纤维素热解过程的分子动力学模拟

本文利用 PM3 方法对生物质主要组分纤维素进行了结构优化并得到了一系列的结构参数.对不同力场下,聚合度为 9 的纤维素单链热分解进行了分子动力学方法模拟研究,得到不同力场下的模拟过程中参数.通过与相关生物质热解实验结果对比,利用 Amber 力场模拟得到的结果与实验值吻合较好.基于 Amber 力场并结合量子力学对纤维素单元热解过程进行了研究,模拟得到纤维素单元分子链在加热过程中的主要分解温度范围、断键顺序以及一次热解的基团,并对一次产物进行了分析.     

相变材料热物理性质的分子动力学模拟

为从微观尺度探寻相变材料的热物性变化机理, 本文采用分子动力学的方法, 构建了由正二十二烷组成的无定形结构的相变材料体系, 采用周期性边界条件以及COMPASS力场对相变材料的比热以及导热系数进行了模拟, 并对纯正二十二烷进行了DSC测试. 结果表明, 模拟所得的相变材料热容与文献实验值的偏差是6.5%, 熔点与DSC实验值的偏差是0.98%. 当温度为288–318 K时, 相变材料的导热系数在0.1–0.4 W·m^-1·K^-1 范围内波动, 且随着压力增大略呈下降趋势. 关键词： 扩散系数 比热 导热系数 分子动力学     

噬菌体T4溶菌酶溶液构象模拟中分子力场和水模型的选择

蛋白质在溶液中可能以不同构象的集合形式存在,不能用单一的静态结构来表示. 分子动力学模拟已成为对溶液中蛋白质构象进行采样的有用工具,但分子力场和水模型的选择是关键问题. 这项工作介绍了噬菌体T4溶菌酶的个例研究. 本文发现,使用经典的AMBER99SB力场和TIP4P水模型,分子动力学模拟不能很好地描述野生型噬菌体T4溶菌酶在微秒时间尺度上的铰链弯曲结构域运动. 其它新型力场和水模型的组合,如被称为RSFF2+的残基特异性力场和离散校正的水模型TIP4P-D,能够对噬菌体T4溶菌酶溶液构象进行合理的采样,与实验数据有良好的一致性. 这项工作为进一步研究噬菌体T4溶菌酶的溶液构象转变提供了分子力场和水模型的参考.     

极化蛋白专一性电荷在HIV-1蛋白酶-抑制剂结合自由能预测中的应用

对人类免疫缺陷病毒（HIV-1）蛋白酶-抑制剂复合物分别在AMBER力场及极化专一性蛋白电荷（PPC）下进行10 ns的分子动力学模拟（MD）,并用MM/PBSA方法计算结合自由能.PPC是基于线性标度的量子力学计算的静电势拟合的蛋白质电荷,能够更准确地描述蛋白质所处的静电环境.结果表明：PPC电荷计算的结合自由能比AMBER力场计算的结合自由能更接近实验值.     

噬菌体T4溶菌酶溶液构象模拟中分子力场和水模型的选择（英文）

蛋白质在溶液中可能以不同构象的集合形式存在,不能用单一的静态结构来表示.分子动力学模拟已成为对溶液中蛋白质构象进行采样的有用工具,但分子力场和水模型的选择是关键问题.这项工作介绍了噬菌体T4溶菌酶的个例研究.本文发现,使用经典的AMBER99SB力场和TIP4P水模型,分子动力学模拟不能很好地描述野生型噬菌体T4溶菌酶在微秒时间尺度上的铰链弯曲结构域运动.其它新型力场和水模型的组合,如被称为RSFF2+的残基特异性力场和离散校正的水模型TIP4P-D,能够对噬菌体T4溶菌酶溶液构象进行合理的采样,与实验数据有良好的一致性.这项工作为进一步研究噬菌体T4溶菌酶的溶液构象转变提供了分子力场和水模型的参考.     

Fe合金FCC-BCC原子尺度台阶型马氏体相界面迁移行为的分子动力学模拟研究

两相界面的原子尺度结构对相界面迁移行为具有重要影响.高分辨透射电子显微分析表明钢中马氏体相界面具有高度为若干原子层间距的台阶结构,然而目前Fe合金马氏体相变的模拟研究工作中绝大多数使用非台阶型相界面结构作为模拟初始模型.本文基于拓扑模型和相变位错理论构建了Fe合金FCC/BCC台阶型相界面初始模型,采用分子动力学模拟方法研究了Fe合金马氏体相界面的迁移行为.研究结果表明,当两相界面具有约束共格匹配关系及台阶结构时,体系发生FCC→BCC马氏体相变并呈现典型的非扩散切变特征;相变过程中FCC/BCC宏观尺度相界面沿其法线方向以(4.4±0.3)×10~2 m/s的速度迁移,且相界面在迁移过程中始终保持稳定的台阶结构和相对平直的宏观界面形貌特征;相变位错的滑移速度高达(2.8±0.2)×10~3 m/s,相变位错阵列沿台阶面的协同侧向滑移不仅是马氏体台阶结构宏观相界面迁移的微观机制,也是马氏体相变宏观形状应变的主要来源;采用分子动力学模拟方法获得的Fe合金马氏体相变晶体学特征参量与拓扑模型的解析解数值非常接近,相变产生的整体宏观形状应变由平行于相界面的剪切应变和垂直于相界面的法向应变两部分组成.     

