Vibrational spectrum at a water surface: a hybrid quantum mechanics/molecular mechanics molecular dynamics approach

A hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation is applied to the calculation of surface orientational structure and vibrational spectrum (second-order nonlinear susceptibility) at the vapor/water interface for the first time. The surface orientational structure of the QM water molecules is consistent with the previous MD studies, and the calculated susceptibility reproduces the experimentally reported one, supporting the previous results using the classical force field MD simulation. The present QM/MM MD simulation also demonstrates that the positive sign of the imaginary part of the second-order nonlinear susceptibility at the lower hydrogen bonding OH frequency region originates not from individual molecular orientational structure, but from cooperative electronic structure through the hydrogen bonding network.     

Dielectric constants of binary mixtures of propylene carbonate with dimethyl carbonate and ethylene carbonate from molecular dynamics simulation: comparison between non-polarizable and polarizable force fields

Using non-polarizable and polarizable molecular dynamics simulations, binary mixtures of propylene carbonate?+?dimethyl carbonate and propylene carbonate?+?ethylene carbonate with various compositions were investigated. The polarizable model produces more reasonable estimation of dielectric constants than the non-polarizable model; however, combining the electronic continuum model with the non-polarizable MD improves the comparison between the two models. Fair agreement was found between the results from these simulations and available experimental data. In addition, for a better understanding of the mixing behaviour, the excess dielectric constants over the entire composition were calculated. By comparison of the two mixtures in various mole fractions, distinctive mixing behaviours of propylene carbonate?+?dimethyl carbonate (poorly symmetric mixture) and propylene carbonate?+?ethylene carbonate (highly symmetric mixture) were observed.     

A definitive test of the Percus-Yevick and hypernetted chain approximations in liquid metals

Pair correlation functions calculated via molecular dynamics (MD) are inverted using the Percus-Yevick and Hypernetted Chain approximations to obtain approximate pair potentials for Li and Al. The results turn out to be quite sensitive to the calculated compressibility. These approximate pair potentials are compared with the ones that were used in the MD calculation. Although some qualitative features of the original potentials are reproduced, the agreement is very poor making it clear that the PY and HNC approximations are of very little use for liquid metal calculations.     

The effects of vacancy defects and nitrogen doping on the thermal conductivity of armchair (10, 10) single-wall carbon nanotubes

The influence of vacancy defects and nitrogen doping on the thermal conductivity of typical armchair (10, 10) single-walled carbon nanotubes is investigated using molecular dynamics (MD) simulation. The second-generation reactive empirical bond order potential and Tersoff potential are used to describe the interatomic interactions and the thermal conductivities are calculated using the Müller-Plathe approach (also called non-equilibrium MD simulation). Vacancy defects decrease the thermal conductivity whereas the substitution of nitrogen at vacancy sites improves the thermal conductivity. Quantum correction of the calculated results produces a thermal conductance temperature dependence that is in qualitative agreement with experimental data.     

Diffusion of 1,2,3-Benzotriazole as a Volatile Corrosion Inhibitor through Common Polymer Films Using the Molecular Dynamics Simulation Method

Diffusion of 1,2,3-benzotriazole (BT), as one of the volatile corrosion inhibitors (VCI) for copper and steel, through several polymers was investigated using molecular dynamics simulation (MD). MD were performed by employing the COMPASS force field to estimate the diffusivity of BT through polyethylene (PE), polypropylene (PP), polyvinyl chloride (PVC), and Nylon 6 as potential hosts for anticorrosion film packaging purposes. The diffusion coefficients (D) of BT in these polymers were calculated by constructing an amorphous cell, each containing BT and one of these polymers. After constructing the cell, a molecular dynamics simulation was performed to calculate the mean square displacement of the BT molecule. Simulation results showed that BT can diffuse through PVC easier than the other polymers. Among these hosts the Nylon 6 had the lowest D value, implying that this polymer can maintain BT for a long time. The temperature dependence of diffusion through PE, as the most common VCI film, was studied and the activation energy (Q_d) and pre-exponential diffusion coefficient (D₀) in Arrhenius equation were calculated.     

Calculation of diffusion coefficient of long chain molecules using molecular dynamics

Molecular dynamics (MD) is a powerful tool for calculating several thermo-physical properties of wide range of materials. In this study, the diffusivities (D) of two widely used long chain molecules MHA and ODT are calculated at various temperatures using MD simulations coupled with Einstein relationship. Four different kinds of forcefields COMPASS, UFF, CVFF and PCFF are employed in the MD simulation and the results are compared. Diffusivity values are evaluated in a humid environment in presence of water molecules.     

