bluuebunny/crossref_metadata_2025 huggingface dataset:
Reply to “Comment on ‘Elimination of translational and rotational motions in nuclear orbital plus molecular orbital theory’ ” [J. Chem. Phys. 123, 237101 (2005)]
Authors: Nakai Hiromi , Hoshino Minoru , Miyamoto Kaito , Hyodo Shi-aki
Published: December 2005

The reply to “Comment on ‘Elimination of transitional and rotational motions in nuclear orbital plus molecular orbital theory’ ” [J. Chem. Phys. 122, 164101 (2005)] is discussed. Sutcliffe pointed out in his Comment that it is impossible to rigorously construct a translation- and rotation-free (TRF)-nuclear orbital plus molecular orbital (NOMO) Hamiltonian. The essential problems pointed out in the Comment undoubtedly exist and the TRF treatment for a nonrigid rotator system cannot rigorously succeed in general cases, as well as in the NOMO theory. However, the localized nuclear wave function represented by the Gaussian basis functions enables us to separate the nuclear motion into the zeroth-order rigid-body rotation and the higher-order coupling. The TRF-NOMO method adopts the unique definition of the center of mass, angular, and internal coordinates for the zeroth-order rotator. This treatment can numerically avoid the essential problems pointed out by Sutcliffe.
Simulation of the photodynamics of azobenzene on its first excited state: Comparison of full multiple spawning and surface hopping treatments
Authors: Toniolo A. , Ciminelli C. , Persico M. , Martínez T. J.
Published: December 2005

We have studied the cis→trans and trans→cis photoisomerization of azobenzene after n→π* excitation using the full multiple spawning (FMS) method for nonadiabatic wave-packet dynamics with potential-energy surfaces and couplings determined “on the fly” from a reparametrized multiconfigurational semiempirical method. We compare the FMS results with a previous direct dynamics treatment using the same potential-energy surfaces and couplings, but with the nonadiabatic dynamics modeled using a semiclassical surface hopping (SH) method. We concentrate on the dynamical effects that determine the photoisomerization quantum yields, namely, the rate of radiationless electronic relaxation and the character of motion along the reaction coordinate. The quantal and semiclassical results are in good general agreement, confirming our previous analysis of the photodynamics. The SH method slightly overestimates the rate of excited state decay, leading in this case to lower quantum yields.
Production and characterization of micron-sized filaments of solid argon
Authors: Grams Michael , Stasicki Boleslaw , Toennies J. Peter
Published: December 2005

A continuous 50-μm-diam filament of solid argon is produced in a moderate vacuum (4.2×10−3mbar) by cooling argon gas to 70–90K over the last 8mm of a long fused silica capillary. Prior to formation of the straight filament the jet shows different stages characterized by spraying, snowballing, or spiraling filaments as documented by charge-coupled device (CCD) camera microscope pictures. Consecutive CCD pictures are used to measure the filament velocities, which increase with the driving gas pressure P0 up to about 4.0cm∕s at P0=400bars with an intermediate peak at about 80bars. This technique may find applications for producing wall-less cryogenic matrices, targets for laser plasma sources of extreme UV and soft-x-ray sources, plasma implosion experiments, or H2 pellets for injection into fusion reactors.
Global optimization and folding pathways of selected α-helical proteins
Authors: Carr Joanne M. , Wales David J.
Published: December 2005

The results of basin-hopping global optimization simulations are presented for four small, α-helical proteins described by a coarse-grained potential. A step-taking scheme that incorporates the local conformational preferences extracted from a large number of high-resolution protein structures is compared with an unbiased scheme. In addition, the discrete path sampling method is used to investigate the folding of one of the proteins, namely, the villin headpiece subdomain. Folding times from kinetic Monte Carlo simulations and iterative calculations based on a Markovian first-step analysis for the resulting stationary-point database are in good mutual agreement, but differ significantly from the experimental values, probably because the native state is not the global free energy minimum for the potential employed.
Long-term stabilization of the length of an optical reference cavity
Authors: Hagel Gaëtan , Houssin Marie , Knoop Martina , Champenois Caroline , Vedel Michel , Vedel Fernande
Published: December 2005

To obtain a high degree of long-term length stabilization of an optical reference cavity, its free-spectral range is locked by means of an accurate and stable frequency synthesizer. The locking scheme is twofold: a laser is locked on the Nth mode of a reference Fabry-Perot cavity and part of the laser light is shifted in frequency to be in resonance with the (N+1)th mode of the cavity. This shift is generated by an acousto-optical modulator (AOM) mounted in a double-pass scheme, matching half of the free-spectral range of the reference cavity. The resulting absolute stabilization of the length of the cavity reaches the 10−11 level per second, limited by the lock transfer properties and the frequency stability of the AOM control synthesizer.
Closed, heated reaction chamber design for dynamic high-temperature x-ray-diffraction analyses of gas/solid displacement reactions
Authors: Haluska Michael S. , Snyder Robert L. , Sandhage Kenneth H. , Misture Scott T.
Published: December 2005

