金属纳米棒弯曲力学行为的分子动力学模拟

纳米结构的力学性能是纳米超微型器件设计的基础,分子动力学是研究纳米结构力学行为的有效方法.本文采用镶嵌原子方法模拟金属铜纳米棒的弯曲力学行为.计算结果表明由于尺寸效应和表面效应的影响,在纳观尺度下纳米结构表现出与宏观尺度下完全不同的力学特征.金属纳米棒弯曲力学过程分为初始变形迟滞阶段、线弹性变形阶段和塑性变形阶段.塑性变形阶段表现出“刚化”、“台阶”和较强的延性等特征. 关键词： 纳米结构 纳米棒 弯曲性能 分子动力学     

Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules

All atom molecular dynamics simulations with explicit water were done to study the interaction between two parallel double-stranded DNA molecules in the presence of the multivalent counterions putrescine (2+), spermidine (3+), spermine (4+) and cobalt hexamine (3+). The inter-DNA interaction potential is obtained with the umbrella sampling technique. The attractive force is rationalized in terms of the formation of ion bridges, i.e., multivalent ions which are simultaneously bound to the two opposing DNA molecules. The lifetime of the ion bridges is short on the order of a few nanoseconds.     

分子动力学模拟H原子与Si的表面相互作用

通过分子动力学模拟了入射能量对H原子与晶Si表面相互作用的影响. 通过模拟数据与实验数据的比较, 得到H原子吸附率随入射量的增加 呈先增加后趋于平衡的趋势. 沉积的H原子在Si表面形成一层氢化非晶硅薄膜, 刻蚀产物(H₂, SiH₂, SiH₃和SiH₄)对H原子吸附率趋于平衡有重要影响, 并且也决定了样品的表面粗糙度. 当入射能量为1 eV时, 样品表面粗糙度最小. 随着入射能量的增加, 氢化非晶硅薄膜中各成分(SiH, SiH₂, SiH₃)的量以及分布均有所变化. 关键词： 分子动力学 吸附率 表面粗糙度 氢化非晶硅薄膜     

Molecular dynamics simulation of the interaction between a mixed dislocation and a stacking fault tetrahedron

A high number-density of nanometer-sized stacking fault tetrahedra are commonly found during irradiation of low stacking fault energy metals. The stacking fault tetrahedra act as obstacles to dislocation motion leading to increased yield strength and decreased ductility. Thus, an improved understanding of the interaction between gliding dislocations and stacking fault tetrahedra are critical to reliably predict the mechanical properties of irradiated materials. Many studies have investigated the interaction of a screw or edge dislocation with a stacking fault tetrahedron (SFT). However, atomistic studies of a mixed dislocation interaction with an SFT are not available, even though mixed dislocations are the most common. In this paper, molecular dynamics simulation results of the interaction between a mixed dislocation and an SFT in face-centered cubic copper are presented. The interaction results in shearing, partial absorption, destabilization or simple bypass of the SFT, depending on the interaction geometry. However, the SFT was not completely annihilated, absorbed or collapsed during a single interaction with a mixed dislocation. These observations, combined with simulation results of edge or screw dislocations, suggest that defect-free channel formation in irradiated copper is not likely by a single dislocation sweeping or destruction process, but rather by a complex mix of multiple shearing, partial absorption and defect cluster transportation that ultimately reduces the size of stacking fault tetrahedra within a localized region.     

Molecular dynamics simulation of gas adsorption on defected graphene

Gas sensing is one of the most promising applications for graphene. Using molecular dynamics simulation method, adsorption isotherm of xenon (Xe) gas on defected and perfect graphene is studied in order to investigate sensing properties of graphene for Xe gas. In this method, first generation of Brenner many-body potential is used to simulate the interaction of carbon–carbon (C) atoms in graphene, and Lennard–Jones two-body potential is used to simulate interaction of Xe–Xe and Xe–C atoms. In the simulated systems, adsorption coverage, radial distribution function, heat of adsorption, binding energy and specific heat capacity at constant volume are calculated for several temperatures between 90 K and 130 K, and various pressures. It was found that both of the defected and perfect graphene could be introduced as very good candidates for adsorption of Xe gas.     

