纳米尺度下毛细流动的分子动力学模拟

采用分子动力学模拟研究纳米尺度下壁面润湿性对毛细流动的影响,主要考虑纳米通道两侧壁面润湿性相同与不同两种情况。研究表明：两侧壁面润湿性相同条件下,毛细流动随着壁面润湿性增强而加快, 毛细高度随时间的变化早期偏离Lucas-Washburn理论,但后期与其预测符合。在纳米通道两侧壁面润湿性不同的情况下,液面会发生振荡,两侧壁面毛细高度也不相等,且液面振荡的幅度和两侧壁面毛细高度差都随着两侧壁面润湿性差异的增大而增大。基于能量转化分析,提出两侧壁面湿润性不同情况下纳米通道中毛细流动发生的条件以及毛细流动快慢的判别依据。研究结果加深了对纳米尺度下毛细流动机理的认识,并为相关工程应用提供理论参考。     

CaF2熔化温度的分子动力学模拟

利用壳层模型分子动力学方法,研究了高温高压条件下CaF2的熔化温度,同时计算了温度为300K、压强上升到100GPa时CaF2 的状态方程.研究中考虑了分子动力学模拟的过热熔化,通过晶体的现代熔化理论,对CaF2 的分子动力学模拟熔化温度进行了修正, 获得了高温高压下CaF2的熔化温度.因此,常压下壳层模型分子动力学方法为研究物质熔化提供了一个很好的方法.     

不同温度下二氧化硅纳米管的结构和振动性质的分子动力学模拟

采用三种势能模型, 利用分子动力学模拟研究了在300～1600 K内4、6和8元环的二氧化硅纳米管. 结果表明,三种纳米管的末端环的稳定性随温度的升高而降低. 通过振动态密度考察了二氧化硅纳米管的有效振动特性. 以及不同温度下二氧化硅纳米管的红外光谱.     

Molecular Dynamics Simulations of Liquid Phosphorus at High Temperature and Pressure

By performing ab initio molecular dynamics simulations, we have investigated the microstructure, dynamical and electronic properties of liquid phosphorus （P） under high temperature and pressure. In our simulations, the calculated coordination number （CN） changes discontinuously with density, and seems to increase rapidly after liquid P is compressed to 2.5 g/cm3. Under compression, liquid P shows the first-order liquid-liquid phase transition from the molecular liquid composed of the tetrahedral P4 molecules to complex polymeric form with three-dimensional network structure, accompanied by the nonmetal to metal transition of the electronic structure. The order parameters Q6 and Q4 are sensitive to the microstructural change of liquid P. By calculating diffusion coefficients, we show the dynamical anomaly of liquid P by compression. At lower temperatures, a maximum exists at the diffusion coefficients as a function of density; at higher temperatures, the anomalous behavior is weakened. The excess entropy shows the same phenomena as the diffusion coefficients. By analysis of the angle distribution functions and angular limited triplet correlation functions, we can clearly find that the Peierls distortion in polymeric form of liquid P is reduced by further compression.     

量子分子动力学模拟液体钚的输运性质

采用第一原理分子动力学（QMD）方法模拟液体钚的输运性质.计算的粘性和扩散系数在较低温度时与文献有明显差异,在实验测量范围内,模拟结果与实验一致,温度升高时数值模拟结果趋于一致.利用QMD的模拟结果计算了应力自相关函数和速度自相关函数,结果表明：在温度较低时,液体钚呈现明显的强关联特性.对于具有强关联特性的液体,利用较短时间的QMD模拟结果,通过简单e指数拟合外推到t→∞得到的扩散系数和粘性具有较大偏差,这是造成本文模拟结果与文献结果出现差异的主要原因.通过增加QMD模拟时间步数,获得了更为准确的输运性质.     

增强采样分子动力学模拟在生物分子研究中的进展

分子动力学模拟能够描述蛋白质分子在行使生物学功能过程中涉及的构象变化,已发展成为中物学研究中重要的计算工具.由于生物分子的构象分布存在崎岖的自由能面,在较为复杂的生物体系的模拟中,传统的分子动力学模拟的构象采样能力受到极大限制,模拟的时间尺度与真实的生物学过程之间仍存在差距.增强采样是解决这一问题的有效手段.本文综述了两类增强采样方法即约束型和无约束型增强采样算法的理论基础、最新进展及其在生物分子中的典型应用,同时也简要总结了组合型增强采样算法近些年的发展.     