A closed, x-ray transparent chamber for containing a hot reactive gas (generated from an internal condensed source) has been designed and evaluated for use in dynamic x-ray-diffraction analysis of a gas/solid displacement reaction. The chamber consisted of a square-bottom base and lid machined from dense pyrolytic graphite. The base contained a flat pedestal, upon which SiO2 microshells (the reactant oxide) were placed, raised above adjacent cavities holding Mg flakes (the condensed precursor to the reactive gas). Upon heating to 650 °C, the Mg evaporated and reacted with the SiO2 inside the sealed chamber. By passing incident and diffracted x rays through the vertical side walls of the chamber and by blocking undesired graphite-diffracted x rays with platinum, the Mg(g)∕SiO2(s) displacement reaction could be tracked with time. This is the first use of dynamic high-temperature x-ray diffraction analysis to monitor the progress of a displacement reaction involving a reactant gas that was generated and confined within a closed reaction chamber.
Circular dichroism in the angle-resolved C 1s photoemission spectra of gas-phase carvone enantiomers
Authors: Harding Chris J. , Mikajlo Elisabeth , Powis Ivan , Barth Silko , Joshi Sanjeev , Ulrich Volker , Hergenhahn Uwe
Published: December 2005

The inner-shell C 1s photoionization of randomly oriented molecules of the chiral compound carvone has been investigated using circularly polarized synchrotron radiation up to 30eV above threshold. Binding energies of the C̱O and C̱H2 carbon 1s orbitals were determined to be 292.8±0.2 and 289.8±0.2eV, respectively. The remaining C̱–H C 1s levels substantially overlap under an intense central peak centered at 290.5±0.2eV. The angle-resolved photoemission from the carbonyl carbon C̱O core orbital in pure carvone enantiomers shows a pronounced circular dichroism of ∼6% at the magic angle of 54.7° to the light beam propagation direction. This corresponds to an expected 0°–180° forward-backward electron emission asymmetry of ∼10%. On changing between the R and S enantiomers of carvone the sense or sign of the asymmetry and associated dichroism effectively reverses. The observed circular dichroism, and its energy dependence, is well accounted for by calculations performed in the pure electric dipole approximation.
Minimizing broadband excitation under dissipative conditions
Authors: Gelman David , Kosloff Ronnie
Published: December 2005

Optimal control theory is employed for the task of minimizing the excited-state population of a dye molecule in solution. The spectrum of the excitation pulse is contained completely in the absorption band of the molecule. Only phase control is studied which is equivalent to optimizing the transmission of the pulse through the medium. The molecular model explicitly includes two electronic states and a single vibrational mode. The other degrees of freedom are classified as bath modes. The surrogate Hamiltonian method is employed to incorporate these bath degrees of freedom. Their influence can be classified as electronic dephasing and vibrational relaxation. In accordance with experimental results, minimal excitation is associated with a negatively chirped pulses. Optimal pulses with more complex transient structure are found to be superior to linearly chirped pulses. The difference is enhanced when the fluence is increased. The improvement degrades when dissipative effects become more dominant.
Reverse polarization in charged π-conjugated oligomers
Authors: Gao Kun , Liu Xiao-jing , Liu De-sheng , Xie Shi-jie
Published: December 2005

Single-photon excitation in a charged π-conjugated oligomer is studied theoretically. An apparent reverse polarization is obtained through single-photon excitation, which is different from that obtained through a double-photon excitation. The polarizability is calculated and it is found that a maximum reverse polarization will appear at a suitable conjugation length. In addition, we indicate that the reverse polarization is a nonlinear behavior with the induced electric field. Effects of nondegenerate confinement and interchain interactions on the reverse polarization are also discussed.
Phase stability of the intermetallic L21 Heusler alloys of A2(Hf1−xZrx)Al (where A=Pd and Pt) for an Nb-based high-temperature materials design
Authors: Kim Miyoung , Freeman A. J. , Kim Sungtae , Perepezko J. H. , Olson G. B.
Published: December 2005

First principles phase stability calculations are used to predict the lattice mismatches between Nb and the A2(Hf1−xZrx)AlL21 Heusler phases and the L21 phase formation energies, where A=Pd and∕or Pt, and x=0, 0.25, 0.75 and 1. The calculated L21 phase mixing energy demonstrates that the Hf-Zr solution phases in the form of A2(Hf1−xZrx)Al (x≠0 and 1) are energetically favored, although the Zr-rich alloys exhibit a smaller lattice mismatch than the Hf-rich alloys. The introduction of Pt reduces the lattice mismatch, and forms the energetically favorable (PtPd)XAl Heusler phase, where X=Hf and Zr. A number of critical diffusion couple experiments confirm the phase stability predictions and establish new microstructural design parameters.
Frequency response of cantilever beams immersed in viscous fluids near a solid surface with applications to the atomic force microscope
Authors: Green Christopher P. , Sader John E.
Published: December 2005

