Relations between intergranular diffusion and structure: A molecular dynamics study

The high temperature (T > 0.5T_m) structure of the previously studied fcc (310)[001] Σ = 5 grain boundary is reinvestigated in order to determine the nature of the diffusion mechanism. The obtained results confirm our earlier conclusion that the grain boundary remains crystalline, but highly disordered, up to the melting point. In addition, we explored the diffusion mechanisms in the fcc (210)[001] Σ = 5 grain boundary. As expected, diffusion occurs mainly by the vacancy migration. The jump frequencies determined by the molecular dynamics simulation have been used to evaluate the tracer correlation factor and the anisotropy of the intergranular diffusion coefficient through a random walk model simulation of the vacancy migration.     

Twisting carbon nanotubes: A molecular dynamics study

We simulate the twist of carbon nanotubes using atomic molecular dynamic simulations. The ultimate twist angle per unit length and the deformation energy are calculated for nanotubes of different geometries. It is found that the thick tube is harder to be twisted while the thin tube exhibits higher ultimate twisting ratio. For multi-walled nanotubes, the zigzag tube is found to be able to stand more deformation than the armchair one. We observed the surface transformation during twisting. Formation of structural defects is observed prior to fracture.     

Kinetic and molecular dynamics analysis of carbon diffusion in austenite

A kinetic 10-frequency model for interstitial diffusion via octahedral interstices in the fcc lattice is developed. In this model, the specific role of the transition probabilities during association and dissociation of the first nearest neighbour interstitial pairs through the second nearest neighbour sites is considered. Application of the model is made to carbon diffusion in austenite. Molecular dynamics is used to investigate carbon interstitial diffusion in austenite at low carbon contents. The assumption that carbon atoms can interact with each other only indirectly (via neighbouring iron atoms) is used. The Arrhenius parameters of interstitial carbon jump frequencies consistent with the 10-frequency model are determined. Comparison of the molecular dynamics results with experimental data at 1273?K in the context of the 10-frequency model is performed. It is shown that a small direct repulsion between carbon atoms at first nearest neighbours should be included. It is found that the initial increase (with increasing carbon content) in both the tracer and the chemical diffusion coefficients is shown to be a result of increased rates of dissociation of carbon from first and second nearest neighbour pairs to third nearest neighbour sites.     

Elastic properties of anatase titanium dioxide nanotubes:A molecular dynamics study

The elastic properties of anatase nanotubes are investigated by molecular dynamics(MD) simulations. Young's modulus, Poisson ratio, and shear modulus are calculated by transversely isotropic structure model. The calculated elastic constants of bulk rutile, anatase, and Young's modulus of nanotube are in good agreement with experimental values, respectively, demonstrating that the Matsui and Akaogi(MA) potential function used in the simulation can accurately present the elastic properties of anatase titanium dioxide nanotubes. For single wall anatase titanium dioxide nanotube, the elastic moduli are shown to be sensitive to structural details such as the chirality and radius. For different chirality nanotubes with the same radius, the elastic constants are not proportional to the chiral angle. The elastic properties of the nanotubes with the chiral angle of 0° are worse than those of other chiral nanotubes. For nanotubes with the same chirality but different radii, the elastic constant, Young's modulus, and shear modulus decrease as the radius increases. But there exist maximal values in a radius range of 10 nm–15 nm. Such information can not only provide a deep understanding of the influence of geometrical structure on nanotubes mechanical properties, but also present important guidance to optimize the composite behavior by using nanotubes as the addition.     

Ab initio molecular dynamics investigations of structural, electronic and dynamical properties of water in supercritical carbon dioxide

Ab initio molecular dynamics simulations of a solitary perdeuterated water molecule solvated in supercritical carbon dioxide have been performed along an isotherm at three different densities. Electron donor-acceptor interactions between the oxygen atom of water and the carbon atom of CO₂ as well as hydrogen bonded interactions between the two molecules have been shown to play a dominant role in the solvation. The mean dipole moment of the water molecule increases with the density of the solution, from a value of 1.85 D at low density to around 2.15 D at the highest density. The increase in the solvent density causes the water molecule to exhibit a range of behavior, from a free molecule to one that interacts strongly with CO₂. A blue shift in the bending mode of water has been observed with increasing solvent density. The carbon dioxide molecules which are present in the first neighbor shell of water are found to exhibit larger propensity to deviate from a linear geometry in their instantaneous configurations.      

