六硝基六氮杂异伍兹烷转晶中的分子动力学模拟

利用六硝基六氮杂异伍兹烷(HNIW)晶体生长及添加剂附着晶面的模拟,来优选添加剂使转晶得到的ε型HNIW晶体形状更规则;构立了ε型HNIW晶胞模型,采用分子动力学方法模拟了晶体生长的外部形态.应用分子动力学计算,筛选到能修改ε-HNIW晶体生长外形的T1、T2和T3添加剂.在转晶实验中利用T1、T2和T3添加剂修改了ε-HNIW晶体的外形,与分子动力学模拟结果基本一致.结果表明,分子动力学模拟可预示添加剂对ε-HNIW晶体生长的影响.借助这种模拟,易选择添加剂,使ε-HNIW晶体具有更规则的形貌.     

分子动力学模拟在环氧基复合材料中的应用

综述了分子动力学模拟在环氧基复合材料研究中的应用以及模拟结果的有效性,概叙了分子动力学模拟中应用的几种分子力场,以及固化剂的选择对固化材料的密度、热机械性能及玻璃化转变温度(T_g)的影响,并对分子动力学模拟的发展趋势作了展望。     

蛋白质体系分子动力学模拟的前沿进展-从介科学角度重新审视

蛋白质是生命的物质基础,是生命活动的主要承担者,对蛋白质时空多尺度结构及其控制机制的深入理解是探索生命起源、病理认知及新药开发的基础. 受实验表征手段及时空分辨率的限制,计算机模拟已成为研究蛋白质体系结构及功能的重要手段之一. 由于蛋白质体系模拟所涉及的时间和空间跨度均相当大,因此,准确且快速地描述其时空多尺度结构,从而分析体系的控制机制及相关生理过程,成为分子动力学模拟面临的巨大挑战. 本工作对近半个世纪以来的分子模拟方法,特别是分子动力学方法和相关的增强采样技术在蛋白质体系研究中的应用进行了总结,综述了近年来分子动力学的理论模型和算法的发展,并介绍了这些方法在结构化蛋白质的天然结构与构象变化、固有无序蛋白质的动态结构及其结合底物的动力学过程及分子机理、分子伴侣及病毒等蛋白质复合物体系中的研究成果;汇总了高性能计算的飞速发展所带动的分子动力学模拟软件的变革,拓展了蛋白质模拟的时空尺度,重点阐述了大规模高性能分子动力学模拟在蛋白质研究中的应用;最后,基于介科学理论的飞速发展及其在多种复杂体系的成功运用,对未来蛋白质体系的模拟方法和理论研究的趋势进行了思考和展望.     

基于蒙特卡洛分子动力学模拟的算法在天然产物小分子与蛋白质相互作用中的应用

天然产物小分子与蛋白质相互作用的研究对于天然产物的功能研究有着非常重要的意义。作为一种快速而低成本的手段,基于分子动力学模拟的方法正在受到越来越多的重视,而基于蒙特卡洛分子动力学模拟的算法是其典型的代表。本文详细的阐述了基于蒙特卡洛分子动力学模拟的算法在天然产物小分子与蛋白质相互作用中的应用。     

六硝基六氮杂异伍兹烷转晶中的分子动力学模拟

利用六硝基六氮杂异伍兹烷（HNIW）晶体生长及添加剂附着晶面的模拟，来优选添加剂使转晶得到的ε型HNIW晶体形状更规则；构立了￡型HNIW晶胞模型，采用分子动力学方法模拟了晶体生长的外部形态。应用分子动力学计算，筛选到能修改ε-HNIW晶体生长外形的T1、T2和T3添加剂。在转晶实验中利用T1、T2和T3添加剂修改了ε-HNIW晶体的外形，与分子动力学模拟结果基本一致。结果表明，分子动力学模拟可预示添加剂对ε-HNIW晶体生长的影响。借助这种模拟，易选择添加剂，使ε-HNIW晶体具有更规则的形貌。     

氨的自扩散系数的分子动力学模拟研究

采用分子动力学模拟方法研究了氨在较宽温度和压力范围的分子自扩散系数。从常温到高温,自扩散系数的模拟值与实验值吻合得很好,这表明可以采用分子动力学模拟来代替实验,获得高温高压条件下实验难以测量的自扩散系数。     

超临界或高压CO2中无限稀释扩散系数的模拟

采用分子动力学模拟的方法对超临界二氧化碳的自扩散系数及甲醇和乙醇在超临界二氧化碳中的无限稀释扩散系数进行了模拟计算。结果表明,分子动力学模拟方法可较准确地反映二氧化碳的扩散性质,计算无限稀释扩散系数取得了与实验值较吻合的结果。采用这种新方法可以准确有效的地预测超临界体系的扩散性质,将会更加广泛应用于工程设计,因此分子动力学模拟作为先进的研究手段会得到越来越广泛的应用。     

分子模拟技术在分子筛的吸附扩散研究中的应用

二分子模拟是近年发展起来的一门新兴计算化学技术.简要介绍了分子模拟技术的基本原理及其优点和缺点,重点阐述了分子模拟中的Monte Carlo分子模拟和分子动力学模拟两种方法及其在分子筛的吸附扩散研究中的应用.同时介绍了这两种组合方法的应用,最后展望了分子模拟技术的发展方向.     

