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

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.

Semiconductor nanocrystals were prepared for use as fluorescent probes in biological staining and diagnostics. Compared with conventional fluorophores, the nanocrystals have a narrow, tunable, symmetric emission spectrum and are photochemically stable. The advantages of the broad, continuous excitation spectrum were demonstrated in a dual-emission, single-excitation labeling experiment on mouse fibroblasts. These nanocrystal probes are thus complementary and in some cases may be superior to existing fluorophores.

https://science.sciencemag.org/content/sci/281/5385/2013.full.pdf

Semiconductor Nanocrystals as Fluorescent Biological Labels

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Self-assembled monolayers of thiolates on metals as a form of nanotechnology.

The use of optical measurements to monitor electrochemical changes on the surface of nanosized metal particles is discussed within the Drude model. The absorption spectrum of a metal sol in water is shown to be strongly affected by cathodic or anodic polarization, chemisorption, metal adatom deposition, and alloying. Anion adsorption leads to strong damping of the free electron absorption. Cathodic polarization leads to anion desorption. Underpotential deposition (upd) of electropositive metal layers results in dramatic blue-shifts of the surface plasmon band of the substrate. The deposition of just 0.1 monolayer can be readily detected by eye. In some cases alloying occurs spontaneously during upd. Alloy formation can be ascertained from the optical absorption spectrum in the case of gold deposition onto silver sols. The underpotential deposition of silver adatoms onto palladium leads to the formation of a homogeneous silver shell, but the mean free path is less than predicted, due to lattice strain in t...

Surface Plasmon Spectroscopy of Nanosized Metal Particles

A method to determine the spring constant of a rectangular atomic force microscope cantilever is proposed that relies solely on the measurement of the resonant frequency and quality factor of the cantilever in fluid (typically air), and knowledge of its plan view dimensions. This method gives very good accuracy and improves upon the previous formulation by Sader et al. [Rev. Sci. Instrum. 66, 3789 (1995)] which, unlike the present method, requires knowledge of both the cantilever density and thickness.

/pdf/calibration-of-rectangular-atomic-force-microscope-290lry8thn.pdf

Calibration of rectangular atomic force microscope cantilevers

Gold nanorods: Synthesis, characterization and applications

Gold colloids have been homogeneously coated with silica using the silane coupling agent (3-aminopropyl)trimethoxysilane as a primer to render the gold surface vitreophilic. After the formation of a thin silica layer in aqueous solution, the particles can be transferred into ethanol for further growth using the Stober method. The thickness of the silica layer can be completely controlled, and (after surface modification) the particles can be transferred into practically any solvent. Varying the silica shell thickness and the refractive index of the solvent allows control over the optical properties of the dispersions. The optical spectra of the coated particles are in good agreement with calculations using Mie's theory for core−shell particles.

http://nathan.instras.com/documentDB/paper-29.pdf

Synthesis of Nanosized Gold−Silica Core−Shell Particles

In this tutorial review, we summarise recent research into the controlled growth of gold nanoparticles of different morphologies and discuss the various chemical mechanisms that have been proposed to explain anisotropic growth. With the overview and discussion, we intended to select those published procedures that we consider more reliable and promising for synthesis of morphologies of interest. We expect this to be interesting to researchers in the wide variety of fields that can make use of metal nanoparticles.

Paul Mulvaney

Papers

Surface Plasmon Spectroscopy of Nanosized Metal Particles

Calibration of rectangular atomic force microscope cantilevers

Gold nanorods: Synthesis, characterization and applications

Synthesis of Nanosized Gold−Silica Core−Shell Particles

Shape control in gold nanoparticle synthesis