The collapsing bubble in a liquid by molecular dynamics simulations

Molecular dynamics simulations have been made of a collapsing bubble or cavity in a simple liquid. Simulations of a Lennard-Jones liquid reveal that the collapsing process takes place in a series of stages. First, the ‘hottest’ molecules from the high kinetic energy tail in the Maxwell—Boltzmann distribution diffuse into the empty cavity. This is followed by a gradual filling in of the cavity until the density in the centre is a little lower than that of the bulk liquid. The system eventually reaches a final new equilibrium liquid state through a subsequent slower equilibration phase. The bubble fills in an oscillatory manner, by partly filling in, and then partially emptying, and so on, with ever decreasing amplitude towards the final uniform liquid state. These density oscillations are more obvious in systems with a larger bubble. Similar oscillations are observed in the kinetic energy of the molecules at selected radii from the centre of the initial bubble. The maximum temperature occurs typically at the end of the initial fillingin stage during which the density of the core undergoes a vapour-to-liquid phase transition, the released latent heat probably contributing to the temperatures achieved in this region. The average maximum temperature found in the smallest system examined is about nine times the critical temperature, which is about 6000 K for water, thus suggesting a simple mechanism for producing molecules with the sorts of kinetic energies and lifetimes required for sonoluminescence.     

Orientation restraints in molecular dynamics simulations using time and ensemble averaging

In this article we present methodology for simulating protein dynamics while imposing restraints derived from NMR measurements on partially ordered molecules. Such measurements may include residual dipolar couplings and chemical-shift anisotropies. We define a restraint potential for use in molecular dynamics and energy minimization. The presented potential is consistent with the simultaneously optimized molecular order tensor. Restraining can be performed with time and ensemble averaging. We performed a large number of molecular dynamics simulations of the histidine containing phosphocarrier protein with restraints on backbone N-H vector orientations derived from residual dipolar couplings. From these simulations it is evident that the use of time- or ensemble-averaged restraints is essential to leave the fluctuations of the restrained vectors unaffected. Without averaging the fluctuations of the restrained vectors are reduced significantly. This also has the effect of decreasing the apparent molecular order-parameter tensor.     

Brownian dynamics in Fourier space: membrane simulations over long length and time scales

A simulation algorithm for elastic membrane sheets is presented. Overdamped stochastic dynamics including hydrodynamic coupling to surrounding solvent and arbitrary external forces are generated by employing Fourier modes of the sheet as the primary dynamic variables. Simulations over the micron length scale and second time scale are easily achieved. The dynamics of a lipid bilayer attached to an underlying network of cytoskeletal filaments is used to estimate the diffusion constant of membrane-bound proteins on the surface of the red blood cell.     

基于分子动力学模拟的主链型液晶聚合物的新模型

在传统的Gay-Berne (GB)/Lennard-Jones (LJ)模型的基础上，发展了一种用于模拟半刚性主链型液晶聚合物(LCP)的分子级模型，命名为Solo-LJ-SP-GB 模型.单一的LJ联合体和非线性弹簧被用于描述LCP分子中的间隔体.用分子动力学模拟半刚性主链型LCP系统(该系统由169条分子链组成，每两个刚性体之间的间隔体个数为6)时，该模型所需的计算时间不到传统的GB/LJ 模型所需时间的十分之一，大大地提高了计算效率.通过采用该模型模拟半刚性主链型LCP的相变问题，观察到了与半刚性主链型LCP分子中间隔体个数相关的热力学的奇偶效应以及从等方相到向列相的相转变过程.这些模拟结果与当前的试验结果相当符合，从而表明了该模型可以较为准确地描述出半刚性主链型LCP的结构特性. 关键词： Solo-LJ-SP-GB模型 液晶聚合物 分子动力学模拟     

Atomic structure and diffusivity in liquid Al80Ni20 by ab initio molecular dynamics simulations

The atomic structure and diffusivity in liquid Al₈₀Ni₂₀ are studied by ab initio molecular dynamics simulations. The local structures are analyzed by the pair correlation function, structure factor, coordinate number, Honneycutt–Anderson bond pair, and Voronoi tessellation methods. It is observed that the amount of icosahedral clusters increases, and the liquid becomes more ordered as the temperature decreases. The predicted self-diffusion coefficients of Al and Ni via the mean square displacements are very close to each other and agree well with the quasi-elastic neutron scattering measurements in the literature. The observation of equal self-diffusivity of Al and Ni is attributed to the formation of local solute-centered polyhedra, coupling the migration of Al and Ni. The Manning dynamic correlation factor is evaluated and found to be close to unity. The predicted interdiffusion coefficients using the Darken equation agree well with experimental data in the literature.     

