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.

The optical properties of metal nanoparticles have long been of interest in physical chemistry, starting with Faraday's investigations of colloidal gold in the middle 1800s. More recently, new lithographic techniques as well as improvements to classical wet chemistry methods have made it possible to synthesize noble metal nanoparticles with a wide range of sizes, shapes, and dielectric environments. In this feature article, we describe recent progress in the theory of nanoparticle optical properties, particularly methods for solving Maxwell's equations for light scattering from particles of arbitrary shape in a complex environment. Included is a description of the qualitative features of dipole and quadrupole plasmon resonances for spherical particles; a discussion of analytical and numerical methods for calculating extinction and scattering cross-sections, local fields, and other optical properties for nonspherical particles; and a survey of applications to problems of recent interest involving triangula...

/pdf/the-optical-properties-of-metal-nanoparticles-the-influence-16vrpkvhkg.pdf

The Optical Properties of Metal Nanoparticles: The Influence of Size, Shape, and Dielectric Environment

The surface science of titanium dioxide

The richness of optical and electronic properties of graphene attracts enormous interest. Graphene has high mobility and optical transparency, in addition to flexibility, robustness and environmental stability. So far, the main focus has been on fundamental physics and electronic devices. However, we believe its true potential lies in photonics and optoelectronics, where the combination of its unique optical and electronic properties can be fully exploited, even in the absence of a bandgap, and the linear dispersion of the Dirac electrons enables ultrawideband tunability. The rise of graphene in photonics and optoelectronics is shown by several recent results, ranging from solar cells and light-emitting devices to touch screens, photodetectors and ultrafast lasers. Here we review the state-of-the-art in this emerging field.

/pdf/graphene-photonics-and-optoelectronics-3ddg6ukzcu.pdf

Graphene photonics and optoelectronics

Optical second-harmonic generation and sum-frequency generation as novel spectroscopic tools to probe molecular chirality are currently being developed. The latter in particular allows studies of chirality associated with both electronic and vibrational transitions of molecules in isotropic bulk, thin films, and monolayers. We review here the recent theoretical and experimental progress in the field. It is shown theoretically and experimentally that both processes can have monolayer sensitivity to detect chirality in electronic and vibrational transitions and that the sensitivity of the sum-frequency spectroscopy of chirality in vibrational transitions can be greatly enhanced through vibrational-electronic double-resonance. Measurements with short-pulsed lasers provide opportunities for time-resolved in situ studies of chirality. Contents PAGE 1. Introduction 258 2. Basics of chiral responses in SFG and SHG 259  2.1. General considerations of SFG and SHG 259  2.2. Non-linear susceptibility for an azimutha...

Non-linear optical spectroscopy as a novel probe for molecular chirality

Surface lamellar decoration (SLD), surface enhanced Raman scattering (SERS) and optical second harmonic generation (SHG) experiments have been utilized to study the molecular orientation and conformation changes at a rubbed polyimide alignment-layer surface. This aromatic polyimide containing pendent cyanobiphenyl mesogens was synthesized via a polycondensation of 2,2'-bis(3,4-dicarboxy-phenyl)hexafluoropropane dianhydride (6FDA) with bis[omega-[4-(4-cyanophenyl)phenoxy]hexyl] 4,4'-diamino-2,2'-biphenyldicarboxylate (nCBBP, n = 6), abbreviated as 6FDA--6CBBP. Uniform alignment layers, possessing high pretilt angles ranging from 39 degrees to 43 degrees, have been achieved after mechanical rubbing of the polyimide thin film surface at room temperature and subsequent annealing. This is the first time that high pretilt angles have been detected to possess a negative angle (-theta(c)) with respect to the rubbing direction (i.e., opposite to the rubbing direction), considerably different from the conventional pretilt angle (theta(c)) observed along the rubbing direction. This observation is confirmed using magnetic null and SHG methods. Combined polyethylene (PE) SLD and atomic force microscopy experiments reveal that the azimuthal orientation distribution of the long axis of the edge-on PE lamellar crystals is oriented normal to the rubbing direction, indicating that the PE chains are aligned parallel to the rubbing direction. This SLD technique probes the anisotropic surface orientation of the outermost molecules of the rubbed polyimide layer. The SERS results show that prior to rubbing the surface, both the pendent cyanobiphenyls in the side chains and backbones possess nearly planar chain conformations at the polyimide surface. Mechanical rubbing causes not only tilting of the backbone moieties, such as imide-phenylene structure, but also significant conformational rearrangements of the pendent side chains at the surfaces. The molecular mechanism of this unusual alignment is due to the fact that the pendent cyanobiphenyls forms a uniformly tilted conformation on the rubbed surface, and the polar cyano groups point down toward the layer surface deduced from SHG phase measurements. This conformational rearrangement of the side chains results in the formation of fold-like bent structures on the surface, which directly leads to the long axis of cyanobiphenyls having the -theta(c) pretilt angle with respect to the rubbing direction.

Rubbing-Induced Molecular Reorientation on an Alignment Surface of an Aromatic Polyimide Containing Cyanobiphenyl Side Chains

We have studied theoretically and experimentally the dynamic behavior of a nonlinear Fabry-Perot interferrometer filled with a Kerr medium. The Fabry-Perot responses ranging from extremely transient to quasi-steady-state in various modes of operation are considered. The experimental results are in excellent agreement with theory. It is shown that the quasi-steady-state operation requires not only a medium response time much smaller than the cavity round-trip time, but also a characteristic time of the input intensity variation several hundred times larger than the cavity round-trip time. Even in the quasi-steady-state limit, optical switching is often featured by overshoot and ringing after switching. The switching speed is limited by the cavity buildup time.

/pdf/theoretical-and-experimental-study-of-the-dynamic-behavior-480if59pck.pdf

Theoretical and experimental study of the dynamic behavior of a nonlinear Fabry-Perot interferrometer

Electrostriction, optical Kerr effect and self-focusing of laser beams

Molecular Characterization of Polymer and Polymer Blend Surfaces. Combined Sum Frequency Generation Surface Vibrational Spectroscopy and Scanning Force Microscopy Studies

Y. R. Shen

Papers

Non-linear optical spectroscopy as a novel probe for molecular chirality

Rubbing-Induced Molecular Reorientation on an Alignment Surface of an Aromatic Polyimide Containing Cyanobiphenyl Side Chains

Theoretical and experimental study of the dynamic behavior of a nonlinear Fabry-Perot interferrometer

Electrostriction, optical Kerr effect and self-focusing of laser beams

Molecular Characterization of Polymer and Polymer Blend Surfaces. Combined Sum Frequency Generation Surface Vibrational Spectroscopy and Scanning Force Microscopy Studies