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

Photocatalyticwatersplittingrepresentsapromisingwaytoproducerenewablehydrogenfuel from solar energy. Ultrathin semiconductor electrodes for water splitting are of particular interest because the optical absorption occurs in the region where photogenerated charge carriers can effectively contribute to the chemical reactions on the surface. It is therefore important to manipulate and concentrate the incident light so that more photons can be absorbed within the thin film. Here we show an enhanced photocurrent in a thin-film iron oxide photoanode coated on arrays of Au nanopillars. The enhancement can be attributed primarily to the increased optical absorption originating from both surface plasmon resonances and photonic-mode light trapping in the nanostructured topography. The resonances can be tuned to a desirable wavelength by varying the thickness of the iron oxide layer. A net enhancement as high as 50% was observed over the solar spectrum.

/pdf/plasmon-enhanced-photocatalytic-activity-of-iron-oxide-on-5cxhhs79a4.pdf

Plasmon-Enhanced Photocatalytic Activity of Iron Oxide on Gold

Detection and characterization of molecular interactions on membrane surfaces is important to biological and pharmacological research. In one embodiment, silver nanocubes interfaced with glass-supported model membranes form a label-free sensor that measures protein binding to the membrane. The present device and technique utilizes plasmon resonance scattering of nanoparticles, which are chemically coupled to the membrane. In contrast to other plasmonic sensing techniques, this method features simple, solution-based device fabrication and readout. Static and dynamic protein/membrane binding are monitored and quantified.

Plasmonic system for detecting binding of biological molecules

(Invited) Atomically Thin Two-Dimensional Organic-Inorganic Hybrid Perovskites

Solid-solid interfacial processes greatly affect the performance of electronic and composite materials, but probing the dynamics of buried interfaces is challenging and often involves lengthy or invasive sample preparation. We show that bilayer nanoribbons-made here of tin dioxide and copper-are convenient structures for observing as-made interfaces as they respond to changing temperature in a transmission electron microscope (TEM). At low temperatures (<200 degrees C), differential thermal expansion causes the bilayers to bend when heated or cooled, with the motion determined by the extent of Cu-SnO(2) epitaxy. At higher temperatures, we are able to watch-in real time and with nanometer resolution-a progression of grain growth, interdiffusion, island formation, solid-state chemical reactions, and melting. This novel TEM geometry is readily applicable to other nanoribbon/coating combinations and is well suited to observing interfacial phenomena driven thermally or by the application of mechanical, electrical, or magnetic forces.

http://nanowires.berkeley.edu/wp-content/uploads/2013/01/106.pdf

Thermally driven interfacial dynamics of metal/oxide bilayer nanoribbons.

Ferroelectric semiconductors are rare materials with both spontaneous polarizations and visible light absorptions that are promising for designing functional photoferroelectrics, such as optical switches and ferroelectric photovoltaics. The emerging halide perovskites with remarkable semiconducting properties also have the potential of being ferroelectric, yet the evidence of robust ferroelectricity in the typical three-dimensional hybrid halide perovskites has been elusive. Here, we report on the investigation of ferroelectricity in all-inorganic halide perovskites, CsGeX3, with bandgaps of 1.6 to 3.3 eV. Their ferroelectricity originates from the lone pair stereochemical activity in Ge (II) that promotes the ion displacement. This gives rise to their spontaneous polarizations of ~10 to 20 μC/cm2, evidenced by both ab initio calculations and key experiments including atomic-level ionic displacement vector mapping and ferroelectric hysteresis loop measurement. Furthermore, characteristic ferroelectric domain patterns on the well-defined CsGeBr3 nanoplates are imaged with both piezo-response force microscopy and nonlinear optical microscopic method.

https://escholarship.org/content/qt4vj925mz/qt4vj925mz.pdf

Peidong Yang

Papers

Plasmon-Enhanced Photocatalytic Activity of Iron Oxide on Gold

Plasmonic system for detecting binding of biological molecules

(Invited) Atomically Thin Two-Dimensional Organic-Inorganic Hybrid Perovskites

Thermally driven interfacial dynamics of metal/oxide bilayer nanoribbons.

Ferroelectricity in a semiconducting all-inorganic halide perovskite.