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

/pdf/self-assembled-monolayers-of-thiolates-on-metals-as-a-form-1neb0hj3k4.pdf

Self-assembled monolayers of thiolates on metals as a form of nanotechnology.

The richness of optical and electronic properties of graphene attracts enormous interest. Graphene has high mobility and optical transparency, in addition to flexibility, robustness and environmental stability. So far, the main focus has been on fundamental physics and electronic devices. However, we believe its true potential lies in photonics and optoelectronics, where the combination of its unique optical and electronic properties can be fully exploited, even in the absence of a bandgap, and the linear dispersion of the Dirac electrons enables ultrawideband tunability. The rise of graphene in photonics and optoelectronics is shown by several recent results, ranging from solar cells and light-emitting devices to touch screens, photodetectors and ultrafast lasers. Here we review the state-of-the-art in this emerging field.

/pdf/graphene-photonics-and-optoelectronics-3ddg6ukzcu.pdf

Graphene photonics and optoelectronics

BACKGROUND Materials by design is an appealing idea that is very hard to realize in practice. Combining the best of different ingredients in one ultimate material is a task for which we currently have no general solution. However, we do have some successful examples to draw upon: Composite materials and III-V heterostructures have revolutionized many aspects of our lives. Still, we need a general strategy to solve the problem of mixing and matching crystals with different properties, creating combinations with predetermined attributes and functionalities. ADVANCES Two-dimensional (2D) materials offer a platform that allows creation of heterostructures with a variety of properties. One-atom-thick crystals now comprise a large family of these materials, collectively covering a very broad range of properties. The first material to be included was graphene, a zero-overlap semimetal. The family of 2D crystals has grown to includes metals (e.g., NbSe 2 ), semiconductors (e.g., MoS 2 ), and insulators [e.g., hexagonal boron nitride (hBN)]. Many of these materials are stable at ambient conditions, and we have come up with strategies for handling those that are not. Surprisingly, the properties of such 2D materials are often very different from those of their 3D counterparts. Furthermore, even the study of familiar phenomena (like superconductivity or ferromagnetism) in the 2D case, where there is no long-range order, raises many thought-provoking questions. A plethora of opportunities appear when we start to combine several 2D crystals in one vertical stack. Held together by van der Waals forces (the same forces that hold layered materials together), such heterostructures allow a far greater number of combinations than any traditional growth method. As the family of 2D crystals is expanding day by day, so too is the complexity of the heterostructures that could be created with atomic precision. When stacking different crystals together, the synergetic effects become very important. In the first-order approximation, charge redistribution might occur between the neighboring (and even more distant) crystals in the stack. Neighboring crystals can also induce structural changes in each other. Furthermore, such changes can be controlled by adjusting the relative orientation between the individual elements. Such heterostructures have already led to the observation of numerous exciting physical phenomena. Thus, spectrum reconstruction in graphene interacting with hBN allowed several groups to study the Hofstadter butterfly effect and topological currents in such a system. The possibility of positioning crystals in very close (but controlled) proximity to one another allows for the study of tunneling and drag effects. The use of semiconducting monolayers leads to the creation of optically active heterostructures. The extended range of functionalities of such heterostructures yields a range of possible applications. Now the highest-mobility graphene transistors are achieved by encapsulating graphene with hBN. Photovoltaic and light-emitting devices have been demonstrated by combining optically active semiconducting layers and graphene as transparent electrodes. OUTLOOK Currently, most 2D heterostructures are composed by direct stacking of individual monolayer flakes of different materials. Although this method allows ultimate flexibility, it is slow and cumbersome. Thus, techniques involving transfer of large-area crystals grown by chemical vapor deposition (CVD), direct growth of heterostructures by CVD or physical epitaxy, or one-step growth in solution are being developed. Currently, we are at the same level as we were with graphene 10 years ago: plenty of interesting science and unclear prospects for mass production. Given the fast progress of graphene technology over the past few years, we can expect similar advances in the production of the heterostructures, making the science and applications more achievable.

