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

New materials hold the key to fundamental advances in energy conversion and storage, both of which are vital in order to meet the challenge of global warming and the finite nature of fossil fuels. Nanomaterials in particular offer unique properties or combinations of properties as electrodes and electrolytes in a range of energy devices. This review describes some recent developments in the discovery of nanoelectrolytes and nanoelectrodes for lithium batteries, fuel cells and supercapacitors. The advantages and disadvantages of the nanoscale in materials design for such devices are highlighted.

https://img62.chem17.com/1/20140715/635410323829886334962.pdf

Nanostructured materials for advanced energy conversion and storage devices

2.1. Solvents 4307 2.1.1. Propylene Carbonate (PC) 4308 2.1.2. Ethers 4308 2.1.3. Ethylene Carbonate (EC) 4309 2.1.4. Linear Dialkyl Carbonates 4310 2.2. Lithium Salts 4310 2.2.1. Lithium Perchlorate (LiClO4) 4311 2.2.2. Lithium Hexafluoroarsenate (LiAsF6) 4312 2.2.3. Lithium Tetrafluoroborate (LiBF4) 4312 2.2.4. Lithium Trifluoromethanesulfonate (LiTf) 4312 2.2.5. Lithium Bis(trifluoromethanesulfonyl)imide (LiIm) and Its Derivatives 4313

/pdf/nonaqueous-liquid-electrolytes-for-lithium-based-uxm5ffbi18.pdf

Nonaqueous liquid electrolytes for lithium-based rechargeable batteries.

The Li-S battery has been under intense scrutiny for over two decades, as it offers the possibility of high gravimetric capacities and theoretical energy densities ranging up to a factor of five beyond conventional Li-ion systems. Herein, we report the feasibility to approach such capacities by creating highly ordered interwoven composites. The conductive mesoporous carbon framework precisely constrains sulphur nanofiller growth within its channels and generates essential electrical contact to the insulating sulphur. The structure provides access to Li+ ingress/egress for reactivity with the sulphur, and we speculate that the kinetic inhibition to diffusion within the framework and the sorption properties of the carbon aid in trapping the polysulphides formed during redox. Polymer modification of the carbon surface further provides a chemical gradient that retards diffusion of these large anions out of the electrode, thus facilitating more complete reaction. Reversible capacities up to 1,320 mA h g(-1) are attained. The assembly process is simple and broadly applicable, conceptually providing new opportunities for materials scientists for tailored design that can be extended to many different electrode materials.

http://dns2.asia.edu.tw/~ysho/YSHO-English/1000%20WC/PDF/Nat%20Mat8,%20500.pdf

A highly ordered nanostructured carbon–sulphur cathode for lithium–sulphur batteries

Glasses can be formed by many routes. In some cases, distinct polyamorphic forms are found. The normal mode of glass formation is cooling of a viscous liquid. Liquid behavior during cooling is classified between "strong" and "fragile," and the three canonical characteristics of relaxing liquids are correlated through the fragility. Strong liquids become fragile liquids on compression. In some cases, such conversions occur during cooling by a weak first-order transition. This behavior can be related to the polymorphism in a glass state through a recent simple modification of the van der Waals model for tetrahedrally bonded liquids. The sudden loss of some liquid degrees of freedom through such first-order transitions is suggestive of the polyamorphic transition between native and denatured hydrated proteins, which can be interpreted as single-chain glass-forming polymers plasticized by water and cross-linked by hydrogen bonds. The onset of a sharp change in d dT( is the Debye-Waller factor and T is temperature) in proteins, which is controversially indentified with the glass transition in liquids, is shown to be general for glass formers and observable in computer simulations of strong and fragile ionic liquids, where it proves to be close to the experimental glass transition temperature. The latter may originate in strong anharmonicity in modes ("bosons"), which permits the system to access multiple minima of its configuration space. These modes, the Kauzmann temperature T(K), and the fragility of the liquid, may thus be connected.

https://science.sciencemag.org/content/sci/267/5206/1924.full.pdf

Formation of glasses from liquids and biopolymers.