Configurational Entropy Relaxation of Silica Glass—Molecular Dynamics Simulations

Vitreous silica was modelled using molecular dynamics (MD). The glass structure was transferred into an undirected graph and decomposed into disjoint structural units that were ideally mixed to calculate the configurational entropy. The Debye relaxation model was suggested to simulate the evolution of entropy during the cooling of the system. It was found that the relaxation of the configurational entropy of MD corresponds to the effective cooling rate of 6.3 × 10⁶ Ks⁻¹ and its extrapolation to 0.33 Ks⁻¹ mimics the glass transition with T_g; close to the experimental value. Debye relaxation correctly describes the observed MD evolution of configurational entropy and explains the existence of freezing-in temperature and the shape of the curve in the transition region.     

Application of Connection in Molecular Dynamics

The evolution of electronic states in molecule has two origins: dynamical one produced by Schr¨odinger equation and kinematical one caused by base transformation due to nuclear motion.In current theories,the former gets analytic expression; the latter depends on heavy numerical calculation,which contains uncertainty.By using connection of fiber bundles,this paper establishes an analytic formula for the latter,and the numerical work is simplified.It shows the mathematical structure of molecule is fiber bundle.     

纳米流体分散稳定性的分子动力学研究初探

纳米流体的制备和分散稳定性是纳米流体研究工作的前提。本文利用平衡分子动力学模拟方法,尝试从微观角度研究纳米流体的分散稳定性。以纳米颗粒Cu在液态CO_2中的分散稳定为算例,通过跟踪每个固体分子和液体分子的位置,分别观察了颗粒周围的液体吸附现象和颗粒的团聚现象。通过改变固液分子间的引力和斥力,观察其对颗粒周围液体分子的密...     

Active Control of Molecular Dynamics: Coherence versus Chaos

The status of theoretical and experimental studies of the active control of molecular dynamics is surveyed, with attention focused on the control of product formation in a branching unimolecular reaction.     

势能模型对石墨烯导热性质分子动力学模拟的影响

针对常用的Tersoff势、Rebo势和Airebo势,系统性地分析势能模型对分子动力学模拟计算石墨烯色散关系、声子态密度、群速度和热导率的影响. 结果表明：Rebo势和Airebo势描述的声子色散关系接近实验值,Airebo势对应的声子态密度与第一性原理计算的结果较为符合,Rebo势和Airebo势计算的Γ点处声子群速度高于Tersoff势. 采用Airebo势得到石墨烯热导率约为1 150 W·（m·K）^-1,与实验值相近. 综合各种影响,相比于Tersoff势和Rebo势,Airebo势能模型更适合计算石墨烯的导热性质.     

Multimillion Atom Molecular Dynamics Simulations of Nanostructures on Parallel Computers

Scalable space–time multiresolution algorithms implemented on massively parallel computers enable large-scale molecular dynamics (MD) simulations involving up to a billion atoms. Multimillion atom MD simulations are performed to study critical issues in the area of structural and dynamical correlations in nanostructures. Our simulation research is focused on a few semiconductor, ceramic, and metallic nanostructures. These nanostructures systems include: nanometer-scale stress patterns in silicon/silicon nitride nanopixels; self-limiting growth and critical lateral sizes in gallium arsenide/indium arsenide nanomesas; structural transformation in colloidal semiconductor nanocrystals; nanoindentation of crystalline and amorphous silicon nitride films; and dynamics of oxidation of metallic aluminum nanoparticles.     

Molecular Dynamics Study of gases H2,D2 and T2

The classical Molecular dynamics simulation has been used to study the equation of state of gas H2,D2 and T2.It has also been investigated that the isotope mass affects on the accuracy of equation of state.Our calculated Iesults show that the classical effect is principal and the isotope mass effects on the equation of state are obvious for the much light gases.At the same time,some useful theoretical data of equation of state for these gases have been provided.It is found that the classical simulation is still effective to the quantum gas.However,the quantum mechanics simulation and the improvement of intermolecular interaction potential are necessary if more accurate computational results are expected.     

Deep Learning Unravels a Dynamic Hierarchy While Empowering Molecular Dynamics Simulations

Molecular dynamics (MD) provide predictive understanding of the behavior of condensed matter. However, its true potential remains largely untested because relevant timescales are often inaccessible, limited portions of conformation space get sampled, and infrequent events are usually irreproducible. A culprit is the huge informational burden required to iterate integration steps. To address the problem, deep learning is applied to encode the dynamics into a shorthand embodiment retaining only essential topological features of the vector field that steers MD integration. The flow is simplified via an equivalence relation that identifies conformations within basins of attraction in potential energy and encodes the dynamics onto a modulo-basin “quotient space” where fast motions are averaged out. The quotient space projection enables coverage of realistic timescales while unraveling the underlying dynamic hierarchy. Deep learning is exploited to propagate the simplified trajectory beyond MD-accessible timescales and to reconstruct it at atomistic level. As shown, the quotient-encoding-propagating-decoding scheme generates within a few hours protein folding pathways with experimentally verified outcomes. By contrast, MD computations covering comparable timespans would take over a hundred days on special-purpose supercomputers. Thus, quotient space constitutes a model for hierarchical understanding of MD simulation while enabling access to realistic timescales.     