2D materials and van der Waals heterostructures

CoO/Fe thin films were grown epitaxially onto vicinal Ag(001) and investigated using magneto-optic Kerr effect, x-ray magnetic circular dichroism (XMCD), and x-ray magnetic linear dichroism (XMLD) techniques. We show that the CoO film in the ultrathin regime does not induce a uniaxial magnetic anisotropy but a coercivity enhancement. This result provides a mechanism for the microscopic origin of the rotatable magnetic anisotropy. XMLD measurement further reveals that the underlying mechanism is that the CoO spins are totally rotatable in the ultrathin regime to follow the Fe magnetization.

https://escholarship.org/content/qt3vq9n23c/qt3vq9n23c.pdf?t=p06n7b

Rotatable magnetic anisotropy of CoO/Fe/Ag(001) in ultrathin regime of the CoO layer

Near-field optical spectroscopy with nanometer spatial resolution using transition radiation from a focused, relativistic electron beam is demonstrated for Ge nanowires. The excitation of the waveguide modes is absent in theoretical treatments that neglect retardation because the coupling of the swift electron to the optical modes of the nanowire is a consequence of its relativistic nature. Here, relativistic energy loss probabilities for aloof electron trajectories near a perpendicularly oriented single nanowire are analytically calculated using a local dielectric theory. Multimode and zero-mode Ge nanowires are experimentally measured in this geometry with a approx2-nm-size electron probe. Observations fall in excellent agreement with the retarded calculations. Optical eigenmodes are identified from comparison of the experimental electron energy loss spectra to theoretical dispersion maps. Adding a Drude-type metallic shell to a dielectric nanowire provides surface-plasmon modes in the same energy range as the dielectric waveguide, leading to strongly coupled hybrid modes that can be efficiently excited by the incident electron. Such results demonstrate a powerful solution for optical studies of nanosystems with nanometer spatial resolution over a broadband energy range.

Relativistic electron energy loss spectroscopy of solid and core-shell nanowires

We report the spatially resolved electrical response of bottom-contact pentacene thin-film transistors to a scanning, focused laser. We find that pentacene films make point-like electrical contacts to the underlying gold electrodes and are able to image them with diffraction-limited resolution. We can further estimate the interfacial resistance associated with hole-injection at an individual point contact, and show that optical activation of one alone increases device current significantly.

Photoelectrical imaging and characterization of point contacts in pentacene thin-film transistors

Scanning electron microscopes (SEMs) require a high vacuum environment to generate and shape an electron beam for imaging; however, the vacuum conditions greatly limit the nature of specimens that can be examined. From a purely scattering physics perspective, it is not necessary to place the specimen inside the vacuum chamber—the mean free paths (MFPs) for electron scattering in air at typical SEM beam voltages are 50–100 μm. This is the idea behind the airSEM, which removes the specimen vacuum chamber from the SEM and places the sample in air. The thickness of the gas layer is less than a MFP from an electron-transparent window to preserve the shape and resolution of the incident beam, resulting in comparable imaging quality to an all-vacuum SEM. Present silicon nitride windows scatter far more strongly than the air gap and are currently the contrast and resolution limiting factor in the airSEM. Graphene windows have been used previously to wrap or seal samples in vacuum for imaging. Here we demonstrate ...

Atomically Thin Graphene Windows That Enable High Contrast Electron Microscopy without a Specimen Vacuum Chamber

Lateral single-layer transition metal dichalcogenide (TMD) heterostructures are promising building blocks for future ultrathin devices. Recent advances in the growth of coherent heterostructures have improved the structural precision of lateral heterojunctions, but an understanding of the electronic effects of the chemical transition at the interface and associated strain is lacking. Here we present a scanning tunneling microscopy study of single-layer coherent TMD heterostructures with nearly uniform strain on each side of the heterojunction interface. We have characterized the local topography and electronic structure of single-layer WS2/WSe2 heterojunctions exhibiting ultrasharp coherent interfaces. Uniform built-in strain on each side of the interface arising from lattice mismatch results in a reduction of the bandgap of WS2. By mapping the tunneling differential conductance across the interface, we find type-II band alignment and an ultranarrow electronic transition region only ∼3 nm in width that arises from wave function mixing between the two materials.

Jiwoong Park

Papers

Rotatable magnetic anisotropy of CoO/Fe/Ag(001) in ultrathin regime of the CoO layer

Relativistic electron energy loss spectroscopy of solid and core-shell nanowires

Photoelectrical imaging and characterization of point contacts in pentacene thin-film transistors

Atomically Thin Graphene Windows That Enable High Contrast Electron Microscopy without a Specimen Vacuum Chamber

Local Electronic Properties of Coherent Single-Layer WS2/WSe2 Lateral Heterostructures