Molecular dynamics simulation for surface melting and self-preservation effect of methane hydrate

The surface melting process of structure sI methane hydrate is simulated at T = 240, 260, 280, and 300 K using NVT molecular dynamics method. The simulation results show that a quasi-liquid layer will be formed during the melting process. The density distribution, translation, orientation, and dynamic properties of water molecules in the quasi-liquid layer are calculated as a function of the distance normal to the interface, which indicates the performance of quasi-liquid layer exhibits a continuous change from crystal-like to liquid-like. The quasi-liquid layer plays as a resistance of mass transfer restraining the diffusion of water and methane molecules during the melting process. The resistance of quasi-liquid layer will restrain methane molecules diffuse from hydrate phase to gas phase and slow the melting process, which can be considered as a possible mechanism of self-preservation effect. The performance of quasi-liquid layer is more crystal-like when the temperature is lower than the melt- ing-point of water, which will exhibit an obvious self-preservation. The self-preservation will weaken while the temperature is higher than the melting-point of water because of the liquid-like performance of the quasi-liquid layer.     

Numerical simulation of droplet coalescence behavior in gas phase under the coupling of electric field and flow field

The coalescence behavior of droplets in an electric field belongs to the important research contents of electrohydrodynamics. Based on the phase field method of the Cahn–Hilliard equation, the electric field and the flow field are coupled to establish the numerical model of twin droplet coalescence in a coupled field. The effects of flow rate, electric field strength, droplet diameter, and interfacial tension on the coalescence behavior of droplets during the coalescence process were investigated. The results show that the dynamic behavior of the droplets is divided into coalescence, after coalescence rupture, and no coalescence under the coupling of electric field and flow field. The proper increase of the electric field strength will accelerate the coalescence of the droplets, and the high electric field strength causes the droplets to burst after coalescence. Excessive flow rates make droplets less prone to coalescence. Under the coupling field, the larger the droplet interface tension, the smaller the droplet diameter, the smaller the flow rate, and the shorter the droplet coalescence time. The results provide a theoretical basis for the application of electrostatic coalescence in gas–liquid separation technology.     

Molecular dynamics simulation of hydrated DPPC monolayers using charge equilibration force fields

We present results of molecular dynamics simulations of a model DPPC-water monolayer using charge equilibration (CHEQ) force fields, which explicitly account for electronic polarization in a classical treatment of intermolecular interactions. The surface pressure, determined as the difference between the monolayer and pure water surface tensions at 323 K, is predicted to be 22.92 ±1.29 dyne/cm, just slightly below the broad range of experimental values reported for this system. The surface tension for the DPPC-water monolayer is predicted to be 42.35 ±1.16 dyne/cm, in close agreement with the experimentally determined value of 40.9 dyne/cm. This surface tension is also consistent with the value obtained from DPPC monolayer simulations using state-of-the-art nonpolarizable force fields. The current results of simulations predict a monolayer-water potential difference relative to the pure water-air interface of 0.64 ±0.02 Volts, an improved prediction compared to the fixed-charge CHARMM27 force field, yet still overestimating the experimental range of 0.3 to 0.45 Volts. As the charge equilibration model is a purely charge-based model for polarization, the current results suggest that explicitly modeled polarization effects can offer improvements in describing interfacial electrostatics in such systems.     

甲烷水合物导热机理的分子动力学模拟

甲烷水合物导热系数是甲烷水合物勘探、开采、储运以及其他应用过程中一个十分重要的物理参数.我们采用平衡分子动力学（EMD）方法Green-Kubo理论计算温度203.15～263.15K、压力范围3～100MPa、晶穴占有率为0～1的sI甲烷水合物的导热系数,采用的水分子模型包括TIP4P、TIP4P-Ew、TIP4P-FQ、TIP4P/2005、TIP4P/Ice.研究了主客体分子、外界温压条件等对甲烷水合物导热性能的影响.研究结果显示甲烷水合物的低导热性能由主体分子构建的sI笼型结构决定,而客体分子进入笼型结构后,使得笼型结构导热性能增强,同时进入笼型结构的客体分子越多,甲烷水合物导热性能越强.研究结果还显示在高温区域（T〉TDebye/3）内不同温度作用下,所有sI水合物具有相似的导热规律.压力对导热系数有一定影响,尤其是在较高压力条件下,压力越高,导热系数越大.而在不同温度和不同压力作用过程中,密度的改变对导热系数的增大或减小几乎没有影响.     

