Whydration effects on DNA double helix stability modulates ligand binding to natural DNA in response to changes in water activity

In this work we present evidence that water molecules are actively involved on the control of binding affinity and binding site discrimination of a drug to natural DNA. In a previous study, the effect of water activity (a(w)) on the energetic parameters of actinomycin-D intercalation to natural DNA was determined using the osmotic stress method (39). This earlier study has shown evidence that water molecules act as an allosteric regulator of ligand binding to DNA via the effect of water activity on the long-range stability of the DNA secondary structure. In this work we have carried out DNA circularization experiments using the plasmid pUC18 in the absence of drugs and in the presence of different neutral solutes to evaluate the contribution of water activity to the energetics of DNA helix unwinding. The contribution of water to these independent reactions were made explicit by the description of how the changes in the free energy of ligand binding to DNA and in the free energy associated with DNA helix torsional deformation are linked to a(w) via changes in structural hydration. Taken together, the results of these studies reveal an extensive linkage between ligand binding affinity and site binding discrimination, and long range helix conformational changes and DNA hydration, This is strong evidence that water molecules work as a classical allosteric regulator of ligand binding to the DNA via its contribution to the stability of the double helix secondary structure, suggesting a possible mechanism by which the biochemical machinery of DNA processing takes advantage of the low activity of water into the cellular milieu.

Cation-oxygen interaction and oxygen stability in CaCu3Ti4O12 and CdCu3Ti4O12 lattices

The cubic perovskite related material CaCu3Ti4O12 has attracted a great deal of attention due to the high values of the static dielectric constant, of order 104, approximately constant in the temperature range 100-600 K. The substitution of Ca by Cd results in a similar temperature dependence but a static dielectric constant more than one order of magnitude lower. A theoretical electronic structure study is performed on CaCu3Ti4O12 (CCTO) and CdCu3Ti4O12 (CdCTO) using a tight binding with overlap method. Although the calculations are performed in a paramagnetic configuration, excellent agreement with experiment was found for the calculated band gap of CCTO. In spite of the fact that the band structures of both systems look practically the same, a significant difference is found in the calculated bond strength of Ca-O and Cd-O pairs, driven by the presence of Ti, with Ca-O interaction in CCTO loosened with respect to Cd-O interaction in the cadmium compound. It is suggested that O vacancies are more easily formed in CCTO, this being related to the lower electronegativity of Ca as compared to Cd. The formation of oxygen vacancies could be the origin of the difference in the static dielectric constant of the two compounds.

The thermohydrodynamical picture of Brownian motion via a generalized Smoluchowsky equation

Via an operator continued fraction scheme, we expand Kramers equation in the high friction limit. Then all distribution moments are expressed in terms of the first momemt (particle density). The latter satisfies a generalized Smoluchowsky equation. As an application, we present the nonequilibrium thermodynamics and hydrodynamical picture for the one-dimensional Brownian motion. (C) 2000 Elsevier B.V. B.V. All rights reserved.

A critical investigation of the Tanford-Kirkwood scheme by means of Monte Carlo simulations

Monte Carlo simulations are used to assess the adequacy of the Tanford-Kirkwood prescription for electrostatic interactions in macromolecules. Within a continuum dielectric framework, the approach accurately describes salt screening of electrostatic interactions for moderately charged systems consistent with common proteins at physiological conditions. The limitations of the Debye-Huckel theory, which forms the statistical mechanical basis for the Tanford-Kirkwood result, become apparent for highly charged systems. It is shown, both by an analysis of the Debye-Huckel theory and by numerical simulations, that the difference in dielectric permittivity between macromolecule and surrounding solvent does not play a significant role for salt effects if the macromolecule is highly charged. By comparison to experimental data, the continuum dielectric model (combined with either an approximate effective Hamiltonian as in the Tanford-Kirkwood treatment or with exact Monte Carlo simulations) satisfactorily predicts the effects of charge mutation on metal ion binding constants, but only if the macromolecule and solvent are assigned the same or similar permittivities.

EXPLICIT SOLUTIONS FOR TRUNCATED COULOMB POTENTIAL OBTAINED FROM SUPERSYMMETRY

The Schrodinger equation with the truncated Coulomb potential is solved using the supersymmetric quantum mechanics formalism, with and without the cutoff in the angular momentum potential. We obtain some analytical eigenfunctions and eigenvalues for particular values of the cutoff parameter.