Theoretical models for the frequency response of a cantilever beam immersed in a viscous fluid commonly assume that the fluid is unbounded. Experimental measurements show, however, that proximity to a surface can significantly affect the frequency response of a cantilever beam. In this article, we rigorously calculate the effect of a nearby surface on the frequency response of a cantilever beam immersed in a viscous fluid, and present a general theoretical model. Due to its practical relevance to applications of the atomic force microscope and microelectromechanical systems, detailed results are presented for cantilever beams with rectangular geometries executing flexural and torsional oscillations. It is found that dissipative loading in the fluid is primarily responsible for the observed variation in the frequency response, whereas inertial loading exerts a relatively weak influence.
Effects of unsteady strain rate on scalar dissipation structures in turbulent planar jets
Authors: Kothnur P. S. , Clemens N. T.
Published: December 2005

An analysis of previously acquired experimental data is performed with the objective of investigating the relationship between strain rate and scalar dissipation rate structures in gas-phase turbulent planar jet flows at local Reynolds numbers ranging from 1000 to 6100. The data analyzed were simultaneously acquired two-dimensional (2D) velocity and 2D conserved scalar fields. The measurements show that, in agreement with previous work, the scalar dissipation structures tend to align orthogonally to the axis of the principal compressive strain rate, and the magnitude of the strain rates acting on the dissipation layers is consistent with theoretical turbulent inner-scale values. Furthermore, the spatially resolved data show that profiles of scalar dissipation, taken across the sheet-like scalar dissipation structures, are approximately Gaussian, whereas the strain rate profiles across the same structures exhibit no characteristic shape, and rarely reach a maximum at the same location as the scalar dissipation. When the scalar dissipation layer thicknesses are cast in nondimensional form and plotted as a function of the instantaneous relative strain rate, the data at all Reynolds numbers exhibit similar characteristics. The measurements from the turbulent flow were compared to a simple one-dimensional (1D) unsteady strained laminar diffusion-layer model, where the imposed strain rate varied harmonically. The simplified model shows remarkable agreement with the experimental data as it predicts the correct trend of layer thickness with strain rate and captures the range of scalar dissipation layer thicknesses that are present in the turbulent flows. The model and experiments show that the layers with greater-than-average strain rate tend to be thicker than expected by steady-state theory, whereas at low strain rates the layers are significantly thinner than at steady state. The 1D model shows best agreement with the measurements when the imposed strain rates are allowed to be positive in the direction of the scalar gradient over some part of the oscillation cycle. This suggests that dissipation layers in turbulent flows experience significant positive strain over their lifetimes.
Debris characteristics of a laser-produced tin plasma for extreme ultraviolet source
Authors: Higashiguchi Takeshi , Rajyaguru Chirag , Dojyo Naoto , Taniguchi Yosuke , Sakita Koji , Kubodera Shoichi , Sasaki Wataru
Published: December 2005

We measured debris characteristics of a tin (Sn) plasma produced by a 10-ns infrared Nd:YAG laser. A maximum kinetic energy of 7keV of tin ions was observed. Such suprathermal tin ions emitted from a solid planar target consisted of singly and doubly ionized tin ions. Both suprathermal ions and neutral fragments emitted from a target showed the angular distributions of cos4θ which were narrower than the 13.5-nm extreme ultraviolet (EUV) emission distribution of cos0.5θ. These measurements would give important information on debris mitigation for efficient EUV sources in the next generation lithography.
New approach to the calculation of the refractive index of liquid and solid xenon
Authors: Hitachi Akira , Chepel Vitaly , Lopes M. Isabel , Solovov Vladimir N.
Published: December 2005

A model for the calculation of the refractive index based on a dispersion relation that incorporates the exciton transition energies is presented. The refractive indices of liquid and solid xenon for different wavelengths are evaluated using this model. Comparison between calculated and experimental values existing in the literature is presented.
Polarization mode dispersion: Characterization of optical fiber using cross-correlation interferometry
Authors: Gibbon T. B. , Conibear A. B. , Leitch A. W. R.
Published: December 2005

The interferometric measurement technique is known to be a quick and reliable method for accurately measuring polarization mode dispersion (PMD) in an optical fiber. In this paper we present the means by which this technique may further be used to obtain qualitative information about the birefringent properties of the fiber under test. Polarization maintaining fiber segments are used to show that a concatenation of n birefringent segments gives rise to an interferogram with 3n interference peaks. The peak positions are further related to the total birefringent contribution of each of the fiber segments. These findings are then used to interpret measurement results and comment on the PMD and related birefringent properties of numerous single mode fibers. Stress is shown to introduce PMD in uncabled single mode fiber. Interferometric measurements are also used to determine the number of birefringent segments in both undeployed and deployed cabled fibers. Polarization optical time domain reflectometry is used successfully to verify these results.
Fingering of exothermic reaction-diffusion fronts in Hele-Shaw cells with conducting walls
Authors: D’Hernoncourt J. , Kalliadasis S. , De Wit A.
Published: December 2005

