Irreversible thermodynamics of Poisson processes with reaction

A kinetic model is derived to study the successive movements of particles, described by a Poisson process, as well as their generation. The irreversible thermodynamics of this system is also studied from the kinetic model. This makes it possible to evaluate the differences between thermodynamical quantities computed exactly and up to second-order. Such differences determine the range of validity of the second-order approximation to extended irreversible thermodynamics

Speed of wave-front solutions to hyperbolic reaction-diffusion equations

The asymptotic speed problem of front solutions to hyperbolic reaction-diffusion (HRD) equations is studied in detail. We perform linear and variational analyses to obtain bounds for the speed. In contrast to what has been done in previous work, here we derive upper bounds in addition to lower ones in such a way that we can obtain improved bounds. For some functions it is possible to determine the speed without any uncertainty. This is also achieved for some systems of HRD (i.e., time-delayed Lotka-Volterra) equations that take into account the interaction among different species. An analytical analysis is performed for several systems of biological interest, and we find good agreement with the results of numerical simulations as well as with available observations for a system discussed recently

Chemoconvection patterns in the Methylene-blue-glucose system: Weakly nonlinear analysis

The oxidation of solutions of glucose with methylene-blue as a catalyst in basic media can induce hydrodynamic overturning instabilities, termed chemoconvection in recognition of their similarity to convective instabilities. The phenomenon is due to gluconic acid, the marginally dense product of the reaction, which gradually builds an unstable density profile. Experiments indicate that dominant pattern wavenumbers initially increase before gradually decreasing or can even oscillate for long times. Here, we perform a weakly nonlinear analysis for an established model of the system with simple kinetics, and show that the resulting amplitude equation is analogous to that obtained in convection with insulating walls. We show that the amplitude description predicts that dominant pattern wavenumbers should decrease in the long term, but does not reproduce the aforementioned increasing wavenumber behavior in the initial stages of pattern development. We hypothesize that this is due to horizontally homogeneous steady states not being attained before pattern onset. We show that the behavior can be explained using a combination of pseudo-steady-state linear and steady-state weakly nonlinear theories. The results obtained are in qualitative agreement with the analysis of experiments.

Nonlinear chemoconvection in the Methylene-blue-glucose system

Interfacial hydrodynamic instabilities arise in a range of chemical systems. One mechanism for instability is the occurrence of unstable density gradients due to the accumulation of reaction products. In this paper we conduct two-dimensional nonlinear numerical simulations for a member of this class of system: the methylene-blue¿glucose reaction. The result of these reactions is the oxidation of glucose to a relatively, but marginally, dense product, gluconic acid, that accumulates at oxygen permeable interfaces, such as the surface open to the atmosphere. The reaction is catalyzed by methylene-blue. We show that simulations help to disassemble the mechanisms responsible for the onset of instability and evolution of patterns, and we demonstrate that some of the results are remarkably consistent with experiments. We probe the impact of the upper oxygen boundary condition, for fixed flux, fixed concentration, or mixed boundary conditions, and find significant qualitative differences in solution behavior; structures either attract or repel one another depending on the boundary condition imposed. We suggest that measurement of the form of the boundary condition is possible via observation of oxygen penetration, and improved product yields may be obtained via proper control of boundary conditions in an engineering setting. We also investigate the dependence on parameters such as the Rayleigh number and depth. Finally, we find that pseudo-steady linear and weakly nonlinear techniques described elsewhere are useful tools for predicting the behavior of instabilities beyond their formal range of validity, as good agreement is obtained with the simulations.

