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

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

Graphene has emerged as a subject of enormous scientific interest due to its exceptional electron transport, mechanical properties, and high surface area. When incorporated appropriately, these atomically thin carbon sheets can significantly improve physical properties of host polymers at extremely small loading. We first review production routes to exfoliated graphite with an emphasis on top-down strategies starting from graphite oxide, including advantages and disadvantages of each method. Then solvent- and melt-based strategies to disperse chemically or thermally reduced graphene oxide in polymers are discussed. Analytical techniques for characterizing particle dimensions, surface characteristics, and dispersion in matrix polymers are also introduced. We summarize electrical, thermal, mechanical, and gas barrier properties of the graphene/polymer nanocomposites. We conclude this review listing current challenges associated with processing and scalability of graphene composites and future perspectives f...

/pdf/graphene-polymer-nanocomposites-19884oy559.pdf

Graphene/Polymer Nanocomposites

Carbon nanotubes (CNTs) hold the promise of delivering exceptional mechanical properties and multi-functional characteristics. Ever-increasing interest in applying CNTs in many different fields has led to continued efforts to develop dispersion and functionalization techniques. To employ CNTs as effective reinforcement in polymer nanocomposites, proper dispersion and appropriate interfacial adhesion between the CNTs and polymer matrix have to be guaranteed. This paper reviews the current understanding of CNTs and CNT/polymer nanocomposites with two particular topics: (i) the principles and techniques for CNT dispersion and functionalization and (ii) the effects of CNT dispersion and functionalization on the properties of CNT/polymer nanocomposites. The fabrication techniques and potential applications of CNT/polymer nanocomposites are also highlighted.

Dispersion and functionalization of carbon nanotubes for polymer-based nanocomposites: a review

We present an analytical treatment of a set of coupled kinetic equations that governs the self-assembly of filamentous molecular structures. Application to the case of protein aggregation demonstrates that the kinetics of amyloid growth can often be dominated by secondary rather than by primary nucleation events. Our results further reveal a range of general features of the growth kinetics of fragmenting filamentous structures, including the existence of generic scaling laws that provide mechanistic information in contexts ranging from in vitro amyloid growth to the in vivo development of mammalian prion diseases.

http://science.sciencemag.org/content/sci/326/5959/1533.full.pdf

An analytical solution to the kinetics of breakable filament assembly

1. A bird's eye view of liquid crystal elastomers 2. Liquid crystals 3. Polymers, elastomers and rubber elasticity 4. Classical elasticity 5. Nematic elastomers 6. Nematic rubber elasticity 7. Soft elasticity 8. Distortions of nematic elastomers 9. Cholesteric elastomers 10. Continuum theory of nematic elastomers 11. Dynamics of liquid crystal elastomers 12. Smectic elastomers A. Nematic order in elastomers under strain B. Biaxial soft elasticity C. Stripe microstructure D. Couple-stress and Cosserat elasticity E. Expansion at small deformations and rotations

/pdf/liquid-crystal-elastomers-49je3ntl73.pdf

Liquid Crystal Elastomers

A requirement for the reversible mechanical actuation of liquid-crystal elastomers is macroscale alignment. However, current processing techniques do not achieve reliable and robust alignment, which limits the practical use of these materials as actuators and artificial muscles. It is now shown that by introducing polymers with exchangeable covalent bonds, liquid-crystal elastomers can be easily processed and aligned, and subsequently remodelled.

Mouldable liquid-crystalline elastomer actuators with exchangeable covalent bonds

Advances in functionality and reliability of carbon nanotube (CNT) composite materials require careful formulation of processing methods to ultimately realize the desired properties. To date, controlled dispersion of CNTs in a solution or a composite matrix remains a challenge, due to the strong van der Waals binding energies associated with the CNT aggregates. There is also insufficiently defined correlation between the microstructure and the physical properties of the composite. Here, we offer a review of the dispersion processes of pristine (non-covalently functionalized) CNTs in a solvent or a polymer solution. We summarize and adapt relevant theoretical analysis to guide the dispersion design and selection, from the processes of mixing/sonication, to the application of surfactants for stabilization, to the final testing of composite properties. The same approaches are expected to be also applicable to the fabrication of other composite materials involving homogeneously dispersed nanoparticles.

https://www.mdpi.com/2073-4360/4/1/275/pdf

Dispersion of Carbon Nanotubes: Mixing, Sonication, Stabilization, and Composite Properties

For some systems, energy from an external source can trigger changes in the internal state of the structure, leading to a mechanical response much larger than the initial input. The ability to unlock this internal work in a solid-state structure is of key importance for many potential applications. We report a novel phenomenon of photo-induced mechanical actuation observed in a polymer-nanotube composite when exposed to infrared radiation. At small strains the sample tends to expand, when stimulated by photons, by an amount that is orders of magnitude greater than the pristine polymer. Conversely, at larger applied pre-strain, it will contract under identical infrared excitation. The behaviour is modelled as a function of orientational ordering of nanotubes induced by the uniaxial extension. It is thought that no other materials can display this continuously reversible response of so large a magnitude, making rubber nanocomposites important for actuator applications.

Eugene M. Terentjev

Papers

An analytical solution to the kinetics of breakable filament assembly

Liquid Crystal Elastomers

Mouldable liquid-crystalline elastomer actuators with exchangeable covalent bonds

Dispersion of Carbon Nanotubes: Mixing, Sonication, Stabilization, and Composite Properties

Photomechanical actuation in polymer-nanotube composites.