Theoretical investigations of rotational phenomena and dielectric properties in a nematic liquid crystal

The molecular dynamics (MD) simulation, based on a realistic atom-atom interaction potential, was performed on 4-n-pentyl-4'-cyanobiphenyl (5CB) in the nematic phase. The rotational viscosity coefficients (RVCs) γ _i, (i = 1, 2) and the ratio of the RVCs λ = - γ ₂/γ ₁ were investigated. Furthermore, static and frequency-dependent dielectric constants and ε were calculated using parameters obtained from the MD simulation. Time correlation functions were computed and used to determine the rotational diffusion coefficient, D _⊥. The RVCs and λ were evaluated using the existing statistical-mechanical approach (SMA), based on a rotational diffusion model. The SMA rests on a model in which it is assumed that the reorientation of an individual molecule is a stochastic Brownian motion in a certain potential of mean torque. According to the SMA, γ _i are dependent on the orientational order and rotational diffusion coefficients. The former was characterized using: i) orientational distribution function (ODF), and ii) a set of order parameters, both derived from analyses of the MD trajectory. A reasonable agreement between the calculated and experimental values of γ _i and λ was obtained. Received 22 March 2000 and Received in final form 8 October 2000     

Momentum distribution dynamics of a Tonks-Girardeau gas: Bragg reflections of a quantum many-body wave packet

The momentum distribution (MD) dynamics of a Tonks-Girardeau (TG) gas is studied in the context of Bragg reflections of a many-body wave packet. We find strong suppression of a Bragg reflection peak for a large and dense TG wave packet; our observation illustrates the dependence of the MD on the interactions and wave function symmetry. The MD is calculated from the reduced single-particle density matrix (RSPDM). We develop a method for calculating the RSPDM of a TG gas, which is operative for a large number of particles, and does not depend on the external potential and the state of the system. The method is based on a formula expressing the RSPDM via a dynamically evolving single-particle basis.     

Simple theoretical model of shear viscosity in isotopic fluid mixtures

We propose a simple hybrid model for the shear viscosity of isotopic fluid mixtures by coupling the contribution of the Stokes–Einstein relation with the existing linear model of Roults's law for the shear viscosity. The calculated values of shear viscosity using this simple hybrid model are found to be in excellent agreement with the molecular dynamics (MD) simulation results. The calculated value of the shear viscosity obtained from the theoretical model as well as the MD simulation increases with increasing mass ratio.     

Roles of V/III ratio and mixture degree in GaN growth: CFD and MD simulation study

To understand the mechanism of Gallium nitride (GaN) film growth is of great importance for their potential applica- tions. In this paper, we investigate the growth behavior of the GaN film by combining computational fluid dynamics (CFD) and molecular dynamics (MD) simulations. Both of the simulations show that V/III mixture degree can have important impacts on the deposition behavior, and it is found that the more uniform the mixture is, the better the growth is. Besides, by using MD simulations, we illustrate the whole process of the GaN growth. Furthermore, we also find that the V/III ratio can affect the final roughness of the GaN film. When the V/III ratio is high, the surface of final GaN film is smooth. The present study provides insights into GaN growth from the macroscopic and microscopic views, which may provide some suggestions on better experimental GaN preparation.     

Assessment of Compatibility in Polypropylene/Poly(lactic acid)/Ethylene Vinyl Alcohol Ternary Blends: Relating Experiments and Molecular Dynamics Simulation Results

Two systems of polypropylene (PP), poly(lactic acid) (PLA) and ethylene vinyl alcohol copolymer (EVOH) ternary blends having different compositions were extruded in a co-rotating twin screw extruder. The first system was PP/PLA (75/25) with various EVOH contents, the second one was PP/EVOH (75/25) having various PLA contents. The effects of composition on the morphology and the tensile and impact properties of the blends were investigated. There were increases in the tensile modulus and tensile strength with an increase in the EVOH and PLA contents in the first and second systems, respectively. A molecular dynamics (MD) simulation was used to investigate the compatibility between the components. Prediction of the miscibility of the blends was carried out by determining the interaction parameters (χ), mixing energies (ΔH_mix), phase diagrams and Gibbs free energies. The MD simulation showed a UCST behavior for the components. Moreover, the simulation results showed a compatibilizer effect for the EVOH component. The experimental values of the dynamic mechanical thermal analysis (DMTA) and mechanical properties were correlated to the MD results. There was a good correlation between the MD and DMTA results. The modulus values using the parallel and Davis models were near to the experimental ones. A good fitting to the mixture law with addition of EVOH confirmed a good compatibilzing effect of it between the PP and PLA components.     

Study of the feature of lattice dynamic and ferroelectric transition in perovskites using molecular-dynamics modeling

Static and dynamic correlation functions of the BaTiO₃ crystal are calculated using molecular-dynamics (MD) modeling. Based on time-dependent pair correlation functions, phonon spectra of BaTiO₃ are calculated and the central peak of inelastic scattering is studied. It is shown that the phonon frequencies calculated by the MD method are in quite good agreement with those we obtained previously in the quasiharmonic approximation [1, 2]. It is demonstrated that the central peak of inelastic scattering is mainly associated with the soft optical mode and has the same symmetry. The coincidence of symmetries makes it possible to explain both the features in the X-ray scattering and the EXAFS spectroscopy.     

