A dielectric continuum molecular dynamics method

We introduce a novel method to simulate hydrated macromolecules with a dielectric continuum representation of the surrounding solvent. In our approach, the interaction between the solvent and the molecular degrees of freedom is described by means of a polarization density free energy functional which is minimum at electrostatic equilibrium. After a pseudospectral expansion of the polarization and a discretization of the functional, we construct the equations of motion for the system based on a Car-Parrinello technique. In the limit of the adiabatic evolution of the polarization field variables, our method provides the solution of the dielectric continuum problem "on the fly," while the molecular coordinates are propagated. In this first study, we show how our dielectric continuum molecular dynamics method can be successfully applied to hydrated biomolecules, with low cost compared to free energy simulations with explicit solvent. To our knowledge, this is the first time that stable and conservative molecular dynamic simulations of solutes can be performed for a dielectric continuum model of the solvent. (C) 2001 American Institute of Physics.

Asymptotic layer-type model of high pressure direct current glow discharge in electronegative gases

Here a self-consistent one-dimensional continuum model is presented for a narrow gap plane-parallel dc glow discharge. The governing equations consist of continuity and momentum equations for positive and negative ions and electrons coupled with Poisson's equation. A singular perturbation method is developed for the analysis of high pressure dc glow discharge. The kinetic processes of the ionization, electron attachment, and ion-ion recombination are included in the model. Explicit results are obtained for the asymptotic limits: delta=(r(D)/L)(2)--> 0, omega=(r(S)/L)(2)--> 0, where r(D) is the Debye radius, r(S) is recombination length, and L is the gap length. The discharge gap divides naturally into four layers with multiple space scales: anode fall region, positive column, transitional region, cathode fall region and diffusion layer adjacent to the cathode surface, its formation is discussed. The effects of the gas pressure, gap spacing and dc voltage on the electrical properties of the layers and its dimension are investigated. (C) 2000 American Institute of Physics. [S0021-8979(00)00813-6].

Changes in surface stress caused by the adsorption of an epitaxial metal monolayer

The adsorption of a metal monolayer on a foreign substrate generates a change in the surface stress. We calculate this change for a number of substrate/adsorbate systems using the embedded-atom method. The results are compared with those obtained from a continuum model. A cycle, in which the stretching of a substrate/adsorbate system is decomposed into several steps, helps in understanding the numerical results. (C) 2000 Elsevier Science B.V. All rights reserved.

Nitrile-Functionalized Pyridinium, Pyrrolidinium, and Piperidinium Ionic Liquids

Two series of 1-alkylpyridinium and N-alkyl-N-methylpiperidinium ionic liquids fiinctionalized with a nitrile group at the end of the alkyl chain have been synthesized. Structural modifications include a change of the alkyl spacer length between the nitrile group and the heterocycle of the cationic core, as well as adding methyl or ethyl substituents on different positions of the pyridinium ring. The anions are the bromide and the bis(trifluoromethylsulfonyl)imide ion. All the bis(trifluoromethylsulfonyl)imide salts as well as the bromide salts with a long alkyl spacer were obtained as viscous liquids at room temperature, but some turned out to be supercooled liquids. In addition, pyrrolidinium and piperidinium ionic liquids with two nitrile functions attached to the heterocyclic core have been prepared. The crystal structures of seven pyridinium bis(trifluoromethylsulfonyl)imide salts are reported. Quantum chemical calculations have been performed on model cations and ion pairs with the bis(trifluoromethylsulfonyl)imide anion. A continuum model has been used to take solvation effects into account. These calculations show that the natural partial charge on the nitrogen atom of the nitrile group becomes more negative when the length of the alkyl spacer between the nitrile functional group and the heterocyclic core of the cation is increased. Methyl or methoxy substituents on the pyridinium ring slightly increase the negative charge on the nitrile nitrogen atom due to their electron-donating abilities. The position of the substituent (ortho, meta, or para) has only a very minor effect on the charge of the nitrogen atom. The N-15 NMR spectra of the bis(trifluoromethylsulfonyl)imide ionic liquids were recorded with the nitrogen-15 nucleus at its natural abundance. The chemical shift of the N-15 nucleus of the nitrile nitrogen atom could be correlated with the calculated negative partial charge on the nitrogen atom.

