Computer simulation of the thermodynamics of the B → Z-DNA transition: effect of the ionic size and charge

The B- to Z-DNA transition free energy as a function of the size and charge of added ions is investigated by Monte Carlo simulation for simple grooved B- and Z-DNA models. It is shown that the electrostatic contribution to the free energy depends almost linearly on the logarithm of the salt concentration for all the systems. The effect of increasing the size of the ions is to make the curves steeper, although its influence on the transition midpoint is more complex. Divalent cations markedly reduce both the slope and the transition midpoint with respect to monovalent ions. These conclusions are in agreement with the experimental findings. The effect of increasing the charge of the anions—not yet experimentally studied—is less pronounced.     

Molecular dynamics simulation of dielectric constant and cluster structure of liquid methanol: the role of cluster–cluster dipole correlations

A molecular dynamics simulation of liquid methanol at ambient conditions with two different three-site potential models was performed and the evaluated dielectric constant was discussed in the light of the cluster structure of the liquid. The distribution of the pair interaction energy of molecules and the cluster size distribution were calculated. An aggregation contribution to dielectric constant was defined and calculated as a function of the threshold H-bond energy using energetic criterion of H-bond. The structural information on dipole–dipole correlations of molecules incorporated in the size and structure distribution of aggregates proved to cover about 80% of the calculated dielectric constant of methanol. The other 20% should be attributed to the cluster–cluster dipole correlations.     

New mean-field theories for the liquid–vapour transition of charged hard spheres

The phase behaviour of the primitive model of electrolytes is studied in the framework of the various mean-field approximations obtained recently by means of methods pertaining to statistical field theory (J.-M. Caillol, J. statist. Phys., 115, 1461 (2004); extended version: arXiv:cond-mat/0305465). The role of the regularization of the Coulomb potential at short distances is discussed in detail and the link to more traditional approximations of the theory of liquids is discussed. The values computed for the critical temperatures, chemical potentials, and densities are compared with available Monte Carlo data and other theoretical predictions.     

Molecular dynamics simulation of the melting of a twist Σ=5 grain boundary

The existence of a possible grain boundary disordering transition of the melting type in a =5 (001) twist boundary of aluminium bicrystal below the melting temperature was investigated using a constant pressure molecular dynamics simulation. The calculated melting temperature T _cm of the bulk Al is about 960 K. The total internal energy, the structure factor, and the pair distribution function were calculated at different layers across the grain boundary. The mean atomic volume, the grain boundary energy, and the thermal expansion coefficients were also calculated using the same simulation method. This simulation also allows us to image the grain boundary structure at different temperatures. The equilibrium grain boundary structure at 300 K retains the periodicity of the coincident site lattice, so that the lowest energy structure corresponds to the coincident site arrangement of the two ideal crystals. With increasing temperature, the total internal energy of the atoms for both the perfect crystal and the grain boundary increases, as do the number of layers in the grain boundary. The grain boundary core exists and the perfect crystal structure still exists outside the grain boundary at 0.9375 T _cm. However, two atomic layers of the equilibrium grain boundary structure at 0.9375 T _cm lose the coincident site lattice periodicity and attain a structure with liquid-like disorder. Therefore, partial melting of the grain boundary has occurred at the temperature above 0.9375 T _cm which is in agreement with the experimental results.     

Molecular dynamics simulation of surface melting behaviours of the V（110） plane

The modified analytic embedded-atom method and molecular dynamics simulations are applied to the investigation of the surface premelting and melting behaviours of the V（110） plane by calculating the interlayer relaxation, the layer structure factor and atomic snapshots in this paper. The results obtained indicate that the premelting phenomenon occurs on the V（110） surface at about 1800K and then a liquid-like layer, which approximately keeps the same thickness up to 2020K, emerges on it. We discover that the temperature 2020K the V（110） surface starts to melt and is in a completely disordered state at the temperature of 2140K under the melting point for the bulk vanadium.     

Molecular dynamics simulation of latent track formation in α-quartz

The latent ion track in α-quartz is studied by molecular dynamics simulations. The latent track is created by depositing electron energies into a cylindrical region with a radius of 3nm. In this study, the electron stopping power varies from 3.0keV/nm to 12.0keV/nm, and a continuous latent track is observed for all the simulated values of electron stopping power except 3.0keV/nm. The simulation results indicate that the threshold electron stopping power for a continous latent track lies between 3.0keV/nm and 3.7 keV/nm. In addition, the coordination defects produced in the latent track are analyzed for all the simulation conditions, and the results show that the latent track in α-quartz consists of an O-rich amorphous phase and Si-rich point defects. At the end of this paper, the influence of the energy deposition model on the latent track in α-quartz is investigated. The results indicate that different energy deposition models reveal similar latent track properties. However, the values of the threshold electron stopping power and the ion track radius are dependent on the choice of energy deposition model.     

