Langevin dynamics for rigid bodies of arbitrary shape

We present an algorithm for carrying out Langevin dynamics simulations on complex rigid bodies by incorporating the hydrodynamic resistance tensors for arbitrary shapes into an advanced rotational integration scheme. The integrator gives quantitative agreement with both analytic and approximate hydrodynamic theories for a number of model rigid bodies and works well at reproducing the solute dynamical properties (diffusion constants and orientational relaxation times) obtained from explicitly solvated simulations.     

A gentler approach to RNEMD: nonisotropic velocity scaling for computing thermal conductivity and shear viscosity

We present a new method for introducing stable nonequilibrium velocity and temperature gradients in molecular dynamics simulations of heterogeneous systems. This method extends earlier reverse nonequilibrium molecular dynamics (RNEMD) methods which use momentum exchange swapping moves. The standard swapping moves can create nonthermal velocity distributions and are difficult to use for interfacial calculations. By using nonisotropic velocity scaling (NIVS) on the molecules in specific regions of a system, it is possible to impose momentum or thermal flux between regions of a simulation while conserving the linear momentum and total energy of the system. To test the method, we have computed the thermal conductivity of model liquid and solid systems as well as the interfacial thermal conductivity of a metal-water interface. We find that the NIVS-RNEMD improves the problematic velocity distributions that develop in other RNEMD methods.     

高T_c超导体YBCO磁通钉扎的计算机模拟研究

临界电流密度Jc是影响高温超导体在强电领域应用的一个重要参数,在实际应用中,特别在外加磁场下,临界电流密度与超导材料的磁通钉扎性质密切相关.因此,磁通钉扎一直是高温超导体研究中的一个重要领域.由于高温超导体磁通钉扎力密度Fp的标度律存在,本文根据D.Dew-Hughes总结的钉扎力函数,主要存在两种主要作用类型(正常相和△K).我们将D.Dew-HugBes给出的钉扎力密度Fp标度函数改进为一个简化的具有物理意义的函数表达式.结合文献中已有的实验数据,我们对YBcO进行了计算机模拟,确定了它的磁通钉扎类型,模拟的研究结果与实际情况比较吻合.     

OOPSE: an object-oriented parallel simulation engine for molecular dynamics

OOPSE is a new molecular dynamics simulation program that is capable of efficiently integrating equations of motion for atom types with orientational degrees of freedom (e.g. "sticky" atoms and point dipoles). Transition metals can also be simulated using the embedded atom method (EAM) potential included in the code. Parallel simulations are carried out using the force-based decomposition method. Simulations are specified using a very simple C-based meta-data language. A number of advanced integrators are included, and the basic integrator for orientational dynamics provides substantial improvements over older quaternion-based schemes.     

Breathing mode dynamics and elastic properties of gold nanoparticles

We present calculations of the bulk modulus, heat capacity, and the period of the breathing mode for spherical nanoparticles following excitation by ultrafast laser pulses. The bulk modulus and heat capacities both exhibit clear transitions upon bulk melting of the particles. Equilibrium calculations of the heat capacity show that the melting transition is sharper and occurs at a lower temperature than one would observe from an ultrafast experiment. We also observe an intriguing splitting in the low-frequency spectra of the nanoparticles and analyze this splitting in terms of Lamb's classical theory of elastic spheres. We conclude that the particles either (1) melt during the observation period following laser excitation or (2) melt an outer shell while maintaining a crystalline core. Both mechanisms for melting are commensurate with our observations.     

On the structural and transport properties of the soft sticky dipole and related single-point water models

The density maximum and temperature dependence of the self-diffusion constant were investigated for the soft sticky dipole (SSD) water model and two related reparametrizations of this single-point model. A combination of microcanonical and isobaric-isothermal molecular dynamics simulations was used to calculate these properties, both with and without the use of reaction field to handle long-range electrostatics. The isobaric-isothermal simulations of the melting of both ice-Ih and ice-Ic showed a density maximum near 260 K. In most cases, the use of the reaction field resulted in calculated densities which were significantly lower than experimental densities. Analysis of self-diffusion constants shows that the original SSD model captures the transport properties of experimental water very well in both the normal and supercooled liquid regimes. We also present our reparametrized versions of SSD for use both with the reaction field or without any long-range electrostatic corrections. These are called the SSD/RF and SSD/E models, respectively. These modified models were shown to maintain or improve upon the experimental agreement with the structural and transport properties that can be obtained with either the original SSD or the density-corrected version of the original model (SSD1). Additionally, a novel low-density ice structure is presented which appears to be the most stable ice structure for the entire SSD family.