Dimension-Splitting for Simplifying Diffusion in Lattice-Gas Models

We introduce a simplified technique for incorporating diffusive phenomena into lattice-gas molecular dynamics models. In this method, spatial interactions take place one dimension at a time, with a separate fractional timestep devoted to each dimension, and with all dimensions treated identically. We show that the model resulting from this technique is equivalent to the macroscopic diffusion equation in the appropriate limit. This technique saves computational resources and reduces the complexity of model design, programming, debugging, simulation and analysis. For example, a reaction-diffusion simulation can be designed and tested as a one-dimensional system, and then directly extended to two or more dimensions. We illustrate the use of this approach in constructing a microscopically reversible model of diffusion-limited aggregation as well as in a model of growth of biological films.     

Phase separation in a three-dimensional,two-phase,hydrodynamic lattice gas

The dynamics of phase separation is explored using an immiscible 3D lattice-gas model. Scaling laws for the growth rate and power spectraS(k) of the growth patterns are computed. For small wavenumbersS(k) shows a crossover fromk ² tok ⁴ behavior. The theoretical prediction for the asymptotic domain growthRt ^2/3 is supported by our results. We discuss the possibility to observe an intermediatet scaling. We show the influence of hydrodynamic forces in symmetric and asymmetric mixtures by comparing simulations with and without momentum conservation. The structure functionS(k) is not significantly modified by hydrodynamics, but the growth rate changes clearly. As a general result, it is shown that, in spite of the unusual thermodynamics of this model, many characteristics of the growth dynamics are surprisingly in agreement with the classical theoretical and experimental results.     

Critical behaviour of the hard-core lattice gas on the honeycomb lattice

The hard triangle lattice-gas model (lattice-gas on the honeycomb lattice with first neighbour exclusion) is studied by the phenomenological renormalization method. The critical activity is found to be z = 7.85 and the critical exponents suggest that this model belongs to the 2-D Ising universality class.     

高磁场核磁共振波谱学在临床医学上的应用

本篇是有关以高磁场核磁共振(非成像)探讨生物体液如体尿及血浆于临床医学上、采样前处理以及一般用到之核磁共振技术,并从文献上举例说明如何利用核磁共振来诊断新陈代谢及病发状态。其成份组成在波谱上观察得到与否,主要靠分子运动以及浓度来决定,分子运动影响了核弛豫,各组成间所显现之不同弛豫可用来做波谱编排,因此不同之分子运动亦有可能做为诊断之依据。     

液态金属及非晶态中的电导率——相干势近似

本文在紧束缚模型内得到了液态金属和非晶态中电子电导率的相干势近似(CPA)结果,用文献[4]提出的处理单格点图形的系统方法可以得到平均双粒子格林函数的近似方程,这里采用具有短程序的点阵-气体模型,液态金属和非晶态金属相对应的CPA方程可以从点阵-气体模型的极限求得,这样得到的目洽方程包括所有的单格点图形,具有CPA的所有性质。 关键词：     

Renormalization Group Maps for Ising Models in Lattice-Gas Variables

Real-space renormalization group maps, e.g., the majority rule transformation, map Ising-type models to Ising-type models on a coarser lattice. We show that each coefficient in the renormalized Hamiltonian in the lattice-gas variables depends on only a finite number of values of the renormalized Hamiltonian. We introduce a method which computes the values of the renormalized Hamiltonian with high accuracy and so computes the coefficients in the lattice-gas variables with high accuracy. For the critical nearest neighbor Ising model on the square lattice with the majority rule transformation, we compute over 1,000 different coefficients in the lattice-gas variable representation of the renormalized Hamiltonian and study the decay of these coefficients. We find that they decay exponentially in some sense but with a slow decay rate. We also show that the coefficients in the spin variables are sensitive to the truncation method used to compute them.     