Thermal diffusion in micropores by molecular dynamics computer simulations

This work focuses on the identification of the main microscopic processes that influence thermal diffusion (the Soret effect) in a fluid mixture confined in an uncorrugated slit pore. To achieve this purpose, a boundary driven nonequilibrium molecular dynamics scheme is applied on binary mixtures of super-critical Lennard–Jones (LJ) spheres representing methane and n-decane. Following previous work, we perform a systematic study of the influence of the parameters used to describe a model slit pore on an effective thermal diffusion factor. Among these parameters are: The nature of the reflection of the diffusing particles on the walls (specular or diffusive), the pore width with respect to the particle size and the fluid-wall potential strength. Simulations were run both on equimolar and non-equimolar mixtures. The results indicate that thermal diffusion is effectively lowered only for strong fluid–wall interactions. It is shown that the general trends, which are different under sub- and super-critical conditions, can be explained by a careful analysis of the relative sorption energies of the two compounds.     

Study of nanoscratching of polymers by using molecular dynamics simulations

Molecular dynamic simulations are performed to study the nanoscratching behavior of polymers.The effects of scratching depth,scratching velocity and indenter/polymer interaction strength are investigated.It is found that polymer material in the scratching zone around the indenter can be removed in a ductile manner as the local temperature in the scratching zone exceeds glass transition temperature Tg.The recovery of polymer can be more significant when the temperature approaches or exceeds Tg.The tangential force,normal force and friction coefficient increase as the scratching depth increases.A larger scratching velocity leads to more material deformation and higher pile-up.The tangential force and normal force are larger for a larger scratching velocity whereas the friction coefficient is almost independent of the scratching velocities studied.It is also found that stronger indenter/polymer interaction strength results in a larger tangential force and friction coefficient.     

Interpretation of NMR data on proteins by molecular dynamics simulations

The stability and the internal mobility of the recently determined solution structure of the activation domain of porcine procarboxypeptidase B (ADB; Vendrell J., Billeter M., Wider G., Avilés F.X., Wüthrich K.: EMBO J.10, 11–15 (1991)) was studied by unrestrained molecular dynamics. A 66 residue long polypeptide corresponding to the structurally well-defined fragment of ADB was immersed in a water bath and carefully equilibrated. A trajectory of 90 ps was then recorded at room temperature, using no constraints deduced from NMR distance measurements. The averages of the inverse third power of the proton-proton distances, for which NMR distance measurements are available, were calculated and converted to time averages of the distances. Comparison of these time averaged distances with the corresponding distance constraints used in the determination of the solution structure show that the dynamic structure described by the molecular dynamics trajectory is consistent with the NMR data for the polypeptide backbone and for most side chains. In the course of the 90 ps trajectory, the ß-sheet of ADB remains intact and well-defined. The last helix of the protein domain is also stable, but moves with respect to the rest of the protein, while the first helix shows increased instability. The structural fluctuations of the side chain do in general not exceed those observed among the 20 conformers describing the solution structure.     

Microscopic structure of liquid dimethyl sulphoxide and its electrolyte solutions: molecular dynamics simulations

Molecular dynamics (MD) simulations of pure dimethyl sulphoxide (DMSO) and solutions of Na⁺, Ca²⁺, Cl^?, NaCl and CaCl₂ in DMSO have been performed at 298.15 K and 398.15 K in NVT ensembles by using a four-interaction-site model of DMSO and reaction field method for Coulombic interactions. The structure of solvent, ion-solvation shells and ion-pairs have been analysed by employing a concept of coordination centres and characteristic vectors of the solvent molecule. Results are given for atom-atom (corresponding to DMSO), ion-atom and ion-ion radial distribution functions (RDFs), orientation of the DMSO molecules and their geometrical arrangements in the first solvation shells of the ions (Na⁺, Ca²⁺, Cl^?). A preferential formation of cyclic dimers with antiparallel alignment between dipole moments of nearest-neighbour molecules in the pure solvent is found. Geometrical models of the first coordination shells of the ions in ‘infinitely dilute solutions’ are proposed. Ion-ion RDFs in NaCl-DMSO and CaCl₂-DMSO solutions reveal the presence of both solvent separated (SSIP) and contact (CIP) ion pairs. The structures of the solvation shells of such ion pairs are also discussed.     

