Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The American Society for Testing and Materials (ASTM) is an independent organization devoted to the development of standards.

American Society for Testing and Materials

/pdf/introduction-to-the-modern-theory-of-dynamical-systems-1eced70mum.pdf

Introduction to the Modern Theory of Dynamical Systems

Numerical Initial Value Problems in Ordinary Differential Equations

We use nonequilibrium molecular dynamics (NEMD) to explore the effect of shear flow on heat flux. By simulating a simple fluid in a channel bounded by tethered atoms, the heat flux is computed for two systems: a temperature driven one with no flow and a wall driven, Couette flow system. The results for the temperature driven system give the Fourier's law thermal conductivity, which is shown to agree well with experiments. Through comparison of the two systems, we quantify the additional components of the heat flux parallel and normal to the walls due to shear flow. To compute the heat flux in the flow direction, the Irving-Kirkwood equations are integrated over a volume, giving the so-called volume average form, and they are also manipulated to get expressions for the surface averaged and method of planes forms. The method of planes and volume average forms are shown to give equivalent results for the heat flux when using small volumes. The heat flux in the flow direction is obtained consistently over a range of simulations, and it is shown to vary linearly with strain rate, as predicted by theory. The additional strain rate dependent component of the heat flux normal to the wall is obtained by fitting the strain rate dependence of the heat flux to the expected form. As a result, the additional terms in the thermal conductivity tensor quantified in this work should be experimentally testable.

Measuring Heat Flux Beyond Fourier's law

Electropumping has shown great potential as an effective means of inducing a net positive flow of water in confined channels. In this paper we present the first nonequilibrium molecular dynamics study and continuum based numerical solutions that demonstrate an effective net positive flow between concentric carbon nanotubes (CNT) using electropumping. We apply a spatially uniform rotating electric field that couples to the water's permanent dipole moment. Taking advantage of the coupling between the spin angular momentum and the linear momentum we break the symmetry of the channel radius by functionalizing the inner CNT's outer surface with carboxyl groups to induce a net positive flow. We also show that our results for concentric nanotubes are consistent with our previous work where we demonstrated that an increase in functionalization beyond an optimal point in a single walled carbon nanotube resulted in a decrease in positive net flow. We then numerically solve the coupled hydrodynamic momentum equations to show that the nonequilibrium molecular dynamics results are consistent with the continuum theory.

Inducing a Net Positive Flow of Water in Functionalized Concentric Carbon Nanotubes Using Rotating Electric Fields.

Molecular dynamics simulations of liquid systems under planar elongational flow have mainly been performed in the NVT ensemble. However, in most material processing techniques and common experimental settings, at least one surface of the fluid is kept in contact with the atmosphere, thus maintaining the sample in the NpT ensemble. For this reason, an implementation of the Nose-Hoover integral-feedback mechanism for constant pressure is presented, implemented via the SLLOD algorithm for elongational flow. The authors test their procedure for an atomic liquid and compare the viscosity obtained with that in the NVT ensemble. The scheme is easy to implement, self-starting and reliable, and can be a useful tool for the simulation of more complex liquid systems, such as polymer melts and solutions.

https://researchbank.swinburne.edu.au/file/e52da340-959e-47d4-87a7-233326078d46/1/PDF (Published version).pdf

Molecular dynamics simulation of planar elongational flow at constant pressure and constant temperature.

Molecular simulation methods such as Monte Carlo simulation and both equilibrium and nonequilibrium molecular dynamics are powerful computational techniques that allow the exact calculation of molecular properties with minimal approximations. The main approximations are the choice of intermolecular potential and the number of particles involved in each interaction. Typically, only pairwise interactions are counted using a simple effective intermolecular potential such as the Lennard-Jones potential. The use of accurate two-body potentials and calculations that explicitly include three or more body interactions are rare because of the large increase in computational cost involved. Here, we report recent progress in the use of both genuine two-body potentials and calculations involving three-body interactions. We show that in some cases, the contribution of three-body interactions can be accurately estimated from two-body interactions without the increase in computational cost involved in explicitly accounting for three-body interactions. As an example of the benefit of including three-body interactions, the improvement in the prediction of vapour-liquid equilibria is examined.

/pdf/beyond-traditional-effective-intermolecular-potentials-and-zexsaeslv8.pdf

Beyond Traditional Effective Intermolecular Potentials and Pairwise Interactions in Molecular Simulation

In this paper we investigate the spatiotemporal dynamics of a diatomic fluid undergoing zero mean oscillatory flow in a slit pore. The study is based on nonequilibrium molecular dynamics simulations together with two limiting solutions to the Navier-Stokes equations which include the effect of molecular rotation. By examining the viscoelastic properties of the system we can estimate the extent of the Newtonian regime, and a direct comparison between the molecular dynamics data and the solutions to the Navier-Stokes equations is then possible. It is found that the agreement is excellent, and that the vortex viscosity can be estimated by fitting the data obtained in the molecular dynamics simulations to the solutions to the Navier-Stokes equations. The quantitative effect of the coupling between the linear momentum and the spin angular momentum on flow is also investigated. We find that the maximum flow can be reduced up to 3-4 % due to the coupling.

https://researchbank.swinburne.edu.au/file/29f7a6f0-05dd-4031-a015-c57876d343fe/1/PDF (Published version).pdf

Billy D. Todd

Papers

Measuring Heat Flux Beyond Fourier's law

Inducing a Net Positive Flow of Water in Functionalized Concentric Carbon Nanotubes Using Rotating Electric Fields.

Molecular dynamics simulation of planar elongational flow at constant pressure and constant temperature.

Beyond Traditional Effective Intermolecular Potentials and Pairwise Interactions in Molecular Simulation

Dynamical properties of a confined diatomic fluid undergoing zero mean oscillatory flow: effect of molecular rotation.