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

A software package for the analysis of X-ray absorption spectroscopy (XAS) data is presented. This package is based on the IFEFFIT library of numerical and XAS algorithms and is written in the Perl programming language using the Perl/Tk graphics toolkit. The programs described here are: (i) ATHENA, a program for XAS data processing, (ii) ARTEMIS, a program for EXAFS data analysis using theoretical standards from FEFF and (iii) HEPHAESTUS, a collection of beamline utilities based on tables of atomic absorption data. These programs enable high-quality data analysis that is accessible to novices while still powerful enough to meet the demands of an expert practitioner. The programs run on all major computer platforms and are freely available under the terms of a free software license.

http://cars9.uchicago.edu/xafs_school/Material/Articles/Horae%20JSR2005.pdf

ATHENA, ARTEMIS, HEPHAESTUS: data analysis for X-ray absorption spectroscopy using IFEFFIT.

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.

5.1. Nanoalloys of Group 11 (Cu, Ag, Au) 865 5.1.1. Cu−Ag 866 5.1.2. Cu−Au 867 5.1.3. Ag−Au 870 5.1.4. Cu−Ag−Au 872 5.2. Nanoalloys of Group 10 (Ni, Pd, Pt) 872 5.2.1. Ni−Pd 872 * To whom correspondence should be addressed. Phone: +39010 3536214. Fax:+39010 311066. E-mail: ferrando@fisica.unige.it. † Universita di Genova. ‡ Argonne National Laboratory. § University of Birmingham. | As of October 1, 2007, Chemical Sciences and Engineering Division. Volume 108, Number 3

Nanoalloys: From Theory to Applications of Alloy Clusters and Nanoparticles

The emergence of semiconductor nanocrystals as the building blocks of nanotechnology has opened up new ways to utilize them in next generation solar cells. This paper focuses on the recent developments in the utilization of semiconductor quantum dots for light energy conversion. Three major ways to utilize semiconductor dots in solar cell include (i) metal−semiconductor or Schottky junction photovoltaic cell (ii) polymer−semiconductor hybrid solar cell, and (iii) quantum dot sensitized solar cell. Modulation of band energies through size control offers new ways to control photoresponse and photoconversion efficiency of the solar cell. Various strategies to maximize photoinduced charge separation and electron transfer processes for improving the overall efficiency of light energy conversion are discussed. Capture and transport of charge carriers within the semiconductor nanocrystal network to achieve efficient charge separation at the electrode surface remains a major challenge. Directing the future resear...

http://wiki.phy.queensu.ca/shughes/images/d/d1/Quantum_Dot_Solar_Cells._Semiconductor_Nanocrystals_as_Light_Harvesters.pdf

Quantum Dot Solar Cells. Semiconductor Nanocrystals as Light Harvesters

Single-Walled Carbon Nanotube–CdS Nanocomposites as Light-Harvesting Assemblies: Photoinduced Charge-Transfer Interactions†

We report on systematic studies of size-dependent alloy formation of silver-coated gold nanoparticles (NPs) in aqueous solution at ambient temperature using X-ray absorption fine structure spectroscopy (XAFS). Various Au-core sizes (2.5−20 nm diameter) and Ag shell thicknesses were synthesized using radiolytic wet techniques. The equilibrium structures (alloy versus core−shell) of these NPs were determined in the suspensions. We observed remarkable size dependence in the room temperature interdiffusion of the two metals. The interdiffusion is limited to the subinterface layers of the bimetallic NPs and depends on both the core size and the total particle size. For the very small particles (≤4.6 nm initial Au-core size), the two metals are nearly randomly distributed within the particle. However, even for these small Au-core NPs, the interdiffusion occurs primarily in the vicinity of the original interface. Features from the Ag shells do remain. For the larger particles, the boundary is maintained to withi...

Size-dependent spontaneous alloying of Au-Ag nanoparticles.

X-ray absorption fine structure determination of pH-dependent U-bacterial cell wall interactions

Adsorption of cadmium to Bacillus subtilis bacterial cell walls: a pH-dependent X-ray absorption fine structure spectroscopy study

Molecular dynamics simulation is used to study the mechanisms involved in the adsorption of various ions to the basal surfaces of kaolinite. Analysis of simulation data indicates that cations and anions adsorb preferably on the siloxane and gibbsite surfaces of kaolinite, respectively. Strong inner-sphere adsorption of chlorine at aluminum vacancies on the gibbsite surface and the occurrence of chlorine-driven inner-sphere adsorption of cesium and sodium on the gibbsite surface for high ionic strengths are observed. Cesium ions form strong inner-sphere complexes at ditrigonal cavities on the siloxane surface. Outer-sphere cesium is highly mobile and only weak adsorption may occur. A small amount of sodium adsorbs on the siloxane surface as inner-sphere complexes at less clearly defined sites. Like cesium, sodium only forms very weak outer-sphere complexes on this surface. Inner-sphere complexes of cadmium and lead do not occur on either surface. Relatively strong outer-sphere cadmium and lead complexes are present on the siloxane surface at ditrigonal cavities.

Bruce A. Bunker

Papers

Single-Walled Carbon Nanotube–CdS Nanocomposites as Light-Harvesting Assemblies: Photoinduced Charge-Transfer Interactions†

Size-dependent spontaneous alloying of Au-Ag nanoparticles.

X-ray absorption fine structure determination of pH-dependent U-bacterial cell wall interactions

Adsorption of cadmium to Bacillus subtilis bacterial cell walls: a pH-dependent X-ray absorption fine structure spectroscopy study

Molecular Dynamics Modeling of Ion Adsorption to the Basal Surfaces of Kaolinite