Fast, scalable master equation solution algorithms. IV. Lanczos iteration with diffusion approximation preconditioned iterative inversion

In this paper we propose a second linearly scalable method for solving large master equations arising in the context of gas-phase reactive systems. The new method is based on the well-known shift-invert Lanczos iteration using the GMRES iteration preconditioned using the diffusion approximation to the master equation to provide the inverse of the master equation matrix. In this way we avoid the cubic scaling of traditional master equation solution methods while maintaining the speed of a partial spectral decomposition. The method is tested using a master equation modeling the formation of propargyl from the reaction of singlet methylene with acetylene, proceeding through long-lived isomerizing intermediates. (C) 2003 American Institute of Physics.

Fast, scalable master equation solution algorithms. III. Direct time propagation accelerated by a diffusion approximation preconditioned iterative solver

In this paper we propose a novel fast and linearly scalable method for solving master equations arising in the context of gas-phase reactive systems, based on an existent stiff ordinary differential equation integrator. The required solution of a linear system involving the Jacobian matrix is achieved using the GMRES iteration preconditioned using the diffusion approximation to the master equation. In this way we avoid the cubic scaling of traditional master equation solution methods and maintain the low temperature robustness of numerical integration. The method is tested using a master equation modelling the formation of propargyl from the reaction of singlet methylene with acetylene, proceeding through long lived isomerizing intermediates. (C) 2003 American Institute of Physics.

Postbuckling of piezoelectric FGM plates subject to thermo-electro-mechanical loading

In this paper, we examine the postbuckling behavior of functionally graded material FGM rectangular plates that are integrated with surface-bonded piezoelectric actuators and are subjected to the combined action of uniform temperature change, in-plane forces, and constant applied actuator voltage. A Galerkin-differential quadrature iteration algorithm is proposed for solution of the non-linear partial differential governing equations. To account for the transverse shear strains, the Reddy higher-order shear deformation plate theory is employed. The bifurcation-type thermo-mechanical buckling of fully clamped plates, and the postbuckling behavior of plates with more general boundary conditions subject to various thermo-electro-mechanical loads, are discussed in detail. Parametric studies are also undertaken, and show the effects of applied actuator voltage, in-plane forces, volume fraction exponents, temperature change, and the character of boundary conditions on the buckling and postbuckling characteristics of the plates. (C) 2003 Elsevier Science Ltd. All rights reserved.

API documentation with executable examples

The rise of component-based software development has created an urgent need for effective application program interface (API) documentation. Experience has shown that it is hard to create precise and readable documentation. Prose documentation can provide a good overview but lacks precision. Formal methods offer precision but the resulting documentation is expensive to develop. Worse, few developers have the skill or inclination to read formal documentation. We present a pragmatic solution to the problem of API documentation. We augment the prose documentation with executable test cases, including expected outputs, and use the prose plus the test cases as the documentation. With appropriate tool support, the test cases are easy to develop and read. Such test cases constitute a completely formal, albeit partial, specification of input/output behavior. Equally important, consistency between code and documentation is demonstrated by running the test cases. This approach provides an attractive bridge between formal and informal documentation. We also present a tool that supports compact and readable test cases; and generation of test drivers and documentation, and illustrate the approach with detailed case studies. (C) 2002 Elsevier Science Inc. All rights reserved.

Dynamic stability of laminated FGM plates based on higher-order shear deformation theory

This paper conducts a dynamic stability analysis of symmetrically laminated FGM rectangular plates with general out-of-plane supporting conditions, subjected to a uniaxial periodic in-plane load and undergoing uniform temperature change. Theoretical formulations are based on Reddy's third-order shear deformation plate theory, and account for the temperature dependence of material properties. A semi-analytical Galerkin-differential quadrature approach is employed to convert the governing equations into a linear system of Mathieu-Hill equations from which the boundary points on the unstable regions are determined by Bolotin's method. Free vibration and bifurcation buckling are also discussed as subset problems. Numerical results are presented in both dimensionless tabular and graphical forms for laminated plates with FGM layers made of silicon nitride and stainless steel. The influences of various parameters such as material composition, layer thickness ratio, temperature change, static load level, boundary constraints on the dynamic stability, buckling and vibration frequencies are examined in detail through parametric studies.

