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

A theoretical approach is presented which represents the first attempt known to the authors to develop molecular dynamics algorithms capable of modeling phase coexistence between two nonequilibrium steady state phases confined in a closed (E,V,N) system. We deal exclusively with shearing liquids because of their importance in rheology. In the present paper, as in the equilibrium Gibbs ensemble Monte Carlo technique for systems at equilibrium, the coexisting phases have no physical contact but their dynamics are coupled in order to reach mechanical, thermal, and composition balance between bulk regions of the two phases. The thermal balance is maintained by requiring zero net heat flow across a hypothetical boundary. This can be achieved by starting from equilibrium and gradually increasing the strength of the external field (the shear rate) in a quasistatic process. For particle interchanges we invoke the Evans–Baranyai variational principle which is at the very least a good approximation for similar simulated steady state systems far from equilibrium. Results of several model calculations are presented. The limitations and the implications of the methods are discussed.

Towards the atomistic simulation of phase coexistence in nonequilibrium systems

In a recent work (Dyer et al., J. Chem. Phys. 129 (2008), 024508), we demonstrated that by accounting for the polarisability of small non-polar solutes, in an explicit manner, it is possible to approach quantitative agreement with experimental values of the excess chemical potential of the molecules in pure water. Here, we continue this line of research by considering the effects of ionic co-solutes (i.e. salts) on the solubility of an explicitly polarisable model suitable for a variety of small non-polar solutes. In doing so, we calculate the excess chemical potential that is related to the solubility of the solute in the solution, and investigate how the solubility of hydrophobic solutes varies with ion concentration, i.e. salting-out/salting-in effects, as measured by the Setchenow parameter. In particular, we consider the solubility of Ne, Ar, Kr, Xe and CH4 in aqueous NaCl solutions for the TIP3P, TIP4P-Ew and TIP4P/2005 models of water. Using these models, we discover that the addition of explicit p...

The importance of polarisability in the modelling of solubility: quantifying the effect of charged co-solutes on the solubility of small non-polar solutes

Ligands can control the surface chemistry, physicochemical properties, processing, and applications of nanomaterials. MXenes are the fastest growing family of two-dimensional (2D) nanomaterials, showing promise for energy, electronic, and environmental applications. However, complex oxidation states, surface terminal groups, and interaction with the environment have hindered the development of organic ligands suitable for MXenes. Here, we demonstrate a simple, fast, scalable, and universally applicable ligand chemistry for MXenes using alkylated 3,4-dihydroxy-l-phenylalanine (ADOPA). Due to the strong hydrogen-bonding and π-electron interactions between the catechol head and surface terminal groups of MXenes and the presence of a hydrophobic fluorinated alkyl tail compatible with organic solvents, the ADOPA ligands functionalize MXene surfaces under mild reaction conditions without sacrificing their properties. Stable colloidal solutions and highly concentrated liquid crystals of various MXenes, including Ti2CTx, Nb2CTx, V2CTx, Mo2CTx, Ti3C2Tx, Ti3CNTx, Mo2TiC2Tx, Mo2Ti2C3Tx, and Ti4N3Tx, have been produced in various organic solvents. Such products offer excellent electrical conductivity, improved oxidation stability, and excellent processability, enabling applications in flexible electrodes and electromagnetic interference shielding.

Universal Ligands for Dispersion of Two-Dimensional MXene in Organic Solvents.

The analytical solution of the Ornstein-Zernike equation in the mean-spherical approximation for a Yukawa fluid and adhesive hard sphere Yukawa fluid with factorizable coefficients is used to derive a simple form for the thermodynamic properties for both mixtures. The second system contains an additional interaction. However, the general thermodynamic expressions were obtained in similar form for both systems. Some particular cases are discussed in terms of Γ, the principal parameter to be calculated for these systems. These results complement the recent work of Yasutomi, M., and Ginoza, M., 1996, Molec. Phys., 89, 1755.

Thermodynamic properties of an asymmetric fluid mixture with adhesive hard sphere Yukawa interaction in the mean spherical approximation

In a recent paper [Mol. Sim., 16, 229 (1996)], we reported non-equilibrium molecular dynamics (NEMD) simulation of planar Couette flow for normal (n-butane) and isomeric butane (i-butane) molecules using two collapsed atom models and an atomistically detailed model. It was found that the collapsed atom models predict the viscosity of the n-butane quite well, but the viscosity of i-butane by those models is underpredicted. It was also found that the atomistically detailed model does not yield quantitative agreement with the viscosity of either the n-butane or i-butane, but it does have the one positive feature that the calculated viscosity of i-butane is higher than that of n-butane (branching increases viscosity) as observed experimentally. In the present paper, we present results of NEMD simulations of observed experimentally. In the present paper, we present results of NEMD simulations of planar Couette flow for normal decane and 4-propyl heptane molecules using the same models. The results sho...

Peter T. Cummings

Papers

Towards the atomistic simulation of phase coexistence in nonequilibrium systems

The importance of polarisability in the modelling of solubility: quantifying the effect of charged co-solutes on the solubility of small non-polar solutes

Universal Ligands for Dispersion of Two-Dimensional MXene in Organic Solvents.

Thermodynamic properties of an asymmetric fluid mixture with adhesive hard sphere Yukawa interaction in the mean spherical approximation

The Rheology of n-Decane and 4-Propyl Heptane by Non Equilibrium Molecular Dynamics Simulations