Molecular dynamics simulation on diffusion of 13 kinds of small molecules in polyethylene terephthalate

Understanding the diffusion of migrants in polyethylene terephthalate (PET) and calculating the diffusion coefficients are very important for migration research. In this study, the diffusion coefficients of 13 kinds of small molecules with molecular weights ranging from 32 to 339 g/mol in amorphous PET are calculated based on molecular dynamics (MD) simulation. By comparison of diffusion coefficients simulated by MD simulation techniques, predicted by the Piringer model and by experiments, the accuracy of the Piringer model and MD simulation techniques for the estimation of diffusion coefficients of migrants in PET is evaluated. The MD simulation shows that D_simu is very close to D_exp, within one order of magnitude of the experimental diffusion coefficients except for a few samples. The possible reasons for the differences among D_simu, D_pred and D_exp are analysed from the molecular weight and temperature. The results show that the Piringer‐model‐predicted values at high temperatures overestimate significantly higher than that at lower temperatures. The activation energy is calculated by the Arrhenius equation, which shows the relationship between diffusion coefficient and temperature. It is shown that the MD simulation yields acceptable activation energy. The study suggests that MD simulation may be a useful approach to calculate the diffusion coefficients of small molecules in PET. Copyright © 2010 John Wiley & Sons, Ltd.     

Molecular dynamics simulation of adsorption of ozone and nitrate ions by water clusters

Coadsorption of ozone molecules and nitrate ions by water clusters was studied by the molecular dynamics technique. The maximum value of an average O-H…O bond length in a water carcass is realized at the minimum specific number of such bonds when the ratio of adsorbed ozone molecules to nitrate ions captured by a cluster is two. IR absorption and reflection spectra were reshaped significantly, and new peaks appeared at Raman spectra due to the addition of ozone and nitrate ions to the disperse water system. After ozone and nitrate ions were captured, the average (in frequency) IR reflection coefficient of the water disperse system increased drastically and the absorption coefficient fell.     

Molecular dynamics calculation of the isotope effect for vacancy diffusion

The relative jump frequencies of tracer atoms with masses 1.00 and 1.05 times the host atom mass have been computed by molecular dynamics in a system of 255 Lennard-Jones atoms comparable with solid argon at 80 °K. The chief error of previous theoretical treatments of the isotope effect is found to be their neglect of unsuccessful saddle point crossings (e.g. U turns) which become more prevalent the lighter the diffusing atom. In the system studied, this effect lowers the ΔK factor from its harmonic value of 0.98 to an effective value of 0.89±0.05.     

铜纳米丝的应变率和尺寸效应的分子动力学模拟

用分子动力学方法对铜纳米丝的应变率效应和尺寸效应进行了模拟研究．结果表明，随着加载应变率的增大，铜纳米丝从低应变率下的静态响应逐渐呈现出较高应变率下的准静态以及高应变率下的动态响应特征，其变形机制以及应力一应变曲线的形态也随之发生变化．在静态和准静态区域，位错运动是铜纳米丝塑性变形的主要来源，而在高应变率动态加载时，铜纳米丝出现整体结构的非品化，最大屈服应力也随着应变率的升高而增大，强化现象明显．当铜纳米丝的截面尺寸变化时，其弹性摸量、屈服应力以及屈服应变、进入强化区域的临界应变率等都发生相应的变化，尺寸效应显著。     

Molecular dynamics simulation of pressure effect on phase transition behaviour and dynamics in the isotropic and discotic nematic phases

Molecular dynamics simulation was performed at constant temperature and pressure to investigate the effect of pressure on molecular dynamics for disc-shaped molecules. The generic Gay-Berne model, GB(0.345, 5.0, 1, 3), was used to study the phase transition behaviour, and translational and rotational dynamics, under two different reduced pressures P^?, 10.0 and 20.0. Obvious shifts were detected in the transition temperatures. Both systems have the same phase sequence with different pressures: isotropic, discotic nematic and columnar phases. Translational motion is characterised by the parallel and perpendicular components of diffusion coefficients, with respect to the director in the orientational ordered phase. With regard to rotational dynamics, the correlation time of the first-rank orientational time autocorrelation function, which corresponds to end-over-end rotational motion of a molecule, has been investigated. A clear jump in the temperature dependence of the correlation time has been found at the isotropic-nematic phase transition point. The retardation factor g_|| as a function of the reduced temperature T^?/T_NI^? shows an apparent pressure effect on the rotational dynamics.     