Deviations from thermally activated and from exponential response are typical features of the vitrification phenomenon and previously have been studied using viscoelastic, dielectric, calorimetric, optical, and other techniques. Linear response data from literature on about 70 covalent glass formers, ionic melts, supercooled liquids, amorphous polymers, and glassy crystals are surveyed. Except for orientational glasses and monohydric aliphatic alcohols a distinct but broad correlation of non‐Debye behavior with non‐Arrhenius relaxations is found. Within the broad trend several groups of materials, distinguished by their respective molecular complexity, can be identified and are shown to exhibit narrow correlations. At a given degree of deviation from Arrhenius behavior externally imposed stresses are relaxed with a departure from exponential behavior which is stronger the more the molecular or atomic subunits of the glassforming material are interconnected with each other.

Nonexponential relaxations in strong and fragile glass formers

The field of viscous liquid and glassy solid dynamics is reviewed by a process of posing the key questions that need to be answered, and then providing the best answers available to the authors and their advisors at this time. The subject is divided into four parts, three of them dealing with behavior in different domains of temperature with respect to the glass transition temperature, Tg , and a fourth dealing with ‘‘short time processes.’’ The first part tackles the high temperature regime T.Tg ,i n which the system is ergodic and the evolution of the viscous liquid toward the condition at Tg is in focus. The second part deals with the regime T;Tg , where the system is nonergodic except for very long annealing times, hence has time-dependent properties ~aging and annealing!. The third part discusses behavior when the system is completely frozen with respect to the primary relaxation process but in which secondary processes, particularly those responsible for ‘‘superionic’’ conductivity, and dopart mobility in amorphous silicon, remain active. In the fourth part we focus on the behavior of the system at the crossover between the low frequency vibrational components of the molecular motion and its high frequency relaxational components, paying particular attention to very recent developments in the short time dielectric response and the high Q mechanical response. © 2000 American Institute of Physics.@S0021-8979~00!02213-1#

https://lib.dr.iastate.edu/cgi/viewcontent.cgi?article=1065&context=mse_pubs

Relaxation in glassforming liquids and amorphous solids

An overview of relaxational phenomenology is given in a manner intended to highlight a number of the important problems which, notwithstanding much recent sophisticated investigation, continue to confront the field. The rapidly lengthening timescale for diffusional and/or reorientational motion, which provokes the glass transition, is examined within the framework of the ‘strong’ and ‘fragile’ classification of both liquids and plastic crystals. The behavior patterns observed are related to the topological features of the potential energy hypersurfaces which may characterize each extreme. In view of the implication that the observed glass transition is the kinetically obscured reflection of an underlying higher order thermodynamic transition which could be associated with a diverging length scale (at least for fragile systems), the problem of the basic diffusional length scale at the glass transition, using a probe molecule approach, is considered. Then, details of the kinetics of relaxation under isothermal conditions are reviewed to decide on the range of deviations from Debye behavior which may be encountered. A correlation with fragility is strongly indicated. The phenomena of serial decoupling of relaxational modes from the main structural relaxation as T g is approached is outlined and, finally, the additional phenomena that may be encountered in experiments that explore the state-dependence (or non-linearity) of relaxation are briefly examined.

Relaxation in liquids, polymers and plastic crystals — strong/fragile patterns and problems☆

Selected aspects of recent progress in the study of supercooled liquids and glasses are presented in this review. As an introduction for nonspecialists, several basic features of the dynamics and thermodynamics of supercooled liquids and glasses are described. Among these are nonexponential relaxation functions, non-Arrhenius temperature dependences, and the Kauzmann temperature. Various theoretical models which attempt to explain these basic features are presented next. These models are conveniently categorized according to the temperature regimes deemed important by their authors. The major portion of this review is given to a summary of current experimental and computational research. The utility of mode coupling theory is addressed. Evidence is discussed for new relaxation mechanisms and new time and length scales in supercooled liquids. Relaxations in the glassy state and significance of the “boson peak” are also addressed.

Charles Angell

Papers

Formation of glasses from liquids and biopolymers.

Nonexponential relaxations in strong and fragile glass formers

Relaxation in glassforming liquids and amorphous solids

Relaxation in liquids, polymers and plastic crystals — strong/fragile patterns and problems☆

Supercooled Liquids and Glasses