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Sample records for acid reaction-diffusion system

  1. Resilience in reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    van Vuuren, J. H.

    1999-10-01

    Reaction-diffusion systems with zero-flux Neumann boundaries are widely used to model various kinds of interaction in, for example, the scientific fields of ecology, biology, chemistry, medicine and industry. The physical systems within these fields are often known to be (conditionally or unconditionally) resilient with respect to shocks, disturbances or catastrophies in the immediate environment. In order to be good mathematical models of such situations the reaction-diffusion systems must have the same resilient or asymptotic behaviour as that of the physical situation. Three fundamentally different kinds of reaction terms are usually distinguished according to the entry signs of the reaction Jacobian: mutualism, mixed (predator-prey) interaction and competition. The asymptotic stability (in the Poincare sense) of mutualistic systems has already been studied extensively, but the results cannot be generalized (globally) to the other two fundamental types, which are not order-preserving. A partial (local) generalization is, however given here for these two types, involving simple Jacobian inequalities and knowledge (often prompted by the underlying physical situation) of invariant sets in solution space. The return time of resilient systems and the approach rate of asymptotically stable solutions are also estimated. Key words: reaction-diffusion system; competition; resilience; asymptotic stability.

  2. Parametric spatiotemporal oscillation in reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Ghosh, Shyamolina; Ray, Deb Shankar

    2016-03-01

    We consider a reaction-diffusion system in a homogeneous stable steady state. On perturbation by a time-dependent sinusoidal forcing of a suitable scaling parameter the system exhibits parametric spatiotemporal instability beyond a critical threshold frequency. We have formulated a general scheme to calculate the threshold condition for oscillation and the range of unstable spatial modes lying within a V-shaped region reminiscent of Arnold's tongue. Full numerical simulations show that depending on the specificity of nonlinearity of the models, the instability may result in time-periodic stationary patterns in the form of standing clusters or spatially localized breathing patterns with characteristic wavelengths. Our theoretical analysis of the parametric oscillation in reaction-diffusion system is corroborated by full numerical simulation of two well-known chemical dynamical models: chlorite-iodine-malonic acid and Briggs-Rauscher reactions.

  3. Parametric spatiotemporal oscillation in reaction-diffusion systems.

    PubMed

    Ghosh, Shyamolina; Ray, Deb Shankar

    2016-03-01

    We consider a reaction-diffusion system in a homogeneous stable steady state. On perturbation by a time-dependent sinusoidal forcing of a suitable scaling parameter the system exhibits parametric spatiotemporal instability beyond a critical threshold frequency. We have formulated a general scheme to calculate the threshold condition for oscillation and the range of unstable spatial modes lying within a V-shaped region reminiscent of Arnold's tongue. Full numerical simulations show that depending on the specificity of nonlinearity of the models, the instability may result in time-periodic stationary patterns in the form of standing clusters or spatially localized breathing patterns with characteristic wavelengths. Our theoretical analysis of the parametric oscillation in reaction-diffusion system is corroborated by full numerical simulation of two well-known chemical dynamical models: chlorite-iodine-malonic acid and Briggs-Rauscher reactions. PMID:27078346

  4. Design and control of patterns in reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Vanag, Vladimir K.; Epstein, Irving R.

    2008-06-01

    We discuss the design of reaction-diffusion systems that display a variety of spatiotemporal patterns. We also consider how these patterns may be controlled by external perturbation, typically using photochemistry or temperature. Systems treated include the Belousov-Zhabotinsky (BZ) reaction, the chlorite-iodide-malonic acid and chlorine dioxide-malonic acid-iodine reactions, and the BZ-AOT system, i.e., the BZ reaction in a water-in-oil reverse microemulsion stabilized by the surfactant sodium bis(2-ethylhexyl) sulfosuccinate (AOT).

  5. Design and control of patterns in reaction-diffusion systems

    SciTech Connect

    Vanag, Vladimir K.; Epstein, Irving R.

