Up-Hill Diffusion of Phase-Separated FeCu Melt by Molecular Dynamics Simulation

Molecular dynamics simulation is performed to characterize the concentration fluctuation of FeCu melts during the liquid-liquid phase separation process, which undergoes the following stages: the formation of interconnected structure and its coarsening, migration and coagulation of droplets driven by the decreasing of potential energy.The up-hill diffusion happens at the early relaxation period in which Cu atoms in Fe-rich region are forced to move toward Cu-rich region by spinodal decomposition with 90% Cu content in Cu-rich region and 95% Fe content in Fe-rich region at temperature of 1500 K. The higher diffusion rate of homogeneous atom can be observed at lower temperature, which is attributed to the larger potential energy difference between Cu-rich region and Fe-rich region. It also exhibits energy heterogeneity in the separated liquid. The domain size decreases sharply during the aggregation and coarsening of droplets, after that it keeps unchanged until the coagulation of droplets begins.The studies characterize concentration and energy heterogeneity of phase-separated liquid on the atomic scale.     

单轴应力场下钨中氦扩散行为的分子动力学模拟研究

本文采用分子动力学方法研究了沿<100>及<111>晶向的单轴应变对钨中单个氦原子扩散的影响。结果表明,应变会使得金属钨材料发生相变,且引起相变的临界应变随温度升高而减小。相变起始的应变在达到抗拉强度的应变附近。计算结果表明,拉应变使得单个氦原子在钨中的扩散系数发生骤降,在不同应变下扩散系数变化平缓。沿<100>晶向氦扩散系数随应变的增大而线性减小,而<111>晶向则出现了震荡变化趋势。研究结果表明,沿<100>晶向应变达到+0.15%时阿纽列斯方程不再适用,而沿<111>晶向应变大+5%阿纽列斯方程仍然适用;沿<111>晶向随应变增加氦扩散激活能减小,说明应变使得单个氦原子在钨中迁移性增强。     

Tracing Nucleation and Growth on Atomic Level in Amorphous Sodium by Molecular Dynamics Simulation

Crystallization of amorphous Na is simulated by using the molecular dynamics method, and the evolutions of atomic clusters are traced by the cluster-type index method （CTIM） we proposed previously. It is demonstrated that the crystallization process exhibits three distinct stages of nucleation, subsequent growth of nuclei and coarsening of crystal grains. Both the size and the internal structure of a cluster play crucial roles in determining whether it is a nucleus. The cluster tracing analysis can identify different crystallization stages more clearly and accurately than other methods. Meanwhile, the simulation results can provide a reasonable explanation at an atomic level for the experimental phenomenon obtained previously.     

基于缠结微结构的非晶态玻璃态高分子材料屈服行为的分子动力学研究

非晶态玻璃态高分子材料作为结构材料在工程领域应用广泛,其机械力学性能特别是屈服变形行为受到热处理、加载应变率和环境温度的影响.采用分子动力学模拟方法研究非晶态玻璃态高分子材料不同工况下的单轴拉伸变形,基于分子链缠结微结构的概念,阐明了非晶态玻璃态高分子材料屈服和应变软化过程的内在变形机制.结果表明,拓扑缠结具有较为稳定的空间结构,难以发生解缠,决定了非晶态高分子材料屈服后的软化平台.由相邻分子链的局部链段相互作用形成的次级缠结在一定外界条件下可发生破坏或重新生成,次级缠结微结构及其演化是非晶态高分子材料发生屈服及软化的内在物理原因.     

Structural and Dynamic Properties of Amorphous Silicon： Tight-Binding Molecular Dynamics Simulation

The tight-binding molecular dynamics simulation has been performed to study structural and dynamical properties of amorphous silicon. It is found that the radial distribution function and static structure factor are in good agreement with the experimental measurements. The bond order parameters Q1 are sensitive to the structure change at different quenching rates. For the dynamical properties, we have calculated the vibration and electronic density of states. The simulation results show that the transverse acoustic is in good agreement with the experimental data, and the high frequency transverse optical (TO) peak shifts to the right of the experimental TO peak.     

