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

Conventional optical components rely on gradual phase shifts accumulated during light propagation to shape light beams. New degrees of freedom are attained by introducing abrupt phase changes over the scale of the wavelength. A two-dimensional array of optical resonators with spatially varying phase response and subwavelength separation can imprint such phase discontinuities on propagating light as it traverses the interface between two media. Anomalous reflection and refraction phenomena are observed in this regime in optically thin arrays of metallic antennas on silicon with a linear phase variation along the interface, which are in excellent agreement with generalized laws derived from Fermat’s principle. Phase discontinuities provide great flexibility in the design of light beams, as illustrated by the generation of optical vortices through use of planar designer metallic interfaces.

http://www.zenogaburro.it/papers/LightPropagation.pdf

Light Propagation with Phase Discontinuities: Generalized Laws of Reflection and Refraction

Metamaterials are artificially fabricated materials that allow for the control of light and acoustic waves in a manner that is not possible in nature. This Review covers the recent developments in the study of so-called metasurfaces, which offer the possibility of controlling light with ultrathin, planar optical components. Conventional optical components such as lenses, waveplates and holograms rely on light propagation over distances much larger than the wavelength to shape wavefronts. In this way substantial changes of the amplitude, phase or polarization of light waves are gradually accumulated along the optical path. This Review focuses on recent developments on flat, ultrathin optical components dubbed 'metasurfaces' that produce abrupt changes over the scale of the free-space wavelength in the phase, amplitude and/or polarization of a light beam. Metasurfaces are generally created by assembling arrays of miniature, anisotropic light scatterers (that is, resonators such as optical antennas). The spacing between antennas and their dimensions are much smaller than the wavelength. As a result the metasurfaces, on account of Huygens principle, are able to mould optical wavefronts into arbitrary shapes with subwavelength resolution by introducing spatial variations in the optical response of the light scatterers. Such gradient metasurfaces go beyond the well-established technology of frequency selective surfaces made of periodic structures and are extending to new spectral regions the functionalities of conventional microwave and millimetre-wave transmit-arrays and reflect-arrays. Metasurfaces can also be created by using ultrathin films of materials with large optical losses. By using the controllable abrupt phase shifts associated with reflection or transmission of light waves at the interface between lossy materials, such metasurfaces operate like optically thin cavities that strongly modify the light spectrum. Technology opportunities in various spectral regions and their potential advantages in replacing existing optical components are discussed.

Flat Optics With Designer Metasurfaces

“Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks”の学習報告

Chemical looping methane partial oxidation provides an energy and cost effective route for methane utilization. However, there is considerable CO2 co-production in current chemical looping systems, rendering a decreased productivity in value-added fuels or chemicals. In this work, we demonstrate that the co-production of CO2 can be dramatically suppressed in methane partial oxidation reactions using iron oxide nanoparticles embedded in mesoporous silica matrix. We experimentally obtain near 100% CO selectivity in a cyclic redox system at 750–935 °C, which is a significantly lower temperature range than in conventional oxygen carrier systems. Density functional theory calculations elucidate the origins for such selectivity and show that low-coordinated lattice oxygen atoms on the surface of nanoparticles significantly promote Fe–O bond cleavage and CO formation. We envision that embedded nanostructured oxygen carriers have the potential to serve as a general materials platform for redox reactions with nanomaterials at high temperatures. Chemical looping methane partial oxidation is an effective technology to produce syngas with a minimal energy penalty. Here, the authors design and develop a mesoporous silica supported nanoparticle oxygen carrier that enables a near 100% CO generation with high recyclability and substantially lower operating temperature.

/pdf/near-100-co-selectivity-in-nanoscaled-iron-based-oxygen-mkg864a4yy.pdf

Near 100% CO selectivity in nanoscaled iron-based oxygen carriers for chemical looping methane partial oxidation.

We propose and experimentally demonstrate a new method of generating correlated photons in a microstructure fiber by means of a reversed degenerate four-wave-mixing process. Here one photon is annihilated from each of the bichromatic pump pulses to generate a pair of photons at the mean frequency. For a microstructure fiber as short as 1.5?m the measured coincidence counting rate is approximately eight times that of the accidental coincidences with a peak pump power of 0.25?W.

Generation of correlated photon pairs in a microstructure fiber.