    2008-06-15

    We discuss the design of reaction-diffusion systems that display a variety of spatiotemporal patterns. We also consider how these patterns may be controlled by external perturbation, typically using photochemistry or temperature. Systems treated include the Belousov-Zhabotinsky (BZ) reaction, the chlorite-iodide-malonic acid and chlorine dioxide-malonic acid-iodine reactions, and the BZ-AOT system, i.e., the BZ reaction in a water-in-oil reverse microemulsion stabilized by the surfactant sodium bis(2-ethylhexyl) sulfosuccinate (AOT)

  6. Wave Phenomena in Reaction-Diffusion Systems

    NASA Astrophysics Data System (ADS)

    Steinbock, Oliver; Engel, Harald

    2013-12-01

    Pattern formation in excitable and oscillatory reaction-diffusion systems provides intriguing examples for the emergence of macroscopic order from molecular reaction events and Brownian motion. Here we review recent results on several aspects of excitation waves including anomalous dispersion, vortex pinning, and three-dimensional scroll waves. Anomalies in the speed-wavelength dependence of pulse trains include nonmonotonic behavior, bistability, and velocity gaps. We further report on the hysteresis effects during the pinning-depinning transition of twodimensional spiral waves. The pinning of three-dimensional scroll waves shows even richer dynamic complexity, partly due to the possibility of geometric and topological mismatches between the unexcitable, pinning heterogeneities and the one-dimensional rotation backbone of the vortex. As examples we present results on the pinning of scroll rings to spherical, C-shaped, and genus-2-type heterogeneities. We also review the main results of several experimental studies employing the Belousov-Zhabotinsky reaction and briefly discuss the biomedical relevance of this research especially in the context of cardiology.

  7. Multifold Increases in Turing Pattern Wavelength in the Chlorine Dioxide-Iodine-Malonic Acid Reaction-Diffusion System

    NASA Astrophysics Data System (ADS)

    Gaskins, Delora K.; Pruc, Emily E.; Epstein, Irving R.; Dolnik, Milos

    2016-07-01

    Turing patterns in the chlorine dioxide-iodine-malonic acid reaction were modified through additions of sodium halide salt solutions. The range of wavelengths obtained is several times larger than in the previously reported literature. Pattern wavelength was observed to significantly increase with sodium bromide or sodium chloride. A transition to a uniform state was found at high halide concentrations. The observed experimental results are qualitatively well reproduced in numerical simulations with the Lengyel-Epstein model with an additional chemically realistic kinetic term to account for the added halide and an adjustment of the activator diffusion rate to allow for interhalogen formation.

  8. Multifold Increases in Turing Pattern Wavelength in the Chlorine Dioxide-Iodine-Malonic Acid Reaction-Diffusion System.

    PubMed

    Gaskins, Delora K; Pruc, Emily E; Epstein, Irving R; Dolnik, Milos

    2016-07-29

    Turing patterns in the chlorine dioxide-iodine-malonic acid reaction were modified through additions of sodium halide salt solutions. The range of wavelengths obtained is several times larger than in the previously reported literature. Pattern wavelength was observed to significantly increase with sodium bromide or sodium chloride. A transition to a uniform state was found at high halide concentrations. The observed experimental results are qualitatively well reproduced in numerical simulations with the Lengyel-Epstein model with an additional chemically realistic kinetic term to account for the added halide and an adjustment of the activator diffusion rate to allow for interhalogen formation. PMID:27517779

  9. Stochastic resonance with a mesoscopic reaction-diffusion system.

    PubMed

    Mahara, Hitoshi; Yamaguchi, Tomohiko; Parmananda, P

    2014-06-01

    In a mesoscopic reaction-diffusion system with an Oregonator reaction model, we show that intrinsic noise can drive a resonant stable pattern in the presence of the initial subthreshold perturbations. Both spatially periodic and aperiodic stochastic resonances are demonstrated by employing the Gillespies stochastic simulation algorithm. The mechanisms for these phenomena are discussed. PMID:25019857