We consider the influence of heat losses through the walls of a Hele-Shaw cell on the linear stability and nonlinear dynamics of exothermic chemical fronts whose solutal and thermal contributions to density changes have the same signs. Our analysis is based on the reaction-diffusion-convection equations obtained from the Darcy-Boussinesq approximation. The parameters governing the equations are the Damköhler number, a kinetic parameter d, the Lewis number Le, the thermal-expansion coefficient γT, and a heat-transfer coefficient α which measures heat losses through the walls. We show that for thermally insulating walls, the temperature profile is a front that follows the concentration profile, while in the presence of heat losses, the temperature profile becomes a pulse that leads to a nonmonotonic density profile which in turn may lead to a destabilization of an otherwise stable front.
Derivation of a quantitative minimal model from a detailed elementary-step mechanism supported by mathematical coupling analysis
Authors: Shaik O. S. , Kammerer J. , Gorecki J. , Lebiedz D.
Published: December 2005

Accurate experimental data increasingly allow the development of detailed elementary-step mechanisms for complex chemical and biochemical reaction systems. Model reduction techniques are widely applied to obtain representations in lower-dimensional phase space which are more suitable for mathematical analysis, efficient numerical simulation, and model-based control tasks. Here, we exploit a recently implemented numerical algorithm for error-controlled computation of the minimum dimension required for a still accurate reduced mechanism based on automatic time scale decomposition and relaxation of fast modes. We determine species contributions to the active (slow) dynamical modes of the reaction system and exploit this information in combination with quasi-steady-state and partial-equilibrium approximations for explicit model reduction of a novel detailed chemical mechanism for the Ru-catalyzed light-sensitive Belousov-Zhabotinsky reaction. The existence of a minimum dimension of seven is demonstrated to be mandatory for the reduced model to show good quantitative consistency with the full model in numerical simulations. We derive such a maximally reduced seven-variable model from the detailed elementary-step mechanism and demonstrate that it reproduces quantitatively accurately the dynamical features of the full model within a given accuracy tolerance.
Contact values of the particle-particle and wall-particle correlation functions in a hard-sphere polydisperse fluid
Authors: Santos Andrés , Yuste Santos B. , López de Haro Mariano
Published: December 2005

The contact values g(σ,σ′) of the radial distribution functions of a fluid of (additive) hard spheres with a given size distribution f(σ) are considered. A “universality” assumption is introduced, according to which, at a given packing fraction η,g(σ,σ′)=G(z(σ,σ′)), where G is a common function independent of the number of components (either finite or infinite) and z(σ,σ′)=[2σσ′∕(σ+σ′)]μ2∕μ3 is a dimensionless parameter, μn being the nth moment of the diameter distribution. A cubic form proposal for the z dependence of G is made and known exact consistency conditions for the point particle and equal size limits, as well as between two different routes to compute the pressure of the system in the presence of a hard wall, are used to express G(z) in terms of the radial distribution at contact of the one-component system. For polydisperse systems we compare the contact values of the wall-particle correlation function and the compressibility factor with those obtained from recent Monte Carlo simulations.
Concurrent dual-resolution Monte Carlo simulation of liquid methane
Authors: Abrams Cameron F.
Published: December 2005

We conduct molecular simulations of liquid methane in a system where molecular resolution fluctuates between atomically explicit and spherically symmetric united atoms. An appropriate dual-resolution canonical ensemble is constructed using (a) effective united atom pair potentials and (b) resolution-control potentials that confine explicit and united atoms chiefly to different slabs in the simulation domain. A Monte Carlo simulation is developed to sample this ensemble. We show that compatibility of the united-atom potentials with the explicit potentials in a concurrent simulation can be tuned by adjusting the width of the interface between the two resolution regions and by direct modification of the united-atom pair potentials. Our results lay the groundwork for treatment of larger atomically specific molecules with similar concurrent multiresolution techniques.
Dielectric and shear mechanical relaxations in glass-forming liquids: A test of the Gemant-DiMarzio-Bishop model
Authors: Niss Kristine , Jakobsen Bo , Olsen Niels Boye
Published: December 2005

The Gemant-DiMarzio-Bishop model, which connects the frequency-dependent shear modulus to the frequency-dependent dielectric constant, is reviewed and a new consistent macroscopic formulation is derived. It is moreover shown that this version of the model can be tested without fitting parameters. The reformulated version of the model is analyzed and experimentally tested. It is demonstrated that the model has several nontrivial qualitative predictions: the existence of an elastic contribution to the high-frequency limit of the dielectric constant, a shift of the shear modulus loss peak frequency to higher frequencies compared with the loss peak frequency of the dielectric constant, a broader alpha peak, and a more pronounced beta peak in the shear modulus when compared with the dielectric constant. It is shown that these predictions generally agree with experimental findings and it is therefore suggested that the Gemant-DiMarzio-Bishop model is correct on a qualitative level. The quantitative agreement between the model and the data is on the other hand moderate to poor. It is discussed if a model-free comparison between the dielectric and shear mechanical relaxations is relevant, and it is concluded that the shear modulus should be compared with the rotational dielectric modulus, 1∕(ϵ(ω)−n2), which is extracted from the Gemant-DiMarzio-Bishop model, rather than to the dielectric susceptibility or the conventional dielectric modulus M=1∕ϵ(ω).
Dielectric and shear mechanical alpha and beta relaxations in seven glass-forming liquids
Authors: Jakobsen Bo , Niss Kristine , Olsen Niels Boye
Published: December 2005