Vehicle influence on calcium hydroxide pastes diffusion in human and bovine teeth

The purpose of this study was to compare the pH and calcium ion liberation after use of calcium hydroxide pastes with different paste vehicles in human or bovine teeth. Ninety-two single-rooted human and bovine roots were used. The roots were instrumented and an external cavity preparation was performed. The roots were divided in to human and bovine groups. Each group was subdivided into four subgroups (SB) according to the vehicle:SB1, detergent; SB2, saline; SB3, polyethylenoglycol + camphorated paramonochlorophenol (Calen PMCC) and SB4, polyethylenoglycol + furacyn paramonochlorophenol (FPMC). Specimens were immersed into saline solution at 37 degrees C and after 7 and 14 days pH and calcium ion measurements were made. The results were analyzed by ANOVA and Tukey tests (P < 0.05). There was no statistical difference between bovine and human teeth in the pH analysis (P < 0.05), but bovine teeth provided larger calcium ion liberation than human teeth. Calen PMCC was statistically more effective for pH increase and calcium ion liberation in all analyses, followed by FPMC and saline. Detergent showed the lowest pH alterations and calcium ion liberation. The period of 14 days showed more calcium ionic liberation than the 7-day period.

Diffusion-controlled growth of aggregates in layer-by-layer films of poly(o-methoxyaniline)

The adsorption process in layer-by-layer (LBL) films of poly(o-methoxyaniline) alternated with poly(vinyl sulfonic acid) is explained using the Avrami equation. This equation was used due to its mathematical simplicity and adequate description of experimental data in real polymer systems. The Avrami parameters are a convenient means to represent empirical data of crystallization, and if microscopic knowledge is available these parameters can also be associated with adsorption mechanisms. The growth of spherulites in the LBL films was studied as a function of time using atomic force microscopy and the data were used to estimate the number and radii of aggregates, from which the Avrami parameters were determined. We find that the adsorption mechanism may correspond to a tri dimensional, diffusion-controlled growth, with increasing nucleation rate, consistent with results from kinetics of adsorption.

Thermal structure, heat content and stability of two lakes in The National Park of Rio Doce Valley (Minas Gerais, Brazil)

The thermal structure, heat content and stability were studied in Lakes Dom Helvécio and Carioca during an annual cycle. It was found that the maximum heat content, stability and work of the wind in Lake Dom Helvécio correspond to two, four and four times, respectively, the values for the Lake Carioca. These difference can be attributed to morphometric differences in the lakes. A long-term record of heat content and stability for lake Carioca is also presented. Diel variations were studied in summer and winter. The tropicality of the lakes is discussed and compared with other lacustrine systems. © 1989 Kluwer Academic Publishers.

Numerical simulation of viscous three-dimensional flow over aerospace vehicles using Euler/boundary-layer zonal approach

This paper presents a viscous three-dimensional simulations coupling Euler and boundary layer codes for calculating flows over arbitrary surfaces. The governing equations are written in a general non orthogonal coordinate system. The Levy-Lees transformation generalized to three-dimensional flows is utilized. The inviscid properties are obtained from the Euler equations using the Beam and Warming implicit approximate factorization scheme. The resulting equations are discretized and approximated by a two-point fmitedifference numerical scheme. The code developed is validated and applied to the simulation of the flowfield over aerospace vehicle configurations. The results present good correlation with the available data.

Some results on stability of retarded functional differential equations using dichotomic map techniques

This paper deals with the study of the stability of nonautonomous retarded functional differential equations using the theory of dichotomic maps. After some preliminaries, we prove the theorems on simple and asymptotic stability. Some examples are given to illustrate the application of the method. Main results about asymptotic stability of the equation x′(t) = -b(t)x(t - r) and of its nonlinear generalization x′(t) = b(t) f (x(t - r)) are established. © 1998 Kluwer Academic Publishers.

