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

/pdf/quantum-mechanical-continuum-solvation-models-3edv963g14.pdf

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

Hydrophobic hydration is considered to have a key role in biological processes ranging from membrane formation to protein folding and ligand binding. Historically, hydrophobic hydration shells were thought to resemble solid clathrate hydrates, with solutes surrounded by polyhedral cages composed of tetrahedrally hydrogen-bonded water molecules. But more recent experimental and theoretical studies have challenged this view and emphasized the importance of the length scales involved. Here we report combined polarized, isotopic and temperature-dependent Raman scattering measurements with multivariate curve resolution (Raman-MCR) that explore hydrophobic hydration by mapping the vibrational spectroscopic features arising from the hydrophobic hydration shells of linear alcohols ranging from methanol to heptanol. Our data, covering the entire 0-100 °C temperature range, show clear evidence that at low temperatures the hydration shells have a hydrophobically enhanced water structure with greater tetrahedral order and fewer weak hydrogen bonds than the surrounding bulk water. This structure disappears with increasing temperature and is then, for hydrophobic chains longer than ~1 nm, replaced by a more disordered structure with weaker hydrogen bonds than bulk water. These observations support our current understanding of hydrophobic hydration, including the thermally induced water structural transformation that is suggestive of the hydrophobic crossover predicted to occur at lengths of ~1 nm (refs 5, 9, 10, 14).

Water structural transformation at molecular hydrophobic interfaces

Effective diameters of atoms and molecules can typically be estimated within about 1% from equation-of state or compressibility data. These estimates correlate well with critical volumes, with molar refractivities, and with tabulated van der Waals volume increments. The correlations hold well even for markedly aspherical or polar molecules. Comparison of a simple perturbed hard-sphere equation of state (the Carnahan-Starling-van der Waals equation, denoted CS-vdW) with molecular dynamics simulations shows that surprisingly good values for both the Lennard-Jones radius and well depth (typically within 1% for {sigma}{sub LJ}, 10% for {epsilon}{sub LJ}) can be obtained by using pressure-density isotherms or equivalent data. Together with empirical correlations, this permits the LJ potential parameters to be estimated simply from the density (at atmospheric pressure) and the heat of vaporization or boiling point temperature. The temperature dependence of the effective diameter can be estimated from a simple model originally introduced by Boltzmann. More sophisticated perturbative theories of liquids predict a small additional density dependence of the effective diameter. Simple analytical expressions for these theoretical models are presented. In particular, the CS-vdW equation is found to predict reliable absolute densities (within 1%) for liquids at high pressures where direct measurements become difficult.

Estimation of effective diameters for molecular fluids

Spectroscopic imaging has been an increasingly critical approach for unveiling specific molecules in biological environments. Toward this goal, we demonstrate hyperspectral stimulated Raman loss (SRL) imaging by intrapulse spectral scanning through a femtosecond pulse shaper. The hyperspectral stack of SRL images is further analyzed by a multivariate curve resolution (MCR) method to reconstruct quantitative concentration images for each individual component and retrieve the corresponding vibrational Raman spectra. Using these methods, we demonstrate quantitative mapping of dimethyl sulfoxide concentration in aqueous solutions and in fat tissue. Moreover, MCR is performed on SRL images of breast cancer cells to generate maps of principal chemical components along with their respective vibrational spectra. These results show the great capability and potential of hyperspectral SRL microscopy for quantitative imaging of complicated biomolecule mixtures through resolving overlapped Raman bands.

/pdf/quantitative-vibrational-imaging-by-hyperspectral-stimulated-2979rfjucl.pdf

Quantitative Vibrational Imaging by Hyperspectral Stimulated Raman Scattering Microscopy and Multivariate Curve Resolution Analysis

The compatibility of nonenhanced Raman spectroscopy with chromatographic and mass spectroscopic proteomic sensing is demonstrated for the first time. High-quality normal Raman spectra are derived from protein solutions with concentrations down to 1 μM and 1 fmol of protein nondestructively probed within the excitation laser beam. These results are obtained using a drop coating deposition Raman (DCDR) method in which the solution of interest is microdeposited (or microprinted) on a compatible substrate, followed by solvent evaporation and backscattering detection. Representative applications include the DCDR detection of insulin derived from an HPLC fraction, nondestructive DCDR followed by MALDI-TOF of lysozyme, the DCDR detection of protein spots deposited using an ink-jet microprinter, and the identification of spectral differences between glycan isomers of equal mass (such as those derived from posttranslationally modified proteins).

Dor Ben-Amotz

Papers

Water structural transformation at molecular hydrophobic interfaces

Estimation of effective diameters for molecular fluids

Quantitative Vibrational Imaging by Hyperspectral Stimulated Raman Scattering Microscopy and Multivariate Curve Resolution Analysis

Raman Detection of Proteomic Analytes

Oxygen and methylene adducts of C60 and C70