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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

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

Single-layer metal dichalcogenides are two-dimensional semiconductors that present strong potential for electronic and sensing applications complementary to that of graphene.

/pdf/electronics-and-optoelectronics-of-two-dimensional-2jbqr1unvw.pdf

Electronics and optoelectronics of two-dimensional transition metal dichalcogenides.

The semiconductor ZnO has gained substantial interest in the research community in part because of its large exciton binding energy (60meV) which could lead to lasing action based on exciton recombination even above room temperature. Even though research focusing on ZnO goes back many decades, the renewed interest is fueled by availability of high-quality substrates and reports of p-type conduction and ferromagnetic behavior when doped with transitions metals, both of which remain controversial. It is this renewed interest in ZnO which forms the basis of this review. As mentioned already, ZnO is not new to the semiconductor field, with studies of its lattice parameter dating back to 1935 by Bunn [Proc. Phys. Soc. London 47, 836 (1935)], studies of its vibrational properties with Raman scattering in 1966 by Damen et al. [Phys. Rev. 142, 570 (1966)], detailed optical studies in 1954 by Mollwo [Z. Angew. Phys. 6, 257 (1954)], and its growth by chemical-vapor transport in 1970 by Galli and Coker [Appl. Phys. ...

/pdf/a-comprehensive-review-of-zno-materials-and-devices-21a3zjadem.pdf

A comprehensive review of zno materials and devices

and deformations are obtained after removal of the silica matrix using aqueous HF. Our study indicates that mesoporous silicas such as C16MCM-41, C22MCM-41, and SBA-15 can act as good templates for the synthesis of Pd nanowires. Moreover, a significantly depressed melting point of the Pd nanowires is observed around 300 C. To the best of our knowledge, this is the first report on the synthesis and thermal behavior of Pd nanowires of less than 10 nm diameter. Along with our matrix-assisted process, in particular, our low-temperature CVI approach is attractive because it can be carried out under conditions mild enough to avoid any disruption of both the desired material and the template structure. The combined matrix-assisted and CVI process can be extended not only to other sizes of nanowires but also to multidimensional structures using appropriate host architectures.

/pdf/melting-and-welding-semiconductor-nanowires-in-nanotubes-4elqch15y6.pdf

Melting and Welding Semiconductor Nanowires in Nanotubes

Metal nanostructures that support surface plasmons are compelling as plasmonic circuit elements and as the building blocks for metamaterials. We demonstrate here the spontaneous self-assembly of shaped silver nanoparticles into three-dimensional plasmonic crystals that display a frequency-selective response in the visible wavelengths. Extensive long-range order mediated by exceptional colloid monodispersity gives rise to optical passbands that can be tuned by particle volume fraction. These metallic supercrystals present a new paradigm for the fabrication of plasmonic materials, delivering a functional, tunable, completely bottom-up optical element that can be constructed on a massively parallel scale without lithography.

/pdf/self-organized-silver-nanoparticles-for-three-dimensional-52yw7upruk.pdf

Self-organized silver nanoparticles for three-dimensional plasmonic crystals.

Semiconductor nanowires represent an important class of nanostructure building block for photovoltaics as well as direct solar-to-fuel application because of their high surface area, tunable bandgap and efficient charge transport and collection. In this talk, I will highlight several recent examples in this lab using semiconductor nanowires and their heterostructures for the purpose of solar energy harvesting. In addition, we have also discovered that the thermoconductivity of the silicon nanowires can be significantly reduced due to phonon scattering, pointing to a very promising approach to design better thermoelectrical materials. It is important to note that the engines that generate most of the world's power typically operate at only 30–40 per cent efficiency, releasing roughly 15 terawatts of heat to the environment. If this “wasted heat” could be recycled, the impact globally would be enormous. Our silicon nanowire thermoelectric technology could have a significant impact in alternative energy generation.

