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

The optical properties of metal nanoparticles have long been of interest in physical chemistry, starting with Faraday's investigations of colloidal gold in the middle 1800s. More recently, new lithographic techniques as well as improvements to classical wet chemistry methods have made it possible to synthesize noble metal nanoparticles with a wide range of sizes, shapes, and dielectric environments. In this feature article, we describe recent progress in the theory of nanoparticle optical properties, particularly methods for solving Maxwell's equations for light scattering from particles of arbitrary shape in a complex environment. Included is a description of the qualitative features of dipole and quadrupole plasmon resonances for spherical particles; a discussion of analytical and numerical methods for calculating extinction and scattering cross-sections, local fields, and other optical properties for nonspherical particles; and a survey of applications to problems of recent interest involving triangula...

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The Optical Properties of Metal Nanoparticles: The Influence of Size, Shape, and Dielectric Environment

Dye-sensitized solar cells (DSCs) offer the possibilities to design solar cells with a large flexibility in shape, color, and transparency. DSC research groups have been established around the worl ...

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Dye-Sensitized Solar Cells

Highly luminescent semiconductor quantum dots (zinc sulfide-capped cadmium selenide) have been covalently coupled to biomolecules for use in ultrasensitive biological detection. In comparison with organic dyes such as rhodamine, this class of luminescent labels is 20 times as bright, 100 times as stable against photobleaching, and one-third as wide in spectral linewidth. These nanometer-sized conjugates are water-soluble and biocompatible. Quantum dots that were labeled with the protein transferrin underwent receptor-mediated endocytosis in cultured HeLa cells, and those dots that were labeled with immunomolecules recognized specific antibodies or antigens.

http://science.sciencemag.org/content/sci/281/5385/2016.full.pdf

Quantum Dot Bioconjugates for Ultrasensitive Nonisotopic Detection

Strong infrared optogalvanic signals have been observed in the region from 3600–4100 cm−1 for H, He, Li, Ne, and Ar excited in hollow cathode discharges as a result of transitions induced among low Rydberg states of the atoms by a cw F-center laser. On the order of fifty transitions have been assigned in both neon and argon, eleven in helium, and one each in lithium and hydrogen. Studies of the quenching of helium and neon optogalvanic signals by the addition of hydrogen, deuterium and nitrogen to the inert gas plasmas indicate that a quasi-resonant process is occurring for the quenching of helium n = 4 → 6 transitions by H2. The high signal-to-noise ratios observed for many of these transitions with only a few milliwatts of laser power illustrates the potential of this technique for studying excited states of atoms and molecules in plasma environments and suggests the use of atomic Rydberg optogalvanic spectra for frequency calibration in the infrared.

Optogalvanic Spectroscopy in Recombination-Limited Plasmas with Color Center Lasers

Milliwatt average power terahertz quantum cascade lasers (THz-QCLs, 2 THz to 5 THz) have been developed for spectroscopy and as local oscillators for heterodyne receivers. Novel DFB THz-QCLs have been fabricated and show single-mode operation. The narrow line widths of <10 MHz and stark shift tuning of of 6 GHz, allows for wavelength modulation spectroscopy of low pressure gasses in the unexplored THz frequency band. The same devices also act as local-oscillators for heterodyne receivers for remote-sensing and astronomy. Lastly we report on improved tunable DFB devices for use in spectroscopy.

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THz QCLs for heterodyne receivers and wavelength modulation spectroscopy

By exploiting the strong charge-transfer-to-solvent (CTTS) resonances characteristic of all anions in aqueous electrolytes, their interfacial properties are measured using SHG spectroscopy in the deep ultraviolet.

Resonant UV SHG Studies of Ion Adsorption at Aqueous Interfaces

COMMUNICATIONS Infrared laser spectroscopy of uracil in a pulsed slit jet

Ultrafast time-resolved extreme ultraviolet (EUV) reflectivity measurements of optically pumped amorphous carbon (a-C) have been performed with the FERMI free electron laser (FEL). This work extends the energy range used in previous reflectivity studies and adds polarization dependence. The EUV probe is known to be sensitive to lattice dynamics, since in this range the reflectivity is essentially unaffected by the photo-excited surface plasma. The exploitation of both s- and p-polarized EUV radiation permits variation of the penetration depth of the probe; a significant increase in the characteristic time is observed upon increasing the probing depth (1 vs. 5 ps) due to hydrodynamic expansion and consequent destruction of the excited region, implying that there is only a short window during which the probed region is in the isochoric regime. A weak wavelength dependence of the reflectivity is found, consistent with previous measurements and implying a maximum electronic temperature of 0.8 eV ± 0.4.

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Richard J. Saykally

Papers

Optogalvanic Spectroscopy in Recombination-Limited Plasmas with Color Center Lasers

THz QCLs for heterodyne receivers and wavelength modulation spectroscopy

Resonant UV SHG Studies of Ion Adsorption at Aqueous Interfaces

COMMUNICATIONS Infrared laser spectroscopy of uracil in a pulsed slit jet

Free Electron Laser Measurement of Liquid Carbon Reflectivity in the Extreme Ultraviolet