Manifestation of spinodal singularities in the liquid–vapor phase transition during simulation of nanosecond vaporization of a liquid film

The recent results of molecular-dynamics simulation of nanosecond vaporization of a thin liquid film are analyzed within the continual approach. The analysis shows a significant increase in the thermal conductivity at the film temperature maximum before its explosive decomposition, which indicates the closeness of the achievable limiting overheating temperature to the spinodal.     

Liquid–vapour transition of the long range Yukawa fluid

Two liquid state theories, the self-consistent Ornstein–Zernike equation (SCOZA) and the hierarchical reference theory (HRT) are shown, by comparison with Monte Carlo simulations, to perform extremely well in predicting the liquid–vapour coexistence of the hard-core Yukawa (HCY) fluid when the interaction is long range. The long range of the potential is treated in the simulations using both an Ewald sum and hyperspherical boundary conditions. In addition, we present an analytical optimized mean field theory which is exact in the limit of an infinitely long-range interaction. The work extends a previous one by C. Caccamo, G. Pellicane, D. Costa, D. Pini, and G. Stell, Phys. Rev. E 60, 5533 (1999) for short-range interactions.     

Temperature range of the liquid–glass transition

It has been shown that the currently used method for calculating the temperature range of δT_g in the glass transition equation qτ_g = δT_g as the difference δT_g = (T₁₂–T₁₃) results in overestimated values, which is explained by the assumption of a constant activation energy of glass transition in deriving the calculation equation (T₁₂ and T₁₃ are the temperatures corresponding to the logarithmic viscosity values of logη = 12 and logη = 13). The methods for the evaluation of δT_g using the Williams–Landel–Ferry equation and the model of delocalized atoms are considered, the results of which are in satisfactory agreement with the product qτ_g (q is the cooling rate of the melt and τ_g is the structural relaxation time at the glass transition temperature). The calculation of τ_g for inorganic glasses and amorphous organic polymers is proposed.     

Simulating the vapour–liquid equilibria of large cyclic alkanes

Self-adapting fixed endpoint configurational-bias Monte Carlo simulations in the Gibbs ensemble were carried out to determine the vapour–liquid coexistence curves of cyclic alkanes from c-pentane to c-octadecane. In general, the critical temperatures and densities of the cyclic alkanes are substantially higher than those of their linear counterparts. Furthermore, the simulation data point to a maximum in the critical density for cyclic alkanes with about eight carbon atoms as also observed for the linear alkanes.     

Experimental and computer simulation determination of the structural changes occurring through the liquid–glass transition in Cu–Zr alloys

Molecular dynamics (MD) simulations were performed of the structural changes occurring through the liquid–glass transition in Cu–Zr alloys. The total scattering functions (TSF), and their associated primary diffuse scattering peak positions (K _p), heights (K _h) and full-widths at half maximum (K _FWHM) were used as metrics to compare the simulations to high-energy X-ray scattering data. The residuals of difference between the model and experimental TSFs are ～0.03 for the liquids and about 0.07 for the glasses. Over the compositional range studied, Zr_{1? x} Cu _x (0.1 ≤ x ≤ 0.9), K _p, K _h and K _FWHM show a strong dependence on composition and temperature. The simulation and experimental data correlate well between each other. MD simulation revealed that the Cu–Zr bonds undergo the largest changes during cooling of the liquid, whereas the Cu–Cu bonds change the least. Changes in the partial-pair correlations are more readily seen in the second and third shells. The Voronoi polyhedra (VP) in glasses are dominated by only a few select types that are compositionally dependent. The relative concentrations of the dominant VPs rapidly change in their relative proportion in the deeply undercooled liquid. The experimentally determined region of best glass formability, x _Cu ～ 65%, shows the largest temperature dependent changes for the deeply undercooled liquid in the MD simulation. This region also exhibits very strong temperature dependence for the diffusivity and the total energy of the system. These data point to a strong topological change in the best glass-forming alloys and a concurrent change in the VP chemistry in the deeply undercooled liquid.     

Molecular simulation of binary phase diagrams from the osmotic equilibrium method: vapour pressure and activity in water–ethanol mixtures

ABSTRACT

Herein, an approach for simulating phase diagrams of binary mixtures is presented, where a bulk liquid and its corresponding vapour phase are simulated by means of molecular dynamics using explicit polarisation. Time-averaged density profiles for the pure compounds and mixtures at different mole fractions provide information about the spatial distribution in the bulk liquid and the amount of evaporated species in the adjacent vapour phase. The activities in the liquid phase are calculated from the mean vapour phase densities at a given composition, providing a good qualitative agreement compared to experimental data and the precision of the method follows a previously developed Poisson model of evaporation. With the Redlich–Kister approach for the activities in a binary mixture, the directly obtained activities are fitted providing corrected activity coefficients of the two species. This method is applied to ethanol water mixtures at different mole fractions. The obtained structural data are in good agreement with experimental data and time-averaged density profiles provide a detailed insight into the composition of the liquid–vapour interface. An azeotropic point is obtained for an excess concentration of ethanol at 87% as percentage by mass compared to the experimental value of 95%.     

