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

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 ability to control the size, shape, and material of a surface has reinvigorated the field of surface-enhanced Raman spectroscopy (SERS). Because excitation of the localized surface plasmon resonance of a nanostructured surface or nanoparticle lies at the heart of SERS, the ability to reliably control the surface characteristics has taken SERS from an interesting surface phenomenon to a rapidly developing analytical tool. This article first explains many fundamental features of SERS and then describes the use of nanosphere lithography for the fabrication of highly reproducible and robust SERS substrates. In particular, we review metal film over nanosphere surfaces as excellent candidates for several experiments that were once impossible with more primitive SERS substrates (e.g., metal island films). The article also describes progress in applying SERS to the detection of chemical warfare agents and several biological molecules.

Surface-Enhanced Raman Spectroscopy

6. Rehybridization of the Acceptor (RICT) 3908 7. Planarization of the Molecule (PICT) 3909 III. Fluorescence Spectroscopy 3909 A. Solvent Effects and the Model Compounds 3909 1. Solvent Effects on the Spectra 3909 2. Steric Effects and Model Compounds 3911 3. Bandwidths 3913 4. Isoemissive Points 3914 B. Dipole Moments 3915 C. Radiative Rates and Transition Moments 3916 1. Quantum Yields and Radiationless Deactivation Processes 3916

Structural Changes Accompanying Intramolecular Electron Transfer: Focus on Twisted Intramolecular Charge-Transfer States and Structures

The design and realization of metallic nanostructures with tunable plasmon resonances has been greatly advanced by combining a wealth of nanofabrication techniques with advances in computational electromagnetic design. Plasmonics — a rapidly emerging subdiscipline of nanophotonics — is aimed at exploiting both localized and propagating surface plasmons for technologically important applications, specifically in sensing and waveguiding. Here we present a brief overview of this rapidly growing research field.

https://dsl.nju.edu.cn/litao/res/Plasmonic%20review/%5bReview%20article%5d%20nphoton.2007%20Photonic-Nano-optics%20from%20sensing%20to%20waveguiding.pdf

Nano-optics from sensing to waveguiding

Excluded-volume-anisotropy (EVA) model predictions for the cavity formation free energies of rigid linear polyatomic chains dissolved in hard sphere fluids are tested against Monte Carlo Widom insertion simulation measurements performed as a function of chain length (1⩽N⩽6), the ratio of the chain bead diameter to the solvent diameter (0⩽σ/σS⩽3), and solvent density (0.1⩽ρσS3⩽0.8). The results reveal a linear dependence of cavity formation energy on chain length for N⩾2. This allows extrapolation to chain lengths larger than can be measured by direct insertion. EVA predictions are found to be in good agreement with direct simulation results as well as long chain length extrapolations (up to N=50). As an illustration of potential practical application of these results, the EVA model is used to predict the cavity formation free energy of n-hexane dissolved in water and in the pure n-hexane liquid as a function of temperature and pressure, throughout the liquid temperature range.

Cavity formation free energies for rigid chains in hard sphere fluids

The chemical potentials of spherical and diatomic dumbbell particles dissolved in a hard dumbbell fluid are determined using the Widom insertion Monte Carlo simulation method. Results obtained as a function of fluid density and solute–solvent size ratio are compared with previous simulation results and analytical hard body fluid expressions derived from bonded hard sphere (BHS), scaled particle theory (SPT), and corresponding hard sphere (CHS) equations of state. The BHS predictions best represent all the simulation results, while SPT predictions are comparably accurate except for small solute particles dissolved in high-density fluids, and CHS predictions are exact to first order in solute size and solvent density but somewhat less accurate for large particles at high densities. Simulations of the excess reaction free energy for model dissociation and isomerization processes illustrate the subtle effects of solute shape on cavity formation energy for particles with identical molecular volumes.

Cavity formation energies for diatomic and spherical solutes in a diatomic hard body fluid

Quantitative applications of surface-enhanced resonance Raman scattering (SERRS) are often limited by the reproducibility of SERRS intensities, given the difficulty of controlling analyte-substrate interactions and the associated local field enhancement. As demonstrated here, SERRS from dye molecules even within the same structural class that compete with similar substrates display distinct spectral intensities that are not proportional to analyte concentrations, which limits their use as internal standardization probes and/or for multiplex analysis. Recently, we demonstrated that isotopic variants of rhodamine 6G (R6G), namely R6G-d0 and R6G-d4, can be used for internal standards in SERRS experiments with a linear optical response from picomolar to micromolar concentrations (of total analytes). Here we extend these results by describing a straightforward method for obtaining isotopomeric pairs of other Raman active dyes by hydrogen-deuterium exchange conditions for substitution at electron rich aromatic heterocycles. Most of the known SERRS active probes can be converted into the corresponding isotopomeric molecule by this exchange method, which significantly expands the scope of the isotopic edited internal standard (IEIS) approach. The relative quantification using IEIS enables accurate, reproducible (residual standard deviation+/-2.2%) concentration measurements over a range of 200 pM to 2 microM. These studies enable easy access to a variety of isotopically substituted Raman active dyes and establish the generality of the methodology for quantitative SERRS measurements. For the first time, three rhodamine 6G isotopomers have been created and show distinct Raman spectra, demonstrating the principle of the approach for application as a multiplex technique in biomolecular detection/quantification.

Accurate concentration measurements using surface-enhanced Raman and deuterium exchanged dye pairs.

Direct (solute–water) and indirect (water–water) contributions to adsorption at an air–water interface are identified using the Widom potential distribution theorem and quantified using molecular dynamics simulations of a liquid water droplet containing either neopentane or iodide-like solutes with charges of 0 or ±1. The results are used to quantitatively compare direct and indirect energetic and entropic contributions to adsorption, as well as to critically test surface capillary wave, linear response (LR), and mean field (MF) predictions. The negative signs of the total adsorption energies and entropies of both the anionic and cationic solutes are found to result from indirect adsorption induced changes in water–water interactions, rather than from surface capillary wave perturbations, which are found to be asymmetric with respect to solute charge. The LR and MF approximations both accurately describe the adsorption of neutral (hydrophobic) solutes, while for ionic solutes the MF approximation is entir...

Interfacial Adsorption of Neutral and Ionic Solutes in a Water Droplet.

The Clausius inequality is converted to an equality in which a positive quantity with units of energy, termed the deficit function, is used to track entropy production and other effects of irreversible processes. This inequality rectification procedure is shown to yield particularly transparent new derivations of several important results based on the Second Law, with some consequences that have apparently not been previously recognized. For example, the Helmholtz free energy of any system is shown to decrease towards a minimum as the result of any spontaneous processes which begin and end at the same temperature and involve no work exchange, without the need to invoke the stricter requirements of fixed system volume and/or chemical composition.

Dor Ben-Amotz

Papers

Cavity formation free energies for rigid chains in hard sphere fluids

Cavity formation energies for diatomic and spherical solutes in a diatomic hard body fluid

Accurate concentration measurements using surface-enhanced Raman and deuterium exchanged dye pairs.

Interfacial Adsorption of Neutral and Ionic Solutes in a Water Droplet.

Rectification of thermodynamic inequalities