Molecular dynamics simulation of copper nano-cluster melting on the graphite substrate

The melting processes of different-sized copper nano-clusters supported on graphite (0001) plane are investigated by the molecular dynamics method. In this work, the melting point is predicted through the caloric curve. The simulation results show that the melting point of the supported copper nano-cluster is higher than that of the isolated one with the same Cu atoms. In the heating process, the copper nano-particle will adhere to the (0001) face of graphite with its (111) face. Pair analysis results show that the copper atoms close to the graphite can keep with order arrangement even when the temperature is higher than the melt point of the isolated nano-cluster.     

Molecular dynamics simulation in the grand canonical ensemble

An extended system Hamiltonian is proposed to perform molecular dynamics (MD) simulation in the grand canonical ensemble. The Hamiltonian is similar to the one proposed by Lynch and Pettitt (Lynch and Pettitt, J Chem Phys 1997, 107, 8594), which consists of the kinetic and potential energies for real and fractional particles as well as the kinetic and potential energy terms for material and heat reservoirs interacting with the system. We perform a nonlinear scaling of the potential energy parameters of the fractional particle, as well as its mass to vary the number of particles dynamically. On the basis of the equations of motion derived from this Hamiltonian, an algorithm has been proposed for MD simulation at constant chemical potential. The algorithm has been tested for the ideal gas, for the Lennard-Jones fluid over a wide range of temperatures and densities, and for water. The results for the low-density Lennard-Jones fluid are compared with the predictions from a truncated virial equation of state. In the case of the dense Lennard-Jones fluid and water our predicted results are compared with the results reported using other available methods for the calculation of the chemical potential. The method is also applied to the case of vapor-liquid coexistence point predictions.     

金属晶体间微观静摩擦特性的分子动力学模拟研究

以光滑干摩擦接触平面为对象,利用金属晶体间的强体积效应特征,建立了简化计算静摩擦力的界面势能模型.根据第一性原理的方法模拟得出界面分子势能的变化,通过界面分子势能计算出静摩擦力大小,并将数据结果通过通用黏附能量函数计算出的静摩擦力大小进行验证,也将计算结果与超高真空原子力显微镜试验结果进行对比.最后拟合出最大静摩擦力与法向载荷的线性函数关系,得出摩擦力的数值为真实接触面积的函数,并与法向载荷成正比的结论.从微观上对同种金属材料间库伦摩擦定律进行验证与研究.     

分子动力学模拟研究荧光分子芘在磺基甜菜碱胶束中的增溶

采用分子动力学模拟研究了荧光分子芘在磺基甜菜碱两性表面活性剂聚集体中的增溶现象．结果表明,芘分子自发地自溶液中增溶进入胶束疏水内核的栅栏层区域．当胶束溶液中芘分子的局部浓度增大时,两个芘分子可以同时增溶进胶束的栅栏层区域,此时两个芘分子形成π-π共轭堆积的激发态络合物．但是由于荧光分子之间的弱兀．兀相互作用,激发态络合物在胶束中是不稳定的,表现为两个芘分子的多次结合和分离．模拟表明,分子动力学方法可以在分子水平上研究荧光探针分子在表面活性剂胶束中的增溶位点,解释荧光分子在胶束中的动力学现象．     

Molecular dynamics simulation study on the inhibitory effects of choline-O-sulfate on hIAPP protofibrilation

Type 2 diabetes mellitus (T2Dm) is a neurodegenerative disease, which occurs due to the self-association of human islet amyloid polypeptide (hIAPP), also known as human amylin. It was reported experimentally that choline-O-sulfate (COS), a small organic molecule having a tertiary amino group and sulfate group, can prevent the aggregation of human amylin without providing the mechanism of the action of COS in the inhibition process. In this work, we investigate the influence of COS on the full-length hIAPP peptide by performing 500 ns classical molecular dynamics simulations. From pure water simulation (without COS), we have identified the residues 11–20 and 23–36 that mainly participate in the fibril formation, but in the presence of 1.07 M COS these residues become totally free of β-sheet conformation. Our results also show that the sulfate oxygen of COS directly interacts with the peptide backbone, which leads to the local disruption of peptide–peptide interaction. Moreover, the presence of favorable peptide-COS vdW interaction energy and high coordination number of COS molecules in the first solvation shell of the peptide indicates the hydrophobic solvation of the peptide residues by COS molecules, which also play a crucial role in the prevention of β-sheet formation. Finally, from the potential of mean force (PMFs) calculations, we observe that the free energy between two peptides is more negative in the absence of COS and with increasing concentration of COS, it becomes unfavorable significantly indicating that the peptide dimer formation is most stable in pure water, which becomes less favorable in the presence of COS. © 2019 Wiley Periodicals, Inc.     