Molecular dynamics simulation on mechanicalproperty of carbon nanotube torsional deformation

In this paper torsional deformation of the carbon nanotubes is simulated by molecular dynamics method. The Brenner potential is used to set up thesimulation system. Simulation results show that the carbon nanotubes can bear larger torsional deformation, for the armchair type (10,10) single wall carbon nanotubes, with a yielding phenomenon taking place when the torsional angle is up to 63$^{\circ}$(1.1rad). The influence of carbon nanotube helicity in torsional deformation is very small. The shear modulus of single wall carbon nanotubes should be several hundred GPa, not 1\,GPa as others reports.     

多晶银纳米线拉伸变形的分子动力学模拟研究

纳米尺度金属Ag以其独特的导电和导热性,广泛应用于微电子、光电子学、催化等领域,特别是在纳米微电极和纳米器件方面的应用.本文采用分子动力学方法模拟了不同晶粒尺寸下多晶银纳米线的拉伸变形行为,详细分析了晶粒尺寸对多晶银纳米线弹性模量、屈服强度、塑性变形机理的影响.发现当晶粒尺寸小于13.49 nm时,多晶Ag纳米线呈现软化现象,出现反Hall-Petch关系,此时的塑性变形机理主要以晶界滑移、晶粒转动为主,变形后期形成五重孪晶;当晶粒尺寸大于13.49 nm时,塑性变形以位错滑移为主,变形后期产生大量的孪晶组织.     

DNA与组蛋白相互作用的布朗动力学研究

在真核生物中,DNA按左手手征性的方式,缠绕在组蛋白八聚体的周围,形成稳定的核小体结构.文章作者运用布朗动力学,数值模拟了DNA与组蛋白相互作用最终形成核小体的动力学过程,揭示了DNA与组蛋白相互作用的详细图景,并提出了组蛋白八聚体旋转模型,以解释这一过程.文章作者还计算了组成核小体的DNA在受到拉伸力时,组蛋白被从核小体中剥离下来的动力学过程,得到了组装和剥离过程的详细图像,给出了与前人单分子实验一致的拉伸力与拉伸长度的关系曲线和拉伸台阶.此外,还通过建立的组蛋白手征性模型,模拟了核小体手征性的形成过程,发现DNA的缠绕方向强烈依赖于组蛋白的手征性,显示出环境温度对核小体手征性有重要影响.     

用分子模拟方法研究羟基乙叉二膦酸(HEDP)在方解石表面的吸附行为

建立了基于分子力学计算方法的分子模拟手段,用于研究羟基乙叉二膦酸(HEDP)在方解石{104}表面的吸附特性.分子模拟三维吸附图像显示,HEDP中的膦酸基团中的氧原子具有强烈的负电性,能与晶体表面的阳离子产生强烈的静电吸引作用,形成“立体匹配”吸附结构.计算结果显示,HEDP在方解石面上、台阶和扭折点位置的平均吸附能依次约为-5.2eV,-7.0eV和-23.5eV,表明HEDP强烈地吸附到扭折点位置上,从而影响和抑制台阶的生长. 关键词： 分子模拟 方解石 阻垢剂 表面吸附     

应变效应对金属Cu表面熔化影响的分子动力学模拟

采用Mishin镶嵌原子势，通过分子动力学方法模拟了金属Cu 的(110)表面在不同应变下的熔 化行为，分析了表面熔化过程中系统结构组态和能量的变化以及固液界面迁移情况.金属Cu 的(110)表面在低于热力学熔点的温度下发生预熔化，准液体层的厚度随温度升高而增加.当 温度高于热力学熔点时，固液界面的移动速度与温度成正比，外推得到热力学熔点为1380K ，与实验结果1358K吻合良好.应变效应（包括拉伸和压缩）导致热力学熔点降低，并促进表 面预熔化进程.在相同温度条件下，准液体层的厚度随应变绝对值的增加而增大.应变效应导 致的固相自由能增加是金属Cu(110)表面热稳定性下降的主要因素，且表面应力和应变方向 的异同也会影响表面预熔化的进程. 关键词： 表面预熔化 热力学熔点 表面应力 分子动力学     

葛根素与乙酰胆碱酯酶作用的分子动力学模拟

旨在阐明葛根素与乙酰胆碱酯酶(AChE)的分子作用机制,并为基于葛根素的类似物的AChE抑制剂的研发提供参考.运用AutoDock 4.2进行葛根素与AChE的分子对接,采用YASARA进行分子动力学模拟,利用MMPBSA.py模块计算复合体系的结合自由能,分析氨基酸的能量贡献.结果显示,葛根素与AChE对接体系含有4个氢键,2个π-π键. 5 ns后,体系均方根偏差(RMSD)趋于平衡,体系结合自由能为-18.19 kcal/mol.促体系结合的主要作用力是范德华力、静电作用力,非溶剂化能是主要的结合阻力.能量贡献最大的残基依次为Asn533、Lys530、Ala534、Pro529.这些研究为新型抑制剂的研发提供理论参考.     

