Scaling laws and memory effects in the dynamics of liquids and proteins

Recent progress in the numerical calculation of memory functions from molecular dynamics simulations allowed the gaining of deeper insight into the relaxation dynamics of liquids and proteins. The concept of memory functions goes back to the work of R. Zwanzig on the generalized Langevin equation, and it was the basis for the development of various dynamical models for liquids. In this article we present briefly a method for the numerical calculation of memory functions, which is then applied to study their scaling behavior in normal and fractional Brownian dynamics. It has been shown recently that the model of fractional Brownian dynamics constitutes effectively a link between protein dynamics on the nanosecond time scale, which is accessible to molecular dynamics simulations and thermal neutron scattering, and the much longer time scale of functional protein dynamics, which can be studied by fluorescence correlation spectroscopy. The text was submitted by the authors in English. Affiliated with the University of Orléans.     

Collective dynamics near a phase transition in confined fluids

We performed molecular dynamics simulations in the microcanonical ensemble (MEMD) for a "simple" fluid confined between two solid substrates. From the calculation of the intermediate scattering function F(k( parallel ),t) and through the memory function formalism, we extract material ( i.e. transport and thermodynamics) coefficients in the vicinity of the liquid-gas phase transition. Our results show that approaching the limit of stability ( i.e. the spinodal), the dynamics of the system changes markedly.     

Hydration water in dynamics of a hydrated beta-lactoglobulin

Incoherent spin-echo signals of a hydrated β-lactoglobulin protein were investigated, at 275 and 293 K. The intermediate scattering functions I(Q,t) were divided in two contributions from surface water and protein, respectively. On one hand, the dynamics of the surface water follows a KWW stretched exponential function (the exponent is ~0.5), on the other hand, that of the protein follows a single exponential. The present results are consistent with our previous results of hydrated C-phycocyanin combining elastic and quasielastic neutron scattering and by molecular dynamics simulation.     

Molecular dynamics simulations of translational thermal accommodation coefficients for time-resolved LII

Time-resolved laser-induced incandescence demands precise knowledge of the thermal accommodation coefficient, but little is known about the gas-surface scattering physics that underlies this parameter. This paper presents a molecular dynamics simulation that shows how the thermal accommodation coefficient is influenced by the gas molecular mass and gas temperature. The molecular dynamics results also define scattering kernels that can be used as boundary conditions in Direct Simulation Monte Carlo simulations of heat and momentum transfer between soot aggregates and surrounding gas molecules.     

A comparison of ion scattering spectra and molecular dynamics simulations at the surface of silicate glasses

Molecular dynamics simulations are correlated with experimental ion scattering spectra to elucidate the surface structure and composition of fused silica and potassium trisilicate glass. The ion scattering spectra and molecular dynamics simulations both show that the oxygen atoms dominate the surface monolayer of fused silica. The ion scattering spectra of fracture surfaces of potassium trisilicate glass show a large potassium signal with little scattering signal from the oxygen or silicon atoms indicating a predominance of potassium in the surface monolayer. This local enrichment of potassium in the surface monolayer is due to their shielding of the charged silicate tetrahedra at the surface. This is also consistent with the simulations.     

Collective dynamics of lipid membranes studied by inelastic neutron scattering

We have studied the collective short wavelength dynamics in deuterated 1,2-dimyristoyl-sn-glycero-3-phoshatidylcholine (DMPC) bilayers by inelastic neutron scattering. The corresponding dispersion relation variant Planck's over 2pi omega(Q) is presented for the gel and the fluid phase of this model system. The temperature dependence of the inelastic excitations indicates a phase coexistence between the two phases over a broad range and leads to a different assignment of excitations from that reported in a preceding inelastic x-ray scattering study [Phys. Rev. Lett. 86, 740 (2001)]]. As a consequence, we find that the minimum in the dispersion relation is actually deeper in the gel than in the fluid phase. Finally, we can clearly identify an additional nondispersive (optical) mode predicted by molecular dynamics simulations [Phys. Rev. Lett. 87, 238101 (2001)]].     