甲烷的自扩散系数的分子动力学模拟研究

运用分子动力学模拟方法研究了甲烷在较宽温度和压力范围的分子自扩散系数。结果表明,甲烷自扩散系数的模拟值与文献实验值吻合得较好。因此,可以采用分子动力学模拟来代替实验,获得高温高压条件下实验难以测量的甲烷自扩散系数。     

十二烷基-β-D-葡萄糖苷单层膜界面性质的分子动力学模拟

表面活性剂分子的界面组装结构是关系其应用性能的重要指标,分子动力学模拟是考察该体系性质的有力工具.采用分子动力学模拟方法研究了不同界面浓度下非离子表面活性剂十二烷基-β-D-葡萄糖苷的单层膜在水气界面的结构和动力学性质;通过密度分布、均方根位移曲线以及界面形成能等参数表征不同界面浓度条件下单层膜的结构及稳定性;并根据烷...     

Molecular Dynamics Simulation of the Structure of Borate Glasses

The structures of borate glasses have been simulated by use of molecular dynamics. A new type of potential calculated by means of the intermediate neglect of differential overlap (INDO) method and a three-body potential were introduced into the molecular dynamics simulation. Boroxyl rings and diborate groups have been successfully reproduced in the structure models obtained from the present molecular dynamics simulation. Calculated radial distribution functions agreed well with the observed one obtained from X-ray diffraction data. The distribution of O–B–O and B–O–B bond angles is also given.     

分子模拟方法在聚合物性质研究中的应用

综述了四种常用的分子模拟方法:即量子力学方法、分子力学方法、蒙特卡洛方法和分子动力学方法在聚合物性质研究中的应用。四种方法各有优势,共同与计算机模拟成为密不可分的组成部分。     

Simulation of mechanical properties of epoxy-based chemically amplified resist by coarse-grained molecular dynamics

The mechanical properties of an epoxy-based chemically amplified resists with various cross-linking ratios were simulated using a newly developed coarse-grained molecular dynamics simulation that employs a bead–spring model. Models with the different cross-linking ratios were created in the molecular dynamics calculation step and uniaxial elongation simulations were performed. The results reveal that the simulated elastic modulus of the resist modeled by the Kremer–Grest model with an extended angle bending potential depends on the cross-linking ratio, its dependency exhibits good agreement with that determined by nanoindentation tests.     

钾基蒙脱石的分子力学和分子动力学模拟

利用分子力学(molecular mechanics,MM)和分子动力学(molecular dynamics,MD)模拟了K-蒙脱石层间阳离子和水的结构及动力学特征,并将模拟的X射线衍射结果与实验值进行比较.结果显示:在K-蒙脱石的最优构型中,层间距随着水含量的增加而增大;X射线衍射的模拟结果和实验结果一致;K+的位置和蒙脱石层间电荷位置有关,K+在1,2层水合物中依附于黏十的表面附近,而在3层水合物中K+则脱离表面开始向层中其它方向扩散.水分子在黏土层间分散于各个方向,而且存在水质子和K+竞争电荷位置的现象.水和K+在钾基蒙脱石中的活动性低于其在水中和溶液中的活动性.径向分布函数分析结果表明K+组织水分子的能力有限,说明K+对蒙脱石的水化膨胀起抑制作用.     

优化温度相关力场预测正构烷烃热力学性质

为了实现不同温度下正构烷烃及其混合物热力学性质的准确预测,以正构烷烃（n-C₄~C₁₀）为训练集,通过对全原子OPLS-AA力场中非键相互作用参数（ε）的模拟优化,得到了ε与对比温度（T_r）以及正构烷烃碳原子个数（N_C）的经验关系式。利用该关系式计算出不同温度不同种类的正构烷烃的ε值,预测了正构烷烃纯物质及其混合物的黏度、密度、扩散系数等物性,并将新力场模拟计算值与理论估算值以及实验值进行比较。结果表明,采用优化温度相关力场预测烷烃及其混合物的物性与实验值最为吻合。密度、黏度和扩散系数的预测值与实验值的相对偏差分别小于2%、5%和10%,显著优于目前的理论方法和原OPLS-AA力场模拟计算的预测值。上述温度相关力场参数的确立,对于利用分子动力学模拟方法准确地预测正构烷烃及其混合物的热力学性质具有重要的实际应用价值。     

Estimation of the modulus of elasticity of N-A-S-H and slag-based geopolymer structures containing calcium and magnesium ions as impurities using molecular dynamics simulations