Prediction of the temperature dependence of binary diffusion coefficients of gaseous systems from thermal diffusion factors and diffusion coefficients at 300 K

Data are presented which enable binary diffusion coefficients and their concentration dependences to be predicted from diffusion coefficients and thermal diffusion factors at 300 K. The results up to 2000 K are compared with corresponding values derived from the complication of Mason and Marrero. Paper dedicated to Professor Edward A. Mason.     

Molecular dynamics simulation of the enhancement of cobra cardiotoxin and E6 protein binding on mixed self-assembled monolayer molecules

Molecular dynamics simulations are performed on n-alkinethiol self-assembled monolayers (SAMs) and their mixture on a gold surface so that the orientations of the binding of cobra cardiotoxin and E6 protein molecules can be selected using the mixing ratio of CH3-terminated SAMs with different chain lengths. The simulations suggest that a SAM surface with different mixing ratios may provide a possible platform for aligning protein molecules with a desired orientation and for enhancing the binding energy of the protein on the designed surface.     

Molecular dynamics simulation of the rate of dissociation and of the time of vibrational relaxation of diatomic molecules

A method is described for molecular dynamics calculation of the rate of dissociation and of the time of vibrational relaxation of N₂ and O₂ diatomic molecules, which involves simultaneous simulation of the entire ensemble of particles based on the classical concepts of the dynamics of molecules with internal degrees of freedom. Agreement between the calculation results and experimental data is discussed.     

Molecular dynamics simulation of asphalt-aggregate interface adhesion strength with moisture effect

This study developed an atomistic simulation framework based on the classical molecular dynamics (MD) method to study the moisture-induced damage at the asphalt-aggregate interface. The interface adhesion strength of the asphalt–quartz system was predicted using MD simulation for the first time. The interface stress-separation curve under tension that was obtained from MD simulation resembles the failure behaviour measured from the pull-off strength conducted at the macroscopic scale. The results show that the presence of moisture at the asphalt–quartz interface significantly reduces the interface adhesion strength. The interface failure process is affected by the chemical compositions of asphalt. The interface adhesion strength decreases as the moisture content increases or the temperature increases. It was found that the atomistic model size (number of atoms) and the loading rate in MD simulation have considerable effects on the predicted interface adhesion strength. The findings from MD simulation provide fundamental understanding of material failure at the atomistic scale that cannot be observed at the normal experimental testing environment for asphalt materials. The MD simulation results can be potentially calibrated and utilised as inputs for higher scale micromechanical models to predict bulk mechanical responses of asphalt mixtures.     

Molecular simulation and theory of associating chain molecules

A closed-form statistical mechanical based equation of state for associating chain fluids is presented. A Lennard-Jones chain is used as a reference to account for the repulsive, dispersive and anisotropic (size) contributions, while the short-range directional attraction is treated as a perturbation expansion based on Wertheim's first-order theory of associating fluids. A model fluid composed of a chain of tangently bonded Lennard-Jones spheres with an associating square-well site at one of the end spheres is studied. Isobaric-isothermal Monte Carlo simulations were performed for this model at subcritical and supercritical temperatures at a association strength typical of hydrogen-bonding systems. The theory is seen accurately to predict the simulation results subject to the limitations of the equation of state of the reference fluid. The system studied has some of the main complexities found in associating chain molecules such as organic acids, alkanols, and primary amines.Paper presented at the Twelfth Symposium on Thermophysical Properties, June 19–24, 1994. Boulder, Colorado, U.S.A.     