Insights into positron annihilation lifetime spectroscopy by molecular dynamics simulations

The relationship between free-volume properties measured from positron annihilation lifetime spectroscopy (PALS) and calculated from molecular dynamics simulations has been investigated for glassy and liquid glycerol in the temperature range 150–400 K. A virtual probing procedure has been developed to retrieve information on the basic free-volume properties of the simulated microstructures, i.e. mean cavity volume and free-volume cavity fractions. Our data leads us to infer on the occurrence of experimentally non-detectable small cavities with mean equivalent radius of 1.8–1.9 Å between 250 and 275 K. The size of these limiting cavities is found to be temperature dependent, being smaller at low temperatures. At high temperatures, above a characteristic PALS temperature Tb2L , the formation of very large cavities is predicted. This finding suggests that, when the dimension of the holes in the system exceeds a given value, the PALS measurements become unable to catch the complete structural information and phenomena of dynamical origin enter into play in the PALS signal decay. The calculated number of cavities is found to be almost independent on the temperature from the glassy up to the liquid phase, thus furnishing a certain support to theoretical models proposed to evaluate the free-volume cavity fractions.     

Simulation of screw dislocation motion in iron by molecular dynamics simulations

Molecular dynamics (MD) simulations are used to investigate the response of a/2<111> screw dislocation in iron submitted to pure shear strain. The dislocation glides and remains in a (110) plane; the motion occurs exclusively through the nucleation and propagation of double kinks. The critical stress is calculated as a function of the temperature. A new method is developed and used to determine the activation energy of the double kink mechanism from MD simulations. It is shown that the differences between experimental and simulation conditions lead to a significant difference in activation energy. These differences are explained, and the method developed provides the link between MD and mesoscopic simulations.     

Probing restrictive diffusion dynamics at short time scales

Diffusion imaging gradients serve to spectrally filter the temporally evolving diffusion tensor. In this framework, the design of diffusion sensitizing gradients is reduced to the problem of adequately sampling q-space in the spectral domain. The practical limitations imposed by the requirement for delta-function type diffusion-sensitizing gradients to adequately sample q-space, can be relaxed if these impulse gradients are replaced with chirped oscillatory gradients. It is well known that in many systems of interest, dispersion of velocity will itself produce a peak in the velocity correlation function near w=0, while restricted diffusion will manifest itself in the dispersion spectrum at higher frequencies. In this paper, chirped diffusion-sensitizing gradients are proposed and analytically shown to yield an efficient sampling of q-space in a manner that asymptotically approaches that using delta-function diffusion-sensitizing gradient. The challenge is the consequent reduction in diffusion sensitivity as one probes higher frequency dynamics. This problem is addressed by restricting the gradient power to a spectral bandwidth corresponding to the diffusion spectral range of the underlying restrictive geometry. Simultaneous imaging of diffusion and flow at microscopic resolution and at temporally resolvable diffusion time scales thus becomes possible in vivo. Simulations and experiments validate the proposed approach.     

Molecular dynamics simulations of a flexible liquid crystal

Molecular dynamics simulations have been performed for a liquid crystal composed of a Gay—Berne core site with two alkyl chains of different length (C₇ and C₃) at either end of the molecule. Calculations have been carried out for 512 molecules in the NVT ensemble for simulation times of up to 8.0ns at two distinct densities. The liquid crystal phases of the material have been fully characterized by measurements of orientational order parameters and radial distribution functions in each phase. Results are also presented for conformational distributions and effective torsional potentials of the system. We conclude that models of this nature represent a powerful approach to the study of flexibility in mesogenic systems and open up possibilities for predicting both the phase behaviour and bulk properties of liquid crystals based solely on a prior knowledge of intermolecular interactions.     