Reorientational dynamics in a liquid organized system: Brillouin and depolarized Rayleigh scattering experiments in 1-octanol

Light scattering experiments, with dispersive and interferometric techniques, have been performed to study the orientational relaxation dynamics in 1-octanol, a structured liquid system having quite long living H-bonded clusters. Different temporal windows have been opened with these experiments to investigate the temporal events connected to the orientational relaxation dynamics of this molecular liquid. The present results have been compared with previous Monte Carlo MD simulations and experimental dielectric relaxation functions. They show that in the high frequency domain two additional very fast processes can be detected which have not been revealed by dielectric function relaxation.     

Shear localization in a model glass

Using molecular dynamics simulations, we show that a simple model of a glassy material exhibits the shear localization phenomenon observed in many complex fluids. At low shear rates, the system separates into a fluidized shear band and an unsheared part. The two bands are characterized by a very different dynamics probed by a local intermediate scattering function. Furthermore, a stick-slip motion is observed at very small shear rates. Our results, which open the possibility of exploring complex rheological behavior using simulations, are compared to recent experiments on various soft glasses.     

Reorientational motion in binary mixtures: molecular dynamics simulations

Molecular reorientational motion has been studied in a dilute solution of linear ‘tracer’ molecules in a solvent that exhibits liquid, plastic and crystalline phases. Molecular dynamics simulations have been used to extract reorientational correlation functions for both solvent and solute species as functions of temperature in all phases. The transition from the liquid to the plastic phase (upon cooling) results in less hindered tracer rotation, as evidenced by the more rapid decay of orientational correlation. These surprising dynamics are interpreted in terms of structural changes at freezing that lead to a less confining local tracer environment. The findings support a recent experimental result obtained from polarized Raman scattering on a solution of CS₂ tracers in a cyclohexane host.     

Intramolecular diffusive motion in alkane monolayers studied by high-resolution quasielastic neutron scattering and molecular dynamics simulations

Molecular dynamics simulations of a tetracosane (n-C24H50) monolayer adsorbed on a graphite basal-plane surface show that there are diffusive motions associated with the creation and annihilation of gauche defects occurring on a time scale of approximately 0.1-4 ns. We present evidence that these relatively slow motions are observable by high-energy-resolution quasielastic neutron scattering (QNS) thus demonstrating QNS as a technique, complementary to nuclear magnetic resonance, for studying conformational dynamics on a nanosecond time scale in molecular monolayers.     

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.     

熔融Cu57团簇在急冷过程中弛豫和局域结构转变的分子动力学研究

采用基于嵌入原子方法的正则系综分子动力学研究熔融Cu₅₇团簇在急冷过程中的弛豫及其局域结构变化.通过对弛豫过程中均方位移、非相干中间散射函数和非Gauss参数三种函数和原子键对随急冷温度不同所发生变化的分析表明,在经过短时间的原子剧烈运动后,急冷温度极大地影响着团簇内原子结构弛豫过程.急冷温度较高时,原子在经历短时间剧烈运动的β弛豫后,进入α弛豫区后以扩散运动为主,随后原子运动表现为非扩散性的原子局域结构重排,团簇内没有出现明显的成核结构.随着温度的降低,原子局域结构的变化在经过短时间原子剧烈运动的β弛豫后,在α弛豫区原子运动表现为扩散性运动,并出现一定数量的不稳定二十面体结构.当急冷温度很低时,在进入α弛豫区后,团簇结构变化逐渐表现为非扩散性原子局域结构重排,形成相当数量的稳定成核二十面体结构. 关键词： 团簇 分子动力学 计算机模拟 表面     

High density gas state at water/graphite interface studied by molecular dynamics simulation

In this paper molecular dynamics simulations are performed to study the accumulation behaviour of N2 and H2 at water/graphite interface under ambient temperature and pressure. It finds that both N2 and H2 molecules can accumulate at the interface and form one of two states according to the ratio of gas molecules number to square of graphite surface from our simulation results： gas films （pancake-like） for a larger ratio and nanobubbles for a smaller ratio. In addition, we discuss the stabilities of nanobubbles at different environment temperatures. Surprisingly, it is found that the density of both kinds of gas states can be greatly increased, even comparable with that of the liquid N2 and liquid H2. The present results are expected to be helpful for the understanding of the stable existence of gas film （pancake-like） and nanobubbles.     