We present shear mechanical and dielectric measurements taken on seven liquids: triphenylethylene, tetramethyltetra-phenyltrisiloxane (Dow Corning 704® diffusion pump fluid), polyphenyl ether (Santovac® 5 vacuum pump fluid), perhydrosqualene, polybutadiene, decahydroisoquinoline (DHIQ), and tripropylene glycol. The shear mechanical and dielectric measurements are for each liquid performed under identical thermal conditions close to the glass transition temperature. The liquids span four orders of magnitude in dielectric relaxation strength and include liquids with and without Johari-Goldstein beta relaxation. The shear mechanical data are obtained by the piezoelectric shear modulus gauge method giving a large frequency span (10−3–104.5Hz). This allows us to resolve the shear mechanical Johari-Goldstein beta peak in the equilibrium DHIQ liquid. We moreover report a signature (a pronounced rise in the shear mechanical loss at frequencies above the alpha relaxation) of a Johari-Goldstein beta relaxation in the shear mechanical spectra for all the liquids which show a beta relaxation in the dielectric spectrum. It is found that both the alpha and beta loss peaks are shifted to higher frequencies in the shear mechanical spectrum compared to the dielectric spectrum. It is in both the shear and dielectric responses found that liquids obeying time-temperature superposition also have a high-frequency power law with exponent close to −1∕2. It is moreover seen that the less temperature dependent the spectral shape is, the closer it is to the universal −1∕2 power-law behavior. The deviation from this universal power-law behavior and the temperature dependencies of the spectral shape are rationalized as coming from interactions between the alpha and beta relaxations.
Electron solvation in water clusters following charge transfer from iodide
Authors: Verlet Jan R. R. , Kammrath Aster , Griffin Graham B. , Neumark Daniel M.
Published: December 2005

The dynamics following charge transfer to solvent from iodide to a water cluster are studied using time-resolved photoelectron imaging of I−(H2O)n and I−(D2O)n clusters with n⩽28. The results show spontaneous conversion, on a time scale of ∼1ps, from water cluster anions with surface-bound electrons to structures in which the excess electron is more strongly bound and possibly more internalized within the solvent network. The resulting dynamics provide valuable insight into the electron solvation dynamics in water clusters and the relative stabilities between recently observed isomers of water cluster anions.
Simple approximants for natural orbitals of harmonium
Authors: Cioslowski Jerzy , Buchowiecki Marcin
Published: December 2005

Simple approximations to the natural orbitals (NOs) of harmonium with enforced correct short- and long-range asymptotics yield accurate bounds for the NO occupancies. In particular, expressions involving Padé approximants with just one variational parameter are capable of producing the largest NO occupancies with accuracy better than 10−4. The comparison of two cases with different coupling strengths ω (1.94851<n<1.94860 for ω=1∕2 and 1.82124<n<1.82129 for ω=1∕10) indicates that the bounds actually become tighter with the increasing extent of correlation. The expressions derived for the most strongly occupied NOs can be readily generalized to all natural orbitals of harmonium.
Thermodynamic properties of germanium/carbon microclusters
Authors: Wielgus Pawel , Roszak Szczepan , Majumdar Devashis , Leszczynski Jerzy
Published: December 2005

Theoretical studies on the GenCm (n=1,2; m=1–3) microclusters have been performed using the state of the art calculations. Several alternative structures of these clusters were studied to locate the lowest-energy isomers. It is observed that the structures of the complexes result from the competition between ionic Ge–C, conjugated covalent C–C, and metallic Ge–Ge bonds. The ionization of the molecules enhances the ionic character of the Ge–C bond and has significant structural consequences. Using theoretically determined partition functions, thermodynamic data are computed and experimental enthalpies are enhanced. The ab initio atomization energies of germanium carbides compare well with corrected experimental functions. The experimental appearance potentials are well reproduced by the theoretical ionization potentials.
Dynamics of ionic and hydrophobic solutes in water-methanol mixtures of varying composition
Authors: Chowdhuri Snehasis , Chandra Amalendu
Published: December 2005

We have carried out a series of molecular-dynamics simulations of water-methanol mixtures containing either an ionic or a neutral atomic solute to investigate the effects of composition of the mixture on the diffusion of these solutes. Altogether, we have considered 17 different systems of varying composition ranging from pure water to pure methanol. The diffusion coefficients of ionic solutes are found to show nonideal behavior with variation of composition of the solvent mixture. The extent of nonideality of the solute diffusion is found to be similar to the nonideality that is observed for the diffusion and orientational relaxation of water and methanol molecules in these mixtures and is attributed to the enhanced stability of the hydrogen bonds and formation of interspecies complexes in the mixtures. The neutral solute shows characteristics of hydrophobic solvation and its diffusion decreases monotonically with increase of methanol concentration. The present simulation results are compared with those of experiments wherever available.
A targeted reweighting method for accelerating the exploration of high-dimensional configuration space
Authors: Cukier R. I. , Morillo M.
Published: December 2005