Asymptotic modeling of short plane-parallel high-pressure glow discharge

Here a self-consistent continuum model is presented for a narrow gap plane-parallel dc glow discharge. The set of governing equations consisting of continuity and momentum equations for positive ions, fast (emitted by the cathode) and slow electrons (generated by fast electron impact ionization) coupled with Poisson's equation is treated by the technique of matched asymptotic expansions. Explicit results are obtained in the asymptotic limit: (chi delta) much less than 1, where chi = e Phi(a)/kT, delta = (r(D)/L)(2) (Phi(a) is the applied voltage, r(D) is the Debye radius) and pL much greater than 1(Hg mm cm), where p is the gas pressure and L is the gap length. In the case of high pressure, the electron energy relaxation length is much smaller than the gap length, and so the local field approximation is valid. The discharge space divides naturally into a cathode fall sheath, a quasineutral plasma region, and an anode fall sheath. The electric potential distribution obtained for each region in a (semi)analytical form is asymptotically matched to the adjoining regions in the region of overlap. The effects of the gas pressure, gap length, and applied voltage on the length of each region are investigated. (C) 2000 American Institute of Physics. [S1070-664X(00)01302-1].

Electrooxidation of methanol in an alkaline fuel cell: determination of the nature of the initial adsorbate

It is essential to correctly determine the nature of the initial adsorbate in order to calculate the pathway for any given reaction. Recent literature provides conflicting information on the first step in the methanol decomposition pathway. This work sets out to establish what role the solution and the surface have to play in the initial adsorption-deprotonation process. Density functional theory (DFT) calculations, in combination with a cluster-continuum model approach are used to resolve the nature of the adsorbing species. We show that methanol is the dominant species in solution over methoxide, and also has a smaller barrier to adsorption. The nature of the surface species is revealed to be a methanol-OH complex.

Analytically continued generalized continuum distorted waves

The continuum distorted-wave eikonal-initial-state (CDW-EIS) theory of Crothers and McCann (Crothers DSF and McCann JF, 1983 J. Phys. B: At. Mol. Opt. Phys. 16 3229 ) used to describe ionization in ion-atom collisions is generalized (G) to GCDW-EIS, to incorporate the azimuthal ange dependence into the final-state wavefunction. This is accomplished by the analytic continuation of hydrogenic-like wavefunctions from below to above threshold, using parabolic coordinates and quantum numbers including magnetic quantum numbers, thus providing a more complete set of states. At impact energies lower than 25 ke V u^{-1}, the total CDW-EIS ionization cross section falls off, with decreasing energy, too quickly in comparison with experimental data by Crothers and McCann. The idea behind and motivation for the GCDW-EIS model is to improve the theory with respect to experiment, by including contributions from non-zero magnetic quantum numbers. We also therefore incidentally provide a new derivation of the theory of continuum distorted waves for zero magnetic quantum numbers while simultaneously generalizing it.

Total and single differential cross sections for simple resonant collisions using a fully orthonormal continuum-distorted-wave basis

Simple electron capture processes are studied using an orthonormal two state continuum-distorted-wave (CDW) basis. The suitability of the basis set is tested by comparing predictions for total and differential cross sections with available experimental data. Overall good agreement is obtained and the authors conclude that a relatively small CDW basis set may be suitable to model a wide variety of low-energy collisions if the members of this extended set are astutely chosen.

An exactly solvable four transition point model

Heavy particle collisions, in particular low-energy ion-atom collisions, are amenable to semiclassical JWKB phase integral analysis in the complex plane of the internuclear separation. Analytic continuation in this plane requires due attention to the Stokes phenomenon which parametrizes the physical mechanisms of curve crossing, non-crossing, the hybrid Nikitin model, rotational coupling and predissociation. Complex transition points represent adiabatic degeneracies. In the case of two or more such points, the Stokes constants may only be completely determined by resort to the so-called comparison- equation method involving, in particular, parabolic cylinder functions or Whittaker functions and their strong-coupling asymptotics. In particular, the Nikitin model is a two transition-point one-double-pole problem in each half-plane corresponding to either ingoing or outgoing waves. When the four transition points are closely clustered, new techniques are required to determine Stokes constants. However, such investigations remain incomplete, A model problem is therefore solved exactly for scattering along a one-dimensional z-axis. The energy eigenvalue is b(2)-a(2) and the potential comprises -z(2)/2 (parabolic) and -a(2) + b(2)/2z(2) (centrifugal/centripetal) components. The square of the wavenumber has in the complex z-plane, four zeros each a transition point at z = +/-a +/- ib and has a double pole at z = 0. In cases (a) and (b), a and b are real and unitarity obtains. In case (a) the reflection and transition coefficients are parametrized by exponentials when a(2) + b(2) > 1/2. In case (b) they are parametrized by trigonometrics when a(2) + b(2) <1/2 and total reflection is achievable. In case (c) a and b are complex and in general unitarity is not achieved due to loss of flux to a continuum (O'Rourke and Crothers, 1992 Proc. R. Sec. 438 1). Nevertheless, case (c) coefficients reduce to (a) or (b) under appropriate limiting conditions. Setting z = ht, with h a real constant, an attempt is made to model a two-state collision problem modelled by a pair of coupled first-order impact parameter equations and an appropriate (T) over tilde-tau relation, where (T) over tilde is the Stueckelberg variable and tau is the reduced or scaled time. The attempt fails because (T) over tilde is an odd function of tau, which is unphysical in a real collision problem. However, it is pointed out that by applying the Kummer exponential model to each half-plane (O'Rourke and Crothers 1994 J. Phys. B: At. Mel. Opt. Phys. 27 2497) the current model is in effect extended to a collision problem with four transition points and a double pole in each half-plane. Moreover, the attempt in itself is not a complete failure since it is shown that the result is a perfect diabatic inelastic collision for a traceless Hamiltonian matrix, or at least when both diagonal elements are odd and the off-diagonal elements equal and even.

