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

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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.

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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

We report a systematic study of the optical conductivity of twisted bilayer graphene (tBLG) across a large energy range (1.2 eV to 5.6 eV) for various twist angles, combined with first-principles calculations. At previously unexplored high energies, our data show signatures of multiple van Hove singularities (vHSs) in the tBLG bands, as well as the nonlinearity of the single layer graphene bands and their electron-hole asymmetry. Our data also suggest that excitonic effects play a vital role in the optical spectra of tBLG. Including electron-hole interactions in first-principles calculations is essential to reproduce the shape of the conductivity spectra, and we find evidence of coherent interactions between the states associated with the multiple vHSs in tBLG.

Van Hove Singularities and Excitonic Effects in the Optical Conductivity of Twisted Bilayer Graphene

Atomic‐Scale Visualization of Electrochemical Lithiation Processes in Monolayer MoS2 by Cryogenic Electron Microscopy

The field of two-dimensional (2D) materials has expanded to multilayered systems in which electronic, optical, and mechanical properties change---often dramatically---with stacking order, thickness, twist, and interlayer spacing. For transition metal dichalcogenides (TMDs), bond coordination within a single van der Waals layer changes the out-of-plane symmetry that can cause metal-insulator transitions or emergent quantum behavior. Discerning these structural order parameters is often difficult using real-space measurements; however, we show that 2D materials have distinct, conspicuous three-dimensional (3D) structure in reciprocal space described by nearly infinite oscillating Bragg rods. Combining electron diffraction and specimen tilt we probe Bragg rods in all three dimensions to identify multilayer structure with subangstrom precision across several 2D materials---including TMDs (${\mathrm{MoS}}_{2}$, ${\mathrm{TaSe}}_{2}$, ${\mathrm{TaS}}_{2}$) and multilayer graphene. We demonstrate quantitative determination of key structural parameters such as surface roughness, inter- and intralayer spacings, stacking order, and interlayer twist using a rudimentary transmission electron microscope. We accurately characterize the full interlayer stacking order of multilayer graphene (1, 2, 6, 12 layers) as well the intralayer structure of ${\mathrm{MoS}}_{2}$ and extract a chalcogen-chalcogen layer spacing of $3.07\ifmmode\pm\else\textpm\fi{}0.11$ \AA{}. Furthermore, we demonstrate quick identification of multilayer rhombohedral graphene.

Stacking, strain, and twist in 2D materials quantified by 3D electron diffraction

Experiments reveal the path traced by light-induced electric currents in a monolayer semiconductor by using nitrogen-vacancy centers in diamond to sense magnetic fields from those currents.

https://link.aps.org/pdf/10.1103/PhysRevX.10.011003

Spatiotemporal Mapping of a Photocurrent Vortex in Monolayer MoS 2 Using Diamond Quantum Sensors

Stacking atomically thin two-dimensional materials with a rotational misalignment between their layers produces a van der Waals bilayer in which all mirror symmetries can be broken. A fundamental experimental signature of a twisted multilayer is circular dichroism (CD): the conversion of a linearly polarized incident optical field to an elliptically polarized field in transmission. This work investigates the relations between CD, the twist angle, and interlayer slip. In experiments where bilayers are formed by contacting one layer with another, the relative rotation angle between the symmetry axes of each sheet are controlled, but the lateral shifts between the layers are not. Accounting for the lateral shift between the layers expands the configuration space of twisted bilayer structures. Here we demonstrate how the symmetry constraints in this expanded configuration space are expressed in the CD spectrum of twisted bilayer graphene as a function of the rotation angle and interlayer slip.

Jiwoong Park

Papers

Van Hove Singularities and Excitonic Effects in the Optical Conductivity of Twisted Bilayer Graphene

Atomic‐Scale Visualization of Electrochemical Lithiation Processes in Monolayer MoS2 by Cryogenic Electron Microscopy

Stacking, strain, and twist in 2D materials quantified by 3D electron diffraction

Spatiotemporal Mapping of a Photocurrent Vortex in Monolayer MoS 2 Using Diamond Quantum Sensors

Twist, slip, and circular dichroism in bilayer graphene