Time scales available to biomolecular simulations are limited by barriers among states in a high-dimensional configuration space. If equilibrium averages are to be computed, methods that accelerate barrier passage can be carried out by non-Boltzmann sampling. Barriers can be reduced by modifying the potential-energy function and running dynamics on the modified surface. The Boltzmann average can be restored by reweighting each point along the trajectory. We introduce a targeted reweighting scheme where some barriers are reduced, while others are not modified. If only equilibrium properties are desired, trajectories in configuration space can be generated by Langevin dynamics. Once past a transient time, these trajectories guarantee equilibrium sampling when reweighted. A relatively high-order stochastic integration method can be used to generate trajectories. The targeted reweighting scheme is illustrated by a series of double-well models with varying degrees of freedom and shown to be a very efficient method to provide the correct equilibrium distributions, in comparison with analytic results. The scheme is applied to a protein model consisting of a chain of connected beads characterized by dihedral angles and the van der Waals interactions among the beads. We investigate the sampling of configuration space for a model of a helix-turn-helix motif. The targeted reweighting is found to be essential to permit the original all-helical conformation to bend and generate turn structures while still maintaining the alpha-helical segments.
Contact conditions for the charge in the theory of the electrical double layer
Authors: Holovko M. , Badiali J. P. , di Caprio D.
Published: December 2005

In this paper, from the Born-Green-Yvon equations of the liquid-state theory, we derive a general expression for the charge-density contact value at charged interfaces. This relation is discussed, in particular, for symmetrical electrolytes. We emphasize an essential coupling between the electric properties and the density profile. Limiting behavior at small and large charges at the interface is discussed.
Molecular-dynamics simulation of crystallization in helical polymers
Authors: Yamamoto Takashi , Sawada Kaoru
Published: December 2005

The molecular mechanism of crystallization in helical polymers is a fascinating but very difficult subject of research. We here report our recent efforts toward better understanding of the crystallization in helical polymers by use of molecular-dynamics simulation. With straightforward approaches to the problem being quite difficult, we adopt a different strategy of categorizing the helical polymers into two distinct types: one type is a simple bare helix which is essentially made of backbone atomic groups only and has smoother molecular contours, and the other is a more general helix having large side groups that would considerably hamper molecular motion and crystallization. Both types of helical polymers are here constructed by use of the united atom model, but they show quite distinct crystallization behavior; the crystallization of the former-type polymer is rather fast, while that of the latter-type polymer is extremely slow. We find that the bare helix, when rapidly cooled in free three-dimensional space, freezes into partially ordered state with limited intramolecular and intermolecular orders, and that remarkable improvement of order and growth of an ordered chain-folded crystallite occurs by very long-time annealing of the partially ordered state around the apparent freezing temperature. We also study crystallization of the bare helix upon a growth surface; the crystallization in this case proceeds much faster through highly cooperative process of the intermolecular and the intramolecular degrees of freedom. On the other hand, crystallization of the realistic model of isotactic polypropylene (iPP) having pendant methylene groups is found to be extremely sluggish. By restricting the spatial dimension of the system thereby fully disentangling the chain, we observe that the molecule of iPP crystallizes very quickly onto the crystal substrate made of the same iPP chain. Quite remarkable is that the molecule of iPP strictly recognizes the helical sense of the substrate chain and efficiently selects its chirality during crystallization.
Green’s-function reaction dynamics: A particle-based approach for simulating biochemical networks in time and space
Authors: van Zon Jeroen S. , ten Wolde Pieter Rein
Published: December 2005

We have developed a new numerical technique, called Green’s-function reaction dynamics (GFRD), that makes it possible to simulate biochemical networks at the particle level and in both time and space. In this scheme, a maximum time step is chosen such that only single particles or pairs of particles have to be considered. For these particles, the Smoluchowski equation can be solved analytically using Green’s functions. The main idea of GFRD is to exploit the exact solution of the Smoluchoswki equation to set up an event-driven algorithm, which combines in one step the propagation of the particles in space with the reactions between them. The event-driven nature allows GFRD to make large jumps in time and space when the particles are far apart from each other. Here, we apply the technique to a simple model of gene expression. The simulations reveal that spatial fluctuations can be a major source of noise in biochemical networks. The calculations also show that GFRD is highly efficient. Under biologically relevant conditions, GFRD is up to five orders of magnitude faster than conventional particle-based techniques for simulating biochemical networks in time and space. GFRD is not limited to biochemical networks. It can also be applied to a large number of other reaction-diffusion problems.
Ladder operators and coherent states for the Jaynes-Cummings model in the rotating-wave approximation
Authors: Hussin V. , Nieto L. M.
Published: December 2005

Using algebraic techniques, we realize a systematic search of different types of ladder operators for the Jaynes-Cummings model in the rotating-wave approximation. The link between our results and previous studies on the diagonalization of the associated Hamiltonian is established. Using some of the ladder operators obtained before, examples are given on the possibility of constructing a variety of interesting coherent states for this Hamiltonian.
Harmonic and anharmonic contributions to parity-violating vibrational frequency difference between enantiomers of chiral molecules
Authors: Barone Vincenzo , Viglione Rosario G.
Published: December 2005