光谱法结合分子动力学模拟研究臭氧对肌红蛋白结构的作用机制

臭氧(O₃)是一种具有强氧化性作用的杀菌消毒剂,因其安全无害等特点已被广泛用于肉制品生产加工的减菌处理,但O₃减菌处理对红肉色泽具有较强的负面作用,且其作用机制尚缺乏研究。针对肌红蛋白（Mb）存在状态是决定红色肉色泽关键因素的基础,通过紫外-可见吸收光谱法、荧光光谱法和圆二色光谱法（CD）研究O₃作用下Mb的光谱特性变化,结合蛋白质氧化特征指标分析和分子动力学模拟技术探究O₃对Mb分子的作用效果与机制。光谱研究结果表明,O₃处理可使Mb的紫外-可见光谱图在412 nm左右处的铁卟啉环特征峰及540和580 nm附近的氧合肌红蛋白（OMb）特征峰的强度减弱,其中铁卟啉环特征峰发生蓝移;利用固定激发波长280 nm下测定Mb内源性荧光和同步荧光光谱表明O₃会降低Mb的荧光强度,增大铁卟啉基团贡献的荧光峰强度和造成酪氨酸残基荧光光谱特征峰的蓝移;O₃作用使Mb三维荧光光谱特征峰强度的下降及光散射强度的增加。以上变化推断出O₃会促进Mb的氧化,造成其氨基酸残基疏水基团裸露,使Mb所处微环境及其蛋白构象改变;CD分析表明O₃与肌红蛋白接触时间越久,蛋白质二级结构变化越明显,造成α-螺旋的含量下降,无规则卷曲增加。辅以检测不同强度O₃处理Mb的含量及性质的变化,可知O₃处理使OMb含量下降,高铁肌红蛋白（MMb）含量增加,同时O₃处理Mb的羰基含量增加和巯基含量下降,这也进一步证实O₃作用促进了Mb的氧化,此外,O₃处理Mb表面疏水性的增强,说明O₃造成Mb体系微环境的极性变化。分子动力学模拟结果显示O₃会提高Mb肽链的RMSD值,影响Mb肽链的稳定性,减弱铁卟啉环与Mb肽链的相互作用;RMSF结果表明Mb活性口袋附近氨基酸残基的变化较大;蛋白质二级结构分析与光谱学试验研究结果一致,Mb的α-螺旋的含量下降,无规则卷曲增加。总而言之,O₃可作用于Mb的氨基酸残基,导致蛋白质二级结构和疏水性改变,并发生蛋白氧化及铁卟啉环暴露,进而引起红色肉色泽发生改变。该研究可为生鲜红肉护色技术制定等提供一定理论依据。     

Molecular Dynamics Study of Icosahedral Clusters in Ni-Zr Amorphous Alloys

Formation of icosahedral dusters in rapidly solidified binary amorphous NixZr100-x （x = 15, 33.3, 50, 66.7, 85） is studied by using molecular dynamics simulation methods. A large number of icosahedral dusters with 13 atoms （Ih13） were observed in NixZr100-x alloys, and most of them, even those in Zr-rich alloys, are found to be Ni-centred. Studies on the structures of Ni33.3Z66.7 obtained at different cooling rates demonstrate that most of iscosahedral dusters enhanced by decreasing cooling rates are also Ni-centred, The essentials of Ni atoms preferring to be the core of icosahedral clusters are illustrated with the criterion of energy minimization and the equilibrium interatomic distances between different atoms.     

Temperature Dependence of Elastic Properties for Amorphous SiO2 by Molecular Dynamics Simulation

Large-scale and long-time molecular-dynamics simulations are used to investigate the temperature dependences of elastic properties for amorphous SiO2. The elastic moduli increase in a temperature range up to 1600 K and decrease thereafter. The anomalous behaviour in elasticity is explained by analysing the changes of atomic-scale structure with respect to increment of temperature. The mechanism originates predominantly from distortion of the SiO4 tetrahedra network in low-temperature ranges. At an elevated temperature range, thermal-induced Si-O bond stretching dominates the process and leads to normal temperature dependence of elastic properties.     