Localization phenomena in models of ion-conducting glass formers

The mass transport in soft-sphere mixtures of small and big particles as well as in the disordered Lorentz gas (LG) model is studied using molecular dynamics (MD) computer simulations. The soft-sphere mixture shows anomalous small-particle diffusion signifying a localization transition separate from the big-particle glass transition. Switching off small-particle excluded volume constraints slows down the small-particle dynamics, as indicated by incoherent intermediate scattering functions. A comparison of logarithmic time derivatives of the mean-squared displacements reveals qualitative similarities between the localization transition in the soft-sphere mixture and its counterpart in the LG. Nevertheless, qualitative differences emphasize the need for further research elucidating the connection between both models.     

Molecular dynamic study of volumetric phase change induced by a femtosecond laser pulse

During the last decade, femtosecond laser has been used for micro-machining of various materials. In this work, the phase change phenomena during femtosecond laser ablation are investigated using molecular dynamics (MD) simulation. The process of femtosecond laser ablation of nickel is calculated. The temperature and stress history, and the generation and growth of gas bubbles are traced. For different laser pulse fluences, the material ablation process is analysed to reveal the effect of temperature and stress. PACS 02.70.Ns; 42.62.-b; 64.60.Ht     

Melting and Grüneisen parameters of NaCl at high pressure

The Buckingham potential has been employed to simulate the melting and thermodynamic parameters of sodium chloride (NaCl) using the molecular dynamics (MD) method. The constant-volume heat capacity and Grüneisen parameters have been obtained in a wide range of temperatures. The calculated thermodynamic parameters are found to be in good agreement with the available experimental data. The NaCl melting simulations appear to validate the interpretation of superheating of the solid in the one-phase MD simulations. The melting curve of NaCl is compared with the experiments and other calculations at pressure 0－30GPa range.     

一种危险液体混合物的拉曼光谱定性定量识别方法

危险液体混合物的拉曼光谱定性定量分析一直是现场应用难点,为解决该问题,分析了多种物质混合后拉曼光谱的峰位、峰值、峰型变化情况,选取拉曼光谱关键特征峰进行数学简化,构建了从混合物物质成分到混合物拉曼光谱的映射关系,该映射关系描述多种物质成分混合的混合物拉曼特征峰响应只和混合物中各成分本身拉曼特征峰响应以及各物质成分混合比例有关,各物质成分按混合比例贡献拉曼特征谱峰,共同形成最终的混合物拉曼光谱。由该映射关系求逆,可实现从采集到的混合物拉曼光谱计算出各物质成分的混合比例。基于此,设计了危险液体混合物成分定性定量识别方法,主要方法步骤包括,首先进行拉曼光谱数据采集,然后进行拉曼光谱数据处理并获得拉曼特征峰,再进行测试样品与数据谱库标准品的正反向特征峰匹配,如果正反向特征峰匹配系数都比较高,在满足一定阈值条件下,可认定测试样品是某种纯净物,如果不是纯净物,则进入混合物分析,通过拉曼光谱特征峰反向匹配系数筛选,确定混合物成分构成,混合物成分确定后再进行混合物成分比例计算,最终实现危险液体混合物定性定量分析。实验部分,选定丙酮、甲苯、三氯甲烷、乙醇及其混合物进行实验验证,当混合物样品是丙酮、乙醇两种成分按3∶7比例混合时,经拉曼光谱识别方法计算,混合成分计算值是丙酮占比0.245 7,乙醇占比0.706 0;当混合物样品是甲苯、三氯甲烷两种成分按3∶7比例混合时,经拉曼光谱识别方法计算,混合成分计算值是甲苯占比0.323 4,三氯甲烷占比0.763 0;当混合物样品是丙酮、甲苯、乙醇三种成分按4∶3∶3比例混合时,经拉曼光谱识别方法计算,混合成分计算值是丙酮占比0.795 9、甲苯占比0.303 5、乙醇占比0.287 5,实验结果表明,当危险液体混合物成分是两种或三种成分混合时,混合成分计算值基本和实际值吻合,应用危险液体混合物的拉曼光谱定性定量识别方法,可较准确的从拉曼混合光谱中解析出各混合物成分以及各成分在混合物中的比例,可以判断混合物每个拉曼特征谱峰都来自于哪个成分或哪些成分拉曼特征谱峰的混合,谱图解析结果良好,对危险液体混合物现场分析鉴别有较大应用价值。     

