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

Extensive new spectroscopic measurements are combined with a global analysis of the ground state data in order to re-examine and to refine the description of the excited vibration rotation tunneling (VRT) states of the water dimer. Notably, six new ‘donor torsion’ subbands are analytically identified, current vibrational assignments of the K a = 1 stacks are reassessed, the previously reported (H2O)2 donor torsion overtone (DT)2 and hydrogen bond stretch (S) data sets are augmented, and four new (S) subbands have been measured. Unusually large Coriolis effects are predicted, excited state E2 ↔ E1 assignments are reinforced, and possibilities of experimentally determining ground state AS splitting in (H2O)2 from excited state data are discussed.

/pdf/refinements-in-the-description-of-excited-vrt-states-of-the-2ns19yldag.pdf

Refinements in the description of excited VRT states of the water dimer

Cavity ringdown laser absorption spectroscopy

The behavior of ions at aqueous interfaces influences vital processes in many fields but has long remained a subject of controversy. Over the past decade, counterintuitive surface concentration enhancement of several ions in aqueous solution has been demonstrated via nonlinear laser spectroscopy and mass spectrometry. While the evidence for significant ion enhancement at the air-water interface is convincing, the mechanism remains incompletely understood. Toward this end, we present the full broadband DUV-SFG spectrum of the charge-transfer-to-solvent (CTTS) band of interfacial aqueous iodide measured in a single laser shot with a newly developed broadband deep UV-SFG technique, clearly revealing a ∼8 nm redshift and a significant linewidth narrowing relative to bulk solution spectra. KI and NaI solutions yield indistinguishable results. Additionally, we observe a dramatic change in the relative intensities of the J = 3/2 and 1/2 CTTS transitions.

/pdf/broadband-deep-uv-spectra-of-interfacial-aqueous-iodide-2fznmsmdlc.pdf

Broadband Deep UV Spectra of Interfacial Aqueous Iodide

Coherent anti-Stokes Raman scattering (CARS) microscopy is a promising tool for chemically selective imaging based on molecular vibrations. While CARS is currently used as a biological imaging tool, many variations are still being developed, perhaps the most important being multiplex CARS microscopy. Multiplex CARS has the advantage of comparing images based on different molecular vibrations without changing the excitation wavelengths. Here we demonstrate both high-spectral- and spatial-resolution multiplex CARS imaging of polymer films, using a simple scheme for chirped CARS with a spectral bandwidth of 300 cm(-1).

/pdf/chirped-coherent-anti-stokes-raman-scattering-as-a-high-1htchbn7zk.pdf

Chirped coherent anti-Stokes Raman scattering as a high-spectral- and spatial-resolution microscopy

The J= 0–1 transitions of a 3Π carbon monoxide have been measured in several isotopic forms and vibrational states: CO (v=0–4), 13CO (v=0–3), and C18O (v=0–4). These new data were combined with the many lambda doublet transition frequencies previously available from the molecular beam electric resonance experiments of Klemperer and co‐workers and fit to a model Hamiltonian essentially the same as that used for previously published fits of combined optical–lambda doubling data. Many different fits were made including single state–single isotope, multistate–single isotope, single state–multi‐isotope, and multistate–multi‐isotope ones. Among the important conclusions are (1) that the explicit perturbation due to the v′=0 level of the a′ 3∑+ state must be included for adequate fits of the v=0–3 data (and of course the more strongly perturbed v=4 data), (2) that the spin–orbit coupling constant A can be determined well from just the microwave–rf data if several isotopic forms are fitted together, and (3) that ...

Richard J. Saykally

Papers

Refinements in the description of excited VRT states of the water dimer

Cavity ringdown laser absorption spectroscopy

Broadband Deep UV Spectra of Interfacial Aqueous Iodide

Chirped coherent anti-Stokes Raman scattering as a high-spectral- and spatial-resolution microscopy

The microwave spectrum of CO in the a 3Π state. I. The J=0–1 transitions in CO, 13CO, and C18O