Stability of trapped Bose-Einstein condensates

In three-dimensional trapped Bose-Einstein condensate (BEC), described by the time-dependent Gross-Pitaevskii-Ginzburg equation, we study the effect of initial conditions on stability using a Gaussian variational approach and exact numerical simulations. We also discuss the validity of the criterion for stability suggested by Vakhitov and Kolokolov. The maximum initial chirp (initial focusing defocusing of cloud) that can lead a stable condensate to collapse even before the number of atoms reaches its critical limit is obtained for several specific cases. When we consider two- and three-body nonlinear terms, with negative cubic and positive quintic terms, we have the conditions for the existence of two phases in the condensate. In this case, the magnitude of the oscillations between the two phases are studied considering sufficient large initial chirps. The occurrence of collapse in a BEC with repulsive two-body interaction is also shown to be possible.

Gluon mass generation in the PT-BFM scheme

In this article we study the general structure and special properties of the Schwinger-Dyson equation for the gluon propagator constructed with the pinch technique, together with the question of how to obtain infrared finite solutions, associated with the generation of an effective gluon mass. Exploiting the known all-order correspondence between the pinch technique and the background field method, we demonstrate that, contrary to the standard formulation, the non-perturbative gluon self-energy is transverse order-by-order in the dressed loop expansion, and separately for gluonic and ghost contributions. We next present a comprehensive review of several subtle issues relevant to the search of infrared finite solutions, paying particular attention to the role of the seagull graph in enforcing transversality, the necessity of introducing massless poles in the three-gluon vertex, and the incorporation of the correct renormalization group properties. In addition, we present a method for regulating the seagull-type contributions based on dimensional regularization; its applicability depends crucially on the asymptotic behavior of the solutions in the deep ultraviolet, and in particular on the anomalous dimension of the dynamically generated gluon mass. A linearized version of the truncated Schwinger-Dyson equation is derived, using a vertex that satisfies the required Ward identity and contains massless poles belonging to different Lorentz structures. The resulting integral equation is then solved numerically, the infrared and ultraviolet properties of the obtained solutions are examined in detail, and the allowed range for the effective gluon mass is determined. Various open questions and possible connections with different approaches in the literature are discussed. © SISSA 2006.

The Canny detector with edge region focusing using an anisotropic diffusion process

This paper proposes a methodology for edge detection in digital images using the Canny detector, but associated with a priori edge structure focusing by a nonlinear anisotropic diffusion via the partial differential equation (PDE). This strategy aims at minimizing the effect of the well-known duality of the Canny detector, under which is not possible to simultaneously enhance the insensitivity to image noise and the localization precision of detected edges. The process of anisotropic diffusion via thePDE is used to a priori focus the edge structure due to its notable characteristic in selectively smoothing the image, leaving the homogeneous regions strongly smoothed and mainly preserving the physical edges, i.e., those that are actually related to objects presented in the image. The solution for the mentioned duality consists in applying the Canny detector to a fine gaussian scale but only along the edge regions focused by the process of anisotropic diffusion via the PDE. The results have shown that the method is appropriate for applications involving automatic feature extraction, since it allowed the high-precision localization of thinned edges, which are usually related to objects present in the image. © Nauka/Interperiodica 2006.

Compositional modulation and surface stability in InGaP films: Understanding and controlling surface properties

We investigate the formation of compositional modulation and atomic ordering in InGaP films. Such bulk properties - as well as surface morphologies - present a strong dependence on growth parameters, mainly the V/III ratio. Our results indicate the importance of surface diffusion and, particularly, surface reconstruction for these processes. Most importantly from the application point of view, we show that the compositional modulation is not necessarily coupled to the surface instabilities, so that smooth InGaP films with periodic compositional variation could be obtained. This opens a new route for the generation of templates for quantum dot positioning and three-dimensional arrays of nanostructures. © 2007 American Institute of Physics.

A regularized nonlinear diffusion approach for texture image denoising

In this paper a new partial differential equation based method is presented with a view to denoising images having textures. The proposed model combines a nonlinear anisotropic diffusion filter with recent harmonic analysis techniques. A wave atom shrinkage allied to detection by gradient technique is used to guide the diffusion process so as to smooth and maintain essential image characteristics. Two forcing terms are used to maintain and improve edges, boundaries and oscillatory features of an image having irregular details and texture. Experimental results show the performance of our model for texture preserving denoising when compared to recent methods in literature. © 2009 IEEE.