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

Detection of the N = 3-2 transition of CCH in Orion and determination of the molecular rotational constants

We report the first high resolution spectrum of a librational vibration for a water cluster. Four parallel bands of (H2O)3 were measured between 510 and 525 cm−1 using diode laser vibration–rotation–tunneling (VRT) spectroscopy. The bands lie in the “librational band” region of liquid water and are assigned to the nondegenerate out of plane librational vibration. The observation of at least three distinct bands within 8 cm−1 originating in the vibrational ground state is explained by a dramatically increased splitting of the rovibrational levels relative to the ground state by bifurcation tunneling and is indicative of a greatly reduced barrier height in the excited state. This tunneling motion is of special significance, as it is the lowest energy pathway for breaking and reforming of hydrogen bonds, a salient aspect of liquid water dynamics.

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Far-infrared laser vibration–rotation–tunneling spectroscopy of water clusters in the librational band region of liquid water

A second Ar2HCl intermolecular vibration–rotation band centered at 37.2 cm−1 has been measured and assigned as a b‐type transition originating from the ground state. Nuclear hyperfine splittings were resolved for both chlorine isotopes. The rotational constants determined from the data indicate coupling between an Ar–Ar stretching or bending coordinate and the Ar2 –HCl vibrational coordinates. As a result of this particular vibrational motion, Ar2H 35Cl undergoes an axis‐switching transition while the Ar2H 37Cl isotope does not. In addition, the measured hyperfine projections indicate the possibility of coupling between the Ar2 –HCl stretching and bending modes, preventing an absolute vibrational assignment. These results indicate that the ‘‘reversed adiabatic’’ approximation employed by Hutson, Beswick, and Halberstadt in their theoretical study of Ar2HCl [J. Chem. Phys. 90, 1337 (1989)] is not appropriate for the complicated intramolecular dynamics presently observed in this system.

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An investigation of three‐body effects in intermolecular forces. II. Far‐infrared vibration–rotation–tunneling laser spectroscopy of Ar2HCl

Recent experimental and theoretical work has demonstrated that certain anions can exhibit enhanced concentrations at aqueous interfaces and that the adsorption of bromide is particularly important for chemical reactions on atmospheric aerosols, including the depletion of ozone. UV second harmonic generation resonant with the bromide charge-transfer-to-solvent band and a Langmuir adsorption model are used to determine the affinity of bromide for both the air/water and dodecanol/water interfaces. The Gibbs free energy of adsorption for the former is determined to be −1.4 kJ/mol with a lower 90% confidence limit of −4.1 kJ/mol. For the dodecanol/water interface the data are best fit with a Gibbs free energy of +8 kJ/mol with an estimated lower limit of −4 kJ/mol.

Measurement of Bromide Ion Affinities for the Air/Water and Dodecanol/Water Interfaces at Molar Concentrations by UV Second Harmonic Generation Spectroscopy

A computer controlled velocity modulation dye laser spectrometer is used to measure the A 2Πu←X 2Σ+g (7,3) band of N+2. The Doppler‐limited absorption spectra are fit to a model Hamiltonian to obtain precise parameters for the states. The ion rotational temperature was determined to be 461±11, and the translational temperature was estimated to be near 1200 K.

Richard J. Saykally

Papers

Detection of the N = 3-2 transition of CCH in Orion and determination of the molecular rotational constants

Far-infrared laser vibration–rotation–tunneling spectroscopy of water clusters in the librational band region of liquid water

An investigation of three‐body effects in intermolecular forces. II. Far‐infrared vibration–rotation–tunneling laser spectroscopy of Ar2HCl

Measurement of Bromide Ion Affinities for the Air/Water and Dodecanol/Water Interfaces at Molar Concentrations by UV Second Harmonic Generation Spectroscopy

Electronic absorption spectroscopy of molecular ions in plasmas by dye laser velocity modulation: The A←X system of N+2