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

We report refined results for the equilibrium constant for water dimerization (KP), computed as a function of temperature via fully coupled 6D calculation of the canonical (H2O)2 partition function on VRT(ASP-W)III, the most accurate water dimer potential energy surface currently available. Partial pressure isotherms calculated for a range of temperatures and relative humidities indicate that water dimers can exist in sufficient concentrations (e.g., 1018 m-3 at 30 °C and 100% relative humidity) to affect physical and chemical processes in the atmosphere. The determinations of additional thermodynamic properties (ΔG, ΔH, ΔS, CP, and CV) for (H2O)2 are presented, and the role of quasi-bound states in the calculation of KP is discussed at length.

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Water Dimers in the Atmosphere II: Results from the VRT(ASP-W)III Potential Surface

With the Hamiltonian derived in the preceding paper and the ab initio potentials of T. Burgi, S. Graf, S. Leutwyler, and W. Klopper [J. Chem. Phys. 103, 1077 (1995)] and of J. G. C. M. van Duijneveldt‐van de Rijdt and F. B. van Duijneveldt [Chem. Phys. Lett. 237, 560 (1995)], we calculate the pseudo‐rotation tunneling levels in a rotating water trimer. The internal motions are treated by a three‐dimensional discrete variable representation and the Coriolis coupling with the overall rotation is included. Also the effects of donor tunneling are included, by introducing semi‐empirical coupling matrix elements. New experimental data are presented for the c‐type band at 87.1 cm−1 in (H2O)3, which show that specific levels in the donor tunneling quartets of this band are further split into doublets. With the results of our quantitative calculations and the model of the preceding paper we can understand the mechanisms of all the splittings observed in the earlier high‐resolution spectra of (H2O)3 and (D2O)3, as well as these new splittings, in terms of pseudo‐rotation tunneling, donor tunneling and Coriolis coupling. An unambiguous assignment is given of all the bands observed and analyzed. The ab initio potential of the Van Duijneveldts yields accurate energies of the lower pseudo‐rotation levels, the potential of Burgi et al. performs better for the higher levels. With our analysis we can deduce from the spectra that donor tunneling involves inversion of the trimer.

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Tunneling dynamics, symmetry, and far-infrared spectrum of the rotating water trimer. II. Calculations and experiments

In order to address the well‐known problem that the nearly cyclic structure of (NH3)2 deduced from microwave spectra differs greatly from the hydrogen‐bonded equilibrium structure obtained from ab initio calculations, we have calculated the vibration–rotation–tunneling (VRT) states of this complex, and explicitly studied the effects of vibrational averaging. The potential used is a spherical expansion of a site–site potential which was extracted from ab initio data. The six‐dimensional VRT wave functions for all the lowest states with J=0 and J=1 were expanded in products of radial (van der Waals stretch) functions and free‐rotor states for the internal and overall rotations, which were first adapted to the complete nuclear permutation inversion group G36. Although the (expanded) potential is too approximate to expect quantitative agreement with the observed microwave and far‐infrared spectra, we do find several interesting features: The 14N quadrupole splittings and the dipole moment of the complex, whic...

/pdf/computational-exploration-of-the-six-dimensional-vibration-oyf3tnevgd.pdf

Computational exploration of the six-dimensional vibration-rotation-tunneling dynamics of (NH3)2

Water comes in numerous forms, from isolated clusters to at least one liquid form and 17 known forms of ice. The detailed characterization of water clusters is essential for developing more accurate and detailed models for describing all these different forms. The comparatively simple hydrogen-bond structures in small water clusters help to elucidate the much more complicated cooperative hydrogen bonding in liquid water ( 1 ), which is difficult to reproduce quantitatively from simplified models. The water hexamer has received particular attention as the smallest representative of multicyclic three-dimensional hydrogen-bonded structures. On page 897 of this issue, Perez et al. ( 2 ) report a landmark experimental study that resolves some of the controversies regarding the relative energies of water hexamer isomers.

https://science.sciencemag.org/content/sci/336/6083/814.full.pdf

Pinning Down the Water Hexamer

http://www.cchem.berkeley.edu/rjsgrp/publications/papers/2007/350_otten_2007.pdf

Richard J. Saykally

Papers

Water Dimers in the Atmosphere II: Results from the VRT(ASP-W)III Potential Surface

Tunneling dynamics, symmetry, and far-infrared spectrum of the rotating water trimer. II. Calculations and experiments

Computational exploration of the six-dimensional vibration-rotation-tunneling dynamics of (NH3)2

Pinning Down the Water Hexamer

Observation of nitrate ions at the air/water interface by UV-second harmonic generation