Elastic Constants of Superconducting MgB2 from Molecular Dynamics Simulations with Shell Model

The elastic constants of superconducting MgB₂ are calculated using a molecular dynamics method (MD) with shell model. The lattice parameters, five independent elastic constants, equations of state (EOS), Debye temperature, and bulk modulus of MgB₂ are obtained. Meanwhile, the dependence of the bulk modulus B, the lattice parameters a and c, and the unit cell volume V on the applied pressure are presented. It is demonstrated that the method introduced here can well reproduce the experimental results with a reasonable accuracy.     

碳纳米管与有机小分子官能团相互作用的分子动力学研究

利用Material Studio软件先对不同半径的碳纳米管进行结构优化,再对优化后的纳米管进行分子动力学模拟。得到如下结论：经过优化后小半径纳米管结构基本不变,但是随着半径增大纳米管形变越来越明显。同时通过对多根管簇研究后发现也有相似动力学特性。在以上纳米管结构外面加上一定密度随机排列的对苯二甲酸二辛酯（DOTP）有机分子,发现DOTP有机分子与不同结构、不同半径的纳米管之间都存在相互作用,纳米管半径越大相互作用力也越大,同时DOTP分子在纳米管周围排列也逐渐从无序趋于有序。通过计算以上结构的径向分布函数（RDF）等热力学特性,定性和定量地验证了以上结果。     

Molecular dynamics simulations of compressed hydrogen

Abstract

Molecular dynamics simulations have been performed for highly compressed fluid hydrogen in the density and temperature regime of recent shock-compression experiments. Both density functional and tight-binding electronic structure techniques have been used to describe interatomic forces. Two tight-binding models of hydrogen have been developed with a single s-type orbital on each atom that reproduce properties of the dimer, of various crystalline structures, and of the fluid. The simulations indicate that the rapid rise in the electrical conductivity observed in the gas-gun experiments depends critically on the dissociated atoms (monomers). We find that the internal structure of warm, dense hydrogen has a pronounced time-dependent nature with the continual dissociation of molecules (dimers) and association of atoms (monomers). Finally, Hugoniots derived from the equations-of-state of these models do not exhibit the large compressions predicted by the recent laser experiments.     

Equation of state for warm dense lithium: A first principles investigation

The quantum molecular dynamics based on the density functional theory has been adopted to simulate the equation of state for the shock compressed lithium. In contrary to some earlier experimental measurement and theoretical simulation,there is not any evidence of the ‘kink' in the Hugoniot curve in our accurate simulation. Throughout the shock compression process, only a simple solid-to-liquid melting behavior is demonstrated, instead of complicated solid–solid phase transitions. Moreover, the x-ray absorption near-edge spectroscopy has been predicted as a feasible way to diagnose the structural evolution of warm dense lithium in this density region.     

Molecular Dynamics Simulations for Melting Temperatures of SrF2 and BaF2

利用壳层模型分子动力学方法,考虑萤石结构分子中的预熔化现象,对SrF₂和BaF₂的分子动力学模拟熔化温度进行修正,获得了高压下SrF₂和BaF₂的熔化温度. 同时给出了300 K、0.1 Mpa～7GPa和0.1 Mpa～3 GPa时SrF₂和BaF₂的状态方程,与已有研究结果的最大误差分别为0.3%和2.2%. 计算所得SrF₂和BaF₂常压下的熔点与已有的实验结果符合较好. 对于SrF₂和BaF₂分子体积变化和已有的熔化模拟的差别也做了比较和讨论.     

液态合金NiAl凝固过程中微观结构转变的分子动力学模拟

采用分子动力学模拟方法对液态NiAl凝固过程进行了研究 ,考察了不同冷却速度下液态NiAl结构变化特点 ,原子间相互作用势采用F S多体势 ,结构分析采用键取向序和对分析技术 .计算结果表明 ,冷却速度对液态NiAl结构转变有重要影响 ,在不同的冷却速度下 ,NiAl凝固过程出现了明显不同 ,冷速为 4× 10 13 和4× 10 12 K/s时 ,NiAl快速凝固为无序的非晶体结构 ;而在较慢的 8× 10 11K/s冷速下 ,NiAl凝固为晶态结构 .给出了不同冷却速度下液态NiAl结构转变的微观信息 .