  10. Spiral defect chaos in an advection-reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Affan, H.; Friedrich, R.

    2014-06-01

    This paper comprises numerical and theoretical studies of spatiotemporal patterns in advection-reaction-diffusion systems in which the chemical species interact with the hydrodynamic fluid. Due to the interplay between the two, we obtained the spiral defect chaos in the activator-inhibitor-type model. We formulated the generalized Swift-Hohenberg-type model for this system. Then the evolution of fractal boundaries due to the effect of the strong nonlinearity at the interface of the two chemical species is studied numerically. The purpose of the present paper is to point out that spiral defect chaos, observed in model equations of the extended Swift-Hohenberg equation for low Prandtl number convection, may actually be obtained also in certain advection-reaction-diffusion systems.

  11. Hybrid stochastic simulations of intracellular reaction-diffusion systems

    PubMed Central

    Kalantzis, Georgios

    2009-01-01

    With the observation that stochasticity is important in biological systems, chemical kinetics have begun to receive wider interest. While the use of Monte Carlo discrete event simulations most accurately capture the variability of molecular species, they become computationally costly for complex reaction-diffusion systems with large populations of molecules. On the other hand, continuous time models are computationally efficient but they fail to capture any variability in the molecular species. In this study a novel hybrid stochastic approach is introduced for simulating reaction-diffusion systems. We developed a dynamic partitioning strategy using fractional propensities. In that way processes with high frequency are simulated mostly with deterministic rate-based equations, and those with low frequency mostly with the exact stochastic algorithm of Gillespie. In this way we preserve the stochastic behavior of cellular pathways while being able to apply it to large populations of molecules. In this article we describe this hybrid algorithmic approach, and we demonstrate its accuracy and efficiency compared with the Gillespie algorithm for two different systems. First, a model of intracellular viral kinetics with two steady states and second, a compartmental model of the postsynaptic spine head for studying the dynamics of Ca+2 and NMDA receptors. PMID:19414282

  12. A Discrete Model to Study Reaction-Diffusion-Mechanics Systems

    PubMed Central

    Weise, Louis D.; Nash, Martyn P.; Panfilov, Alexander V.

    2011-01-01

    This article introduces a discrete reaction-diffusion-mechanics (dRDM) model to study the effects of deformation on reaction-diffusion (RD) processes. The dRDM framework employs a FitzHugh-Nagumo type RD model coupled to a mass-lattice model, that undergoes finite deformations. The dRDM model describes a material whose elastic properties are described by a generalized Hooke's law for finite deformations (Seth material). Numerically, the dRDM approach combines a finite difference approach for the RD equations with a Verlet integration scheme for the equations of the mass-lattice system. Using this framework results were reproduced on self-organized pacemaking activity that have been previously found with a continuous RD mechanics model. Mechanisms that determine the period of pacemakers and its dependency on the medium size are identified. Finally it is shown how the drift direction of pacemakers in RDM systems is related to the spatial distribution of deformation and curvature effects. PMID:21804911

  13. Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm

    SciTech Connect

    Bernstein, David

    2004-12-12

    We examine an application of the Gillespie algorithm to simulating spatially inhomogeneous reaction-diffusion systems in mesoscopic volumes such as cells and microchambers. The method involves discretizing the chamber into elements and modeling the diffusion of chemical species by the movement of molecules between neighboring elements. These transitions are expressed in the form of a set of reactions which are added to the chemical system. The derivation of the rates of these diffusion reactions is by comparison with a finite volume discretization of the heat equation on an unevenly spaced grid. The diffusion coefficient of each species is allowed to be inhomogeneous in space, including discontinuities. The resulting system is solved by the Gillespie algorithm using the fast direct method. We show that in an appropriate limit the method reproduces exact solutions of the heat equation for a purely diffusive system and the nonlinear reaction-rate equation describing the cubic autocatalytic reaction.

