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

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

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

Although gold is the subject of one of the most ancient themes of investigation in science, its renaissance now leads to an exponentially increasing number of publications, especially in the context of emerging nanoscience and nanotechnology with nanoparticles and self-assembled monolayers (SAMs). We will limit the present review to gold nanoparticles (AuNPs), also called gold colloids. AuNPs are the most stable metal nanoparticles, and they present fascinating aspects such as their assembly of multiple types involving materials science, the behavior of the individual particles, size-related electronic, magnetic and optical properties (quantum size effect), and their applications to catalysis and biology. Their promises are in these fields as well as in the bottom-up approach of nanotechnology, and they will be key materials and building block in the 21st century. Whereas the extraction of gold started in the 5th millennium B.C. near Varna (Bulgaria) and reached 10 tons per year in Egypt around 1200-1300 B.C. when the marvelous statue of Touthankamon was constructed, it is probable that “soluble” gold appeared around the 5th or 4th century B.C. in Egypt and China. In antiquity, materials were used in an ecological sense for both aesthetic and curative purposes. Colloidal gold was used to make ruby glass 293 Chem. Rev. 2004, 104, 293−346

Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology.

We report a polyol method based on diethylene glycol for the synthesis of Pd icosahedral nanocrystals with uniform sizes controllable in the range of 7–20 nm. Our mechanistic study indicates that Ostwald ripening plays a vital role in the homogeneous nucleation and growth of Pd icosahedral nanocrystals with uniform sizes. As a result of the “size focusing” effect facilitated by Ostwald ripening, the broad distribution in size can be quickly narrowed to generate uniform particles with sizes up to 11 nm depending on the reduction kinetics and duration of reaction time. To obtain particles with larger sizes, one has to rely on seed-mediated growth, with the uniform icosahedral nanocrystals obtained through Ostwald ripening serving as the seeds. In such a synthesis, it is vital to suppress homogeneous nucleation while promoting heterogeneous nucleation and layer-by-layer growth. Experimentally, this condition can be accomplished by adding a PdBr42– solution in one shot for the production of Pd icosahedral nanocrystals with uniform sizes up to 20 nm. The size can be tuned by simply controlling the growth time and/or the amount of the precursor involved in the growth step. These strategies built upon the mechanistic understanding are expected to be extendable to other noble metals, providing a robust and viable route to the synthesis of icosahedral nanocrystals with uniform sizes controllable over a broad range for fundamental studies and catalytic applications. 

Polyol Synthesis of Pd Icosahedral Nanocrystals: Insights into the Growth Mechanism and Size Control

Core-shell nanostructures with platinum overlayers conformally coating palladium nano-substrate cores and facile solution-based methods for the preparation of such core-shell nanostructures are described herein. The obtained Pd@Pt core-shell nanocatalysts showed enhanced specific and mass activities towards oxygen reduction, compared to a commercial Pt/C catalyst.

Layered platinum on freestanding palladium nano-substrates for electrocatalytic applications and methods of making thereof

The new class of contrast enhancement agents can be precisely tuned to aid in vivo photoacoustic tomography.

Improving biomedical imaging with gold nanocages.

This paper describes a solution-phase route to the large-scale synthesis of silver nanowires with diameters in the range of 30-40 nm, and lengths up to ~50 m. The initial step of this synthesis involved the formation of Pt nanoparticles by reducing PtCl 2 with ethylene glycol (EG) refluxed at ~160 o C. These Pt nanoparticles could serve as seeds for the growth of silver (formed by reducing AgNO 3 with EG) through heterogeneous nucleation process because their crystal structures and lattice constants matched closely. In the presence of poly(vinyl pyrrolidone) (PVP), the growth of silver could be led to a highly anisotropic mode with formation of uniform nanowires. UV-visible spectroscopy was used to track the growth process of silver nanowires because different silver nanostructures exhibited distinctive surface plasmon resonance peaks at different frequencies. SEM, TEM, XRD, and electron diffraction were used to characterize these silver nanowires, indicating the formation of a highly pure face-centered cubic phase, as well as uniform diameter and bicrystalline structure. The morphology of these silver nanostructures could be varied from particles and rods to long wires by tuning the reaction conditions, including reaction temperature, and the ratio of PVP to silver nitrate. These silver nanowires could be used as sacrificial templates to synthesize gold nanotubes via a template-engaged replacement reaction. The dispersion of gold nanotubes exhibited a strong extinction peak in the red regime, which was around 760 nm. Keywords: Silver nanowires, seeded-growth, gold nanotubes, surface plasmon resonance

Younan Xia

Papers

Polyol Synthesis of Pd Icosahedral Nanocrystals: Insights into the Growth Mechanism and Size Control

Layered platinum on freestanding palladium nano-substrates for electrocatalytic applications and methods of making thereof

Improving biomedical imaging with gold nanocages.

Synthesis and Optical Properties of Silver Bicrystalline Nanowires

Electrospinning nanofibers with controlled structures and complex architectures