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

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.

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

Fundamentals of Plasmonics.- Electromagnetics of Metals.- Surface Plasmon Polaritons at Metal / Insulator Interfaces.- Excitation of Surface Plasmon Polaritons at Planar Interfaces.- Imaging Surface Plasmon Polariton Propagation.- Localized Surface Plasmons.- Electromagnetic Surface Modes at Low Frequencies.- Applications.- Plasmon Waveguides.- Transmission of Radiation Through Apertures and Films.- Enhancement of Emissive Processes and Nonlinearities.- Spectroscopy and Sensing.- Metamaterials and Imaging with Surface Plasmon Polaritons.- Concluding Remarks.

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Plasmonics: Fundamentals and Applications

The interest in nanoscale materials stems from the fact that new properties are acquired at this length scale and, equally important, that these properties * To whom correspondence should be addressed. Phone, 404-8940292; fax, 404-894-0294; e-mail, mostafa.el-sayed@ chemistry.gatech.edu. † Case Western Reserve UniversitysMillis 2258. ‡ Phone, 216-368-5918; fax, 216-368-3006; e-mail, burda@case.edu. § Georgia Institute of Technology. 1025 Chem. Rev. 2005, 105, 1025−1102

Chemistry and properties of nanocrystals of different shapes.

Arrays of circular pores in silicon can exhibit a phononic bandgap when the lattice constant is smaller than the phonon scattering length, and so have become of interest for use as thermoelectric materials, due to the large reduction in thermal conductivity that this bandgap can cause. The reduction in electrical conductivity is expected to be less, because the lattice constant of these arrays is engineered to be much larger than the electron scattering length. As a result, electron transport through the effective medium is well described by the diffusion equation, and the Seebeck coefficient is expected to increase. In this paper, we develop an expression for the purely diffusive thermal (or electrical) conductivity of a composite comprised of square or hexagonal arrays of parallel circular or elliptic cylinders of one material in a continuum of a second material. The transport parallel to the cylinders is straightforward, so we consider the transport in the two principal directions normal to the cylinders, using a self-consistent local field calculation based on the point dipole approximation. There are two limiting cases: large negative contrast (e.g., pores in a conductor) and large positive contrast (conducting pillars in air). In the large negative contrast case, the transport is only slightly affected parallel to the major axis of the elliptic cylinders but can be significantly affected parallel to the minor axis, even in the limit of zero volume fraction of pores. The positive contrast case is just the opposite: the transport is only slightly affected parallel to the minor axis of the pillars but can be significantly affected parallel to the major axis, even in the limit of zero volume fraction of pillars. The analytical results are compared to extensive FEA calculations obtained using Comsol™ and the agreement is generally very good, provided the cylinders are sufficiently small compared to the lattice constant.

Anisotropic charge and heat conduction through arrays of parallel elliptic cylinders in a continuous medium.

Apart from linear polymers, the dynamic properties of fractal structures are essentially unexplored. This paucity of data is due to the fact that dynamic light scattering, the technique of choice for such studies, is expected to display unique features only for objects which are fractal over dimensional scales comparable to the wavelength of light (5000A). Recently, however, colloidal aggregates were shown 1 both to be fractal over lengths up to and to display interesting dynamics. (2) Our purpose here is not only to discuss the dynamics of such aggregates, but also to review the results for polymers and colloidal particles. In all cases, these systems are studied in a dilute suspension by quasi-elastic light scattering.

Dynamics of Fractals

We have conducted a real time, two-dimensional light scattering study of the nonlinear dynamics of field-induced structures in an electrorheological fluid subjected to oscillatory shear. We have developed a kinetic chain model of the observed dynamics by considering the response of a fragmenting/aggregating particle chain to the prevailing hydrodynamic and electrostatic forces. This structural theory is then used to describe the nonlinear rheology of ER fluids.

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Light scattering studies of an electrorheological fluid in oscillatory shear

Patterning Surfaces for High Resolution Self Alignment

We report a real-time, two-dimensional light scattering study of the evolution of structure in a concentrated electrorheological fluid during the 'liquid-solid' phase transition. We find that after particle chaining along the electric field lines, strong light scattering lobes appear at a finite scattering wavevector q orthogonal to the field lines, and then brighten as they move to q=O. This indicates the existence of an unstable concentration fluctuation that signifies the segregation of chains into columns. In fact, the observed growth kinetics of the characteristic length, as well as the form of the structure factor, are qualitatively similar to two-dimensional spinodal decomposition in a system with a conserved order parameter.

James E. Martin

Papers

Anisotropic charge and heat conduction through arrays of parallel elliptic cylinders in a continuous medium.

Dynamics of Fractals

Light scattering studies of an electrorheological fluid in oscillatory shear

Patterning Surfaces for High Resolution Self Alignment

Coarsening of a quiescent electrorheological fluid I: Experiment