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

Charge transport properties of metal-molecule interfaces depend strongly on the character of molecule-electrode interactions. Although through-bond coupled systems have attracted the most attention, through-space coupling is important in molecular systems when, for example, through-bond coupling is suppressed due to quantum interference effects. To date, a probe that clearly distinguishes these two types of coupling has not yet been demonstrated. Here, we investigate the origin of flicker noise in single molecule junctions and demonstrate how the character of the molecule-electrode coupling influences the flicker noise behavior of single molecule junctions. Importantly, we find that flicker noise shows a power law dependence on conductance in all junctions studied with an exponent that can distinguish through-space and through-bond coupling. Our results provide a new and powerful tool for probing and understanding coupling at the metal-molecule interface.

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Flicker Noise as a Probe of Electronic Interaction at Metal–Single Molecule Interfaces

The surface-state excitation energies for the Si(111)2{times}1 surface have been calculated in the {ital GW} approximation. The energy position and the dispersion of the occupied and empty surface states are in excellent agreement with photoemission and inverse-photoemission experiments. The calculated quasiparticle surface-state band gap, 0.62 eV, is 0.15 eV larger than the measured onset energy for electron-hole pair excitations. The possibility that excitonic effects are responsible for this difference is examined.

Many-body calculation of the surface-state energies for si(111)2 1

The low-energy electronic states in ${\mathrm{La}}_{2\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Sr}}_{\mathit{x}}$${\mathrm{CuO}}_{4}$ have recently been probed by soft-x-ray-absorption measurements as a function of doping (x) from the insulating well into the metallic (superconducting) regime. A model for understanding and interpreting those spectra is presented. The electronic structure of the active Cu-O planes is represented by an extended three-band Hubbard model whose parameters have been previously derived from quantum-chemical calculations. The essential additional Coulomb interaction between the core hole created in the absorption process and the nearby valence electrons has been included by calculating the necessary on-site and nearest-neighbor core-valence Coulomb parameters. The absorption spectra are calculated using exact-diagonalization techniques for finite clusters. The low-energy electronic structure can be represented within an effective one-band Hubbard model whose parameters are obtained by a mapping from the three-band model. The transition operator for the absorption process as well as the core-hole Coulomb potential are also mapped into the one-band model. The final calculations in the one-band model are performed for the insulator (half filling) and for several excess hole concentrations in the metal. The theoretical and experimental spectra are compared in detail. The calculations accurately account for the observed peak intensities as a function of doping. Important features include the gap between the preedge peaks in the metal, core-hole excitonic effects, and transfer of oscillator strength. In particular, the preedge peak separation is the charge-transfer gap (from the insulator) reduced by the core-hole exciton binding energy. The transfer of oscillator strength between the observed peaks, which is a key signature of the correlated band situation, is analyzed in detail. A doped charge-transfer insulator model for the electronic structure of the cuprates explains the essential features of the x-ray-absorption data.

Model for low-energy electronic states probed by x-ray absorption in high-Tc cuprates.

In this letter, we have developed a tandem electroabsorption modulator with an integrated semiconductor optical amplifier that is capable of both nonreturn-to-zero and return-to-zero (RZ) data transmission at 40 Gb/s. The tandem modulator consists of a broad-band data encoder and a narrow-band pulse carver. The pulse carver is able to produce 5-ps pulses with more than 20 dB of extinction. The on-chip semiconductor optical amplifier provides up to 8.5 dB of fiber-to-fiber gain and enables the modulator to be operated with zero insertion loss. Devices have been realized with greater than 40-GHz bandwidth, and 13-dB dynamic extinction for a 2.5-V swing. For optimized designs bandwidths of nearly 60 GHz: have been realized. Using these devices penalty free RZ data transmission over a 100-kin dispersion compensated fiber link has been demonstrated with a received power sensitivity of -29 dBm.

Mark S. Hybertsen

Papers

Flicker Noise as a Probe of Electronic Interaction at Metal–Single Molecule Interfaces

Many-body calculation of the surface-state energies for si(111)2 1

Model for low-energy electronic states probed by x-ray absorption in high-Tc cuprates.

40-Gb/s tandem electroabsorption modulator

Absorption and luminescence studies of free-standing porous silicon films.