Adding a length scale to the polyamorphic ice debate

X-ray scattering and molecular dynamics simulations have been used to correlate the short range oxygen-oxygen structure with the intermediate range ordering (IRO) upon annealing very high density amorphous ice. While it is clear that the IRO that defines the network structure breaks down continuously to a minimum level, where there are weakened correlations extending beyond 7 Angstrom, at this point the local structure (O-O-O angles) is observed to change abruptly, allowing a continuous reemergence of a new IRO network. This is very different from a classic first order transition and helps reconcile previous data.     

Semiclassical dynamics of electron transfer at metal surfaces

In this Letter, we demonstrate that nonadiabatic dynamics of molecular scattering from metal surfaces can be efficiently simulated by semiclassical Gaussian wave packet propagation on a local complex potential. The method relies on the wideband limit decoupling of the nuclear equations of motion on different electronic states. If the continuum diabatic potential surfaces are assumed to be parallel, the number of Gaussian wave packets spawned scales at most linearly with propagation time, allowing efficient propagation of nuclear dynamics.     

Icosahedral order in Cu-Zr amorphous alloys studied by means of X-ray absorption fine structure and molecular dynamics simulations

We have used the X-ray absorption fine structure method and molecular dynamics (MD) simulations to characterize atomic order in Cu-Zr metallic glasses (MGs). The microstructure of these MGs is described in terms of interconnected icosahedral-like clusters (superclusters) which are basic building units reproducing the stoichiometry of the system. The equilibrium MD configurations are used as an input for ab initio calculations of the extended X-ray absorption fine structure (EXAFS) and X-ray absorption near-edge structure (XANES) spectra. The theoretical EXAFS and XANES spectra are compared with those measured for rapidly quenched glassy Cu-Zr alloys. We demonstrate that the experimental results are well reproduced by EXAFS modeling of the population of the superclusters derived from the MD configuration. The average local structural motif can be approximated by Cu-centered icosahedral-like cluster satisfying the condition of maximal local packing efficiency and approximating the system stoichiometry. The simulated XANES exhibits good agreement with experiment, indicating that the atomic order of the MD configuration is consistent with that of the real alloy structure over distances of about 1?nm.     

Suppression of the order parameter correlation length by inhomogeneous strains

Very recently we presented puzzling results of diffuse neutron scattering experiments on KSCN and RbSCN. The data yield an increase of the diffuse intensity with increasing temperature below T(c), whereas the width remains constant. Using molecular dynamics and 3D Monte Carlo simulations, we have shown that below T(c) the width of the correlation functions can be stabilized by strain fields originating from the order parameter strain interactions. Here we construct a novel analytic model which predicts the existence of a second characteristic length scale and explains the suppression of the growth of precursor clusters by the influence of inhomogeneous strain fields.     

气体分子与纳米粒子碰撞的分子动力学仿真分析

当气体分子与纳米粒子碰撞的时候,纳米粒子传输理论预测到当纳米粒子的直径由小变大时,碰撞会由镜面反射转化为漫反射.文章利用分子动力学仿真研究了气体分子与纳米粒子碰撞的过程.在验证了这种转化存在同时,又探讨了碰撞转化的机理,即漫反射的起因.仿真结果揭示了漫反射的起因是由于纳米粒子对气体分子的吸附作用.这种吸附作用是由于纳米粒子对能量的容纳特性而产生的.