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

We present a method for calculating the stability of reaction intermediates of electrochemical processes on the basis of electronic structure calculations. We used that method in combination with detailed density functional calculations to develop a detailed description of the free-energy landscape of the electrochemical oxygen reduction reaction over Pt(111) as a function of applied bias. This allowed us to identify the origin of the overpotential found for this reaction. Adsorbed oxygen and hydroxyl are found to be very stable intermediates at potentials close to equilibrium, and the calculated rate constant for the activated proton/electron transfer to adsorbed oxygen or hydroxyl can account quantitatively for the observed kinetics. On the basis of a database of calculated oxygen and hydroxyl adsorption energies, the trends in the oxygen reduction rate for a large number of different transition and noble metals can be accounted for. Alternative reaction mechanisms involving proton/electron transfer to ...

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Origin of the Overpotential for Oxygen Reduction at a Fuel-Cell Cathode

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.

A fundamental change has been achieved in understanding surface electrochemistry due to the profound knowledge of the nature of electrocatalytic processes accumulated over the past several decades and to the recent technological advances in spectroscopy and high resolution imaging. Nowadays one can preferably design electrocatalysts based on the deep theoretical knowledge of electronic structures, via computer-guided engineering of the surface and (electro)chemical properties of materials, followed by the synthesis of practical materials with high performance for specific reactions. This review provides insights into both theoretical and experimental electrochemistry toward a better understanding of a series of key clean energy conversion reactions including oxygen reduction reaction (ORR), oxygen evolution reaction (OER), and hydrogen evolution reaction (HER). The emphasis of this review is on the origin of the electrocatalytic activity of nanostructured catalysts toward the aforementioned reactions by correlating the apparent electrode performance with their intrinsic electrochemical properties. Also, a rational design of electrocatalysts is proposed starting from the most fundamental aspects of the electronic structure engineering to a more practical level of nanotechnological fabrication.

Design of electrocatalysts for oxygen- and hydrogen-involving energy conversion reactions

This review summarizes theoretical progress in the field of active matter, placing it in the context of recent experiments. This approach offers a unified framework for the mechanical and statistical properties of living matter: biofilaments and molecular motors in vitro or in vivo, collections of motile microorganisms, animal flocks, and chemical or mechanical imitations. A major goal of this review is to integrate several approaches proposed in the literature, from semimicroscopic to phenomenological. In particular, first considered are ``dry'' systems, defined as those where momentum is not conserved due to friction with a substrate or an embedding porous medium. The differences and similarities between two types of orientationally ordered states, the nematic and the polar, are clarified. Next, the active hydrodynamics of suspensions or ``wet'' systems is discussed and the relation with and difference from the dry case, as well as various large-scale instabilities of these nonequilibrium states of matter, are highlighted. Further highlighted are various large-scale instabilities of these nonequilibrium states of matter. Various semimicroscopic derivations of the continuum theory are discussed and connected, highlighting the unifying and generic nature of the continuum model. Throughout the review, the experimental relevance of these theories for describing bacterial swarms and suspensions, the cytoskeleton of living cells, and vibrated granular material is discussed. Promising extensions toward greater realism in specific contexts from cell biology to animal behavior are suggested, and remarks are given on some exotic active-matter analogs. Last, the outlook for a quantitative understanding of active matter, through the interplay of detailed theory with controlled experiments on simplified systems, with living or artificial constituents, is summarized.

Hydrodynamics of soft active matter

Diamond-like carbon (DLC) films are deposited on the interior surface of 100 mm long quartz glass tubes with inner diameters of 6, 4, and 0.9 mm by enhanced glow discharge plasma immersion ion implantation (EGD-PIII) at 10 kV. The acetylene plasma is generated inside the tube by electrons created in the plasma near the substrate and secondary electrons from ion bombardment. Acetylene gas pressure distribution obtained from finite element method shows that the pressure varies linearly from the inlet to the outlet of the tube. The electron mean free path, λ e , and collision frequency, ν e , are introduced to qualitatively explain the non-uniform DLC film thickness. Raman scattering indicates that the DLC films at different locations have a similar structure.

