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

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

Graphene has been attracting great interest because of its distinctive band structure and physical properties. Today, graphene is limited to small sizes because it is produced mostly by exfoliating graphite. We grew large-area graphene films of the order of centimeters on copper substrates by chemical vapor deposition using methane. The films are predominantly single-layer graphene, with a small percentage (less than 5%) of the area having few layers, and are continuous across copper surface steps and grain boundaries. The low solubility of carbon in copper appears to help make this growth process self-limiting. We also developed graphene film transfer processes to arbitrary substrates, and dual-gated field-effect transistors fabricated on silicon/silicon dioxide substrates showed electron mobilities as high as 4050 square centimeters per volt per second at room temperature.

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Large-Area Synthesis of High-Quality and Uniform Graphene Films on Copper Foils

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

Recent years have witnessed many breakthroughs in research on graphene (the first two-dimensional atomic crystal) as well as a significant advance in the mass production of this material. This one-atom-thick fabric of carbon uniquely combines extreme mechanical strength, exceptionally high electronic and thermal conductivities, impermeability to gases, as well as many other supreme properties, all of which make it highly attractive for numerous applications. Here we review recent progress in graphene research and in the development of production methods, and critically analyse the feasibility of various graphene applications.

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A roadmap for graphene

The optical conductance of monolayer graphene is defined solely by the fine structure constant, α =  (where e is the electron charge, is Dirac's constant and c is the speed of light). The absorbance has been predicted to be independent of frequency. In principle, the interband optical absorption in zero-gap graphene could be saturated readily under strong excitation due to Pauli blocking. Here, use of atomic layer graphene as saturable absorber in a mode-locked fiber laser for the generation of ultrashort soliton pulses (756 fs) at the telecommunication band is demonstrated. The modulation depth can be tuned in a wide range from 66.5% to 6.2% by varying the graphene thickness. These results suggest that ultrathin graphene films are potentially useful as optical elements in fiber lasers. Graphene as a laser mode locker can have many merits such as lower saturation intensity, ultrafast recovery time, tunable modulation depth, and wideband tunability.

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Atomic‐Layer Graphene as a Saturable Absorber for Ultrafast Pulsed Lasers

The optical conductance of monolayer graphene is defined solely by the fine structure constant. The absorbance has been predicted to be independent of frequency. In principle, the interband optical absorption in zero-gap graphene could be saturated readily under strong excitation due to Pauli blocking. Here, we demonstrate the use of atomic layer graphene as saturable absorber in a mode-locked fiber laser for the generation of ultrashort soliton pulses (756 fs) at the telecommunication band. The modulation depth can be tuned in a wide range from 66.5% to 6.2% by varying the thickness of graphene. Our results suggest that ultrathin graphene films are potentially useful as optical elements in fiber lasers. Graphene as a laser mode locker can have many merits such as lower saturation intensity, ultrafast recovery time, tunable modulation depth and wideband tuneability.

Atomic layer graphene as saturable absorber for ultrafast pulsed lasers

Graphene was deposited on a transparent and flexible substrate, and tensile strain up to ∼0.8% was loaded by stretching the substrate in one direction. Raman spectra of strained graphene show significant red shifts of 2D and G band (−27.8 and −14.2 cm−1 per 1% strain, respectively) because of the elongation of the carbon−carbon bonds. This indicates that uniaxial strain has been successfully applied on graphene. We also proposed that, by applying uniaxial strain on graphene, tunable band gap at K point can be realized. First-principle calculations predicted a band-gap opening of ∼300 meV for graphene under 1% uniaxial tensile strain. The strained graphene provides an alternative way to experimentally tune the band gap of graphene, which would be more efficient and more controllable than other methods that are used to open the band gap in graphene. Moreover, our results suggest that the flexible substrate is ready for such a strain process, and Raman spectroscopy can be used as an ultrasensitive method to ...

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Uniaxial strain on graphene: Raman spectroscopy study and band-gap opening.

Graphene has many unique properties that make it an ideal material for fundamental studies as well as for potential applications. Here we review recent results on the Raman spectroscopy and imaging of graphene. We show that Raman spectroscopy and imaging can be used as a quick and unambiguous method to determine the number of graphene layers. The strong Raman signal of single layer graphene compared to graphite is explained by an interference enhancement model. We have also studied the effect of substrates, the top layer deposition, the annealing process, as well as folding (stacking order) on the physical and electronic properties of graphene. Finally, Raman spectroscopy of epitaxial graphene grown on a SiC substrate is presented and strong compressive strain on epitaxial graphene is observed. The results presented here are highly relevant to the application of graphene in nano-electronic devices and help in developing a better understanding of the physical and electronic properties of graphene.

https://link.springer.com/content/pdf/10.1007%2Fs12274-008-8036-1.pdf

Raman spectroscopy and imaging of graphene

We have clearly discriminated the single-, bilayer-, and multiple-layer graphene (<10 layers) on Si substrate with a 285 nm SiO2 capping layer by using contrast spectra, which were generated from the reflection light of a white light source. Calculations based on Fresnel's law are in excellent agreement with the experimental results (deviation 2%). The contrast image shows the reliability and efficiency of this new technique. The contrast spectrum is a fast, nondestructive, easy to be carried out, and unambiguous way to identify the numbers of layers of graphene sheet. We provide two easy-to-use methods to determine the number of graphene layers based on contrast spectra: a graphic method and an analytical method. We also show that the refractive index of graphene is different from that of graphite. The results are compared with those obtained using Raman spectroscopy.

Zhenhua Ni

Papers

Atomic‐Layer Graphene as a Saturable Absorber for Ultrafast Pulsed Lasers

Atomic layer graphene as saturable absorber for ultrafast pulsed lasers

Uniaxial strain on graphene: Raman spectroscopy study and band-gap opening.

Raman spectroscopy and imaging of graphene

Graphene Thickness Determination Using Reflection and Contrast Spectroscopy