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

$^{a}$L.B. Braly, et al. ``Terahertz Laser Spectroscopy of the Water Dimer Intermolecular Vibrations. I. $(D_{2}O)_{2}$ II. $(H_{2}O)_{2}$'' J. Chem. Phys. 112, 10293 (2000). $^{b}$F.N. Keutsch, et al. ``Complete Characterization of the $(D_{2}O)_{2}$ Ground State: High $K_{a}$ Rotation-Tunneling Levels.'' Submitted 2000. $^{c}$G.C. Groenenboom, et al. ``Water pair potential of near spectroscopic accuracy. II. Vibration-rotation-tunneling levels of the water dimer.'' J. Chem. Phys. 113, 6702 (2000).

Characterization of the water dimer donor torsion vibration by fir-vrt spectroscopy

The three-dimensional intermolecular potential energy surface (IPS) for Ar-NH, has been determined from a least-squares fit to 61 far infrared and microwave vibration-rotation-tunneling (VRT) measurements and to temperature-dependent second virial coefficients. The three intermolecular coordinates (R ,19,+) are treated without invoking any approximations regarding their separability, and the NH, inversion-tunneling motion is included adiabatically. A surface with 13 variable parameters has been optimized to accurately reproduce the spectroscopic observables, using the collocation method to treat the coupled multidimensional dynamics within a scattering formalism. Anisotropy in the IPS is found to significantly mix the free rotor basis functions. The 149.6 cm-’ global minimum on this surface occurs with the NH, symmetry axis nearly perpendicular to the van der Waals bond axis (@=96.6”), at a center-of-mass separation of 3.57 A, and with the Ar atom midway between two of the NH3 hydrogen atoms (+=60”). The position of the global minimum is very different from the center-of-mass distance extracted from microwave spectroscopic studies. Long-range (R > 3.8 A) attractive interactions are greatest when either a N-H bond or the NH, lone pair is directed toward the argon. Comparisons with ab initio surfaces for this molecule as well as the experimentally determined IPS for Ar-Hz0 are presented.

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Spectroscopic cietermination of the intermolecuBar potential energy surface for Ar-NH3 :

Nitrogen Quadrupole Coupling Constants for HCN and H2CN+: Explanation of the Absence of Fine Structure in the Microwave Spectrum of Interstellar H2CN+.

Richard J. Saykally

Papers

Characterization of the water dimer donor torsion vibration by fir-vrt spectroscopy

Spectroscopic cietermination of the intermolecuBar potential energy surface for Ar-NH3 :

Nitrogen Quadrupole Coupling Constants for HCN and H2CN+: Explanation of the Absence of Fine Structure in the Microwave Spectrum of Interstellar H2CN+.

Multidimensional inte:rmolecular potential surfaces from vibration rotation-tunnel ing (vrt)

Ultraviolet laser induced fluorescence spectroscopy of molecular ions in a radiofrequency ion trap

Richard J. Saykally

Papers

Characterization of the water dimer donor torsion vibration by fir-vrt spectroscopy

Spectroscopic cietermination of the intermolecuBar potential energy surface for Ar-NH3 :

Nitrogen Quadrupole Coupling Constants for HCN and H2CN+: Explanation of the Absence of Fine Structure in the Microwave Spectrum of Interstellar H2CN+.

Multidimensional inte:rmolecular potential surfaces from vibration­ rotation-tunnel ing (vrt)

Ultraviolet laser induced fluorescence spectroscopy of molecular ions in a radiofrequency ion trap

Multidimensional inte:rmolecular potential surfaces from vibration rotation-tunnel ing (vrt)