  14. Simulating mesoscopic reaction-diffusion systems using the Gillespie algorithm.

    PubMed

    Bernstein, David

    2005-04-01

    We examine an application of the Gillespie algorithm to simulating spatially inhomogeneous reaction-diffusion systems in mesoscopic volumes such as cells and microchambers. The method involves discretizing the chamber into elements and modeling the diffusion of chemical species by the movement of molecules between neighboring elements. These transitions are expressed in the form of a set of reactions which are added to the chemical system. The derivation of the rates of these diffusion reactions is by comparison with a finite volume discretization of the heat equation on an unevenly spaced grid. The diffusion coefficient of each species is allowed to be inhomogeneous in space, including discontinuities. The resulting system is solved by the Gillespie algorithm using the fast direct method. We show that in an appropriate limit the method reproduces exact solutions of the heat equation for a purely diffusive system and the nonlinear reaction-rate equation describing the cubic autocatalytic reaction. PMID:15903653

  15. Stochastic operator-splitting method for reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Choi, TaiJung; Maurya, Mano Ram; Tartakovsky, Daniel M.; Subramaniam, Shankar

    2012-11-01

    Many biochemical processes at the sub-cellular level involve a small number of molecules. The local numbers of these molecules vary in space and time, and exhibit random fluctuations that can only be captured with stochastic simulations. We present a novel stochastic operator-splitting algorithm to model such reaction-diffusion phenomena. The reaction and diffusion steps employ stochastic simulation algorithms and Brownian dynamics, respectively. Through theoretical analysis, we have developed an algorithm to identify if the system is reaction-controlled, diffusion-controlled or is in an intermediate regime. The time-step size is chosen accordingly at each step of the simulation. We have used three examples to demonstrate the accuracy and robustness of the proposed algorithm. The first example deals with diffusion of two chemical species undergoing an irreversible bimolecular reaction. It is used to validate our algorithm by comparing its results with the solution obtained from a corresponding deterministic partial differential equation at low and high number of molecules. In this example, we also compare the results from our method to those obtained using a Gillespie multi-particle (GMP) method. The second example, which models simplified RNA synthesis, is used to study the performance of our algorithm in reaction- and diffusion-controlled regimes and to investigate the effects of local inhomogeneity. The third example models reaction-diffusion of CheY molecules through the cytoplasm of Escherichia coli during chemotaxis. It is used to compare the algorithm's performance against the GMP method. Our analysis demonstrates that the proposed algorithm enables accurate simulation of the kinetics of complex and spatially heterogeneous systems. It is also computationally more efficient than commonly used alternatives, such as the GMP method.

  16. Selecting spatio-temporal patterns by substrate injection in a reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Ghosh, Shyamolina; Ray, Deb Shankar

    2015-07-01

    We have explored the growth of patterns in chlorine dioxide-iodine-malonic acid reaction-diffusion system when the injection rate of the activator and inhibitor is varied over a range. The transition from spot to stripe and their mixture and finally the target wave which appears at the Hopf bifurcation boundary are observed. Our numerical simulations have been corroborated by theoretical analysis of amplitude equation for targets.

  17. Reaction -Diffusion Systems in Intracellular Molecular Transport and Control

    PubMed Central

    Soh, Siowling; Byrska, Marta; Kandere-Grzybowska, Kristiana

    2013-01-01

    Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. While most research to date has focused on the so-called active-transport mechanisms, “passive” diffusion is often equally rapid and is always energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions – from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. Despite their apparent diversity, these systems share many common features and are “wired” according to “generic” motifs involving non-linear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times describing constituent sub-processes. Therefore, in reviewing the manifestations of cellular RD, we also attempt to familiarize the reader with the basic theory of these processes. PMID:20518023

  18. Dichotomous-noise-induced pattern formation in a reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Das, Debojyoti; Ray, Deb Shankar

    2013-06-01

    We consider a generic reaction-diffusion system in which one of the parameters is subjected to dichotomous noise by controlling the flow of one of the reacting species in a continuous-flow-stirred-tank reactor (CSTR) -membrane reactor. The linear stability analysis in an extended phase space is carried out by invoking Furutzu-Novikov procedure for exponentially correlated multiplicative noise to derive the instability condition in the plane of the noise parameters (correlation time and strength of the noise). We demonstrate that depending on the correlation time an optimal strength of noise governs the self-organization. Our theoretical analysis is corroborated by numerical simulations on pattern formation in a chlorine-dioxide-iodine-malonic acid reaction-diffusion system.

