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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

The influence of diet on the distribution of nitrogen isotopes in animals was investigated by analyzing animals grown in the laboratory on diets of constant nitrogen isotopic composition. 
The isotopic composition of the nitrogen in an animal reflects the nitrogen isotopic composition of its diet. The δ^(15)N values of the whole bodies of animals are usually more positive than those of their diets. Different individuals of a species raised on the same diet can have significantly different δ^(15)N values. The variability of the relationship between the δ^(15)N values of animals and their diets is greater for different species raised on the same diet than for the same species raised on different diets. Different tissues of mice are also enriched in ^(15)N relative to the diet, with the difference between the δ^(15)N values of a tissue and the diet depending on both the kind of tissue and the diet involved. The δ^(15)N values of collagen and chitin, biochemical components that are often preserved in fossil animal remains, are also related to the δ^(15)N value of the diet. 
The dependence of the δ^(15)N values of whole animals and their tissues and biochemical components on the δ^(15)N value of diet indicates that the isotopic composition of animal nitrogen can be used to obtain information about an animal's diet if its potential food sources had different δ^(15)N values. The nitrogen isotopic method of dietary analysis probably can be used to estimate the relative use of legumes vs non-legumes or of aquatic vs terrestrial organisms as food sources for extant and fossil animals. However, the method probably will not be applicable in those modern ecosystems in which the use of chemical fertilizers has influenced the distribution of nitrogen isotopes in food sources. 
The isotopic method of dietary analysis was used to reconstruct changes in the diet of the human population that occupied the Tehuacan Valley of Mexico over a 7000 yr span. Variations in the δ^(15)C and δ^(15)N values of bone collagen suggest that C_4 and/or CAM plants (presumably mostly corn) and legumes (presumably mostly beans) were introduced into the diet much earlier than suggested by conventional archaeological analysis.

Influence of Diet On the Distribtion of Nitrogen Isotopes in Animals

The Huisgen 1,3-dipolar cycloaddition reaction of organic azides and alkynes has gained considerable attention in recent years due to the introduction in 2001 of Cu(1) catalysis by Tornoe and Meldal, leading to a major improvement in both rate and regioselectivity of the reaction, as realized independently by the Meldal and the Sharpless laboratories. The great success of the Cu(1) catalyzed reaction is rooted in the fact that it is a virtually quantitative, very robust, insensitive, general, and orthogonal ligation reaction, suitable for even biomolecular ligation and in vivo tagging or as a polymerization reaction for synthesis of long linear polymers. The triazole formed is essentially chemically inert to reactive conditions, e.g. oxidation, reduction, and hydrolysis, and has an intermediate polarity with a dipolar moment of ∼5 D. The basis for the unique properties and rate enhancement for triazole formation under Cu(1) catalysis should be found in the high ∆G of the reaction in combination with the low character of polarity of the dipole of the noncatalyzed thermal reaction, which leads to a considerable activation barrier. In order to understand the reaction in detail, it therefore seems important to spend a moment to consider the structural and mechanistic aspects of the catalysis. The reaction is quite insensitive to reaction conditions as long as Cu(1) is present and may be performed in an aqueous or organic environment both in solution and on solid support.

Cu-catalyzed azide-alkyne cycloaddition.

Insights into the Nanostructure, Solvation, and Dynamics of Liquid Electrolytes through Small-Angle X-Ray Scattering

A multilayer coating of Ni/Cu/Al was fabricated on magnesium substrates using laser cladding. The solidification behavior and the phase evolution of the compositionally graded coating were studied. The results of the X-ray diffraction (XRD) analysis together with the metallographic study showed that a series of phase evolutions had occurred along the gradient (Mg) → (Mg) + Al12Mg17 → (Mg) + Q + λ2 → λ1 → λ1 + γ1 → γ1 + (Cu) + λ1 → (Cu) + λ1 → (Cu) → (CuNi) → (Ni). The rapid solidification condition had suppressed the invariant reactions that existed in the ternary Mg-Al-Cu alloy system. As a result, many of the predicted Al-rich brittle intermetallic compounds, which are detrimental to the performance of the coating, were not produced. The solidification path during the laser cladding of the Al and Cu layers was determined and the various phases, as predicted by the corresponding phase diagram, agreed well with the experimental results. Finally, the primary arm spacing (PAS) and the solidification morphology of the dendrites in the Cu and Ni layers were analyzed in relation to the solidification conditions.

Microstructure and Phase Evolution in Laser Cladding of Ni/Cu/Al Multilayer on Magnesium Substrates

Phase change memory (PCM) has great potential for the next-generation nonvolatile memory technology, in which Ge2Sb2Te5 (GST) alloy is commonly used. However, poor thermal stability and short devic...

Atomic-Scale Observation of Carbon Distribution in High-Performance Carbon-Doped Ge2Sb2Te5 and Its Influence on Crystallization Behavior

Efficient activation of oxone by pyrite for the degradation of propanil: Kinetics and degradation pathway.

Herzberg staining, a quick and convenient tool for distinguishing non-wood fibers from wood pulp, and Raman spectroscopy were employed to investigate three paper currencies issued under the reign of the Chinese Ming and Qing Emperors between 15th and 19th centuries - da ming bao chao (AMS C-14 Date: 1410-1435 AD, ±1σ) from the Early Ming Dynasty (1405–1433 AD) and da qing bao chao (1859 AD) and hu bu guan piao (1854–1858 AD) from the Late Qing Dynasty (1840–1911 AD). Fiber staining and microscopic examination revealed a predominance of bast fiber from probably mulberry trees and very few cotton fibers (supposed to be environment contamination) in da ming bao chao; fibers in da qing bao chao and hu bu guan piao turned out to be quite pure, which are also bast fibers but very likely came from ramie and paper mulberry trees, respectively.



Raman analysis of red, blue, and black pigments on the investigated paper currencies showed that: (1) The reddish seal on da ming bao chao is not a vermilion (HgS) paste, as it is traditionally assumed, but instead a red lead (or minium, Pb3O4) one. The red pigments on both da qing bao chao and hu bu guan piao are vermilion (HgS). (2) Prussian blue (Fe7(CN)18⋅14-16H2O), a Western pigment, was identified as blue on both da qing bao chao and hu bu guan piao. (3) The black pigment on all these three paper currencies is amorphous carbon from soot. (4) Raman analysis of evenly distributed white pigment particles among the fibers in da qing bao chao confirmed the use of calcium carbonate (CaCO3) as coating pigment or fillers. Both microscopic examination of stained fibers and Raman analysis allowed, for the first time, the understanding of fiber and pigment use in producing ancient Chinese paper currencies. Copyright © 2013 John Wiley & Sons, Ltd.

Tao Li

Papers

Insights into the Nanostructure, Solvation, and Dynamics of Liquid Electrolytes through Small-Angle X-Ray Scattering

Microstructure and Phase Evolution in Laser Cladding of Ni/Cu/Al Multilayer on Magnesium Substrates

Atomic-Scale Observation of Carbon Distribution in High-Performance Carbon-Doped Ge2Sb2Te5 and Its Influence on Crystallization Behavior

Efficient activation of oxone by pyrite for the degradation of propanil: Kinetics and degradation pathway.

Technical investigation of 15th and 19th century Chinese paper currencies: Fiber use and pigment identification