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...

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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.

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Graphene photonics and optoelectronics

Monolithic integrated photoelectrochemical devices consisting of semiconductors and co-catalysts have always been restricted by the trade-off between light absorption and catalytic activity upon frontside illumination. Herein, we proposed a facile strategy to spatio-selectively deposit Pt catalyst on the top of p-Si micro-pyramids, which not only enables substantial light absorption but also immensely boosts the charge transport and mass transfer. With the help of dark-field microscopy and microscopic photocurrent mapping, it is revealed that the top of p-Si micro-pyramids is an ideal electron-migration channel for efficient charge carrier extraction. This spatio-selective strategy affords the Si photocathode to achieve a high applied bias photon-to-current efficiency of 3.84% for hydrogen production, significantly greater than the control sample with the same amount of Pt catalyst deposited uniformly on the same substrates (0.04%).

Enhanced solar hydrogen production by manipulating the spatial distribution of Pt catalyst onto Si micro-pyramid arrays

We propose SPHARM-OT, an enhanced spherical harmonic (SPHARM) surface modeling method using optimal transport (OT) for spherical parameterization. To demonstrate its effectiveness, we apply it to shape analysis of amygdala atrophy in Alzheimer’s disease (AD). Of note, identifying morphological abnormalities of medial temporal structures such as hippocampus and amygdala is an important research topic for early diagnosis of AD. Our empirical study includes two steps: (1) the newly proposed SPHARM-OT method is used to model amygdala shapes of 101 participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI); (2) using the random field theory to perform surface-based statistical analysis for detecting shape changes between cognitively normal (CN) and AD participants. We demonstrate that (1) the new SPHARM-OT method could effectively reduce surface mapping distortion and lead to a more accurate shape reconstruction result; and (2) significant shape changes between CN and AD participants are identified on certain amygdalar surface regions.

Shape analysis of amygdala atrophy using SPHARM-OT

Guest-host interaction has received a great deal of attention in the field of liquid crystals because of its potential. applications to displays and other optoelectronic devices. In one case, it was found that the unusually strong optical nonlinearity of nematic liquid crystals (LCs) can be further enhanced dramatically by a small amount of dye dissolved in the host. It was suggested that the enhancement is caused by optical excitation of dye molecules and dye-LC interaction. An important question unanswered is whether this effect is specific to liquid crystalline host material or it may have a more generic perspective. In this work, we show that the same guest-host effect also exists in the isotropic phase of liquid crystals, and more generally, in ordinary liquids without a mesomorphic phase. We demonstrate that by using 1-amino-anthroquinone dye as guest material and alkylcyanobiphenyls CN(C/sub 6/H/sub 4/)/sub 2/C/sub n/H/sub 2n+1/ as host materials, and performing optical Kerr effect measurement on such guest-host systems. To understand this guest-host effect on a microscopic level, we use a model based on the selective excitation of dye molecules and the change of guest-host interaction upon excitation.

Guest-host-interaction-induced enhancement of optical nonlinearity of liquids

Electrical poling induces polar ordering of molecules in a grating that has been holographically inscribed on a thin film of polymer functionalized with azobenzene side chains. Depending on the surface relief amplitude, the resulting χ(2) grating, seen by second harmonic generation (SHG) near-field scanning optical microscopy (NSOM), can have a periodic structure significantly different from the topographical image. The far-field linear and SHG diffraction patterns correlate well with the grating structures. Poling of the thin-film grating, which presumably has photo-driven non-uniform material properties within each period, leads to the more complex structure of the χ(2) grating.

Poled polymer thin-film gratings studied by near-field second harmonic optical microscopy and far-field optical diffraction

The sluggish oxygen evolution reaction (OER) kinetics and adverse charge transfer and stability at the multi‐interfaces from Si to electrolyte severely impede the application of Si photoanodes. Herein, oxygen vacancy (OV)‐rich NiFe‐layered hydroxides (NiFe‐OH) nanosheet arrays are vertically orientated on Ni‐protected Si photoanodes by a facile solvothermal method followed by a hot Fe ion‐exchange treatment. By virtue of the formation of OVs on NiFe‐OH nanosheets and the vertical contact between the NiFe‐OH and Si substrate, the as‐prepared Si photoanode not only enables abundant active sites for OER but also boosts charge and mass transfer when compared to traditional electro‐deposit samples. Moreover, the vertical contact of NiFe‐OH on Ni/Si benefits to release the interfacial stress and thereby promotes the electrode stability. Consequently, the optimal Si photoanode shows an ultrahigh applied bias photon‐to‐current efficiency of 5.7% and a good stability of over 200 h, outdoing almost all of the recently reported Si photoanodes.

Y. R. Shen

Papers

Enhanced solar hydrogen production by manipulating the spatial distribution of Pt catalyst onto Si micro-pyramid arrays

Shape analysis of amygdala atrophy using SPHARM-OT

Guest-host-interaction-induced enhancement of optical nonlinearity of liquids

Poled polymer thin-film gratings studied by near-field second harmonic optical microscopy and far-field optical diffraction

5.7% Efficiency Si Photoanodes for Solar Water Splitting Catalyzed by Vertically Grown and Oxygen‐Vacancy‐Rich NiFe Hydroxides