  19. Noisy transport in reaction-diffusion systems with quenched disorder

    NASA Astrophysics Data System (ADS)

    Missel, Andrew Royce

    Reaction-diffusion (RD) models are useful tools for studying a wide variety of natural phenomena. The effects of quenched disorder in the reaction rates on RD models is not completely understood, especially in parameter regimes where internal noise or stochasticity is also important. In the first part of this dissertation, I will examine an RD model in which both quenched disorder and stochasticity are important. The model consists of particles (labeled A) which diffuse around space and reproduce (A → 2A), die (A → 0), and compete with one another (2A → A) with rates that depend on position. Specifically, birth is only allowed in localized patches called "oases," while death is allowed in the "desert" that comprises the rest of space. In the limit of low oasis density, transport through the system is achieved via rare "hopping" events when small concentrations of particles make it through the desert from one oasis to another. To correctly account for this hopping---and to accurately describe the nature of transport in the system---it is necessary to take stochasticity into account. In order to determine the nature of transport in this system analytically, I will use a variety of tools drawn from disparate sources, including the theory of hopping conduction in doped semiconductors and first passage percolation. These tools will allow for predictions to be made for a number of important transport-related features: the infection time, or time needed for the population to traverse the system; the velocity of the front moving through the system; and the dynamic roughening of the front. I will also present the results of simulations of the system that largely confirm the analytical predictions. Finally, in the second part of the dissertation I will study a pair of closely related RD models, one of which exhibits an active to absorbing state phase transition.

  20. A priori [Formula: see text] estimates for solutions of a class of reaction-diffusion systems.

    PubMed

    Du, Zengji; Peng, Rui

    2016-05-01

    In this short paper, we establish a priori [Formula: see text]-norm estimates for solutions of a class of reaction-diffusion systems which can be used to model the spread of infectious disease. The developed technique may find applications in other reaction-diffusion systems. PMID:26141826

  1. Distributed order reaction-diffusion systems associated with Caputo derivatives

    NASA Astrophysics Data System (ADS)

    Saxena, R. K.; Mathai, A. M.; Haubold, H. J.

    2014-08-01

    This paper deals with the investigation of the solution of an unified fractional reaction-diffusion equation of distributed order associated with the Caputo derivatives as the time-derivative and Riesz-Feller fractional derivative as the space-derivative. The solution is derived by the application of the joint Laplace and Fourier transforms in compact and closed form in terms of the H-function. The results derived are of general nature and include the results investigated earlier by other authors, notably by Mainardi et al. ["The fundamental solution of the space-time fractional diffusion equation," Fractional Calculus Appl. Anal. 4, 153-202 (2001); Mainardi et al. "Fox H-functions in fractional diffusion," J. Comput. Appl. Math. 178, 321-331 (2005)] for the fundamental solution of the space-time fractional equation, including Haubold et al. ["Solutions of reaction-diffusion equations in terms of the H-function," Bull. Astron. Soc. India 35, 681-689 (2007)] and Saxena et al. ["Fractional reaction-diffusion equations," Astrophys. Space Sci. 305, 289-296 (2006a)] for fractional reaction-diffusion equations. The advantage of using the Riesz-Feller derivative lies in the fact that the solution of the fractional reaction-diffusion equation, containing this derivative, includes the fundamental solution for space-time fractional diffusion, which itself is a generalization of fractional diffusion, space-time fraction diffusion, and time-fractional diffusion, see Schneider and Wyss ["Fractional diffusion and wave equations," J. Math. Phys. 30, 134-144 (1989)]. These specialized types of diffusion can be interpreted as spatial probability density functions evolving in time and are expressible in terms of the H-function in compact forms. The convergence conditions for the double series occurring in the solutions are investigated. It is interesting to observe that the double series comes out to be a special case of the Srivastava-Daoust hypergeometric function of two variables

  2. A Simple Demonstration of Convective Effects on Reaction-Diffusion Systems: A Burning Cigarette.

    ERIC Educational Resources Information Center

    Pojman, John A.

