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

This article reviews the basic theoretical aspects of graphene, a one-atom-thick allotrope of carbon, with unusual two-dimensional Dirac-like electronic excitations. The Dirac electrons can be controlled by application of external electric and magnetic fields, or by altering sample geometry and/or topology. The Dirac electrons behave in unusual ways in tunneling, confinement, and the integer quantum Hall effect. The electronic properties of graphene stacks are discussed and vary with stacking order and number of layers. Edge (surface) states in graphene depend on the edge termination (zigzag or armchair) and affect the physical properties of nanoribbons. Different types of disorder modify the Dirac equation leading to unusual spectroscopic and transport properties. The effects of electron-electron and electron-phonon interactions in single layer and multilayer graphene are also presented.

/pdf/the-electronic-properties-of-graphene-2siyzsnf5w.pdf

The electronic properties of graphene

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

We measured the elastic properties and intrinsic breaking strength of free-standing monolayer graphene membranes by nanoindentation in an atomic force microscope. The force-displacement behavior is interpreted within a framework of nonlinear elastic stress-strain response, and yields second- and third-order elastic stiffnesses of 340 newtons per meter (N m(-1)) and -690 Nm(-1), respectively. The breaking strength is 42 N m(-1) and represents the intrinsic strength of a defect-free sheet. These quantities correspond to a Young's modulus of E = 1.0 terapascals, third-order elastic stiffness of D = -2.0 terapascals, and intrinsic strength of sigma(int) = 130 gigapascals for bulk graphite. These experiments establish graphene as the strongest material ever measured, and show that atomically perfect nanoscale materials can be mechanically tested to deformations well beyond the linear regime.

/pdf/measurement-of-the-elastic-properties-and-intrinsic-strength-27nythtm75.pdf

Measurement of the Elastic Properties and Intrinsic Strength of Monolayer Graphene

There is intense interest in graphene in fields such as physics, chemistry, and materials science, among others. Interest in graphene's exceptional physical properties, chemical tunability, and potential for applications has generated thousands of publications and an accelerating pace of research, making review of such research timely. Here is an overview of the synthesis, properties, and applications of graphene and related materials (primarily, graphite oxide and its colloidal suspensions and materials made from them), from a materials science perspective.

/pdf/graphene-and-graphene-oxide-synthesis-properties-and-2q80uaujok.pdf

Graphene and Graphene Oxide: Synthesis, Properties, and Applications

Polycrystalline “AgBiNb2O7” (I) and “Ag4/5Bi5/6Ta2O6.65” (II) are synthesized by solid state reaction of Ag2O, Bi2O3, Nb2O5, and Ta2O5 in molar ratios of 0.5:0.5:1 for (I) and 0.4:0.418:1 for (II), resp.

Design of Medium Band Gap Ag—Bi—Nb—O and Ag—Bi—Ta—O Semiconductors for Driving Direct Water Splitting with Visible Light.

X-ray absorption spectroscopy (XAS) is an element-specific materials characterization technique that is sensitive to structural and electronic properties. First-principles simulated XAS has been widely used as a powerful tool to interpret experimental spectra and draw physical insights. Recently, there has also been growing interest in building computational XAS databases to enable data analytics and machine learning applications. However, there are non-trivial differences among commonly used XAS simulation codes, both in underlying theoretical formalism and in technical implementation. Reliable and reproducible computational XAS databases require systematic benchmark studies. In this work, we benchmarked Ti K-edge XAS simulations of ten representative Ti-O binary compounds, which we refer to as the Ti-O-10 dataset, using three state-of-the-art codes: xspectra, ocean and exciting. We systematically studied the convergence behavior with respect to the input parameters and developed a workflow to automate and standardize the calculations to ensure converged spectra. Our benchmark comparison shows: (1) the two Bethe-Salpeter equation (BSE) codes (ocean and exciting) have excellent agreement in the energy range studied (up to 35 eV above the onset) with an average Spearman's rank correlation score of 0.998; (2) good agreement is obtained between the core-hole potential code (xspectra) and BSE codes (ocean and exciting) with an average Spearman's rank correlation score of 0.990. Our benchmark study provides important standards for first-principles XAS simulations with broad impact in data-driven XAS analysis.

Multi-code Benchmark on Simulated Ti K-edge X-ray Absorption Spectra of Ti-O Compounds

Total energy minimization calculations show that the interface bonds are strained in nominally lattice matched In 0.53 Ga 0.47 As/InP (001) heterostructures, in agreement with recent X-ray measurements. Anion intermixing relieves the interface strain. The calculated valence band offset varies with the interface bond lengths so the minimum energy structure must be used for a given composition. Then the calculated offset is independent of composition and is in good agreement with experiment. A simple model exhibits the qualitative features revealed by these calculations.

Interface Strain and the Valence Band Offset at the Lattice Matched In0.53Ga0.47As/InP (001) Interface

The constrained density functional approach is used to calculate the energy surface as a function of local charge fluctuations in La2CuO4. This energy surface is then mapped onto a self consistent mean field solution of the Hubbard model which allows extraction of the Coulomb interaction parameters when combined with oneelectron parameters derived from band structure results. The present calculations indicate that La2CuO4 is intermediate between the extreme spin or charge fluctuation regimes. This severly restricts the range of parameter space for theories of quasiparticles, optical excitations and possible pairing mechanism based on the extended Hubbard model.

Mark S. Hybertsen

Papers

Design of Medium Band Gap Ag—Bi—Nb—O and Ag—Bi—Ta—O Semiconductors for Driving Direct Water Splitting with Visible Light.

Multi-code Benchmark on Simulated Ti K-edge X-ray Absorption Spectra of Ti-O Compounds

Interface Strain and the Valence Band Offset at the Lattice Matched In0.53Ga0.47As/InP (001) Interface

Calculation of the Hubbard-Type Many Body Interaction Parameters using Constrained Density Functional Theory

Microscopic Theory of the Properties of Semiconductor Heterojunctions