/pdf/semiconductor-nanowires-for-energy-conversion-u457c9sby2.pdf

Semiconductor nanowires for energy conversion

We have developed a general method for assembling colloidal particles into one-dimensional lines of single particle thickness. Well-spaced, parallel single particle lines can be readily deposited on a substrate from a dilute Langmuir-Blodgett particle monolayer via a stick-slip motion of the water-substrate contact line. The particle density within the lines is controllable by the particle concentration in the monolayer as well as the pulling speed of the substrate. Lines of a great variety of materials and sizes, ranging from a few nanometers to a few micrometers, have been demonstrated. Multiple depositions create complex patterns such as cross lines, even of different particles. The ability of placing nanoparticles into one-dimensional arrays enables the construction of higher hierarchical device structures. For example, using gold nanoparticle seeds, vertical single nanowire arrays of silicon can be grown replicating the pattern of single particle lines.

/pdf/a-general-method-for-assembling-single-colloidal-particle-dd79f8gdxl.pdf

A general method for assembling single colloidal particle lines.

The acid-catalyzed synthesis of highly ordered mesostructured materials has led to a variety of twoand three-dimensional periodic symmetries, and has proven to be an effective route for the generation of fibers, spheres, thin films, and other monolithic forms of mesoporous materials. Zhao et al. recently used non-ionic poly(alkylene oxide) block copolymers, under acidic conditions, to prepare well-ordered, hexagonal mesoporous silica, denoted SBA-15, featuring uniform and adjustable large pore sizes combined with thick hydrothermally stable walls. The catalytic effect of fluoride in the synthesis of mesoporous silica at neutral to basic pH has been described by Voegtlin et al. Fluoride has been successfully used to extend the pH range over which anionic silica precursors can be utilized to create organized periodic structures; it has been used to diminish framework defects in zeolites, and to improve the organization in MCM-41 molecular sieves and MSU-X materials. However, to the best of our knowledge, no studies have been reported on the role of fluoride on cationic silica species in the aqueous acid-synthesis of ordered porous silica. In this communication, we describe the hierarchical ordering effects induced by small amounts of fluoride added during the synthesis of SBA-15-type mesoporous silica under acidic aqueous conditions. The non-ionic poly(ethylene oxide)-b-poly(propylene oxide)-b-poly(ethylene oxide) triblock copolymer EO20PO70EO20 (Pluronic P123) has been employed as the structure-directing agent. At low pH, remarkably well-ordered, hydrothermally stable, large hexagonal mesoporous silica rods with uniform channels extending over micrometer-sized length scales, and with few defects, have been synthesized. The fluoride-induced enhancement of order has enabled the preparation of SBA-15 materials at moderate acidity (~ pH 2.5±3) without compromising the long-range hexagonal symmetry. The mesoporous silicas possess narrow pore-size distributions, hydrothermally stable frameworks, large surface areas, and pore volumes of up to 0.92 cm/g. This work has been motivated by our interest in i) the patterning of mesoporous materials ranging from mesoscopic to macroscopic length scales while retaining molecular-level structural control and ii) understanding the underlying mechanism for the acid-catalyzed mesoporous silica synthesis. Addition of small amounts of fluoride (F:Si molar ratios of 0.008 and 0.03; fluoride source: NH4F or (NH4)2SiF6) during the aqueous acidic SBA-15-type silica synthesis induces substantial ordering that is manifested on different length scales: both the mesoscopic structure and the macroscopic morphology of the mesoporous silicas are significantly improved. Scanning electron microscopy (SEM) has revealed that small amounts of fluoride bring about the formation of large mesoporous silica rods (Fig. 1a) when pre-

/pdf/fluoride-induced-hierarchical-ordering-of-mesoporous-silica-37o91je1jv.pdf

Peidong Yang

Papers

Melting and Welding Semiconductor Nanowires in Nanotubes

Self-organized silver nanoparticles for three-dimensional plasmonic crystals.

Semiconductor nanowires for energy conversion

A general method for assembling single colloidal particle lines.

Fluoride-Induced Hierarchical Ordering of Mesoporous Silica in Aqueous Acid-Syntheses