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.

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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.

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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.

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Graphene and Graphene Oxide: Synthesis, Properties, and Applications

We present a first-principles theory of the quasiparticle energies in semiconductors and insulators described in terms of the electron self-energy operator. The full dielectric matrix is used to evaluate the self-energy operator in the GW approximation: the first term in an expansion of the self-energy operator in terms of the dynamically screened Coulomb interaction (W) and the dressed Green's function (G). Quasiparticle energies are calculated for the homopolar materials diamond, Si, and Ge as well as for the ionic compound LiCl. The results are in excellent agreement with available experimental data. In particular, the indirect band gap is calculated as 5.5, 1.29, and 0.75 eV as compared with experimental gaps of 5.48, 1.17, and 0.744 eV for diamond, Si, and Ge, respectively. The Ge results include relativistic effects. The calculated direct gap for LiCl is within 5% of experiment. Viewed as a correction to the density-functional eigenvalues calculated with the local-density approximation, the present results show a correction dominated by a large jump at the gap. It is found that because of the charge inhomogeneity, the full dielectric screening matrix must be included, i.e., local-field effects are essential. The dynamical effects are also found to be crucial. The required dielectric matrices are obtained within the density-functional approach for the static case and extended to finite frequency with use of a generalized plasmon-pole model based on sum rules. The model reproduces the \ensuremath{\omega} and ${\ensuremath{\omega}}^{\mathrm{\ensuremath{-}}1}$ moments of the exact many-body response function. The qualitative features of the electron self-energy operator are discussed. Using the static Coulomb-hole--screened-exchange approximation for illustration, the role of local fields in the self-energy operator are explained. The role of dynamical renormalization is illustrated. The same qualitative features are observed in both the homopolar and ionic materials.

Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies.

We have experimentally determined the energies of the ground and first four excited excitonic states of the fundamental optical transition in monolayer ${\mathrm{WS}}_{2}$, a model system for the growing class of atomically thin two-dimensional semiconductor crystals. From the spectra, we establish a large exciton binding energy of 0.32 eV and a pronounced deviation from the usual hydrogenic Rydberg series of energy levels of the excitonic states. We explain both of these results using a microscopic theory in which the nonlocal nature of the effective dielectric screening modifies the functional form of the Coulomb interaction. These strong but unconventional electron-hole interactions are expected to be ubiquitous in atomically thin materials.

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Exciton Binding Energy and Nonhydrogenic Rydberg Series in Monolayer WS 2

Since it was first suggested1 that a single molecule might function as an active electronic component, a number of techniques have been developed to measure the charge transport properties of single molecules2,3,4,5,6,7,8,9,10,11,12. Although scanning tunnelling microscopy observations under high vacuum conditions can allow stable measurements of electron transport, most measurements of a single molecule bonded in a metal–molecule–metal junction exhibit relatively large variations in conductance. As a result, even simple predictions about how molecules behave in such junctions have still not been rigorously tested. For instance, it is well known13,14 that the tunnelling current passing through a molecule depends on its conformation; but although some experiments have verified this effect15,16,17,18, a comprehensive mapping of how junction conductance changes with molecular conformation is not yet available. In the simple case of a biphenyl—a molecule with two phenyl rings linked by a single C–C bond—conductance is expected to change with the relative twist angle between the two rings, with the planar conformation having the highest conductance. Here we use amine link groups to form single-molecule junctions with more reproducible current–voltage characteristics19. This allows us to extract average conductance values from thousands of individual measurements on a series of seven biphenyl molecules with different ring substitutions that alter the twist angle of the molecules. We find that the conductance for the series decreases with increasing twist angle, consistent with a cosine-squared relation predicted for transport through π-conjugated biphenyl systems13.

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Dependence of single-molecule junction conductance on molecular conformation

We present a first-principles theory for the quasiparticle energies of semiconductors and insulators. The full dielectric matrix is used to evaluate the nonlocal, energy-dependent electron self-energy operator. Both local-field effects and dynamical screening are found to be essential for understanding quasiparticle energies. Results for the band gaps, optical transitions, and band dispersions for silicon and diamond are in excellent agreement with existing experimental data.

First-principles theory of quasiparticles: Calculation of band gaps in semiconductors and insulators.

Patterned graphene shows substantial potential for applications in future molecular-scale integrated electronics. Environmental effects are a critical issue in a single-layer material where every atom is on the surface. Especially intriguing is the variety of rich chemical interactions shown by molecular oxygen with aromatic molecules. We find that O2 etching kinetics vary strongly with the number of graphene layers in the sample. Three-layer-thick samples show etching similar to bulk natural graphite. Single-layer graphene reacts faster and shows random etch pits in contrast to natural graphite where nucleation occurs at point defects. In addition, basal plane oxygen species strongly hole dope graphene, with a Fermi level shift of ∼0.5 eV. These oxygen species desorb partially in an Ar gas flow, or under irradiation by far UV light, and readsorb again in an O2 atmosphere at room temperature. This strongly doped graphene is very different from “graphene oxide” made by mineral acid attack.

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Mark S. Hybertsen

Papers

Electron correlation in semiconductors and insulators: Band gaps and quasiparticle energies.

Exciton Binding Energy and Nonhydrogenic Rydberg Series in Monolayer WS 2

Dependence of single-molecule junction conductance on molecular conformation

First-principles theory of quasiparticles: Calculation of band gaps in semiconductors and insulators.

Graphene Oxidation: Thickness-Dependent Etching and Strong Chemical Doping