Modification of glass transition and liquid—liquid transition in PMMA doped with fluorescent dyes

PMMA doped with fluorescent dyes presents important modifications of thermally stimulated current spectra at high temperature. Glass and liquid-liquid transitions are no longer resolved and only one intense peak appears at 127°C. This peak cannot be resolved by the thermal sampling method. It has an Arrhenius behavior, and the plot of τ(1/T) shows the existence of a compensation phenomenon with a characteristic temperature which does not depend on the dye concentration. The modification is induced even if the dye concentration is as weak as some 10s of ppm. Thus it cannot be considered as a plasticization effect.     

Hydrogen motions and the α-relaxation in glass-forming polymers: Molecular dynamics simulation and quasi-elastic neutron scattering results

The combination of molecular dynamics simulations and neutron scattering measurements on three different glass-forming polymers (polyisoprene, poly(vinyl ethylene) and polybutadiene) has allowed to establish the existence of a crossover from Gaussian to non-Gaussian behavior for the incoherent scattering function in the α-relaxation regime. The deviation from Gaussian behavior observed can be reproduced assuming the existence of a distribution of discrete jump lengths underlying the sublinear diffusion of the atomic motions during the structural relaxation.     

Anisotropy of the solid–liquid interface properties of the Ni–Zr B33 phase from molecular dynamics simulation

Solid–liquid interface (SLI) properties of the Ni–Zr B33 phase were determined from molecular dynamics simulations. In order to perform these measurements, a new semi-empirical potential for Ni–Zr alloy was developed that well reproduces the material properties required to model SLIs in the Ni_50.0Zr_50.0 alloy. In particular, the developed potential is shown to provide that the solid phase emerging from the liquid Ni_50.0Zr_50.0 alloy is B33 (apart from a small fraction of point defects), in agreement with the experimental phase diagram. The SLI properties obtained using the developed potential exhibit an extraordinary degree of anisotropy. It is observed that anisotropies in both the interfacial free energy and mobility are an order of magnitude larger than those measured to date in any other metallic compound. Moreover, the [0 1 0] interface is shown to play a significant role in the observed anisotropy. Our data suggest that the [0 1 0] interface simultaneously corresponds to the lowest mobility, the lowest free energy and the highest stiffness of all inclinations in B33 Ni–Zr. This finding can be understood by taking into account a rather complicated crystal structure in this crystallographic direction.     

Surface tension of hydrocarbon chains at the liquid–vapour interface

Molecular dynamics simulations were performed at constant temperature to obtain the surface tension of hydrocarbon chains at the liquid–vapour interface. The Ewald sum was used to calculate the dispersion forces of the Lennard–Jones potential to take into account the full interaction. The NERD and TraPPE_UA flexible force field models were used to simulate molecules from ethane to hexadecane along the coexistence curve. The simulation results for the TraPPE_UA model are in good agreement with experimental data, whereas the NERD model predicts slightly higher values.     

The penetrable sphere and related models of liquid—vapour equilibrium

The equation of state of the penetrable sphere model of liquid—vapour equilibrium is calculated by three different sequences of approximations; the first is based on the virial expansion of the equivalent two-component model in powers of the densities, the second on expansion in powers of the activity, and the third on a cumulant expansion of the configurational energy in powers of the reciprocal temperature. These sequences are examined both with the inclusion of all coefficients and with the sub-sets of coefficients appropriate to the first and second Percus-Yevick (PY) approximations. The first PY approximation gives a classical critical point whose density and temperature are accurately determined. The second PY and the complete set of coefficients yield badly-behaved series from which few conclusions can be drawn.

The penetrable sphere model is generalized to a wider class of potentials and one of these, in which the configurational energy is expressed in terms of gaussian functions is related to a two-component model of Helfand and Stillinger. It is more tractable than the original model and is examined by the same sequences of approximations. They have shown that the complete series leads to a non-classical critical point in their version of the model; here we show that the first PY approximation is classical but the second nonclassical.     

Molecular dynamic simulation of lubricant spreading： effect from the substrate and endbead

Molecular dynamic simulations based on a coarse-grained, bead-spring model are adopted to investigate the spreading of both nonfunctional and functional perfluoropolyether (PFPE) on solid substrates. For nonfunctional PFPE, the spreading generally exhibits a smooth profile with a precursor film. The spreading profiles on different substrates are compared, which indicate that the bead-substrate interaction has a significant effect on the spreading behaviour, especially on the formation of the precursor film. For functional PFPE, the spreading generally exhibits a complicated terraced profile. The spreading profiles with different endbeads are compared, which indicate that the endbead-substrate interaction and the endbead--endbead interaction, especially the latter, have a significant effect on the spreading behaviour.