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

PROBLEM TO BE SOLVED: To provide a monolithic array for a vertical-cavity surface emitting laser(VCSEL) device used to emit light at a plurality of wavelengths, in which the gain peak of every device inside the array is tuned to a cavity mode, and in which the array composed of the devise used to emit light at respective designated wavelengths is realized with high reproducibility and with high accuracy. SOLUTION: An upper-part mirror 235, a lower-part mirror 210, an upper-part confinement layer, a lower-part confinement layer 215, and a quantum well layer 225 which comprises boundary layers on both sides, are provided at every device. The thickness of the lower-part mirror 210, that of the lower-part confinement layer 215 and that of the upper-part mirror 235, are nearly identical through all devices inside an array. The thickness of the quantum well layer in the device which emits light at a first wavelength is different from the thickness of the quantum well layer in the device which emits light at a second wavelength. The devices have a prescribed relationship (e.g. within a range of about 5 nm) between a light emitting wavelength and a peak-gain wavelength.

Monolithic array for vertical-cavity surface emitting laser device

http://absimage.aps.org/image/MAR09/MWS_MAR09-2008-002785.pdf

Conductance of Molecular Wires Measured by STM- Break Junction

The invention is a semiconductor optical device and a method of manufacture.
The device (10) includes a first waveguide (15) having an edge (31), and a second
waveguide (12) adjacent to at least a portion of the first waveguide including the edge so
that light is coupled from the first to the second waveguide. The second waveguide has a
modal index which is essentially constant at least at the edge of the first waveguide. The
method includes forming at least the second waveguide by Selective Area Growth (SAG)
using oxide pads (61, 62) of a particular geometry to achieve the essentially constant
modal index. In one embodiment, the device is an expanded beam laser with an expander
portion (10b) which is less than 300 microns.

Semiconductor optical devices

Erratum: Absorption and luminescence studies of free-standing porous silicon films [Phys. Rev. B 49, 5386 (1994)]

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 partially desorb 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 than graphene oxide made by mineral acid attack.

Mark S. Hybertsen

Papers

Monolithic array for vertical-cavity surface emitting laser device

Conductance of Molecular Wires Measured by STM- Break Junction

Semiconductor optical devices

Erratum: Absorption and luminescence studies of free-standing porous silicon films [Phys. Rev. B 49, 5386 (1994)]

Graphene Oxidation: Thickness Dependent Etching and Strong Chemical Doping