Network-based scoring system for genome-scale metabolic reconstructions

Background: Network reconstructions at the cell level are a major development in Systems Biology. However, we are far from fully exploiting its potentialities. Often, the incremental complexity of the pursued systems overrides experimental capabilities, or increasingly sophisticated protocols are underutilized to merely refine confidence levels of already established interactions. For metabolic networks, the currently employed confidence scoring system rates reactions discretely according to nested categories of experimental evidence or model-based likelihood. Results: Here, we propose a complementary network-based scoring system that exploits the statistical regularities of a metabolic network as a bipartite graph. As an illustration, we apply it to the metabolism of Escherichia coli. The model is adjusted to the observations to derive connection probabilities between individual metabolite-reaction pairs and, after validation, to assess the reliability of each reaction in probabilistic terms. This network-based scoring system uncovers very specific reactions that could be functionally or evolutionary important, identifies prominent experimental targets, and enables further confirmation of modeling results. Conclusions: We foresee a wide range of potential applications at different sub-cellular or supra-cellular levels of biological interactions given the natural bipartivity of many biological networks.

Experimental evidence of localized oscillations in the photosensitive chlorine dioxide-iodine-malonic acid reaction

The interaction between Hopf and Turing modes has been the subject of active research in recent years. We present here experimental evidence of the existence of mixed Turing-Hopf modes in a two-dimensional system. Using the photosensitive chlorine dioxide-iodine-malonic acid reaction (CDIMA) and external constant background illumination as a control parameter, standing spots oscillating in amplitude and with hexagonal ordering were observed. Numerical simulations in the Lengyel-Epstein model for the CDIMA reaction confirmed the results.

FiltekTM Silorane and FiltekTM Supreme XT resins: tissue reaction after subcutaneous implantation in isogenic mice

The aim of this study was to evaluate the tissue compatibility of a silorane-based resin system (FiltekTM Silorane) and a methacrylatebased nanoparticle resin (FiltekTM Supreme XT) after implantation in the subcutaneous connective tissue of isogenic mice. One hundred and thirty five male isogenic BALB/c mice were randomly assigned to 12 experimental and 3 control groups, according to the implanted material and the experimental period of 7, 21 and 63 days. At the end of each period, the animals were killed and the tubes with the surrounding tissues were removed and processed for microscopic analysis. Samples were subjected to a descriptive and a semi-quantitative analyses using a 4-point scoring system (0-3) to evaluate the collagen fiber formation and inflammatory infiltrate. Data were statistically analyzed using the Kruskal Wallis test (a=0.05). The results showed that there was no significant difference between the experimental and control groups considering the three evaluation periods (p>0.05). The silorane-based and the methacrylate-based nanoparticle resins presented similar tissue response to that of the empty tube (control group) after subcutaneous implantation in isogenic mice.

Reaction-diffusion lattice gas: Theory and computer results

We report on the study of nonequilibrium ordering in the reaction-diffusion lattice gas. It is a kinetic model that relaxes towards steady states under the simultaneous competition of a thermally activated creation-annihilation $(reaction$) process at temperature T, and a diffusion process driven by a heat bath at temperature T?T. The phase diagram as one varies T and T, the system dimension d, the relative priori probabilities for the two processes, and their dynamical rates is investigated. We compare mean-field theory, new Monte Carlo data, and known exact results for some limiting cases. In particular, no evidence of Landau critical behavior is found numerically when d=2 for Metropolis rates but Onsager critical points and a variety of first-order phase transitions.

Larock Reaction in the synthesis of heterocyclic compounds

The indole ring is one of the most common features in natural products and small molecules with important bioactivity. Larock reported a new methodology for the synthesis of the indole ring system based on the palladium-catalyzed heteroannulation of 2-iodoaniline and substituted alkyne moieties. This procedure was subsequently extended to the preparation of other nitrogen- and oxygen- containing heterocycles. This is the process of choice for the synthesis of a large number of heterocyclic derivatives, as it provides outstanding regioselectivity and good to excellent yields.

Larock Reaction in the synthesis of heterocyclic compounds

The indole ring is one of the most common features in natural products and small molecules with important bioactivity. Larock reported a new methodology for the synthesis of the indole ring system based on the palladium-catalyzed heteroannulation of 2-iodoaniline and substituted alkyne moieties. This procedure was subsequently extended to the preparation of other nitrogen- and oxygen- containing heterocycles. This is the process of choice for the synthesis of a large number of heterocyclic derivatives, as it provides outstanding regioselectivity and good to excellent yields.