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

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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 develop a simple, efficient, and general statistical mechanical technique for calculating the pressure tensor of an atomic fluid. The method is applied to the case of planar Poiseuille flow through a narrow slit pore, and the results indicate that our technique is accurate and relatively efficient. A second method to calculate shear stress is derived from the momentum continuity equation. This mesoscopic method again is seen to be accurate with low statistical uncertainty. Using both approaches, the viscosity is calculated as a function of position across the pore, and is seen to oscillate because of a wall-induced local structure in the fluid. We discuss these methods in relation to the well-known ambiguity of the pressure tensor.

Pressure tensor for inhomogeneous fluids

In this work we use nonequilibrium molecular dynamics (NEMD) to simulate an atomic liquid undergoing gravity-fed flow down a narrow channel. We compare the simulation results against the predictions of classical Navier-Stokes theory for two different channel widths. For a channel width of 5.1 molecular diameters, we find that the velocity profile deviates significantly from the hydrodynamic prediction. The shape of this velocity profile is found to be independent of the applied field (pressure gradient). We find that the heat flux profile does not agree with the cubic profile predicted by Navier-Stokes hydrodynamics, but shows significant oscillations located about one molecular diameter from the walls. This result differs from the earlier work of Todd and Evans [B. D. Todd and D. J. Evans, J. Chem. Phys. 103, 9804 (1995)], in which an assumption of a purely quadratic velocity profile resulted in very weak oscillations in the heat flux. We find that in narrow channels the viscosity cannot be described by a linear, local constitutive relation. However, classical Navier-Stokes behavior is approached for a channel width of g\ensuremath{\sim}10 molecular diameters.

Departure from navier-stokes hydrodynamics in confined liquids

The purpose of this paper is threefold. First, we review the existing literature on flow rates of water in carbon nanotubes. Data for the slip length which characterizes the flow rate are scattered over 5 orders of magnitude for nanotubes of diameter 0.81-10 nm. Second, we precisely compute the slip length using equilibrium molecular dynamics (EMD) simulations, from which the interfacial friction between water and carbon nanotubes can be found, and also via external field driven non-equilibrium molecular dynamics simulations (NEMD). We discuss some of the issues in simulation studies which may be reasons for the large disagreements reported. By using the EMD method friction coefficient to determine the slip length, we overcome the limitations of NEMD simulations. In NEMD simulations, for each tube we apply a range of external fields to check the linear response of the fluid to the field and reliably extrapolate the results for the slip length to values of the field corresponding to experimentally accessible pressure gradients. Finally, we comment on several issues concerning water flow rates in carbon nanotubes which may lead to some future research directions in this area.

https://researchbank.swinburne.edu.au/file/762e6a29-197f-4d24-b1b5-1cc29c6e8cc4/1/PDF (Published version).pdf

How fast does water flow in carbon nanotubes

Data for the flow rate of water in carbon nanopores is widely scattered, both in experiments and simulations. In this work, we aim at precisely quantifying the characteristic large slip length and flow rate of water flowing in a planar graphene nanochannel. First, we quantify the slip length using the intrinsic interfacial friction coefficient between water and graphene, which is found from equilibrium molecular dynamics (EMD) simulations. We then calculate the flow rate and the slip length from the streaming velocity profiles obtained using non-equilibrium molecular dynamics (NEMD) simulations and compare with the predictions from the EMD simulations. The slip length calculated from NEMD simulations is found to be extremely sensitive to the curvature of the velocity profile and it possesses large statistical errors. We therefore pose the question: Can a micrometer range slip length be reliably determined using velocity profiles obtained from NEMD simulations? Our answer is “not practical, if not impossible” based on the analysis given as the results. In the case of high slip systems such as water in carbon nanochannels, the EMD method results are more reliable, accurate, and computationally more efficient compared to the direct NEMD method for predicting the nanofluidic flow rate and hydrodynamic boundary condition.

/pdf/slip-length-of-water-on-graphene-limitations-of-non-4yepvdt2hl.pdf

Slip length of water on graphene: Limitations of non-equilibrium molecular dynamics simulations

http://physics.ujep.cz/~mlisal/md/sutton-chen_fcc2.pdf

Billy D. Todd

Papers

Pressure tensor for inhomogeneous fluids

Departure from navier-stokes hydrodynamics in confined liquids

How fast does water flow in carbon nanotubes

Slip length of water on graphene: Limitations of non-equilibrium molecular dynamics simulations

Surface and bulk properties of metals modelled with Sutton-Chen potentials