谐振势阱中的布朗运动——磁镊实验与模拟

从磁镊实验和模拟角度研究了处于谐振势阱中的布朗运动. 利用实验和模拟的结果验证了理论.然后通过理论与实验的对照, 对磁镊实验中DNA分子的持久长度大小对小球位移分布的影响, 以及磁镊实验中的测力误差作了相关分析.分析指出:持久长度的变化对沿 DNA链方向上的布朗运动影响更大;小的外力作用下力的测量会出现较大误差.     

水导热系数的分子动力学模拟

本文选用平衡分子动力学模拟方法,应用不同的势能模型对强极性分子水的导热系数进行了模拟计算.结果表明,用分子动力学模拟方法计算水的导热系数时,模拟结果对模型的选取极为敏感.在目前应用较为广泛的几种模型中以TIP4P模型较为适用,所得的导热系数与实验值较为接近.     

β-HMX晶体单轴压缩及绝热压缩的分子动力学模拟

采用COMPASS(Condensed-Phase Optimized Molecular Potential for Atomistic Simulation Studies)力场,对β-HMX晶体的单轴压缩进行了分子动力学模拟,压缩方向分别垂直于β-HMX晶体的(100)、(010)和(001)晶面。模拟结果表明,垂直于不同晶面的单轴压缩得到的状态方程不同,显示出β-HMX晶体单轴压缩的各向异性。利用NpH系综对β-HMX晶体进行了绝热静水压缩模拟,得到的绝热静水压缩线处于等温静水压缩线的上方,与实验结果更加吻合。绝热压缩下,体系温度升高,各压力作用下体系温度的模拟结果与理论计算得到的冲击温度比较接近,说明COMPASS力场和NpH系综适用于模拟β-HMX晶体的绝热压缩。利用分子动力学方法模拟炸药的绝热压缩,可以预估炸药的冲击温度。     

扭转对碳纳米管束热物性的影响

采用非平衡分子动力学方法(NEMD)研究了扭转对碳纳米管(CNT)管束热导率的影响。CNT管束由7根(10,10) CNT组成。通过对CNT管束施加不同程度扭转,结果表明CNT管束热导率随着扭转程度增大迅速下降。采用T形法测量了扭转前后CNT管束热导率随温度的变化,实验结果与模拟预测趋势吻合。声子谱和拉曼光谱的结果表明扭转对原结构的破坏,结构有序性降低造成声子软化,最终导致了热导率的下降。     

Thermodynamic and transport properties of spiro-(1,1')-bipyrrolidinium tetrafluoroborate and acetonitrile mixtures:A molecular dynamics study

Organic salts such as spiro-(1,1')-bipyrrolidinium tetrafluoroborate([SBP][BF4]) dissolved in liquid acetonitrile(ACN) are a new kind of organic salt solution,which is expected to be used as an electrolyte in electrical double layer capacitors(EDLCs).To explore the physicochemical properties of the solution,an all-atom force field is established on the basis of AMBER parameter values and quantum mechanical calculations.Molecular dynamics(MD) simulations are carried out to explore the liquid structure and physicochemical properties of [SBP][BF4] electrolyte at room temperature.The computed thermodynamic and transport properties match the available experimental results very well.The microscopic structures of [SBP][BF4] salt solution are also discussed in detail.The method used in this work provides an efficient way of predicting the properties of organic salt solvent as an electrolyte in EDLCs.     

Reproducible protein folding with the stochastic tunneling method

We report the reproducible folding of the 20 amino-acid protein trp cage using a novel version of the stochastic tunneling method and a recently developed all-atom protein free-energy force field. Six of 25 simulations reached an energy within 1 kcal/mol of the best energy, all of which correctly predicted the native experimental structure of the protein, in total eight simulations converged to the native structure. We find a strong correlation between energy and root-mean-square deviation to the native structure for all simulations.     

Self-organised criticality in base-pair breathing in DNA with a defect

We analyse base-pair breathing in a DNA sequence of 12 base-pairs with a defective base at its centre. We use both all-atom molecular dynamics (MD) simulations and a system of stochastic differential equations (SDEs). In both cases, Fourier analysis of the trajectories reveals self-organised critical behaviour in the breathing of base-pairs. The Fourier Transforms (FTs) of the inter-base distances show power-law behaviour with gradients close to −1. The scale-invariant behaviour we have found provides evidence for the view that base-pair breathing corresponds to the nucleation stage of large-scale DNA opening (or ‘melting’) and that this process is a (second-order) phase transition. Although the random forces in our SDE system were introduced as white noise, FTs of the displacements exhibit pink noise, as do the displacements in the AMBER/MD simulations.     