Molecular dynamics simulations of a mixed DOPC/DOPG bilayer

We have constructed a mixed dioleoylphosphatidylcholine (DOPC) and dioleoylphosphatidylglycerol bilayer (DOPG) bilayer utilizing MD simulations. The aim was to develop an explicit molecular model of biological membranes as a complementary technique to neutron diffraction studies that are well established within the group. A monolayer was constructed by taking a previously customized PDB file of each molecule and arranging them in a seven rows of ten molecules and duplicated and rotated to form a bilayer. The 140-molecule bilayer contained 98 DOPC molecules and 42 DOPG molecules, in a 7:3 ratio in favour of DOPC. Sodium counter ions were placed near the phosphate moiety of DOPG to counteract the negative charge of DOPG. This was representative of the lipid ratio in a sample used for neutron diffraction. The MD package GROMACS was used for confining the bilayer in a triclinic box, adding Simple Polar Charge water molecules, energy minimization (EM). The bilayer/solvent system was subjected to EM using the steepest descent method to nullify bad contacts and reduce the potential energy of the system. Subsequent MD simulation using an initial NVT (constant number of particles, volume and temperature) for a 20 ps MD run followed by a NPT (constant number of particles, pressure and temperature) was performed. Structural parameters including volume of lipid, area of lipid, order parameter of the fatty acyl carbons and electron density profiles generated by the MD simulation were verified with values obtained from experimental data of DOPC, as there are no comparable experimental data available for the mixed bilayer.     

混合物物态方程的计算

 在采用体积相加原理计算混合物物态方程的基础上,建立了一种物理模型确定混合物温度。根据混合物中各组分温度和压强平衡条件,采用压强-密度迭代方法计算给出混合物物态方程,编制了两种组分的混合物物态方程计算程序。为检验建立的温度模型的合理性及程序的有效性,分析了不同密度、温度状态的氢（H2）和钨（W）组成的混合物状态参量,计算了以下情形及其组合情形的混合物物态方程：H₂和W以不同质量比混合;质量比固定,单组分状态不同;温度区间和密度区间不同。研究表明:实际应用中在建立的混合物温度模型基础上确定的混合物物态方程是合理的。     

Diffusion kurtosis imaging for the assessment of renal fibrosis of chronic kidney disease: A preliminary study

Purpose: To investigate the potential of diffusion kurtosis imaging (DKI) for the assessment of renal fibrosis in chronic kidney disease (CKD), using histopathology as the reference standard.Methods: Eighty-nine CKD patients and twenty healthy volunteers were recruited in this study. DKI was performed in all participants and all CKD patients received renal biopsy. The values of mean diffusivity (MD) and mean kurtosis (MK) in the renal cortex and medulla were compared between CKD patients and healthy volunteers. The Spearman correlation coefficient was calculated to assess the relationship between MD, MK values and the estimated glomerular filtration rate (eGFR), serum creatinine (SCr), 24 h urinary protein (24 h-UPRO), histopathological fibrosis score.Results: The medullary MD values were significantly lower than cortex, while the cortical MK values were significantly lower than medulla for all participants. Renal parenchymal MD values were significantly lower in the CKD patients than healthy controls, whereas MK values were significantly higher in the CKD patients than healthy controls. In the CKD patients, the significantly negative correlation was observed between the renal parenchymal MD values and the 24 h-UPRO, SCr, histopathological fibrosis score, as well as between the renal parenchymal MK values and the eGFR, while the significantly positive correlation was found between the renal parenchymal MD values and the eGFR, as well as between the renal parenchymal MK values and the 24 h-UPRO, SCr, histopathological fibrosis score.Conclusion: DKI shows great potential in the noninvasive assessment of renal fibrosis in CKD.     

Prediction of Structure and Energy of Trans-1,4-Polybutadiene Glassy Surface by Atomistic Simulations of Free-Standing Ultrathin Films

Atomistic modeling of amorphous trans-1,4-polybutadiene (TPBD), using molecular mechanics and molecular dynamics (MD) simulations, is performed to generate three-dimensionally periodic bulk and two-dimensionally periodic thin film condensed phases. The condensed structures are constructed using multiple polymer chains. Structural and energetic relaxations and sampling of properties are performed using MD in the canonical ensemble (NVT) by a procedure that relieves local high-energy spots and brings the system to realistic thermodynamic states. The calculated surface energy for TPBD, 30.72 erg/cm², is in excellent agreement with the reported experimental value of 31 erg/cm². The structure of the surface layers is probed in terms of the atomic mass density variations, bond-bond orientation function profiles, and the distribution of the dihedral angles about the rotatable backbone bonds. The thickness of the surface layer over which the density varies smoothly but rapidly is found to be approximately 15 Å. The level of agreement of the calculated surface energy with the experimental value is superior in comparison to previous investigations in the literature using the atomistic approach for flexible polymers.