Molecular dynamics simulation of copper bicrystal response to shear loading

The behavior of a large-angle grain boundary of the Σ = 5 (210)[001] special type in a copper bicrystal under shear loading conditions has been computer simulated. It is established that, simultaneously with the relative slippage of grains in the direction of applied load, the grain boundary shifts in the direction perpendicular to that of shear straining. This motion of the grain boundary exhibits a discrete character and leads to a growth of one grain at the expense of another. The mechanism of this displacement is analyzed and the influence of the loading rate and direction on the character of grain boundary motion is studied. The obtained results provide better understanding of the atomic mechanisms of plastic strain development in polycrystalline materials.     

Radon diffusion coefficients in 360 waterproof materials of different chemical composition

This paper summarises the results of radon diffusion coefficient measurements in 360 common waterproof materials available throughout Europe. The materials were grouped into 26 categories according to their chemical composition. It was found that the diffusion coefficients of materials used for protecting houses against radon vary within eight orders from 10(-15) to 10(-8) m(2) s(-1). The lowest values were obtained for bitumen membranes with an Al carrier film and for ethylene vinyl acetate membranes. The highest radon diffusion coefficient values were discovered for sodium bentonite membranes, rubber membranes made of ethylene propylene diene monomer and polymer cement coatings. The radon diffusion coefficients for waterproofings widely used for protecting houses, i.e. flexible polyvinyl chloride, high-, low-density polyethylene, polypropylene and bitumen membranes, vary in the range from 3 × 10(-12) to 3 × 10(-11) m(2) s(-1). Tests were performed which confirmed that the radon diffusion coefficient is also an effective tool for verifying the air-tightness of joints.     

Molecular dynamics simulation of microcrack healing in copper

The molecular dynamics method is used to simulate microcrack healing during heating or/and under compressive stress. A center microcrack in Cu crystal could be sealed under a compressive stress or by heating. The role of compressive stress and heating in crack healing was additive. During microcrack healing, dislocation generation and motion occurred. If there were pre-existed dislocations around the microcrack, the critical temperature or compressive stress necessary for microcrack healing would decrease, and the higher the number of dislocations, the lower the critical temperature or compressive stress. The critical temperature necessary for microcrack healing depended upon the orientation of crack plane. For example, the critical temperature of the crack along (0 0 1) plane was the lowest, i.e., 770 K.     

Molecular dynamics simulation of the effect of surface roughness and pore on linear friction welding between Ni and Al

Atomic model of Ni–Al linear friction welding is established by molecular dynamics simulation. The effect of surface roughness on linear friction welding and the rules of pore closure are investigated. The simulations results show that rough surfaces are gradually flattened during the friction process. The rough surface of the harder material (Ni) may influence the final structure of the weld. Pores near the interface is closed after linear friction welding. Pore closure in Al slab occurs in friction process by atom diffusion, while it takes place in Ni slab in forging stage mainly by deformation of the interface.     

分子动力学模拟金属玻璃Cu应力晶化的应变率效应

采用Mishin镶嵌原子势，通过分子动力学方法模拟了零温下非晶金属Cu在不同应变率条件下的拉伸变形过程和应力晶化行为，分析了此过程中原子体系应力与结构组态的变化．结果表明：在应变率10^8s^-1-10^9s^-1范围内，金属玻璃Cu的塑性流动应力随着应变率的提高而增大，弹性模量约为55GPa．在塑性流动过程中发生应力晶化现象，伴随着明显的晶核形成与生长过程，晶化程度随着应变率的增加而加剧．应力效应和温度效应都是导致金属玻璃晶化的重要途径，形成的少量纳米晶粒是导致剪切带的形成和扩展的可能因素．     