    1990-01-01

    Described is a demonstration that provides an introduction to nonequilibrium reaction-diffusion systems and the coupling of hydrodynamics to chemical reactions. Experiments that demonstrate autocatalytic behavior that are effected by gravity and convection are included. (KR)

  3. An integration factor method for stochastic and stiff reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Ta, Catherine; Wang, Dongyong; Nie, Qing

    2015-08-01

    Stochastic effects are often present in the biochemical systems involving reactions and diffusions. When the reactions are stiff, existing numerical methods for stochastic reaction diffusion equations require either very small time steps for any explicit schemes or solving large nonlinear systems at each time step for the implicit schemes. Here we present a class of semi-implicit integration factor methods that treat the diffusion term exactly and reaction implicitly for a system of stochastic reaction-diffusion equations. Our linear stability analysis shows the advantage of such methods for both small and large amplitudes of noise. Direct use of the method to solving several linear and nonlinear stochastic reaction-diffusion equations demonstrates good accuracy, efficiency, and stability properties. This new class of methods, which are easy to implement, will have broader applications in solving stochastic reaction-diffusion equations arising from models in biology and physical sciences.

  4. Numerical solutions of the reaction diffusion system by using exponential cubic B-spline collocation algorithms

    NASA Astrophysics Data System (ADS)

    Ersoy, Ozlem; Dag, Idris

    2015-12-01

    The solutions of the reaction-diffusion system are given by method of collocation based on the exponential B-splines. Thus the reaction-diffusion systemturns into an iterative banded algebraic matrix equation. Solution of the matrix equation is carried out byway of Thomas algorithm. The present methods test on both linear and nonlinear problems. The results are documented to compare with some earlier studies by use of L∞ and relative error norm for problems respectively.

  5. Nuclemeter: a reaction-diffusion based method for quantifying nucleic acids undergoing enzymatic amplification.

    PubMed

    Liu, Changchun; Sadik, Mohamed M; Mauk, Michael G; Edelstein, Paul H; Bushman, Frederic D; Gross, Robert; Bau, Haim H

    2014-01-01

    Real-time amplification and quantification of specific nucleic acid sequences plays a major role in medical and biotechnological applications. In the case of infectious diseases, such as HIV, quantification of the pathogen-load in patient specimens is critical to assess disease progression and effectiveness of drug therapy. Typically, nucleic acid quantification requires expensive instruments, such as real-time PCR machines, which are not appropriate for on-site use and for low-resource settings. This paper describes a simple, low-cost, reaction-diffusion based method for end-point quantification of target nucleic acids undergoing enzymatic amplification. The number of target molecules is inferred from the position of the reaction-diffusion front, analogous to reading temperature in a mercury thermometer. The method was tested for HIV viral load monitoring and performed on par with conventional benchtop methods. The proposed method is suitable for nucleic acid quantification at point of care, compatible with multiplexing and high-throughput processing, and can function instrument-free. PMID:25477046

  6. The role of a reaction-diffusion system in the initiation of primary hair follicles.

    PubMed

    Nagorcka, B N; Mooney, J R

    1985-05-21

    A mechanism based on a reaction-diffusion system is proposed for the initiation of hair follicles in the epidermis during fetal development. It is demonstrated that initiation of primary follicles in a series of waves, within the proposed mechanism, is a consequence of the size and shape dependent properties of the reaction-diffusion system without the need for the propagation of signals through the skin. The observed trio grouping of follicles and variation of primary follicle density per unit skin area during development are also correctly predicted. An explanation, based on the reaction-diffusion system and the variation of its characteristic spatial wavelength with time during development, is suggested for the termination of both primary and secondary follicle initiation as well as follicle neogenesis. The proposed initiation mechanism is basically the same as that used to explain various spatial patterns observed in hair fibre formation (Nagorcka & Mooney, 1982). PMID:4033155