Energetics and diffusion of point defects in Au/Ag metals:A molecular dynamics study

To reveal the potential aging mechanism for self-irradiation in Pu–Ga alloy, we choose Au–Ag alloy as its substitutional material in terms of its mass density and lattice structure. As a first step for understanding the microscopic behavior of point defects in Au–Ag alloy, we perform a molecular dynamics(MD) simulation on energetics and diffusion of point defects in Au and Ag metal. Our results indicate that the octahedral self-interstitial atom(SIA) is more stable than the tetrahedral SIA. The stability sequence of point defects for He atom in Au/Ag is: substitutional site octahedral interstitial site tetrahedral interstitial site. The He–V cluster(Hen Vm, V denotes vacancy) is the most stable at n = m. For the mono-vacancy diffusion, the MD calculation shows that the first nearest neighbour(1 NN) site is the most favorable site on the basis of the nudged elastic band(NEB) calculation, which is in agreement with previous experimental data. There are two peaks for the second nearest neighbour(2 NN) and the third nearest neighbour(3 NN) diffusion curve in octahedral interstitial site for He atom, indicating that the 2 NN and 3 NN diffusion for octahedral SIA would undergo an intermediate defect structure similar to the 1 NN site. The 3 NN diffusion for the tetrahedral SIA and He atom would undergo an intermediate site in analogy to its initial structure. For diffusion of point defects, the vacancy, SIA, He atom and He–V cluster may have an analogous effect on the diffusion velocity in Ag.     

Single-particle and collective dynamics of protein hydration water: a molecular dynamics study

We present an analysis based on molecular dynamics simulations of water single particle and collective density fluctuations in a protein crystal at 150 and 300 K. For the collective dynamics, the calculations predict the existence of two sound modes. The first one around 35 meV is highly dispersive and the second one around 9 meV is weakly dispersive in the k range studied here (0.5相似文献   

生物分子结合水的结构与动力学研究进展

生物结合水在维护生物大分子的结构、稳定性以及调控动力学性质和生理功能等方面起着决定性的作用.从分子水平上理解生物结合水分子的结构与性质及其影响生物结构和功能的本质与规律,是揭示生物大分子生理功能机理的关键.目前生物结合水的结构与动力学相关研究尚处于初步阶段.本文从三个方面介绍当前生物结合水的相关研究及其进展:首先介绍结合水对蛋白质折叠、质子给予与迁移、配体结合与药物设计以及变构效应等生物结构和功能的影响;然后介绍生物分子周围的水分子结构研究情况;最后从时间尺度、动力学属性、生物分子与水分子之间的动力学耦合作用、蛋白质表面结合水次扩散运动等角度介绍生物分子水合动力学的研究进展,并归纳出一些目前尚待进一步解决的科学问题.     

Atomistic origin of radial corrugation in a few-walled carbon nanotubes: A molecular dynamics study

We perform molecular dynamics simulations of a few-walled (with 3–4 walls) carbon nanotubes using empirical interatomic potential. We demonstrate that the radial corrugation occurs in such thin nanotubes under hydrostatic pressure, which is apparently similar to the corrugation in thicker (e.g., several tens-walled) nanotubes that had been predicted using continuum mechanics approximation. The mechanism underlying the corrugation of a few-walled nanotubes, however, is found to be much distinct from thick nanotubes; i.e., the sp³ bonds between adjacent concentric walls and registry of atom arrangement take important roles in the formation and stabilization of corrugation modes in a few-walled nanotubes.     

Relaxation dynamics and power spectra of liquid water: a molecular dynamics simulation study

We present molecular dynamics simulations of liquid water at normal and supercooled conditions. Autocorrelation functions (ACFs) of several structural quantities and their fourier transforms are obtained and analysed. Structural correlations and relaxation times increase linearly with degree of supercooling. Power spectra of ACFs show increase in librational motion of liquid water with cooling. These modes intensify with supercooling because of structuring and ordering of water molecules. Overall, liquid water structure is homogenous over the temperatures and pressures studied and undergoes fluctuation–dissipation in its local-density variations [English and Tse, Phys. Rev. Lett. 106, 037801 (2011)].     

The structure and dynamics of water inside armchair carbon nanotube

In this paper we present some simulation results about the behaviour of water molecules inside a single wall carbon nanotube (SWNT). We find that the confinement of water in an SWNT can induce a wave-like pattern distribution along the channel axis, similar phenomena are also observed in biological water channels. Carbon nanotubes(CNTs) can serve as simple nonpolar water channels. Molecular transport through narrow CNTs is highly collective because of tight hydrogen bonds in the protective environment of the pore. The hydrogen bond net is important for proton and other signal transports. The average dipoles of water molecules inside CNTs (7,7), (8,8) and (9,9) are discussed in detail. Simulation results indicate that the states of dipole are affected by the diameter of SWNT. The number of hydrogen bonds, the water--water interaction and water--CNT interaction are also studied in this paper.     

Molecular dynamics simulation of C8E5 micelle in explicit water: structure and hydrophobic solvation thermodynamics

Results are presented from a large scale molecular dynamics (MD) simulation of a non-ionic micelle comprising 80 C₈E₅ surfactant molecules in 9798 explicit TIP3P waters. The results are consistent with the conventional static picture of a simple spherical micelle (‘hydrophilic heads out, hydrophobic tails in’). In addition, the MD simulation reveals structural details that show clearly the dynamic nature of the micellar aggregate. The micelle is roughly spherical with thermal fluctuations leading to instantaneous shapes that are significantly non-spherical. The individual surfactant molecules adopt various nonlinear conformations, predominately in the hydrophilic segment, thereby leading to the overall compact globular shape of the micelle aggregate. Atomic distribution functions and dihedral angle distributions show that the micelle interior is similar to liquid n-octane. Although no water penetration in the micelle hydrophobic core is observed, there is considerable exposure of the hydrophobic tails of the surfactant molecules to water in the interfacial region. The excess chemical potentials of hydrophobic Lennard-Jones (LJ) solutes and their WCA analogs show a preference for the michelle core relative to bulk water. Interestingly, the solvation energies of LJ solutes show a minimum in the interfacial region. A qualitative explanation for this behaviour based on different packing tendencies of water and chain-like molecules is presented.     

