.在受压构形演化方面,与碳纳米管丰富的径向屈曲/扭转/侧向屈曲组合形变不同,112.88°和83.62°锥角的碳纳米锥受压沿轴向完美内陷,而60.0°和38.94°锥角的碳纳米锥受压发生侧向屈曲.     

低能Pt原子与Pt(111)表面相互作用的分子动力学模拟

利用分子动力学模拟方法详细研究了低能Pt原子与Pt(111)表面的相互作用所导致的表面吸附原子、溅射原子、表面空位的产生及分布规律,给出了表面吸附原子产额、溅射原子产额和表面空位产额随入射Pt原子能量的变化关系.模拟结果显示:溅射产额、表面吸附原子产额和表面空位产额随入射原子的能量的增加而增加,溅射原子、表面吸附原子的分布花样呈3度旋转对称性质;当入射粒子能量高于溅射阈值时,表面吸附原子主要是基体最表面原子的贡献,入射粒子直接成为表面吸附原子的概率很小.其主要原因是:当入射粒子能量高于溅射能量阈值时,入射 关键词： 分子动力学 低能粒子 表面原子产额 空位缺陷 溅射     

Computation of some thermodynamics, transport, structural properties, and new equation of state for fluid methane using two-body and three-body intermolecular potentials from molecular dynamics simulation

Molecular dynamics simulation has been performed to obtain pressure, radial distribution function, and self-diffusion coefficient of fluid methane using one site OPLS (optimized potentials for liquid simulations), five sites OPLS-SITE, and two-body HFD (Hartree-Fock dispersion)-like potentials. To take higher-body forces into account, three-body potential of Hauschild and Prausnitz (1993) has been used with the two-body HFD-like potential. The significance of this work is that the three-body potential of Hauschild and Prausnitz extended as a function of density and temperature and used with the HFD-like potential to improve the prediction of the results of pressure of fluid methane without requiring an expensive three-body calculation. The molecular dynamics simulation of methane has been also used to determine a new equation of state. The results are in a good agreement with experimental and theoretical values.     

Cu-Au体系非对称异质外延行为的分子动力学研究

利用分子动力学模拟方法研究了Cu/Au(001)和Au/Cu(001)异质外延岛的演化行为. 研究结果显示：Cu-Au体系的相互外延行为呈现出明显的非对称性. Cu在Au(001)基体表面可以形成完整的外延结构，而Au在Cu(001)基体表面外延将导致失配位错的出现. 导致非对称外延生长行为的根本原因是外延岛的应变状态的差异和外延岛自身性质的不同. 随着外延岛的长大，Cu外延岛与Au(001)基体的微观失配度由最初的接近宏观失配度的9%左右迅速单调下降，并最终趋于晶格匹配；而Au在Cu(001)基体表面外延的微观失配度则呈现出振荡增加趋势. Cu/Au(001)体系的基体形变主要发生在外延岛的边缘，而Au/Cu(001)体系的基体形变主要发生在外延岛内部所对应的区域.     

Diffusion activation energy versus the favourable energy in two-order-parameter model:A molecular dynamics study of liquid Al

In the present work, we find that both diffusion activation energy E_a(D) and E_a(S^ex) increase linearly with pressure and have the same slope (0.022±0.001 eV/GPa) for liquid Al. The temperature and pressure dependence of excess entropy is well fitted by the expression -S^ex(T,P)/k_B=a(P)+b(P)T+c(P)exp(E_f/k_BT), which together with the small ratio of E_f/k_BT leads to the relationship of excess entropy to temperature and pressure, i.e. S^ex≈-cE_f/T, where c is about 12 and E_f (=Δ E-PΔV) is the favourable energy. Therefore, there exists a simple relation between E_a(S^ex) and E_f, i.e. E_a(S^ex)≈cE_f.     