氦热力学性质的分子动力学研究

 利用经典分子动力学和第一性原理分子动力学,研究了氦在高压下的熔化曲线、状态方程和非金属-金属转变。得到了氦在温度小于4.5 eV、 密度0.3~5.0 g/cm³范围内的状态方程,并把氦的熔化曲线的压强范围拓展到了50 GPa。氦的能隙宽度曲线表明,温度大大降低了氦的金属化密度。     

Algorithm for molecular dynamics simulations of spin liquids

A new symplectic time-reversible algorithm for numerical integration of the equations of motion in magnetic liquids is proposed. It is tested and applied to molecular dynamics simulations of a Heisenberg spin fluid. We show that the algorithm exactly conserves spin lengths and can be used with much larger time steps than those inherent in standard predictor-corrector schemes. The results obtained for time correlation functions demonstrate the evident dynamic interplay between the liquid and magnetic subsystems.     

氦热力学性质的分子动力学研究

利用经典分子动力学和第一性原理分子动力学,研究了氦在高压下的熔化曲线、状态方程和非金属-金属转变。得到了氦在温度小于4.5 eV、 密度0.3~5.0 g/cm3范围内的状态方程,并把氦的熔化曲线的压强范围拓展到了50 GPa。氦的能隙宽度曲线表明,温度大大降低了氦的金属化密度。     

Calculation of thermodynamic properties of Ni nanoclusters via selected equations of state based on molecular dynamics simulations

We present an approach for constant-pressure molecular dynamics simulations. This approach is especially designed for finite systems, for which no periodic boundary condition applies. A molecular dynamics (MD) simulation for Ni nanoclusters is used to calculate their pressure–volume–temperature (p–v–T) data for the temperature range 200 K≤T≤400 K, and pressures up to 600 kbar. Isothermal sets of p–v–T data were generated by the simulation; each set was fitted by three equations of state (EoSs): Linear Isotherm Regularity-II (LIRII), Birch–Murnaghan (BM), and EOS III. It is found that the MD data are satisfactorily reproduced by the EoSs with reasonable precision. Some features of the EoSs criteria, such as the temperature dependences of the coefficients, the isothermal bulk modulus and its pressure derivative at the zero-pressure limit, and isobaric thermal expansion for Ni nanoclusters, are investigated. We have found that same EoSs are valid for both bulk Ni and Ni nanoclusters, but with different values of the parameters, which depend on the cluster size and temperature. An increase in bulk modulus with decrease of cluster size can be observed. Also, an increase in isobaric expansion coefficient with decrease of cluster size has been found.     

Diffusion behavior of hydrogen isotopes in tungsten revisited by molecular dynamics simulations

Molecular dynamics simulations were performed to study the diffusion behavior of hydrogen isotopes in single-crystal tungsten in the temperature range of 300–2000 K. The simulations show that the diffusion coefficient of H isotopes exhibits non-Arrhenius behavior, though this deviation from Arrhenius behavior is slight. Many-body and anharmonic effects of the potential surface may induce slight isotope-dependence by the activation energy; however, the dependence of the pre-factor of the diffusion coefficient on the isotope mass is diminished. The simulation results for H-atom migration near W surfaces suggest that no trap mutations occur for H atoms diffusing near either W{100} or W{111} surfaces, in contrast to the findings for He diffusion near W surfaces. Based on the H behavior obtained by our MD simulations, the time evolution of the concentration distribution of interstitial H atoms in a semi-infinite W single crystal irradiated by energetic H projectiles was calculated. The effect of H concentration on H diffusion is discussed, and the applicability of the diffusion coefficients obtained for dilute H in W is assessed.     

Computing the local pressure in molecular dynamics simulations

Computer simulations of inhomogeneous soft matter systems often require accurate methods for computing the local pressure. We present a simple derivation, based on the virial relation, of two equivalent expressions for the local (atomistic) pressure in a molecular dynamics simulation. One of these expressions, previously derived by other authors via a different route, involves summation over interactions between particles within the region of interest; the other involves summation over interactions across the boundary of the region of interest. We illustrate our derivation using simulations of a simple osmotic system; both expressions produce accurate results even when the region of interest over which the pressure is measured is very small.