A study of cavitation nucleation in pure water using molecular dynamics simulation

To discover the microscopic mechanism responsible for cavitation nucleation in pure water, nucleation processes in pure water are simulated using the molecular dynamics method. Cavitation nucleation is generated by uniformly stretching the system under isothermal conditions, and the formation and development of cavitation nuclei are simulated and discussed at the molecular level. The processes of energy, pressure, and density are analyzed, and the tensile strength of the pure water and the critical volume of the bubble nuclei are investigated. The results show that critical states exist in the process of cavitation nucleation. In the critical state, the energy, density, and pressure of the system change abruptly, and a stable cavitation nucleus is produced if the energy barrier is broken and the critical volume is exceeded. System pressure and water density are the key factors in the generation of cavitation nuclei. When the critical state is surpassed, the liquid is completely ruptured, and the volume of the cavitation nucleus rapidly increases to larger than 100 nm³; at this point, the surface tension of the bubble dominates the cavitation nucleus, instead of intermolecular forces. The negative critical pressure for bubble nucleation is -198.6 MPa, the corresponding critical volume is 13.84 nm³, and the nucleation rate is 2.42×10³² m^-3·^-1 in pure water at 300 K. Temperature has a significant effect on nucleation: as the temperature rises, nucleation thresholds decrease, and cavitation nucleation occurs earlier.     

First-principles molecular dynamics simulations of the structure of germanium dioxide under pressures

We have carried out first-principles molecular dynamics simulations of glass and liquid germanium dioxide (GeO₂) over a wide range of pressure. Our results show that in the glass GeO₂ system nearly all Ge–O coordination environments are fourfold at low compression, whereas at high compression five- and sixfold coordination types coexist. In the liquid GeO₂ system although most Ge–O coordination environments are fourfold, some threefold coordination types exist at low compression. Pentahedral units also exist in the liquid state while less than that in the glass state. At high compression, pentahedral units disappear and GeO₆ octahedron is dominant in the liquid state going with some sevenfold coordination.     

The thermodynamics and structure of liquid water

The additive interatomic interaction model has been used to calculate the thermodynamic functions of liquid water. The O … O and H … H nonbonded interactions were described by Kitaigorodsky potential functions of type 6-exp; for the H … O interactions the hydrogen bond potentials were introduced, and refined using sublimation heats of ice modifications and the normal vibrations of the water dimer. The thermodynamic functions of liquid water were obtained by averaging the corresponding thermodynamic quantities by the Monte Carlo method in the NVT ensemble. Different initial configurations were considered and the results were proved to converge, provided the Markov chain is sufficiently long. The calculated thermodynamic functions were in agreement with the experimental data. An analysis of instantaneous equilibrium configurations was carried out, and conclusions were drawn to what degree the previously proposed structures of liquid water correspond to reality.     

The carbon dioxide molecule: A new derivation of the potential,spectroscopic, and molecular constants

A new determination of the potential energy function of the carbon dioxide molecule from its vibrorotational spectrum is presented. Starting from the previous determination made by A. Chédin [J. Mol. Spectrosc.76, 430–491 (1979)] and from a significantly larger set of updated experimental data, the new potential is shown to provide a better agreement between theoretical and experimental eigenenergies. A similar improvement in the prediction of eigenstates is expected.     

Consequences of minimising pair correlations in fluids for dynamics,thermodynamics and structure

ABSTRACT

Liquid-state theory, computer simulation and numerical optimisation are used to investigate the extent to which positional correlations of a hard-sphere fluid – as characterised by the radial distribution function and the two-particle excess entropy – can be suppressed via the introduction of auxiliary pair interactions. The corresponding effects of such interactions on total excess entropy, density fluctuations and single-particle dynamics are explored. Iso-g processes, whereby hard-sphere-fluid pair structure at a given density is preserved at higher densities via the introduction of a density-dependent, soft repulsive contribution to the pair potential, are considered. Such processes eventually terminate at a singular density, resulting in a state that – while incompressible and hyperuniform – remains unjammed and exhibits fluid-like dynamic properties. The extent to which static pair correlations can be suppressed to maximise pair disorder in a fluid with hard cores, determined via direct functional maximisation of two-body excess entropy, is also considered. Systems approaching a state of maximised two-body entropy display a progressively growing bandwidth of suppressed density fluctuations, pointing to a relation between ‘stealthiness’ and maximal pair disorder in materials.