Solution structure of CnErg1 (Ergtoxin), a HERG specific scorpion toxin

The three-dimensional structure of chemically synthesized CnErg1 (Ergtoxin), which specifically blocks HERG (human ether-a-go-go-related gene) K+ channels, was determined by nuclear magnetic resonance spectroscopy. CnErg1 consists of a triple-stranded beta-sheet and an a-helix, as is typical of K+ channel scorpion toxins. The peptide structure differs from the canonical structures in that the first beta-strand is shorter and is nearer to the second beta-strand rather than to the third beta-strand on the C-terminus. There is also a large hydrophobic patch on the surface of the toxin, surrounding a central lysine residue, Lys13. We postulate that this hydrophobic patch is likely to form part of the binding surface of the toxin. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Biochemical Societies.

Water table waves in an unconfined aquifer: Experiments and modeling

[1] Comprehensive measurements are presented of the piezometric head in an unconfined aquifer during steady, simple harmonic oscillations driven by a hydrostatic clear water reservoir through a vertical interface. The results are analyzed and used to test existing hydrostatic and nonhydrostatic, small-amplitude theories along with capillary fringe effects. As expected, the amplitude of the water table wave decays exponentially. However, the decay rates and phase lags indicate the influence of both vertical flow and capillary effects. The capillary effects are reconciled with observations of water table oscillations in a sand column with the same sand. The effects of vertical flows and the corresponding nonhydrostatic pressure are reasonably well described by small-amplitude theory for water table waves in finite depth aquifers. That includes the oscillation amplitudes being greater at the bottom than at the top and the phase lead of the bottom compared with the top. The main problems with respect to interpreting the measurements through existing theory relate to the complicated boundary condition at the interface between the driving head reservoir and the aquifer. That is, the small-amplitude, finite depth expansion solution, which matches a hydrostatic boundary condition between the bottom and the mean driving head level, is unrealistic with respect to the pressure variation above this level. Hence it cannot describe the finer details of the multiple mode behavior close to the driving head boundary. The mean water table height initially increases with distance from the forcing boundary but then decreases again, and its asymptotic value is considerably smaller than that previously predicted for finite depth aquifers without capillary effects. Just as the mean water table over-height is smaller than predicted by capillarity-free shallow aquifer models, so is the amplitude of the second harmonic. In fact, there is no indication of extra second harmonics ( in addition to that contained in the driving head) being generated at the interface or in the interior.

Opening windows into the mind: mothers' preferences for mental state explanations and children's theory of mind

A new questionnaire, the Maternal Mental State Input Inventory (MMSII) was created to measure mothers' preferences for introducing and elaborating on mental states in conversation with their young children. In two studies, the questionnaire was given to mothers of young children, and the children's theory of mind (ToM) development was assessed with standard tasks. In both studies, the questionnaire exhibited good internal reliability, and significant correlations emerged between mothers' self-reported preferences for elaborated, explanatory talk about the mental states and children's theory of mind performance. Further, mothers' conversational preferences, as measured by the MMSII, were the best predictors of children's theory of mind development when relevant control variables were included in the analyses. These results converge with naturalistic observational research that has demonstrated links between mothers' conversational styles and their children's theory of mind. They go further in suggesting that mothers' tendencies toward elaborated, explanatory talk about a range of mental states is particularly beneficial to children's theory of mind development. (C) 2003 Elsevier Inc. All rights reserved.

A review of drainage and spontaneous rupture in free standing thin films with tangentially immobile interfaces

A review of spontaneous rupture in thin films with tangentially immobile interfaces is presented that emphasizes the theoretical developments of film drainage and corrugation growth through the linearization of lubrication theory in a cylindrical geometry. Spontaneous rupture occurs when corrugations from adjacent interfaces become unstable and grow to a critical thickness. A corrugated interface is composed of a number of waveforms and each waveform becomes unstable at a unique transition thickness. The onset of instability occurs at the maximum transition thickness, and it is shown that only upper and lower bounds of this thickness can be predicted from linear stability analysis. The upper bound is equivalent to the Freakel criterion and is obtained from the zeroth order approximation of the H-3 term in the evolution equation. This criterion is determined solely by the film radius, interfacial tension and Hamaker constant. The lower bound is obtained from the first order approximation of the H-3 term in the evolution equation and is dependent on the film thinning velocity A semi-empirical equation, referred to as the MTR equation, is obtained by combining the drainage theory of Manev et al. [J. Dispersion Sci. Technol., 18 (1997) 769] and the experimental measurements of Radoev et al. [J. Colloid Interface Sci. 95 (1983) 254] and is shown to provide accurate predictions of film thinning velocity near the critical thickness of rupture. The MTR equation permits the prediction of the lower bound of the maximum transition thickness based entirely on film radius, Plateau border radius, interfacial tension, temperature and Hamaker constant. The MTR equation extrapolates to Reynolds equation under conditions when the Plateau border pressure is small, which provides a lower bound for the maximum transition thickness that is equivalent to the criterion of Gumerman and Homsy [Chem. Eng. Commun. 2 (1975) 27]. The relative accuracy of either bound is thought to be dependent on the amplitude of the hydrodynamic corrugations, and a semiempirical correlation is also obtained that permits the amplitude to be calculated as a function of the upper and lower bound of the maximum transition thickness. The relationship between the evolving theoretical developments is demonstrated by three film thickness master curves, which reduce to simple analytical expressions under limiting conditions when the drainage pressure drop is controlled by either the Plateau border capillary pressure or the van der Waals disjoining pressure. The master curves simplify solution of the various theoretical predictions enormously over the entire range of the linear approximation. Finally, it is shown that when the Frenkel criterion is used to assess film stability, recent studies reach conclusions that are contrary to the relevance of spontaneous rupture as a cell-opening mechanism in foams. (C) 2003 Elsevier Science B.V. All rights reserved.