聚乙烯在石墨表面结晶的分子动力学模拟

采用分子动力学方法模拟了聚乙烯在石墨(001)表面的吸附和结晶过程;直观的给出了聚乙烯链被石墨(001)面吸附并诱导形成有序的片层晶体的过程;发现结晶温度对得到的有序结构中的聚乙烯链相对石墨表面的特定取向有影响(300 K和600 K时的取向方向不同);表面覆盖率影响聚乙烯吸附层的厚度,对取向的方向无影响.     

Molecular dynamics simulation of single wall carbon nanotubes polymerization under compression

Single wall carbon nanotubes (SWCNTs) often aggregate into bundles of hundreds of weakly interacting tubes. Their cross-polymerization opens new possibilities for the creation of new super-hard materials. New mechanical and electronic properties are expected from these condensed structures, as well as novel potential applications. Previous theoretical results presented geometric modifications involving changes in the radial section of the compressed tubes as the explanation to the experimental measurements of structural changes during tube compression. We report here results from molecular dynamics simulations of the SWCNTs polymerization for small diameter arm chair tubes under compression. Hydrostatic and piston-type compression of SWCNTs have been simulated for different temperatures and rates of compression. Our results indicate that large diameter tubes (10,10) are unlike to polymerize while small diameter ones (around 5 A) polymerize even at room temperature. Other interesting results are the observation of the appearance of spontaneous scroll-like structures and also the so-called tubulane motifs, which were predicted in the literature more than a decade ago.     

Molecular dynamics simulation study on zwitterionic structure to maintain the natural behavior of polyalanine13 in aqueous environment

Molecular dynamics simulations are applied to the initial stage of polyalanine13 conformational transi- tion from α-helix to random coil in aqueous environment and the interaction of polyalanine13 with zwitterionic and hydrophobic surfaces respectively in the same condition. The analysis of secondary structure, hydrogen bonds, RMSD, dihedral distribution, and the degree of adsorption are performed. The results show that zwitterionic structure maintains the natural behavior of polyalanine13 in water to a better extent, which should be an indirect proof of the hypothesis of "maintain of normal structure."     

A steered molecular dynamics simulation on the elastic behavior of adsorbed star polymer chains

<正>Elastic behavior of 4-branched star polymer chain with different chain length N adsorbed on attractive surface is investigated using steered molecular dynamics(SMD) simulation method based on the united-atom(UA) model for branched alkanes.The simulation is realized by pulling up the chain via a linear spring with a constant velocity v = 0.005 nm/ps.At the beginning,the chain lies extensionally on adsorbed surface and suffers continuous deformations during the tensile process.Statistical parameters as mean-square radii of gyration S~2_(xy),S~2_z,shape factor δ,describing the conformational changes,sectional density den which gives the states of the chain,and average surface attractive energy U_a,average total energy U,average force f probed by the spring,which characterize the thermodynamic properties, are calculated in the stimulant process.Remarkably,distinguishing from the case in linear chains that there only exists one long plateau in the curve of f,the force plateau in our study for star chains is multiple,denoting different steps of desorption,and this agrees well with the experimental results in essence.We find during the tensile process,there are three characteristic distances Z_c,Z_t and Z_0 from the attractive surface,and these values vary with N.When Z=Z_c,the chain is stripped from the surface,but due to the form of wall-monomer interaction,the surface retains weak influence on the chain till Z = Z_c.From Z=Z_t,parameters U_a,U and f respectively reach a stable value,while the shape and the size of the chain still need adjustments after Z_t till Z_0 to reach their equilibrium states.Specifically,for short chain of N= 41,Z_t and Z_0 are incorporated.These results may help us to deepen the knowledge about the elastic behavior of adsorbed star polymer chains.     

Molecular dynamics simulation of metastable ices IV and XII

The method of molecular dynamics with the use of Poltev-Malenkov potential is applied to simulate crystalline ices IV and XII, which do not have the regions of stability in the phase diagrams of H₂O and D₂O ices. Ice IV appears to undergo a partial destruction, whereas the ice XII structure is retained during the simulation. For different crystal types of water molecules in considered ices the mean square displacement of the center of mass of a water molecule with time is calculated together with the density of states of translational and librational vibrations.     