液态氧化铝结构的分子动力学模拟

利用分子动力学模拟液态氧化铝从2663 K到过冷温度2223 K的结构变化,通过总双体分布函数得到的液态氧化铝的原子第一、第二近邻距离与Ansell研究小组的实验结果基本一致.通过配位数和偏角分布函数的分析,液态氧化铝的局域结构主要是由氧的三重铝原子配位和铝原子四重(AlO₄)和五重(AlO₅)氧原子配位组成.没有观察到可能因铝原子高、低配位数氧原子的团簇分离而出现的液-液相变.     

Stabilities and Dynamics of Protein Folding Nuclei by Molecular Dynamics Simulation

To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics(MD) simulation in aqueous solution four fragments cut out of a protein G, including oneα-helix(seq B: KVFKQYAN), two β-turns(seq A: LNGKTLKG and seq C: YDDATKTF), and one β-strand(seq D:DGEWTYDD). The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-μs equilibrium MD simulation trajectories. We find that seq A and seq B have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seq D alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seq C is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seq C in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics.     

Molecular Dynamics Study of Stability of Solid Solutions and Amorphous Phase in the Cu-Al System

The relative stability of fee and bcc solid solutions and amorphous phase with different compositions in the Cu-Al system is studied by molecular dynamics simulations with n-body potentials. For CU1-xAlx alloys, the calculations show that the fee solid solution has the lowest energies in the composition region with x 〈 0.32 or x 〉 0.72, while the bcc solid solution has the lowest energies in the central composition range, in agreement with the ball-milling experiments that a single bcc solid solution with 0.30 〈 x 〈 0.70 is obtained. The evolution of structures in solid solutions and amorphous phase is studied by the coordination number （CN） and bond-length analysis so as to unveil the underlying physics. It is found that the energy sequence among three phases is determined by the competition in energy change originating from the bond length and CNs （or the number of bonds）.     

丙烯酰胺聚合物与氧化铝晶体相互作用的分子动力学模拟

将丙烯酰胺单体分别与丙烯酸(AA)、阳离子单体丙烯酰氧乙基二甲基乙基溴化铵(DMB)、疏水性单体丙烯酸十八酯(OA)共聚,分别得到阴离子聚丙烯酰胺P(AA-co-AM)、阳离子聚丙烯酰胺P(DMB-co-AM)、非离子聚丙烯酰胺P(AM)和疏水性聚丙烯酰 胺P(OA-co-AM)等四种丙烯酰胺高分子絮凝剂. 用分子动力学方法,模拟计算了四种聚丙烯酰胺絮凝剂与氧化铝晶体(012)晶面的相互作用,以获得相应的形变能,结合能及理论排序,为阐释四种高分子絮凝剂的絮凝作用机理提供理论依据. 研究结果表明：四种聚合物分子相对Al₂O₃(012)面的初始位置均已贴近Al₂O₃(012)面,且絮凝剂分子中的O原子与Al₂O₃(012)面的Al原子之间存在强烈的相互作用;与Al₂O₃(012)晶面结合的高分子絮凝剂发生扭曲变形,但形变能远小于相应的非键作用能. Al₂O₃(012)晶面结合能的大小排序为P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), 显示四种絮凝剂中P(DMB-co-AM)的絮凝性能最佳,PAM絮凝效果最差.     

孔洞和空位对单晶铝力学性能影响的分子动力学研究

采用分子动力学方法模拟含孔洞的单晶铝单轴拉伸过程,研究晶向、孔洞体积分数、空位体积分数等对孔洞生长的影响.结果表明：对于不同的晶向,决定孔洞生长变形的微观机制不同.[010]晶向单轴拉伸情况下,形变机制主要是｛111｝面位错引起的堆垛层错;[111]晶向单轴拉伸情况下,形变机制主要是位错的移动、堆积与发射.此外,孔洞及空位的体积分数对[010]、[111]晶向的孔洞生长过程也有着明显的影响.总的来说,随着孔洞或者空位体积分数的增加,材料的杨氏模量变小,屈服强度、屈服应变下降.     

The Kinetics of the Liquid Phase Nucleation in a Stretched FCC Crystal: A Molecular Dynamics Simulation

Physics of the Solid State - The kinetics of a spontaneous formation of liquid phase in a stretched (superheated) Lennard-Jones fcc crystal is studied. Molecular dynamics experiments are used to...     

