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

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

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

/pdf/self-assembled-monolayers-of-thiolates-on-metals-as-a-form-1neb0hj3k4.pdf

Self-assembled monolayers of thiolates on metals as a form of nanotechnology.

Molecular conductance junctions are structures in which single molecules or small groups of molecules conduct electrical current between two electrodes. In such junctions, the connection between the molecule and the electrodes greatly affects the current-voltage characteristics. Despite several experimental and theoretical advances, including the understanding of simple systems, there is still limited correspondence between experimental and theoretical studies of these systems.

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Electron transport in molecular wire junctions.

A theory for surface enhanced Raman scattering (SERS) is developed Effects due to realistic surface geometry and dielectric properties are included Three sources of enhanced Raman scattering are noted: the image dipole enhancement effect, the increase of local field (’’lightning rod’’ effect), and the resonant excitation of surface plasmons The surface is modeled as a hemispheroid protruding from a conducting plane, although other models are considered The spherical limit is discussed in some detail and molecular orientation effects are considered Cross sections for Mie, Rayleigh, and Raman scattering are derived

Electromagnetic theory of enhanced Raman scattering by molecules adsorbed on rough surfaces

Electron transmission through molecules and molecular interfaces has been a subject of intensive research due to recent interest in electron-transfer phenomena underlying the operation of the scanning-tunneling microscope on one hand, and in the transmission properties of molecular bridges between conducting leads on the other. In these processes, the traditional molecular view of electron transfer between donor and acceptor species gives rise to a novel view of the molecule as a current-carrying conductor, and observables such as electron-transfer rates and yields are replaced by the conductivities, or more generally by current-voltage relationships, in molecular junctions. Such investigations of electrical junctions, in which single molecules or small molecular assemblies operate as conductors, constitute a major part of the active field of molecular electronics. In this article I review the current knowledge and understanding of this field, with particular emphasis on theoretical issues. Different approaches to computing the conduction properties of molecules and molecular assemblies are reviewed, and the relationships between them are discussed. Following a detailed discussion of static-junctions models, a review of our current understanding of the role played by inelastic processes, dephasing and thermal-relaxation effects is provided. The most important molecular environment for electron transfer and transmission is water, and our current theoretical understanding of electron transmission through water layers is reviewed. Finally, a brief discussion of overbarrier transmission, exemplified by photoemission through adsorbed molecular layers or low-energy electron transmission through such layers, is provided. Similarities and differences between the different systems studied are discussed.

http://atto.tau.ac.il/~nitzan/anrev-published.pdf

Electron transmission through molecules and molecular interfaces

Optical properties of small dielectric spheroids with or without adsorbed molecules are studied theoretically. Expressions for the absorption line shapes, the radiative and nonradiative decay rates, and quantum yields are derived. In the case of a molecule near a spheroid the magnitudes differ dramatically from the corresponding case of a molecule near a plane.

Spectroscopic properties of molecules interacting with small dielectric particles

Transport of electrons in a single molecule junction is the simplest problem in the general subject area of molecular electronics. In the past few years, this area has been extended to probe beyond the simple tunnelling associated with large energy gaps between electrode Fermi level and molecular levels, to deal with smaller gaps, with near-resonance tunnelling and, particularly, with effects due to interaction of electronic and vibrational degrees of freedom. This overview is devoted to the theoretical and computational approaches that have been taken to understanding transport in molecular junctions when these vibronic interactions are involved. After a short experimental overview, and discussion of different test beds and measurements, we define a particular microscopic model Hamiltonian. That overall Hamiltonian can be used to discuss all of the phenomena dealt with subsequently. These include transition from coherent to incoherent transport as electron/vibration interaction increases in strength, inelastic electron tunnelling spectroscopy and its interpretation and measurement, affects of interelectronic repulsion treated at the Hubbard level, noise in molecular transport junctions, non-linear conductance phenomena, heating and heat conduction in molecular transport junctions and current-induced chemical reactions. In each of these areas, we use the same simple model Hamiltonian to analyse energetics and dynamics. While this overview does not attempt survey the literature exhaustively, it does provide appropriate references to the current literature (both experimental and theoretical). We also attempt to point out directions in which further research is required to answer cardinal questions concerning the behaviour and understanding of vibrational effects in molecular transport junctions. (Some figures in this article are in colour only in the electronic version)

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Abraham Nitzan

Papers

Electron transport in molecular wire junctions.

Electromagnetic theory of enhanced Raman scattering by molecules adsorbed on rough surfaces

Electron transmission through molecules and molecular interfaces

Spectroscopic properties of molecules interacting with small dielectric particles

Molecular transport junctions: vibrational effects