Phase equilibria and surface tension of pure fluids using a molecular layer structure theory (MLST) model

This paper presents a new model based on thermodynamic and molecular interaction between molecules to describe the vapour-liquid phase equilibria and surface tension of pure component. The model assumes that the bulk fluid can be characterised as set of parallel layers. Because of this molecular structure, we coin the model as the molecular layer structure theory (MLST). Each layer has two energetic components. One is the interaction energy of one molecule of that layer with all surrounding layers. The other component is the intra-layer Helmholtz free energy, which accounts for the internal energy and the entropy of that layer. The equilibrium between two separating phases is derived from the minimum of the grand potential, and the surface tension is calculated as the excess of the Helmholtz energy of the system. We test this model with a number of components, argon, krypton, ethane, n-butane, iso-butane, ethylene and sulphur hexafluoride, and the results are very satisfactory. (C) 2002 Elsevier Science B.V. All rights reserved.

Quantum theory of the far-off-resonance continuous-wave Raman laser: Heisenberg-Langevin approach

We present the quantum theory of the far-off-resonance continuous-wave Raman laser using the Heisenberg-Langevin approach. We show that the simplified quantum Langevin equations for this system are mathematically identical to those of the nondegenerate optical parametric oscillator in the time domain with the following associations: pump pump, Stokes signal, and Raman coherence idler. We derive analytical results for both the steady-state behavior and the time-dependent noise spectra, using standard linearization procedures. In the semiclassical limit, these results match with previous purely semiclassical treatments, which yield excellent agreement with experimental observations. The analytical time-dependent results predict perfect photon statistics conversion from the pump to the Stokes and nonclassical behavior under certain operational conditions.

Cytotoxic iron chelators: Characterization of the structure, solution chemistry and redox activity of ligands and iron complexes of the di-2-pyridyl ketone isonicotinoyl hydrazone (HPKIH) analogues

Di-2-pyridyl ketone isonicotinoyl hydrazone (HPKIH) and a range of its analogues comprise a series of monobasic acids that are capable of binding iron (Fe) as tridentate (N,N,O) ligands. Recently, we have shown that these chelators are highly cytotoxic, but show selective activity against cancer cells. Particularly interesting was the fact that cytotoxicity of the HPKIH analogues is maintained even after complexation with Fe. To understand the potent anti-tumor activity of these compounds, we have fully characterized their chemical properties. This included examination of the solution chemistry and X-ray crystal structures of both the ligands and Fe complexes from this class and the ability of these complexes to mediate redox reactions. Potentiometric titrations demonstrated that all chelators are present predominantly in their charge-neutral form at physiological pH (7.4), allowing access across biological membranes. Keto-enol tautomerism of the ligands was identified, with the tautomers exhibiting distinctly different protonation constants. Interestingly, the chelators form low-spin (diamagnetic) divalent Fe complexes in solution. The chelators form distorted octahedral complexes with Fe-II, with two tridentate ligands arranged in a meridional fashion. Electrochemistry of the Fe complexes in both aqueous and non-aqueous solutions revealed that the complexes are oxidized to their ferric form at relatively high potentials, but this oxidation is coupled to a rapid reaction with water to form a hydrated (carbinolamine) derivative, leading to irreversible electrochemistry. The Fe complexes of the HPKIH analogues caused marked DNA degradation in the presence of hydrogen peroxide. This observation confirms that Fe complexes from the HPKIH series mediate Fenton chemistry and do not repel DNA. Collectively, studies on the solution chemistry and structure of these HPKIH analogues indicate that they can bind cellular Fe and enhance its redox activity, resulting in oxidative damage to vital biomolecules.