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

In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. (C) 1997 John Wiley & Sons, Inc.

LINCS : A linear constraint solver for molecular simulations

N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

There has been much recent interest in the behavior of integral-equation theories for the distribution functions of a fluid near the critical point and in the two-phase region. For most systems, implementation of these theories necessitates numerical solution of the integral equations. However, for two examples, the adhesive hard sphere fluid in the Percus-Yevick approximation and the hard sphere plus Yukawa tail model in the mean spherical approximation, analytical solutions of the Ornstein-Zernike equation are available. In this work we consider the comparison of results obtained via numerical methods with the analytical solution of the Percus-Yevick equation for the adhesive hard sphere fluid. This complements a recent study by us of the mean spherical approximation for the hard sphere plus Yukawa tail fluid. This allows us to examine carefully how errors arise in the numerical solutions. We examine the accuracy of numerical calculations of the critical exponents as well as the interpretation of solutions obtained in the coexistence region. We discuss the implications of this work for applications to more realistic potentials where only numerical solutions are available.

Solution of the Percus-Yevick equation in the coexistence region of a simple fluid

In a recent paper (1987) the authors reported nonequilibrium molecular dynamics simulations of liquid rubidium using the isokinetic sllod algorithm for the dynamics and the Price potential for the interactions. New and more extensive results are presented which confirm that the results exhibit normal square-root behaviour of the shear viscosity as a function of strain rate at the triple point.

Shear viscosity of liquid rubidium at the triple point

β-Enaminone and its derivatives have emerged among the finest bioactive intermediates. High yields of several β-enaminones (86–97%) are achieved through treatment of substituted aromatic and aliphatic amines with cyclic/acyclic 1,3-diketones, over the magnetically separable cobalt ferrite nanoparticles (CoFe2O4 NPs). The latter was prepared upon co-precipitation. Its purity, fine crystallinity, elemental distributions, morphology, magnetic features, and thermal stability were confirmed by Fourier transform infrared, X-ray diffraction, energy dispersive X-ray spectrometry, scanning electron microscopy, vibrating sample magnetometry, and thermal gravimetric analysis analyses. Thus, CoFe2O4 NPs acted as an excellent green heterogeneous nanocatalyst for synthesis of β-enaminones and gave good recyclability, while showing insignificant loss of their activity.

β -Enaminones over recyclable nano-CoFe 2 O 4 : a highly efficient solvent-free green protocol

https://www.prf.jcu.cz/data/files/87/83fpe.pdf

Peter T. Cummings

Papers

Solution of the Percus-Yevick equation in the coexistence region of a simple fluid

Shear viscosity of liquid rubidium at the triple point

β -Enaminones over recyclable nano-CoFe 2 O 4 : a highly efficient solvent-free green protocol

On the determination of the vapor–liquid envelope for polarizable models by Monte Carlo simulation

Erratum: “Multicomponent mixture of charged hard-sphere chain molecules in the polymer mean-spherical approximation” [J. Chem. Phys. 115, 540 (2001)]