气体-表面相互作用的分子动力学模拟研究

采用分子动力学模拟方法研究了气体分子Ar在光滑和粗糙Pt表面上的散射规律.提出了一种速度抽样方法,计算了不同温度条件下气体分子对光滑和粗糙表面的切向动量适应系数和吸附概率.结果显示：光滑表面条件下,气体分子的切向动量系数和吸附概率都随着温度的升高而降低;粗糙度对气体分子切向动量与表面的适应具有极大的促进作用,当粗糙度足够大时,切向动量适应系数的大小趋近于1.0,对温度的敏感性也逐渐降低.采用粒子束方法对气体分子在光滑和粗糙表面上的散射规律进行了定量分析.总结了散射过程中气体分子的典型轨迹和动量变化规律,将气体分子在光滑表面的散射分为两种类型：单次碰撞后散射和多次碰撞后散射.单次碰撞后散射的气体分子平均切向动量有所减小,而经过多次碰撞后散射的气体分子则倾向于保持原有的平均切向动量.对于粗糙表面,粗糙度的存在使气体分子与表面间的动量和能量适应更加充分,导致气体分子在较粗糙表面上散射后的平均切向动量大幅减小并接近于0,且气体分子在表面上经历的碰撞次数越多,其散射后的能量损失越严重.     

Molecular dynamics studies of the interaction between water and oxide surfaces

The water-surface interaction is a research target of great importance for a broad spectrum of technological applications and fundamental scientific disciplines. In the present study, a comparative analysis is performed to clarify the structural and diffusion properties of water on a number of oxide surfaces. Based on the molecular dynamics (MD) simulation method, the water-surface interaction mechanism was investigated for the oxide materials TiO₂ (anatase), Al₂O₃ (corundum), and Fe₂O₃ (hematite). A comparison of the water-TiO₂ interaction with the water-Al₂O₃ and water-Fe₂O₃ systems demonstrates the specificity of the adsorption and layer formation on the atomic/molecular level scale. The obtained MD analysis data point to a considerable enhancement of water-TiO₂ surface adsorption and a relatively high density distribution profile near the surface. The novel data on water structure and diffusion on oxide surfaces are discussed from the point of view of possible material innovation and design.     

金属Al表面熔化各向异性的分子动力学模拟

采用嵌入原子势,使用分子动力学方法对金属Al不同低指数晶面的表面熔化现象分别进行了模拟.分析了熔化过程中样品结构组态的变化.模拟结果表明对于不同的自由表面,表面熔化呈现出明显的各向异性行为.Al（110）面在低于熔点的温度之下发生预熔化;（111）与（001）面都出现过热现象.与（111）面不同,（001）面发生过热现象时表面原子层为类液层,而（111）面仍然保持很好的晶格结构,即预熔化的Al（001）面在高于熔点的温度下,仍可以在很长的时间内处于相对稳定的亚稳态.由模拟得到Al的热力学熔点为950 K左右,与实验值基本符合. 关键词： 分子动力学 表面熔化 过热     

Effect of stress state on deformation and fracture of nanocrystalline copper:Molecular dynamics simulation

Deformation in a microcomponent is often constrained by surrounding joined material making the component under mixed loading and multiple stress states. In this study, molecular dynamics(MD) simulation are conducted to probe the effect of stress states on the deformation and fracture of nanocrystalline Cu. Tensile strain is applied on a Cu single crystal,bicrystal and polycrystal respectively, under two different tension boundary conditions. Simulations are first conducted on the bicrystal and polycrystal models without lattice imperfection. The results reveal that, compared with the performance of simulation models under free boundary condition, the transverse stress caused by the constrained boundary condition leads to a much higher tensile stress and can severely limit the plastic deformation, which in return promotes cleavage fracture in the model. Simulations are then performed on Cu single crystal and polycrystal with an initial crack. Under constrained boundary condition, the crack tip propagates rapidly in the single crystal in a cleavage manner while the crack becomes blunting and extends along the grain boundaries in the polycrystal. Under free boundary condition, massive dislocation activities dominate the deformation mechanisms and the crack plays a little role in both single crystals and polycrystals.     

Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters

Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion; whereas for large adatoms clusters(hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process; however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster,vacancy formation, filling, and shifting can be observed from the results.     

Molecular dynamics simulation of a graphite-supported copper nanocluster: thermodynamic properties and gas adsorption

Molecular dynamics simulations were conducted for a cubic Cu cluster supported on a graphite bilayer. The Sutten–Chen and Lennard–Jones potentials were used for metal–metal and metal–graphite interactions, respectively. Heating and cooling processes were performed by NVT simulations at different temperatures in the range 200 to 1800?K. The melting point was identified on the basis of caloric and heat capacity curves. The calculated melting point was 770?K, far below the bulk melting point of crystalline copper. Several phenomena such as the appearance of a hysteresis (irreversibility) in caloric curves, surface melting, and cluster-induced surface wetting were justified from the results. The simulation of cluster in the presence of gas atmosphere showed that the CO gas is adsorbed more than H₂ and it has a greater impact on the cluster's structure.     

冲击条件下含纳米空洞的单晶铜的塌缩

利用分子动力学方法研究了单晶铜中不同大小的球形空洞在冲击波下的演化过程.模拟结果表明不同大小空洞的塌缩过程不同.模拟中冲击波由空洞左边扫向空洞右边.在较大尺寸的空洞塌缩过程中会产生系列的位错环.当空洞半径较小时,先在空洞的右侧形成位错环,当空洞半径增大到某一临界大小时,在空洞左右两侧同时产生位错环,当空洞半径较大时,先在空洞左侧形成位错环.当空洞左右两侧的位错环均形成以后,其右侧位错环前端的生长速度大于其左侧的.空洞半径增大,相应的位错环前端的生长速度变化不大.当空洞半径增大时,空洞中心指向位错源的矢量方 关键词： 纳米空洞 位错环 冲击波 塑性变形     

Interaction mechanism between copolymer inhibitor and β-dicalcium silicate surface based on molecular dynamics simulation

Copolymer inhibitor with multifunctional groups has a good effect on inhibiting the secondary reaction in the clinker leaching process for alumina production, but the inhibition mechanism of the copolymer is not clear yet. In this paper, molecular dynamics simulation was used to study the adsorption process of the copolymer inhibitor with multifunctional groups, such as acrylic acid-vinyl alcohol copolymer (PAV) and acrylic acid-hydroxypropyl acrylate copolymer (PAH), on the β-dicalcium silicate (C₂S) crystal surface, and reveal its inhibiting mechanism. Meanwhile, the polyacrylic acid (PAA) with only the carboxyl group also is simulated for comparing the inhibition effect with copolymer inhibitors. The results show that the binding energy between copolymer (PAV, PAH) and β-C₂S is greater than that of PAA with a single functional group. The order of binding energy is as follows: PAH?>?PAV?>?PAA. In aqueous solution, the water molecule can restrict the degree of deformation of polymers, increase the distance between polymers and β-C₂S and then lead to weakening of the adsorption of polymers on the crystal surface. The comprehensive and coordination effect of carboxyl and hydroxyl functional groups in PAV and PAH can strengthen the adsorption of copolymers on the β-C₂S surface. The different spatial distribution of multifunctional groups in the molecular structure has a different influence on the adsorption of the copolymer. The results can provide a theoretical basis for researching new and highly effective copolymer inhibitors with multifunctional groups.

Compared the adsorption state: The comprehensive and coordinate action of carboxyl and hydroxyl groups of the inhibitor with multifunctional groups make the inhibitor have a stronger adsorption ability on the surface of β-C₂S than that with a single functional group. The results obtained in this paper can provide a theoretical basis for the research and development of new and highly effective polymeric inhibitors with multifunctional groups.

Highlights

The interaction between copolymer and β-C₂S was investigated by MD simulation.

The binding energy order between polymers and β-C₂S is PAH?>?PAV?>?PAA.

The presence of water molecules can weaken the adsorption of the copolymer on the surface of β-C₂S.

The comprehensive and coordinate action of carboxyl and hydroxyl groups of the inhibitor with multifunctional groups make the inhibitor have a stronger adsorption ability on the surface of β-C₂S than that with a single functional group.