Deposition of diamond-like carbon films on interior surface of long and slender quartz glass tube by enhanced glow discharge plasma immersion ion implantation

We present the results of a ~250 square degrees CO mapping (+26d 4.1x10^5 Msun in the whole region. In fact, the mass of the molecular gas is dominated by the W40 giant molecular cloud (GMC) at ~474 pc (~1.4x10^5 Msun) and the GMC complex G036.0+01.0 at ~560-670 pc (~2.0x10^5 Msun), while the MCs at ~220-260pc have gas masses of 10^2-10^3 Msun. Interestingly, an ~80pc long filamentary MC G044.0-02.5 at a distance of ~404 pc shows a systematic velocity gradient along and perpendicular to the major axis of the filament. The HI gas with the enhanced emission has the similar spatial morphologies and velocity features compared to the corresponding CO structure, indicating that the large-scale converging HI flows are probably responsible for the formation of the MC. Meanwhile, the long filamentary MC consists of many sub-filaments with the lengths ranging from ~0.5 pc to several pc, as well as prevalent networks of filaments in other large-scale local MCs.

Local Molecular Gas toward the Aquila Rift Region

Background: Nonalcoholic fatty liver disease (NAFLD) was associated with higher risk of cardiovascular disease (CVD). Low-grade albuminuria was recognized as an early indicator of CVD. Epidemiological studies investigating the association between NAFLD and low-grade albuminuria were limited.

Aim: To determine whether NAFLD is independently associated with the presence of low-grade albuminuria in Chinese adults.

Design: A cross-sectional community-based population study was performed in 8270 Chinese adults aged 40 years or older.

Methods: A first-voided early morning spot urine sample was obtained for urinary albumin and creatinine measurements. The highest quartile of urinary albumin-to-creatinine ratio was defined as low-grade albuminuria, after excluding the participants with micro- or macroalbuminuria. NAFLD was diagnosed by using ultrasonography findings after the exclusion of alcohol abuse and other liver diseases.

Results: The prevalence of low-grade albuminuria was significantly higher in participants with NAFLD than in those without NAFLD (33.6% vs. 21.3% in men and 30.4% vs. 22.8% in women, respectively). Multivariate-adjusted logistic regression analysis revealed that NAFLD was significantly associated with increased odds ratio of low-grade albuminuria in men (odds ratio, 1.47; 95% CI, 1.16–1.87) after adjusting for multiple confounders. The significant association was not detected in women.

Conclusions: NAFLD was significantly associated with an increased risk of present low-grade albuminuria in middle-aged and elderly Chinese men.

Nonalcoholic fatty liver disease is associated with low-grade albuminuria in Chinese adults (change not displayed)

Nucleic acid detecting method

We present a large-scale mapping toward the GEM OB1 association in the galactic anti-center direction. The 9^deg * 6.5^deg area was mapped in 12CO, 13CO, and C18O with 50" angular resolution at 30" sampling. The region was divided into four main components based on spatial distribution and velocity: the Gemini OB1 Giant Molecular Cloud (GGMC) Complex, the Lynds Dark Clouds and the West Front Clouds, the Swallow and Horn, and the Remote Clouds. The GGMC Complex is located in the Perseus arm, while the Lynds Dark Clouds and the West Front Clouds are located in the Local arm. Swallow and Horn are revealed for the first time in this paper. The two clouds have a similar velocity interval ([11, 21] km s^-1) and have similar sizes (0.6 and 0.8 deg^2). We analyzed the structure of these clouds in detail and calculated their parameters (mass, temperature, etc.). Two elongated structures were discovered in a longitude-velocity map in the velocity interval [11, 30] km s^-1. We also found an interesting filament that shows a 0.8 km s^-1 pc^-1 gradient perpendicular to the direction of the long axis.

Ye Xu

Papers

Deposition of diamond-like carbon films on interior surface of long and slender quartz glass tube by enhanced glow discharge plasma immersion ion implantation

Local Molecular Gas toward the Aquila Rift Region

Nonalcoholic fatty liver disease is associated with low-grade albuminuria in Chinese adults (change not displayed)

Nucleic acid detecting method

Molecular gas toward the Gemini OB1 Giant Molecular Cloud Complex I: Observation data