金刚石膜的计算机虚拟制备技术中的分子动力学模拟

综述了近年来金刚石薄膜形成过程的分子动力学（Molecular Dynamics，简称MD）模拟研究，详细地阐述了原子间相互作用势的选取，总结了不同沉积条件下MD的计算模型和几种典型情况下的模拟结果。研究表明：在原子尺度上，MD方法能较全面地提供有关膜生长的信息，对进一步了解金刚石膜形成的微观机制以及为细观层次仿真提供基本信息均具有重要意义。     

The effect of instrument resolution on diffusion coefficients measured using NMR spectroscopy

This study presents a numerical simulation of the performance of an NMR spectrometer in which the influence of equipment with both low and high spatial resolutions is investigated. The results indicate that a low resolution NMR with a wide sensitivity curve may be unable to provide an accurate estimation of the moisture profile along the whole length of a test sample where the moisture gradient changes abruptly. It cannot provide accurate moisture information over a distance measured from each end of the test sample equivalent to the effective width of the sensitivity curve. However, a low-resolution spectrometer does not show any significant errors when calculating liquid diffusion coefficients, although the range of moisture contents over which they can be measured is limited. This study suggests that to avoid errors and practical difficulties, NMR spectrometers for moisture measurement should be selected carefully by matching the effective width of the sensitivity curve to the moisture properties of the material to be measured.

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Résumé Cette étude présente une simulation numérique de l'exécution d'un spectromètre RMN étudiant l'influence d'un matériel à basses et hautes résolutions spatiales. Les résultats indiquent qu'il se peut qu'une basse résolution du RMN avec une courbe large de sensibilité ne soit pas en mesure de fjurnir une évaluation précise du profil d'humidité sur la longueur entière d'un échantillon d'essai où le gradient d'humidité change soudainement. Il ne peut pas fournir d'informations précises sur l'humidité au-dessus d'une distance mesurée à partir de chaque extrémité de l'échantillon d'essai équivalant à la largeur effective de la courbe de sensibilité. Cependant, un spectromètre à basse résolution ne montre aucune erreur significative lors du calcul des coefficients de diffusion liquide, bien que l'intervalle du contenu d'humidité au-dessus duquel elles peuvent être mesurées soit limité. Cette étude suggère que pour éviter des erreurs et des difficulté pratiques, les spectromètres RMN mesurant l'humidité soient choisis soigneusement en associat la largeur effective de la courbe de sensibilité aux propriétés d'humidité du matériel à mesurer.

     

Molecular dynamics simulation of incipient plasticity of nickel substrates of different surface orientations during nanoindentation

The present study aims to elucidate the anisotropic characteristics in material responses for crystallographic nickel substrates with (001), (011) and (111) surface orientations during nanoindentation. Molecular dynamic simulation is applied to compensate for the experimental limitation of nanoindentation, particularly for pure nickel substrates. Defect nucleation and evolution in Ni single crystal of these three crystal orientations was examined. Hardness and Young’s modulus are also extracted in different orientations. The Young’s modulus of (111) crystallographic orientation is the largest, while that of (001) surface is the smallest. The sensitivity of the yield point for face centred cubic crystals depends on the crystallographic orientation. The (001) crystallographic orientation reaches the yield point first, while the (111) crystallographic orientation is the most difficult in which to achieve yield. Using a visualisation method of centrosymmetry parameter, the homogeneous nucleation and early evolution of dislocations were investigated, deepening understanding of incipient plasticity at the atomic scale. The present results suggest that defect nucleation and evolution are the root of curve jitter. The indentation depth of the elastic–plastic transition point varies in the different crystallographic orientation models, and appears latest in the (111) model. The strain energy of the substrate exerted by the tip is stored by the formation of homogeneous nucleation and is dissipated by the dislocation slide in the {111} glide plane. The three nickel substrates with different crystallographic orientations exhibit different forms of dislocation propagation.