A general perturbative procedure for the computation of harmonic and anharmonic contributions to parity-violating vibrational shifts is introduced and applied to PHBrF and AsHBrF. The results point out the importance of both diagonal and off-diagonal anharmonic contributions and indicate that some parity-violating shift of AsHBrF approaches the resolution forecasted for next generation experiments. The proposed approach is sufficiently general and computationally effective to allow studies of similar and larger molecular systems.
Construction of new solutions to the fully nonlinear generalized Camassa-Holm equations by an indirect F function method
Authors: Yomba Emmanuel
Published: December 2005

An indirect F function method is introduced to solve the generalized Camassa-Holm equation with fully nonlinear dispersion and fully nonlinear convection C(l,n,p). Taking advantage of elliptic equation, this F function is used to map the solutions of the generalized Camassa-Holm equation to those of the elliptic equation. As a result, we can successfully obtain in a unified way and for special values of the parameters of this equation, many exact solutions expressed by various single and combined nondegenerative Jacobi elliptic function solutions and their degenerative solutions (soliton, combined soliton solutions, and triangular solutions) as the modulus m is driven to 1 and 0.
Off-diagonal magnetoimpedance in field-annealed Co-based amorphous ribbons
Authors: Buznikov N. A. , Kim CheolGi , Kim Chong-Oh , Jin Lan , Yoon Seok-Soo
Published: December 2005

The off-diagonal magnetoimpedance in field-annealed CoFeSiB amorphous ribbons was measured in the low-frequency range using a pickup coil wound around the sample. The asymmetric two-peak behavior of the field dependence of the off-diagonal impedance was observed. The asymmetry is attributed to the formation of a hard magnetic crystalline phase at the ribbon surface. The experimental results are interpreted in terms of the surface impedance tensor. It is assumed that the ribbon consists of an inner amorphous region and surface crystalline layers. The coupling between the crystalline and amorphous phases is described through an effective bias field. A qualitative agreement between the calculated dependences and experimental data is demonstrated. The results obtained may be useful for the development of weak magnetic-field sensors.
Structures and stability of defect-free multiwalled carbon toroidal rings
Authors: Liu P. , Zhang Y. W. , Lu C.
Published: December 2005

Atomistic simulations of the structures and stability of defect-free multiwalled carbon toroidal rings were performed using the second-generation empirical bond-order potential and a Morse-type van der Waals potential. It was found that a multiwalled toroidal ring improves the structural stability over its outermost single-walled counterpart, implying a stabilizing effect from the inner rings. This can be explained by the superlinear relation between the critical ring diameter and its tube diameter existing in single-walled rings. However, the findings that the critical diameter of an armchair ring is larger than that of a zigzag ring with the same tube diameters, and that the inclusion of torsion exhibits a negative effect on the stability of a multiwalled ring, are in contrast to that of a single-walled nanoring. In addition, the instability of a multiwalled nanoring always starts with the formation of many short-wavelength ripples on the compressed side of the outermost tube. Subsequently, some of the ripples develop into buckles, resulting in buckling failures.
Surface-plasmon resonance sensing of alcohol with electrodeposited polythiophene and gold nanoparticle-oligothiophene films
Authors: Sih Bryan C. , Wolf Michael O. , Jarvis David , Young Jeff F.
Published: December 2005

Electrodeposited films of polythiophene or gold nanoparticles (NPs) capped with conjugated oligothiophenes prepared on thin gold films are employed in a Kretschmann-type surface-plasmon resonance detector. The polythiophene films selectively respond to alcohol (ethanol or methanol) and toluene vapors but not to hexanes or water vapors, while the nanoparticle/oligothiophene films respond only to alcohol vapors of the solvents tested. For both films, the response to vapors consisted of the minimum in the reflectance curve (θ0) shifting to a higher angle as the thickness of the film increased. Slight increases in dielectric constant were also observed. The NPs do not result in an enhancement in sensitivity, contrary to theoretical predictions that suggest greater sensitivity may be achieved due to localized surface-plasmon effects associated with the presence of the Au NPs in the dielectric.
Depth-graded multilayers for application in transmission geometry as linear zone plates
Authors: Liu Chian , Conley R. , Macrander A. T. , Maser J. , Kang H. C. , Zurbuchen M. A. , Stephenson G. B.
Published: December 2005

Fresnel zone plates for x-ray focusing optics are typically made using lithographic techniques. To achieve optimum efficiency for hard x rays, a depth of several microns is required, which limits the minimum zone width and hence minimum focal spot size achievable using lithography. We are exploring the fabrication of zone plates by an alternative technique that surmounts these limitations: the growth of a multilayer film to be used in transmission (Laue) diffraction geometry, in which the thickness of consecutive layers gradually increases according to the Fresnel zone formula; the film is sectioned after growth to the required depth. For a planar multilayer, this produces a linear zone plate that can focus x rays in one dimension. Here we report the growth and characterization of a depth-graded multilayer suitable for use as a zone plate for hard x-ray focusing. The multilayer has a total of 470 alternating layers of WSi2 and Si with thicknesses increasing monotonically from 15 to 60 nm, for a total thickness of 11.33μm. One of the major challenges is to understand and select the right material system for this kind of thick multilayer. We have found that WSi2∕Si is a promising system. A comparison between WSi2∕Si and W∕Si multilayers is presented.
Eucentric four-axis ultrahigh vacuum goniometer for reflection high-energy electron diffraction applications
Authors: Schmehl A. , Schulz R. R. , Mannhart J.
Published: December 2005