Wormlike chain theory and bending of short DNA

The probability distributions for bending angles in double helical DNA obtained in all-atom molecular dynamics simulations are compared with theoretical predictions. The computed distributions remarkably agree with the wormlike chain theory and qualitatively differ from predictions of the subelastic chain model. The computed data exhibit only small anomalies in the apparent flexibility of short DNA and cannot account for the recently reported AFM data. It is possible that the current atomistic DNA models miss some essential mechanisms of DNA bending on intermediate length scales. Analysis of bent DNA structures reveal, however, that the bending motion is structurally heterogeneous and directionally anisotropic on the length scales where the experimental anomalies were detected. These effects are essential for interpretation of the experimental data and they also can be responsible for the apparent discrepancy.     

Soot primary particle formation from multiscale coarse-grained molecular dynamics simulation

A new multiscale coarse-graining procedure is used to study carbonaceous nanoparticle agglomeration in combustion environments. The computational methodology is applied to an ensemble of 10,000 nanoparticles (or effectively 2 million total carbon atoms) to simulate, for the first time, the agglomeration of carbonaceous nanoparticles using coarse-grained atomistic-scale information. In particular, with the coarse-graining approach we are able to assess the influence of nanoparticle morphology and temperature on the agglomeration process. The coarse-graining of the interparticle force field is accomplished applying a force-matching procedure to data obtained from trajectories and forces from all-atom MD simulations. The coarse-grained MD results show rich and varied clustering behaviors for different particle morphology and, in some cases, the formation of primary particles with a diameter around 15 nm are observed for the first time by molecular simulation techniques.     

Structures and Hydrogen Bonding Interactions in Urea-water System Studied by All-atom MD Simulation and Chemical Shifts in NMR Spectrum

采用分子动力学模拟方法结合核磁共振化学位移和粘度对尿素水溶液在稀浓度范围内的结构和弱相互作用进行研究. 从径向分布函数(RDF)分析看出,尿素水溶液中存在着几种不同类型、不同氢键形成能力的传统氢键. 氢键网络分析发现尿素水溶液体系在水富集区域,水分子倾向于自身缔合形成稳定的分子簇结构,而随着尿素浓度的逐渐增加,水的有序结构受到破坏,水分子和尿素分子发生了交叉缔合作用形成氢键,尿素分子有形成自身缔合的趋势. 分子动力学统计的平均氢键数与核磁共振化学位移和粘度数据结果进行比较,发现它们的变化趋势一致,证明了实验和理论结果有很强的可靠性.     

Phase behaviour and interfacial properties of ternary system CO2 + n-butane + n-decane: coarse-grained theoretical modelling and molecular simulations

ABSTRACT

This work illustrates the application of a three-party approach based on theoretical modelling, molecular dynamic (MD) simulations and available experimental data for describing the phase equilibrium and interfacial properties for the ternary system: carbon dioxide + n-butane + n-decane and its corresponding binary sub-systems at 344.3 K. Specifically, a coarse-grained force field is employed for both theoretical predictions and MD. The interfacial region is described by the square gradient theory where the homogenous Helmholtz energy density contribution is provided by the Statistical Associated Fluid Theory equation of state for potentials of variable range for molecules conformed of segments interacting through the Mie potential (SAFT-VR Mie) and MD simulations in the canonical ensemble where the molecules are represented by a coarse-grained Mie force field. The novelty here is that both the theory and the simulations uniquely share the same underlying intermolecular potentials; hence, the experimental data are employed to verify both the theory and simulations. In this schema, the ternary mixture is full predictive as its parameters are only based on pure fluids parameters and binary interactions. It is observed that the phase equilibria and the interfacial properties are equally well represented by the used approach.     

Multiscale simulation of loading and electrical resistance in silicon nanoindentation

Nanoindentation experiments are an excellent probe of micromechanical properties, but their interpretation is complicated by their multiscale nature. We report simulations of silicon nanoindentation, based on an extended version of the local quasicontinuum model, capable of handling complex Bravais crystals. Our simulations reproduce the experimental load vs displacement curves and provide microscopic information such as the distribution of transformed metallic phases of silicon underneath the indenter. This information is linked to the macroscopic electrical resistance, giving a satisfactory explanation of experimental results.     

Protein folding kinetics and thermodynamics from atomistic simulations

Determining protein folding kinetics and thermodynamics from all-atom molecular dynamics (MD) simulations without using experimental data represents a formidable scientific challenge because simulations can easily get trapped in local minima on rough free energy landscapes. This necessitates the computation of multiple simulation trajectories, which can be independent from each other or coupled in some manner, as, for example, in the replica exchange MD method. Here we present results obtained with a new analysis tool that allows the deduction of faithful kinetics data from a heterogeneous ensemble of simulation trajectories. The method is demonstrated on the decapeptide Chignolin for which we predict folding and unfolding time constants of 1.0 +/- 0.3 and 2.6 +/- 0.4 micros, respectively. We also derive the energetics of folding, and calculate a realistic melting curve for Chignolin.