Study of lattice thermal conductivity of alpha-zirconium by molecular dynamics simulation

The non-equilibrium molecular dynamics method is adapted to calculate the phonon thermal conductivity of alphazirconium. By exchanging velocities of atoms in different regions, the stable heat flux and the temperature gradient are established to calculate the thermal conductivity. The phonon thermal conductivities under different conditions, such as different heat exchange frequencies, different temperatures, different crystallographic orientations, and crossing grain boundary (GB), are studied in detail with considering the finite size effect. It turns out that the phonon thermal conductivity decreases with the increase of temperature, and displays anisotropies along different crystallographic orientations. The phonon thermal conductivity in [0001] direction (close-packed plane) is largest, while the values in other two directions of [2īī0] and [01ī0] are relatively close. In the region near GB, there is a sharp temperature drop, and the phonon thermal conductivity is about one-tenth of that of the single crystal at 550 K, suggesting that the GB may act as a thermal barrier in the crystal.     

抑制剂8CA与脂肪细胞脂肪酸结合蛋白(A-FABP)结合模式的分子动力学研究

摘要：脂肪细胞脂肪酸结合蛋白A-FABP(Adipocyte fatty-acid binding protein)是治疗脂质调节生物过程相关疾病的重要靶标. 分子动力学模拟和MM-PBSA方法被采用研究抑制剂8CA与A-FABP结合模式. 研究结果表明静电相互作用和范德华作用驱动了抑制剂8CA与A-FABP的结合。基于残基的能量分解表明抑制剂8CA与R126间的极性相互作用为抑制剂与A-FABP的结合提供了重要贡献. 该残基与8CA的相互作用较好地稳定了抑制剂与A-FABP复合物的稳定性. 我们期望这个研究能为治疗炎症、动脉硬化和代谢病药物设计提供一定的理论指导。     

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.     

Influence of line defects on relaxation properties of graphene: A molecular dynamics study

The relaxation properties of single layer graphene sheets containing line defects were investigated using molecular dynamics simulation with AIROBE bond-order interatomic potential. The dynamic evolution of graphene sheets during relaxation condition was analyzed. The simulation results show that the single layer graphene sheets are not perfectly flat in an ideal state, and the graphene sheet shows a significant corrugations at the verge of sheet. The graphene sheet is bent with the line defects at the end of the sheet, and the extent of this bend also increases with the increase of the defect number. Furthemore, the graphene sheet transforms into a paraboloid with the line defects at the middle of the sheet.     

Au/Cu(001)异质外延岛演化的分子动力学研究

利用分子动力学弛豫方法模拟了Au/Cu(001)异质外延生长初期Au异质外延岛的形貌演化，分析了Au外延岛演化过程中的局域应力及与基体结合能随表面岛尺寸的变化. 研究结果表明：当异质外延岛小于7×7时，外延岛原子分布呈现赝Cu点阵形貌；当外延岛达到8×8后，外延岛内开始出现失配位错，失配位错数量随外延岛尺寸的增加而增加. 局域压力分析指出，外延岛上原子之间的近邻环境不同导致了所受应力的差异，而外延岛的形变则是由外延岛原子的应力分布所决定. 研究还发现，失配位错的产生导致错位原子与基体原子之间的结合强度减弱，但相对增加了非错位原子与基体原子之间的结合强度. 关键词： 异质外延 表面形貌 局域压力 分子动力学模拟     

Cu(111)三维表面岛对表面原子扩散影响的分子动力学研究

采用嵌入原子方法的原子间相互作用势，利用分子动力学方法计算了同质外延生长中不同层数的三维Cu(111)表面岛上表面原子扩散激活能，分析了三维表面岛的层数对表面原子交换扩散和跳跃扩散势垒的影响. 研究结果表明，二维Enrilich-Schwoebel(ES)势垒小于三维ES势垒，且三维ES势垒不随表面岛层数的增加而显著变化. 对于侧向表面为(100)的表面岛，表面原子沿〈011〉方向上的扩散行为，随表面岛层数增加而逐渐变化；在表面岛层数达到3层时，扩散路径上的势垒变化趋于稳定，表面原子扩散以下坡扩散为主. 对于侧面取向为(111)的表面岛，当表面岛层数大于3层后，开始呈现上坡扩散的可能. 关键词： 表面原子 扩散 分子动力学模拟