The design and performance of a four-axis low-profile eucentric UHV goniometer for in situ reflection high-energy electron diffraction (RHEED) studies during film deposition is reported. The design provides one translational and three rotational degrees of freedom that are fully independent. Although developed to facilitate high-pressure RHEED during the growth of oxide thin films by pulsed laser deposition, this goniometer design is applicable to other UHV techniques including molecular beam epitaxy. The goniometer requires only a single DN 100 CF flange (6in. o.d., 100mm i.d.), making it suitable for small deposition systems, too. Samples, attached to a resistively heated holder, can be easily transferred on and off of the goniometer without breaking vacuum. The holder accommodates samples up to 10mm×10mm in size and allows them to be heated to 900°C in pure oxygen while being attached to the goniometer. Full eucentric motion of the hot sample is possible with a typical axis precision of <0.1°. Most of the mechanism is located in air, allowing the use of standard materials and lubricants, substantially reducing the in-vacuum mechanics, and increasing the precision, reliability, and robustness of the system.
Global optimization of ionic MgnF2n (n=1–30) clusters
Authors: Francisco E. , Martín Pendás A. , Blanco M. A.
Published: December 2005

The global optimization basin-hopping (BH) method has been used to locate the global minima (GM) of MgnF2n (n=1−30) clusters using a Born-Mayer-type potential. Some of the GM were particularly difficult to find, requiring more than 1.5×104 BH steps. We have found that both the binding energy per MgF2 unit and the effective volume of the GM isomers increase almost linearly with n, and that cluster symmetry decreases with cluster size. The data derived from the BH runs reveal a growing density of local minima just above the GM as n increases. Despite this, the attraction basin around each GM is relatively large, since after all their atomic coordinates are randomly displaced by values as high as 2.0bohrs, the perturbed structures, upon reoptimization, relax back to the GM in more than 50% of the cases (except for n=10 and 11). The relative stabilities derived from energy second differences suggest that n=8,10,13,15, and 20 are probably the magic numbers for these systems. Mass spectrum experiments would be very useful to clarify this issue.
Slice imaging of photodissociation of spatially oriented molecules
Authors: Lipciuc M. Laura , van den Brom Alrik J. , Dinu Laura , Janssen Maurice H. M.
Published: December 2005

An electrostatic ion lens to spatially orient parent molecules and to image the angular distribution of photofragments is presented. Photodissociation of laboratory-oriented molecules makes it possible to study the dynamics of the dissociation process in more detail compared to photodissociation of nonoriented molecules. Using the velocity map imaging technique in combination with the slice imaging technique, the spatial recoil distribution of the photofragments can be measured with high resolution and without symmetry restrictions. Insertion of orientation electrodes between the repeller and the extractor of a velocity mapping electrostatic lens severely distorts the ion trajectories. The position where the ions are focused by the lens, the focal length, can be very different in the directions parallel and perpendicular to the inserted orientation electrodes. The focal length depends on the exact dimensions and positions of the electrodes of the ion lens. As this dependence is different in both directions, this dependence can be used to correct for the distorted ion trajectories. We discuss the design of an electrostatic ion lens, which is able to orient parent molecules and map the velocity of the photofragments. We report sliced images of photofragments from photolysis of spatially oriented CD3I molecules to demonstrate the experimental combination of molecular orientation and velocity map slice imaging with good resolution.
Nanosecond pulsed laser energy and thermal field evolution during second harmonic generation in periodically poled LiNbO3 crystals
Authors: Louchev Oleg A. , Yu Nan Ei , Kurimura Sunao , Kitamura Kenji
Published: December 2005

Computational study of nanosecond pulse laser radiation in periodically poled LiNbO3 (PPLN) crystals reveals the complex spatio-temporal evolution of the 1.064μm fundamental harmonic (FH) and second harmonic (SH) energy fields with associated temperature fields, leading to the thermal dephasing and inhibition of second harmonic generation (SHG). The investigated range of the laser input power is W0=0.5–50W (with the pulse energy Q0=0.01–1mJ∕pulse and repetition rate of 50kHz). For input laser powers W0>10W the FH and SH energy fields are found to strongly couple with nonuniform temperature field, leading to significant thermal dephasing and SHG efficiency loss. Heat generation and temperature distributions also exhibit very significant nonuniformities along and across the laser beam, maximizing at the rear or inside the crystal, depending on the input power. However, conformal temperature tuning along the operating crystal inhibits these nonuniformities, and significantly enhances SHG efficiency under high input powers. For instance, selected PPLN conformal cooling parameters lead to the formation of a temperature-uniform quasi-phase-matching channel for a 300μm diameter laser beam providing a high SHG efficiency (≈64%) at 20W input power.