Geopolymers are alkaline cements composed of aluminosilicate units. The molecular structure of some geopolymers is sodium-aluminosilicate hydrate (N-A-S-H). Impurities containing calcium and magnesium are of significant importance in various types of geopolymer materials, as these impurities affect the mechanical properties of the geopolymer. In this study, the effects of different percentages of impurities on the modulus of elasticity of two types of geopolymer structures (N-A-S-H and slag) were investigated using molecular dynamics simulations. A recently introduced and modified N-A-S-H structure was used in the simulations. The molecular structure of blast furnace slag was also used to confirm and validate the molecular simulation results. The main reason for comparing the results of molecular dynamics simulations of the N-A-S-H structure with those of slag was the availability of laboratory results for slag-based geopolymers in the technical literature. The proposed molecular structure of slag based on its constituents is (N,C)-A-S-H. This structure is the most similar to N-A-S-H. The simulation parameters were selected based on data available in the literature. For the amorphous form of N-A-S-H, several simulations were performed to determine the mean modulus of elasticity. Then, additional simulations were carried out to investigate the effect of impurities on the modulus of elasticity of geopolymer materials. The results were in good agreement with the available laboratory results. The results showed that with an increasing percentage of calcium in the N-A-S-H structure, the modulus of elasticity increased. On the other hand, with an increasing percentage of magnesium impurities in the slag and N-A-S-H structures, the modulus of elasticity decreased. The overall results showed that the molecular dynamics simulation method is a good tool to complement laboratory studies for investigating the mechanical properties of geopolymers.     

Dynamics in self-assembled organic monolayers at the liquid/solid interface revealed by scanning tunneling microscopy

The liquid/solid interface provides an interesting medium for molecular self-assembly and scanning tunneling microscopy is the preferred technique to analyse the structural features of the surface-supported self-assembled monolayers in this medium. An interesting aspect is the phenomenon of molecular dynamics at the liquid/solid interface. In this mini-review, we report on our efforts and strategies to investigate and even induce molecular dynamics at the liquid/solid interface, bringing insight to various kinds of processes such as conformational, translational and adsorption/desorption dynamics.     

枣泉煤分子模型构建及热解的分子模拟

以宁东枣泉煤为研究对象，使用工业分析、元素分析、X射线光电子能谱、¹³C固体核磁等表征手段和计算机辅助，构建获得枣泉煤大分子结构模型。经过分子动力学退火动力学模拟和几何结构全优化，与初始结构相比键长、键角发生明显改变，立体构型显著，芳香层片之间近似平行的排列方式明显。获得的傅里叶变换红外和¹³C固体核磁的实验与计算谱图总体吻合较好，进一步证明了构建模型的合理性。使用反应分子动力学方法模拟枣泉煤的热解过程，考察不同热解终温和升温速率对热解行为的影响。结果发现，随着温度的升高，反应速率逐渐加快。不同升温速率对枣泉煤热解过程中气体的产生有显著影响。在动力学模拟中大多产生C₁₅以下的碎片，大分子的种类则并不多。随着升温速率的增加，气、液、固三相产物整体上都呈现下降的趋势。此外，还根据反应分子动力学模拟结果追踪了热解过程中CO₂的形成机理，获得了三种不同的CO₂形成路径。     

靶向于Galectin-10蛋白的哮喘抑制剂设计

Galectin-10（Gal10）存在于人类嗜酸性细胞中,可经历相变成为晶体而诱发哮喘疾病。通过分子动力学模拟方法结合分子力学-泊松-玻尔兹曼方程-表面积计算自由能分解方法解析Gal10蛋白与溶晶抗体相互作用,发现Gal10蛋白与溶晶抗体结合主要依靠疏水相互作用驱动,对结合起最有利贡献的氨基酸残基包括Gal10蛋白的Y69、K117、D113、E68、I116、H114和溶晶抗体的W53-H、Y104-H、N97-L、K55-L、Y93-L、R100-H。以此为基础,构建Gal10蛋白与溶晶抗体相互作用的亲和结合模型,以设计抑制剂并构建序列为WXYXXNXY的抑制剂库,利用分子对接、分子动力学模拟、构象比对等方法,最终确定获得WGYGWNGY等潜在高效哮喘抑制剂。     

Tracking dynamics of glass formers and modifiers via correlation maps of molecular dynamics simulation

In this study, we describe a method to construct a correlation map that captures the evolution of species-specific dynamic information through the spatial correlation of high-dimensional time-series molecular dynamics (MD) simulation dataset for a series of borosilicate glasses. The correlation is based on ‘displacement’ between a pair of atomic configurations determined by the root mean square distance (RMSD) metric. We implement the correlation map as a quantitative visualization tool that provides a compressed representation of a high-dimensional molecular dynamics dataset to inspect various physical aspects and capture distinct atomic dynamics—from large fluctuations to small local oscillations—for high-temperature melt, linear cooling, and low-temperature equilibration processes during molecular dynamics simulation of glasses. We capture species-specific dynamics using this method that show different cooling dynamics for different glass formers and modifiers, especially the onset of slow dynamics and the variation of atomic dynamics at high temperatures. Furthermore, we show that the species-specific atomic dynamics have structural origins that depend on the composition of the simulated borosilicate glasses. The correlation map serves as a visualization tool to rapidly survey changes in atomic configurations during different simulation conditions.