We demonstrated in simulations and experiments that by defining a properly designed two-dimensional metallic aperture-grating structure on the facet of quantum cascade lasers, a small beam divergence angle can be achieved in directions both perpendicular and parallel to the laser waveguide layers (denoted as θ⊥ and θ‖, respectively). Beam divergence angles as small as θ⊥=2.7o and θ‖=3.7o have been demonstrated. This is a reduction by a factor of ~30 and ~10, respectively, compared to those of the original lasers emitting at a wavelength of 8.06 µm. The devices preserve good room temperature performance with output power as high as ~55% of that of the original unpatterned lasers. We studied in detail the trade-off between beam divergence and power throughput for the fabricated devices. We demonstrated plasmonic collimation for buried heterostructure lasers and ridge lasers; devices with different waveguide structures but with the same plasmonic collimator design showed similar performance. We also studied a device patterned with a “spider’s web” pattern, which gives us insight into the distribution of surface plasmons on the laser facet.

Quantum cascade lasers with integrated plasmonic antenna-array collimators.

Dielectric metasurfaces are ultra-thin devices that can shape optical wavefronts with extreme control. While an assortment of materials possessing a wide range of dielectric constants have been proposed and implemented, the minimum dielectric contrast required for metasurfaces to achieve high-efficiency performance, for a given device function and feature size constraint, is unclear. In this Article, we examine the impact of dielectric material selection on metasurface efficiency at optical frequencies. As a model system, we design transmissive, single-layer periodic metasurfaces (i.e., metagratings) using topology optimization, and we sweep device thickness and light deflection angle for differing material types. We find that for modest deflection angles below 40 degrees, materials with relatively low dielectric constants near 4 can be used to produce metagratings with efficiencies over 80%. However, ultra-high-efficiency devices designed for large deflection angles and multiple functions require materials with high dielectric constants comparable to silicon. We also identify, for all materials, a minimum device thickness required for optimal metagrating performance that scales inversely with dielectric constant. Our work presents materials selection guidelines for high-performance metasurfaces operating at visible and infrared wavelengths.

Analysis of material selection on dielectric metasurface performance

Iron oxide composites are enabling materials in energy conversion systems including chemical looping and photocatalysis. Extensive earlier experimental findings indicate that inert oxides such as titanium oxide can greatly improve the reactivity of iron oxide over multiple redox cycles. Knowledge on the evolution of the nanoscale morphology of the Fe–Ti materials during the oxidation and reduction is thus of considerable importance. It is also of interest to the fundamental understanding of the ion diffusion mechanism in the reaction processes. In this study, Fe–Ti composite microparticles undergoing cycles of oxidation and reduction are examined at the nano-scale, and the interfacial characteristics of the iron titanium oxides within the composites are probed. Nanobelts are observed to simultaneously form on the microparticle surface during the oxidation at 700 °C, while microblades are found at 900 °C. Additionally, unlike pure iron microparticles that become dense on surface due to sintering effect, Fe–Ti microparticles are transformed into porous particles after redox cycles. The atomistic thermodynamics methods and density functional theory calculations are carried out to investigate the ionic diffusion and vacancy formation during the oxidation and reduction process. A number of surface configurations are considered, and the Ti–Ti–O– terminated surface is computed to the most stable surface structure at experimental conditions. It was found that in oxidation processes, surface Ti atoms are more favorable for oxygen adsorption and dissociation than Fe atoms. The energy barrier of Fe ion diffusion towards the surface, on the other hand, is lower than Ti ion diffusion, which contributes to the Fe2O3-dominant nanobelt formation. The volume change due to high temperature associated with the solid state transformation at the Fe2O3/FeTiO3 interface produces compressive stresses, which stimulate Fe2O3 nanobelt growth to accompany the interface reaction. Also, as the vacancy formation energy of FeTiO3 is lower than Fe2O3 in the reduction process, it indicates that it is easier for a FeTiO3 surface to form vacancy defects, thereby enhancing the porous surface structure formation and O2 diffusivity. The good agreements between experiments and DFT calculations further substantiate nanostructure formation mechanism in redox reactions of iron titanium composite materials.

Jonathan A. Fan

Papers

Near 100% CO selectivity in nanoscaled iron-based oxygen carriers for chemical looping methane partial oxidation.

Generation of correlated photon pairs in a microstructure fiber.

Quantum cascade lasers with integrated plasmonic antenna-array collimators.

Analysis of material selection on dielectric metasurface performance

Nanostructure formation mechanism and ion diffusion in iron–titanium composite materials with chemical looping redox reactions