Spinodal decomposition of off-critical quenches with a viscous phase using dissipative particle dynamics in two and three spatial dimensions

We investigate the domain growth and phase separation of hydrodynamically correct binary immiscible fluids of differing viscosity as a function of minority phase concentration in both two and three spatial dimensions using dissipative particle dynamics. We also examine the behavior of equal-viscosity fluids and compare our results to similar lattice-gas simulations in two dimensions.     

Nonequilibriurn discontinuous phase transitions in a fast ionic conductor model: Coexistence and spinodal lines

Two-dimensional lattice-gas models with attractive interactions and particle-conserving hopping dynamics under the influence of a very large external electric field along a principal axis are studied in the case of off-critical densities. We describe the corresponding nonequilibrium first-order phase transitions, evaluate coexistence and spinodal lines, and make some comparisons with experimental observations on fast ionic conductors.See Ref. 1 (henceforth referred to as II) for references.     

A method for tractable dynamical studies of single and double shock compression

A new multiscale simulation method is formulated for the study of shocked materials. The method combines molecular dynamics and the Euler equations for compressible flow. Treatment of the difficult problem of the spontaneous formation of multiple shock waves due to material instabilities is enabled with this approach. The method allows the molecular dynamics simulation of the system under dynamical shock conditions for orders of magnitude longer time periods than is possible using the popular nonequilibrium molecular dynamics approach. An example calculation is given for a model potential for silicon in which a computational speedup of 10(5) is demonstrated. Results of these simulations are consistent with the recent experimental observation of an anomalously large elastic precursor on the nanosecond time scale.     

Structure of interfaces from uniformity of the chemical potential

It is shown that a generalized chemical potential suggested by the potential-distribution theory is uniform even in a nonuniform fluid. Leng, Rowlinson, and Thompson had already observed its uniformity through the liquid-vapor interface in the penetrable-sphere model, in mean-field approximation. Following those authors, we exploit the uniformity of that generalized chemical potential to obtain unified and transparent derivations of the results of Ono and Kondo and of van der Waals on the liquid-vapor interfaces in the lattice-gas model and in the model of attracting hard spheres, respectively, both in mean-field approximation.Work supported by the National Science Foundation and the Cornell University Materials Science Center.     

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.     

Supercomputer simulation of cracks and fractures by quasimolecular dynamics

A modern method for predicting the time and place of crack and fracture development is through molecular dynamics, which studies reactions to external forces in the small, that is, the molecular level. In quasimolecular dynamics, which is an attempt to bridge the gap between atomistic and continuum simulations, molecules are aggregated into larger units, called quasimolecules, to simulate the large scale behavior. In this first paper, quasimolecular dynamics is applied to the study of crack and fracture generation in a stressed, slotted plate made of pure copper. Conservation of mass and energy is basic to the methodology.     

Birefringence effects induced by optical saturation, dispersion effects in the far infra-red.

It has been demonstrated recently, using computer simulation, that a molecular liquid treated with strong electromagnetic radiation becomes birefringent in the far infra red region of the electromagnetic spectrum This appears to be a new observation, opening the way for the spectral investigation of molecular dynamics with powerful laser fields. It is shown in this paper that the birefringence is accompanied by dispersion at frequencies characteristic or the molecular dynamics on the picosecond time scale. Dispersion of the birefringence that accompanies dynamic optical saturation is a new practical method of investigating molecular material at far infra red frequencies.     

Kinetic equation for the processes of local reorganization of molecular systems with charged species

A molecular dynamic theory based on the lattice-gas model for the local reorganization of multi-component systems containing charged species is considered. Expressions for the mono- and bimolecular stages of the elementary processes that describe chemical reactions and displacements and rotations of molecules in dense gases and liquids are derived, with consideration given to direct and indirect effects of the initiation of electron and proton transfer. The proposed kinetic equations describe small-scale restructuring of solutions containing components of different sizes under the influence of changes in the external parameters of the molecular system at the kinetic stage of evolution of the system. The theory retains the effects of direct spatial correlations in the distribution of all the components of the mixture with the help of pair distribution functions in the quasi-chemical approximation. The dynamics of the local reorganization of molecules includes the kinetic equations for the local densities and pair distribution functions. The equations derived are intended to describe liquid-phase reactions, ion charge exchange, mutual diffusion of components of different sizes in multicomponent solutions, extraction processes at liquid phase boundaries, and photochemical processes in condensed phases.     