分子动力学模拟BCC铁中级联碰撞产生的缺陷结构及其演变(英文)

用分子动力学模拟BCC铁中级联碰撞原子的演变过程.结果显示,级联碰撞的原子不仅可以临时地产生自间隙原子、空位、以及<100>,<110>和<111>哑铃型缺陷,也可以产生<110>和<111>,以及<110>和<110>哑铃型缺陷的复合缺陷.模拟显示在模拟的能量范围内,如果初级碰撞原子的能量越大,该原子引起的级联碰撞覆盖区域会越大.发现具有几千电子伏特初级碰撞能量的原子引起的级联碰撞覆盖区域大约为11~15个晶格常数大小.同时还发现在级联碰撞的初始阶段(0.0~0.75 ps)不仅会有自间隙原子与空位的生成,同时也会有少量的自间隙原子与空位缺陷复合而消失.     

含有缺陷3C-SiC陶瓷拉伸性能的分子动力学模拟

SiC纤维增韧SiC基复合材料(SiC_f/SiC)由于其优越的性能而成为新一代核能系统重要候选材料之一.材料中的缺陷会使材料的力学性能发生变化,本文运用分子动力学程序LAMMPS模拟计算了分别含有空位、微空洞和反位替代三种缺陷的3C-SiC结构体系沿[100]方向的拉伸变形过程,原子间相互作用采用Tersoff多体势描述.通过模拟得到不同缺陷体系的应力—应变曲线和拉伸过程中体系能量,通过分析应力-应变曲线,得到了不同缺陷体系的杨氏模量、断裂应变、拉伸强度随缺陷"浓度"的变化关系,最后分析了3C-SiC拉伸断裂机理.研究结果表明,空位和微空洞对杨氏模量、拉升强度的影响类似,都是随着缺陷"浓度"的增加而减小,反位替代缺陷使体系的杨氏模量随缺陷"浓度"的增加而增大.     

硝酸钾电解质溶液水化结构的分子动力学模拟

应用分子动力学方法对硝酸钾溶液中离子团簇的结构和离子的水化性质进行模拟研究．水分子采用简单点电荷模型，钾离子被看作带电硬球，硝酸根离子采用刚性四节点模型，同时考虑了节点间的库仑长程作用和L-J相互作用，库仑长程作用采用EWALD求和方法处理，得到了溶液中各种离子对的微观构型和径向分布函数，考察了溶液浓度对离子水化性质的影响．研究表明, 在KNO3溶液中存在一定程度的离子缔合，在高离子浓度情形，可以观察到二聚体、三聚体、溶剂分离阴阳离子对以及其它更复杂的离子团簇构型；离子水化数随离子浓度的升高而降低，对不同浓度的溶液得到的K+的水化数为5?7，NO3-的水化数为3.5?4.7，与蒙特卡罗模拟结果和飞行时间中子衍射实验的测量结果一致．     

Simulation Study on the Structure and Dynamics of Water in Sodium Tetrafluoroborate/Water

应用分子动力学模拟方法研究了室温条件下四氟硼酸钠(NaBF₄)/水混合体系中水分子的微观结构、IR光谱以及转动动力学. 考察了混合物体系中水分子的摩尔分数浓度分别为6.25%、25.0%、50.0%、75.0%、90.0% 和99.6%时体系的结构和动力学性质. 研究显示在不同水分子含量的混合物中水分子以自由分子存在,随着混合物中水分子摩尔分数的增加,水分子的转动和弯曲振动带红移,而O-H伸缩振动蓝移,混合物中水分子内和分子间的氢键和非谐性相互作用增强,分子平动和转动变得困难和缓慢,研究结果与实验观测一致.     

结构材料辐照损伤的分子动力学程序GPU并行化及优化

基于NIVIDIA公司的CUDA架构对结构材料辐照损伤的分子动力学程序在单个GPU上进行并行化,并对影响程序运行效率的相关因素进行分析和测试.经过一系列优化,当粒子数为两百万时,对比单CPU的执行时间,优化后的GPU程序其双精度加速比可达112倍,单精度加速比达到了三百倍,为后续扩展多GPU结构材料辐照损伤的分子动力学程序奠定基础.