Magnetically quantized continuum distorted-wave theory in atomic and molecular collisions

The continuum distorted-wave eikonal initial-state (CDW-EIS) theory of Crothers and McCann (J Phys B 1983, 16, 3229) used to describe ionization in ion-atom collisions is generalized (G) to GCDW-EIS to incorporate the azimuthal angle dependence of each CDW in the final-state wave function. This is accomplished by the analytic continuation of hydrogenic-like wave functions from below to above threshold, using parabolic coordinates and quantum numbers including magnetic quantum numbers, thus providing a more complete set of states. At impact energies lower than 25 keVu(-1), the total ionization cross-section falls off, with decreasing energy, too quickly in comparison with experimental data. The idea behind and motivation for the GCDW-EIS model is to improve the theory with respect to experiment by including contributions from nonzero magnetic quantum numbers. We also therefore incidentally provide a new derivation of the theory of continuum distorted waves for zero magnetic quantum numbers while simultaneously generalizing it. (C) 2004 Wiley Periodicals, Inc.

A photospheric bright point model

Aims. A magneto-hydrostatic model is constructed with spectropolarimetric properties close to those of solar photospheric magnetic bright points.
Methods. Results of solar radiative magneto-convection simulations are used to produce the spatial structure of the vertical component of the magnetic field. The horizontal component of magnetic field is reconstructed using the self-similarity condition, while the magneto-hydrostatic equilibrium condition is applied to the standard photospheric model with the magnetic field embedded. Partial ionisation processes are found to be necessary for reconstructing the correct temperature structure of the model.
Results. The structures obtained are in good agreement with observational data. By combining the realistic structure of the magnetic field with the temperature structure of the quiet solar photosphere, the continuum formation level above the equipartition layer can be found. Preliminary results are shown of wave propagation through this magnetic structure. The observational consequences of the oscillations are examined in continuum intensity and in the Fe I 6302 angstrom magnetically sensitive line.

How do grazers achieve their distribution? A continuum of models from random diffusion to the ideal free distribution using biased random walks

A conceptual model is described for generating distributions of grazing animals, according to their searching behavior, to investigate the mechanisms animals may use to achieve their distributions. The model simulates behaviors ranging from random diffusion, through taxis and cognitively aided navigation (i.e., using memory), to the optimization extreme of the Ideal Free Distribution. These behaviors are generated from simulation of biased diffusion that operates at multiple scales simultaneously, formalizing ideas of multiple-scale foraging behavior. It uses probabilistic bias to represent decisions, allowing multiple search goals to be combined (e.g., foraging and social goals) and the representation of suboptimal behavior. By allowing bias to arise at multiple scales within the environment, each weighted relative to the others, the model can represent different scales of simultaneous decision-making and scale-dependent behavior. The model also allows different constraints to be applied to the animal's ability (e.g., applying food-patch accessibility and information limits). Simulations show that foraging-decision randomness and spatial scale of decision bias have potentially profound effects on both animal intake rate and the distribution of resources in the environment. Spatial variograms show that foraging strategies can differentially change the spatial pattern of resource abundance in the environment to one characteristic of the foraging strategy.</

A progressive failure model for composite laminates subjected to low velocity impact damage

This paper presents a 3-D failure model for predicting the dynamic material response of composite laminates under impact loading. The formulation is based on the Continuum Damage Mechanics (CDM) approach and enables the control of the energy dissipation associated with each failure mode regardless of mesh refinement and fracture plane orientation. Internal thermodynamically irreversible damage variables were defined in order to quantify damage concentration associated with each possible failure mode and predict the gradual stiffness reduction during the impact damage process. The material model has been implemented into LS-DYNA explicit finite element code within solid elements and it has proven to be capable of reproducing experimental results with good accuracy in terms of static/dynamic responses, absorbed energy and extent of damage.