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.

Gold nanocages with localized surface plasmon resonance peaks in the near-infrared region exhibited a broad two-photon photoluminescence band extending from 450 to 650 nm when excited by a Ti:sapphire laser at 800 nm. The bright luminescence makes it possible to explore the use of Au nanocages as a new class of optical imaging agents for two-photon microscopy. In this work, we have demonstrated the use of two-photon microscopy as a convenient tool to directly examine the uptake of antibody-conjugated and PEGylated Au nanocages by U87MGwtEGFR cells. We have also correlated the results from two-photon microscopy with the data obtained by inductively coupled plasma mass spectrometry. Combined together, these results indicate that the antibody-conjugated Au nanocages were attached to the surface of the cells through antibody−antigen binding and then internalized into the cells via receptor-mediated endocytosis. The cellular uptake process was dependent on a number of parameters, including incubation time, inc...

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Quantifying the Cellular Uptake of Antibody-Conjugated Au Nanocages by Two-Photon Microscopy and Inductively Coupled Plasma Mass Spectrometry

To validate the importance of uniformity in pore size and structure of a scaffold for tissue engineering, we fabricated two types of scaffolds with uniform (inverse opal scaffolds) and nonuniform p...

/pdf/three-dimensional-scaffolds-for-tissue-engineering-the-1xlw8c9wsh.pdf

Three-Dimensional Scaffolds for Tissue Engineering: The Importance of Uniformity in Pore Size and Structure

The concept of shape-controlled synthesis is discussed by investigating the growth mechanisms for silver nanocubes, nanowires, and nanospheres produced through a polymer-mediated polyol process. Experimental parameters, such as the concentration of AgNO(3) (the precursor to silver), the molar ratio between poly(vinylpyrrolidone) (PVP, the capping agent) and AgNO(3), and the strength of chemical interaction between PVP and various crystallographic planes of silver, were found to determine the crystallinity of seeds (e.g., single crystal versus decahedral multiply twinned particles). In turn, the crystallinity of a seed and the extent of the PVP coverage on the seed were both instrumental in controlling the morphology of final product. The ability to generate silver nanostructures with well-defined morphologies provides a great opportunity to experimentally and systematically study the relationship between their properties and geometric shapes.

Shape-Controlled Synthesis of Metal Nanostructures: The Case of Silver

Gold(I) halides, including AuCl and AuBr, were employed for the first time as precursors in the synthesis of Au nanoparticles. The synthesis was accomplished by dissolving Au(I) halides in chloroform in the presence of alkylamines, followed by decomposition at 60 degrees C. The relative low stability of the Au(I) halides and there derivatives eliminated the need for a reducing agent, which is usually required for Au(III)-based precursors to generate Au nanoparticles. Controlled growth of Au nanoparticles with a narrow size distribution was achieved when AuCl and oleylamine were used for the synthesis. FTIR and mass spectra revealed that a complex, [AuCl(oleylamine)], was formed through coordination between oleylamine and AuCl. Thermolysis of the complex in chloroform led to the formation of dioleylamine and Au nanoparticles. When oleylamine was replaced with octadecylamine, much larger nanoparticles were obtained due to the lower stability of [AuCl(octadecylamine)] complex relative to [AuCl(oleylamine)]. Au nanoparticles can also be prepared from AuBr through thermolysis of the [AuBr(oleylamine)] complex. Due to the oxidative etching effect caused by Br(-), the nanoparticles obtained from AuBr exhibited an aspect ratio of 1.28, in contrast to 1.0 for the particles made from AuCl. Compared to the existing methods for preparing Au nanoparticles through the reduction of Au(III) compounds, this new approach based on Au(I) halides offers great flexibility in terms of size control.

/pdf/facile-synthesis-of-gold-nanoparticles-with-narrow-size-4urh2p5ovp.pdf

Younan Xia

Papers

Quantifying the Cellular Uptake of Antibody-Conjugated Au Nanocages by Two-Photon Microscopy and Inductively Coupled Plasma Mass Spectrometry

Three-Dimensional Scaffolds for Tissue Engineering: The Importance of Uniformity in Pore Size and Structure

Shape-Controlled Synthesis of Metal Nanostructures: The Case of Silver

Facile Synthesis of Gold Nanoparticles with Narrow Size Distribution by Using AuCl or AuBr as the Precursor

Assembly of Nanoparticles into Opaline Structures over Large Areas