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

We critically review dissipative particle dynamics (DPD) as a mesoscopic simulation method. We have established useful parameter ranges for simulations, and have made a link between these parameters and χ-parameters in Flory-Huggins-type models. This is possible because the equation of state of the DPD fluid is essentially quadratic in density. This link opens the way to do large scale simulations, effectively describing millions of atoms, by firstly performing simulations of molecular fragments retaining all atomistic details to derive χ-parameters, then secondly using these results as input to a DPD simulation to study the formation of micelles, networks, mesophases and so forth. As an example application, we have calculated the interfacial tension σ between homopolymer melts as a function of χ and N and have found a universal scaling collapse when σ/ρkBTχ0.4 is plotted against χN for N>1. We also discuss the use of DPD to simulate the dynamics of mesoscopic systems, and indicate a possible problem with...

https://www.physics.iitm.ac.in/~iol/lecture_notes/groot-warren.pdf

Dissipative particle dynamics : bridging the gap between atomistic and mesoscopic simulation

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

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

https://cyberleninka.org/article/n/1018032.pdf

Polymer nanotechnology: Nanocomposites

Theory of phase equilibria in mixtures of copolymers and homopolymers. 2. Interfaces near the consolute point

We model the statics and dynamics of wetting of liquids on thin rubber films. We show that at equilibrium the capillary forces deform soft substrates, leading to undulations of the rubber film surface originating at the triple line. Such deformations propagate when a liquid spreads on the rubber film. This induces the dissipation that may control the spreading dynamics. We derive a general expression for this dissipation as a function of the viscoelastic properties of the substrate. We calculate the spreading velocities for various mechanical relaxation models. Using available mechanical relaxation data, we find that our model may well account for the experimental observations of Carre and Shanahan, who demonstrated the importance of viscoelastic braking effects.

Static and Dynamic Wetting Properties of Thin Rubber Films

An analysis of the free energy of distortion of a molten polymer brush, such as a layer of block copolymer at an air interface, is reported. Within the Alexander-de Gennes approximation of a delta function distribution of chain ends, but rigorously enforcing incompressibility, the change in the free energy of a brush associated with a small-amplitude sinusoidal displacement of the free surface about the equilibrium height is calculated. Unlike the surface of a liquid, long-wavelength modes in a brush are suppressed due to the lateral chain stretching required to maintain constant density

Surface modes and deformation energy of a molten polymer brush

We analyse the way grafted polymers modify the slippage of an entangled polymer melt on an ideal surface. We take into account the deformation of the grafted chains in the flow (non-linear effects) and show that it alters significantly their efficiency as anti-slippers. We calculate the relation between the applied shear stress and the slippage velocity. At low velocities the friction of the underformed grafted chains is strong. Above a certain threshold part of the chain relaxes through monomeric friction, and the stress becomes almost velocity independent. For even higher velocities the contribution of the grafted chains become small and a significant slippage is recovered. More generally, non-linear effects due to deformation of chains in flow are shown to be of importance at most experimental and practical velocities.

Slippage of an entangled polymer melt on a grafted surface

Fundamental understanding of how crystals of organic molecules nucleate on a surface remains limited because of the difficulty of probing rare events at the molecular scale. Here we show that single-molecule templates on the surface of carbon nanohorns can nucleate the crystallization of two organic compounds from a supersaturated solution by mediating the formation of disordered and mobile molecular nanoclusters on the templates. Single-molecule real-time transmission electron microscopy indicates that each nanocluster consists of a maximum of approximately 15 molecules, that there are fewer nanoclusters than crystals in solution, and that in the absence of templates physisorption, but not crystal formation, occurs. Our findings suggest that template-induced heterogeneous nucleation mechanistically resembles two-step homogeneous nucleation.

Ludwik Leibler

Papers

Theory of phase equilibria in mixtures of copolymers and homopolymers. 2. Interfaces near the consolute point

Static and Dynamic Wetting Properties of Thin Rubber Films

Surface modes and deformation energy of a molten polymer brush

Slippage of an entangled polymer melt on a grafted surface

Heterogeneous nucleation of organic crystals mediated by single-molecule templates