Coarse-grained model of proteins incorporating atomistic detail of the active site

We present a novel approach to explore the conformational space of globular proteins near their native state. It combines the advantages of coarse-grained models with those of all-atoms simulations, required to treat molecular recognition processes. The comparison between calculated structural properties with those obtained with all-atoms molecular dynamics simulations establishes the accuracy of the model. Our method has the potential to be extended to molecular recognition processes in systems whose characteristic size and time scale prevent an analysis based on all-atoms molecular dynamics.     

Shear viscosity of strongly coupled Yukawa systems on finite length scales

The Yukawa shear viscosity has been calculated using nonequilibrium molecular dynamics. Near the viscosity minimum, we find exponential decay consistent with the Navier-Stokes equation, with significant deviations on finite length scales for larger viscosity values. The viscosity is determined to be nonlocal on a scale length consistent with the correlation length, revealing the length scales necessary for obtaining transport coefficients in the hydrodynamic limit by nonequilibrium molecular dynamics methods. Our results are quasiuniversal with respect to excess entropy for excess entropies well below unity.     

A Mesoscopic Simulation Approach for Modeling Intracellular Reactions

Reactions in the intracellular medium occur in a highly organized and heterogenous environment rendering invalid modeling approaches based on the law of mass action or its stochastic counter-part. This has led to the recent development of a variety of stochastic microscopic approaches based on lattice-gas automata or Brownian dynamics. The main disadvantage of these methods is that they are computationally intensive. We propose a mesoscopic method which permits the efficient simulation of reactions occurring in the complex geometries typical of intracellular environments. This approach is used to model the transport of a substrate through a pore in a semi-permeable membrane, in which its Michaelis–Menten enzyme is embedded. We find that the temporal evolution of the substrate is a sensitive function of the spatial heterogeneity of the environment. The spatial organization and heterogeneities of the intracellular medium seem to be playing an important role in the regulation of biochemical reactions.     

固态高分子体系多尺度分子运动的核磁共振研究

固体核磁共振技术是研究固态高分子材料中结构和分子动力学的一种非常重要和有效的手段. 该技术的一个重要特点是可以通过合理的实验方法,实现对研究体系中从低频(Hz)到中频(kHz)乃至高频(MHz)范围内分子运动的观测. 因此,固体核磁共振技术非常适合研究高分子体系中各类不同尺度分子运动. 该文首先简要介绍核磁共振研究分子运动的基本原理和方法,以及固态高分子体系的结构和分子动力学特点,然后结合固态高分子体系中的一些例子对核磁共振在固态高分子多尺度分子运动方面的一些研究成果展开讨论.     

Efficient formalism for large-scale ab initio molecular dynamics based on time-dependent density functional theory

A new "on the fly" method to perform Born-Oppenheimer ab initio molecular dynamics (AIMD) simulations is presented. Inspired by Ehrenfest dynamics in time-dependent density functional theory, the electronic orbitals are evolved by a Schr?dinger-like equation, where the orbital time derivative is multiplied by a parameter. This parameter controls the time scale of the fictitious electronic motion and speeds up the calculations with respect to standard Ehrenfest dynamics. In contrast with other methods, wave function orthogonality needs not be imposed as it is automatically preserved, which is of paramount relevance for large-scale AIMD simulations.     

多核环境下的分子动力学模拟

本文在多核环境下,使用OpenMP实现了经典分子动力学模拟程序的并行;同时对分子动力学模拟进行了两项主要的优化:分子排序及运用SIMD指令运算.在4核下获得了4.13倍的计算性能提升,将经典分子动力学模拟的模拟规模提高至4000分子×10~7模拟总步数.