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

An enhanced static approximation for the electron self-energy operator is proposed for efficient calculation of quasiparticle energies. Analysis of the static Coulomb-hole screened-exchange (COHSEX) approximation originally proposed by Hedin shows that most of the error derives from the short-wavelength contributions of the assumed adiabatic accumulation of the Coulomb hole. A wave-vector-dependent correction factor can be incorporated as the basis for a new static approximation. This factor can be approximated by a single scaling function, determined from the homogeneous electron-gas model. The local field effect in real materials is captured by a simple ansatz based on symmetry consideration. As inherited from the COHSEX approximation, the new approximation presents a Hermitian self-energy operator and the summation over empty states is eliminated from the evaluation of the self-energy operator. Tests were conducted comparing the new approximation to GW calculations for diverse materials ranging from crystals, molecules, atoms and a carbon nanotube. The accuracy for the minimum gap is about 10% or better. Like in the COHSEX approximation, the occupied bandwidth is overestimated.

Enhanced static approximation to the electron self-energy operator for efficient calculation of quasiparticle energies

Comparison of structurally relaxed models of the Si(001)-SiO2 interface based on different crystalline oxide forms

This study details a scanning tunneling microscopy investigation into the mechanism of chiral grain growth in highly ordered, self-assembled monolayer films composed of cruciform π-systems. Although the molecules themselves are achiral, when they adsorb from solution onto graphite, they adopt a gear-like conformation that, by virtue of the surface, is chiral. These handed subunits arrange themselves into enantiomeric two-dimensional domains. The unique finding from this study is that Ostwald ripening is frustrated between domain boundaries that are of opposite chirality because direct interconversion between the chiral units on the surface is energetically inhibited.

Frustrated Ostwald Ripening in Self-Assembled Monolayers of Cruciform π-Systems

A process for fabricating a waveguide with a desired tapered profile is disclosed. The waveguide has a first section with a first height and a second section with a second height. The first height is greater than the second height. The waveguide height tapers from the first height to the second height. The waveguide is a compound semiconductor material and is formed using selective area growth. In selective area growth, a dielectric mask is formed on a substrate. The dimensions of the dielectric mask are selected to provide a waveguide with the desired dimensions. The compound semiconductor material is deposited on the substrate using chemical vapor deposition. The dielectric mask affects the rate at which the compound material is deposited in areas of the substrate proximate to the mask. Therefore, the profile of the waveguide formed using the selected mask dimensions is modeled and compared with the desired profile. If modeled profile is not acceptably similar to the desired profile, the dimensions of the mask are modified. The profile of the waveguide formed using the modified mask dimensions is again modeled, and the modeled waveguide profile is compared with the desired waveguide profile. This process is repeated until the modeled profile is sufficiently similar to the desired profile. After the mask dimensions are selected, the mask is formed on the substrate, and the compound semiconductor waveguide is formed on the substrate using selective area growth.

Process for fabricating an optical waveguide

Despite mounting evidence that materials imperfections are a major obstacle to practical applications of superconducting qubits, connections between microscopic material properties and qubit coherence are poorly understood. Here, we perform measurements of transmon qubit relaxation times $T_1$ in parallel with spectroscopy and microscopy of the thin polycrystalline niobium films used in qubit fabrication. By comparing results for films deposited using three techniques, we reveal correlations between $T_1$ and grain size, enhanced oxygen diffusion along grain boundaries, and the concentration of suboxides near the surface. Physical mechanisms connect these microscopic properties to residual surface resistance and $T_1$ through losses arising from the grain boundaries and from defects in the suboxides. Further, experiments show that the residual resistance ratio can be used as a figure of merit for qubit lifetime. This comprehensive approach to understanding qubit decoherence charts a pathway for materials-driven improvements of superconducting qubit performance.

Mark S. Hybertsen

Papers

Enhanced static approximation to the electron self-energy operator for efficient calculation of quasiparticle energies

Comparison of structurally relaxed models of the Si(001)-SiO2 interface based on different crystalline oxide forms

Frustrated Ostwald Ripening in Self-Assembled Monolayers of Cruciform π-Systems

Process for fabricating an optical waveguide

Microscopic Relaxation Channels in Materials for Superconducting Qubits