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 Microphase Separation in Block Copolymers

Rubbers exhibit enormous extensibility up to several hundred per cent, compared with a few per cent for ordinary solids, and have the ability to recover their original shape and dimensions on release of stress. Rubber elasticity is a property of macromolecules that are either covalently cross-linked or connected in a network by physical associations such as small glassy or crystalline domains, ionic aggregates or multiple hydrogen bonds. Covalent cross-links or strong physical associations prevent flow and creep. Here we design and synthesize molecules that associate together to form both chains and cross-links via hydrogen bonds. The system shows recoverable extensibility up to several hundred per cent and little creep under load. In striking contrast to conventional cross-linked or thermoreversible rubbers made of macromolecules, these systems, when broken or cut, can be simply repaired by bringing together fractured surfaces to self-heal at room temperature. Repaired samples recuperate their enormous extensibility. The process of breaking and healing can be repeated many times. These materials can be easily processed, re-used and recycled. Their unique self-repairing properties, the simplicity of their synthesis, their availability from renewable resources and the low cost of raw ingredients (fatty acids and urea) bode well for future applications.

Self-healing and thermoreversible rubber from supramolecular assembly

Permanently cross-linked materials have outstanding mechanical properties and solvent resistance, but they cannot be processed and reshaped once synthesized Non–cross-linked polymers and those with reversible cross-links are processable, but they are soluble We designed epoxy networks that can rearrange their topology by exchange reactions without depolymerization and showed that they are insoluble and processable Unlike organic compounds and polymers whose viscosity varies abruptly near the glass transition, these networks show Arrhenius-like gradual viscosity variations like those of vitreous silica Like silica, the materials can be wrought and welded to make complex objects by local heating without the use of molds The concept of a glass made by reversible topology freezing in epoxy networks can be readily scaled up for applications and generalized to other chemistries

Silica-Like Malleable Materials from Permanent Organic Networks

Catalytic control of bond exchange reactions enables healing of cross-linked polymer materials under a wide range of conditions. The healing capability at high temperatures is demonstrated for epoxy–acid and epoxy–anhydride thermoset networks in the presence of transesterification catalysts. At lower temperatures, the exchange reactions are very sluggish, and the materials have properties of classical epoxy thermosets. Studies of model molecules confirmed that the healing kinetics is controlled by the transesterification reaction rate. The possibility of varying the catalyst concentration brings control and flexibility of welding and assembling of epoxy thermosets that do not exist for thermoplastics.

Metal-catalyzed transesterification for healing and assembling of thermosets.

Windmills, cars, and dental restoration demand polymer materials and composites that are easy to process, assemble, and recycle while exhibiting outstanding mechanical, thermal, and chemical resistance. Vitrimers, which are polymer networks able to shuffle chemical bonds through exchange reactions, could address these demands if they were prepared from existing plastics and processed with fast production rates and current equipment. We report the metathesis of dioxaborolanes, which is rapid and thermally robust, and use it to prepare vitrimers from polymers as different as poly(methyl methacrylate), polystyrene, and high-density polyethylene that, although permanently cross-linked, can be processed multiple times by means of extrusion or injection molding. They show superior chemical resistance and dimensional stability and can be efficiently assembled. The strategy is applicable to polymers with backbones made of carbon-carbon single bonds.

Ludwik Leibler

Papers

Theory of Microphase Separation in Block Copolymers

Self-healing and thermoreversible rubber from supramolecular assembly

Silica-Like Malleable Materials from Permanent Organic Networks

Metal-catalyzed transesterification for healing and assembling of thermosets.

High-performance vitrimers from commodity thermoplastics through dioxaborolane metathesis