Molecular dynamics simulation of complex multiphase flow on a computer cluster with GPUs

Compute Unified Device Architecture (CUDA) was used to design and implement molecular dynamics (MD) simulations on graphics processing units (GPU). With an NVIDIA Tesla C870, a 20–60 fold speedup over that of one core of the Intel Xeon 5430 CPU was achieved, reaching up to 150 Gflops. MD simulation of cavity flow and particle-bubble interaction in liquid was implemented on multiple GPUs using a message passing interface (MPI). Up to 200 GPUs were tested on a special network topology, which achieves good scalability. The capability of GPU clusters for large-scale molecular dynamics simulation of meso-scale flow behavior was, therefore, uncovered. Supported by the National Natural Science Foundation of China (Grant Nos. 20336040, 20221603 and 20490201), and the Chinese Academy of Sciences (Grant No. Kgcxz-yw-124)     

Molecular dynamics study on the influence of C-terminal sugar substitution on dynamics and conformation of vancomycin derivatives

Computational investigations were performed to examine the effects of the addition of 2-acetamido-2-deoxy-β-D-galactopyranosylamine or 1-amino-1-deoxy-D-glucitol connected to the C-terminus of vancomycin with different linkers. The purpose of this modification was to find more effective vancomycin derivatives by providing alternative interactions between vancomycin moiety and the peptidoglycan precursor. Each prepared vancomycin–peptidoglycan complex was optimized and submitted to the molecular dynamics study and analysis. The analysis of overall root mean square deviation, changes in position and interactions involving modified part of vancomycin as well as cluster analysis were carried out. One of the proposed vancomycin analogues seems to be efficient vancomycin substitute.     

Molecular dynamics simulation of O3 photolysis by ultraviolet light in solid argon

A technique of time reversal is used to simulate the trapping-site structure of O₃ isolated in an argon matrix. It is found that the most probable trapping site is single substitutional. The UV photodissociation of O₃ in Ar matrices is simulated by molecular dynamics. It is shown that the photolysis channels of O₃ in the single trapping site are seriously hindered by the matrix cage. The photolysis quantum yield obtained via our simulations is in agreement with corresponding measurements. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 623–628, 1999     

Molecular dynamics simulation on the interaction between polymer inhibitors and anhydrite surface

Investigation on the microscopic interaction between polymer inhibitors and calcium sulfate will be helpful for understanding its scale inhibition mechanism and can provide a theoretical guidance to developing new scale inhibitors. In this work, molecular dynamics simulations with COMPASS force field have been performed to simulate the interaction between hydrolyzed polymaleic anhydride (HPMA), polyaspartic acid (PASP), polyepoxysuccinic acid (PESA), polyacrylic acid (PAA) and the (001) and (020) surfaces of anhydrite (AD) crystal with and without water. The results show that the sequence of binding energies between four polymer inhibitors and AD (001) and (020) with water is PESA > PASP > HPMA > PAA. The binding energy of the same polymer inhibitor on AD (001) is smaller than that on AD (020). Water molecules weaken the deformations of HPMA and PAA but aggravate those of PASP and PESA. Natural bond orbital (NBO) charges of the repeat units of polymer inhibitors were calculated by B3LYP/6‐31G* method. The Coulomb interaction is formed between the O atoms of polymer inhibitors and the Ca atoms of AD crystal. The system of polymer–AD is mainly contributed from the non‐bonding interaction. Polymer inhibitors do not interact directly with AD crystal, but indirectly through the interactions between inhibitor–H₂O and H₂O–AD, i.e. water molecules participate in scale inhibition of polymer inhibitors to AD crystal. Water molecules cannot be ignored when the interaction models are constructed, i.e. solvent effect cannot be ignored. Copyright © 2015 John Wiley & Sons, Ltd.     

Steered molecular dynamics simulation of elastic behavior of adsorbed single polyethylene chains

We investigate the dynamics of the detachment of single polyethylene (PE) chains from a strongly adsorbing surface in vacuum using a united atom model. Various statistical properties, including the mean‐square end‐to‐end distance 〈R²〉, the mean‐square radii of gyration , , the shape factor , the torsion angle distribution, the average surface adsorption energy , the average total energy , and the average force , are analyzed. The relationship between the average force and the pulling velocity v shows two distinctive regions: a weakly dependence region at Å/ps and a strongly dependence region at Å/ps. Remarkably, the PE chain manifests force hysteresis under sequential stretching and releasing. These investigations may provide some insights into the elastic behavior of adsorbed polymer chains. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2322–2332, 2007