  7. Solitary travelling auto-waves in fractional reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Datsko, Bohdan; Gafiychuk, Vasyl; Podlubny, Igor

    2015-06-01

    In this article we study properties of solitary auto-waves in nonlinear fractional reaction-diffusion systems. As an example, the generalised FitzHugh-Nagumo model with time-fractional derivatives is considered. By a linear stability analysis and computer simulation it is shown that the order of the fractional derivative can substantially change the properties of solitary auto-waves and significantly enrich nonlinear system dynamics. The main properties of solitary travelling wave solutions, including the shape of the waves, the domain of their existence, as well as the parameters of their propagation in fractional reaction-diffusion systems, are investigated.

  8. Front waves and complex spatiotemporal patterns in a reaction-diffusion-convection system with thermokinetic autocatalysis.

    PubMed

    Trávnícková, Tereza; Kohout, Martin; Schreiber, Igor; Kubícek, Milan

    2009-12-01

    We analyze dynamics of stationary nonuniform patterns, traveling waves, and spatiotemporal chaos in a simple model of a tubular cross-flow reactor. The reactant is supplied continuously via convective flow and/or by diffusion through permeable walls of the reactor. First order exothermic reaction kinetics is assumed and the system is described by mass and energy balances forming coupled reaction-diffusion-convection equations. Dynamical regimes of the reaction-diffusion subsystem range from pulses and fronts to periodic waves and complex chaotic behavior. Two distinct types of chaotic patterns are identified and characterized by Lyapunov dimension. Next we examine the effects of convection on various types of the reaction-diffusion regimes. Remarkable zigzag fronts and steady state patterns are found despite the absence of differential flow. We employ continuation techniques to elucidate the existence and form of these patterns. PMID:20059221

  9. Front waves and complex spatiotemporal patterns in a reaction-diffusion-convection system with thermokinetic autocatalysis

    NASA Astrophysics Data System (ADS)

    Trávníčková, Tereza; Kohout, Martin; Schreiber, Igor; Kubíček, Milan

    2009-12-01

    We analyze dynamics of stationary nonuniform patterns, traveling waves, and spatiotemporal chaos in a simple model of a tubular cross-flow reactor. The reactant is supplied continuously via convective flow and/or by diffusion through permeable walls of the reactor. First order exothermic reaction kinetics is assumed and the system is described by mass and energy balances forming coupled reaction-diffusion-convection equations. Dynamical regimes of the reaction-diffusion subsystem range from pulses and fronts to periodic waves and complex chaotic behavior. Two distinct types of chaotic patterns are identified and characterized by Lyapunov dimension. Next we examine the effects of convection on various types of the reaction-diffusion regimes. Remarkable zigzag fronts and steady state patterns are found despite the absence of differential flow. We employ continuation techniques to elucidate the existence and form of these patterns.

  10. Scaling of morphogenetic patterns in reaction-diffusion systems.

    PubMed

    Rasolonjanahary, Manan'Iarivo; Vasiev, Bakhtier

    2016-09-01

    Development of multicellular organisms is commonly associated with the response of individual cells to concentrations of chemical substances called morphogens. Concentration fields of morphogens form a basis for biological patterning and ensure its properties including ability to scale with the size of the organism. While mechanisms underlying the formation of morphogen gradients are reasonably well understood, little is known about processes responsible for their scaling. Here, we perform a formal analysis of scaling for chemical patterns forming in continuous systems. We introduce a quantity representing the sensitivity of systems to changes in their size and use it to analyse scaling properties of patterns forming in a few different systems. Particularly, we consider how scaling properties of morphogen gradients forming in diffusion-decay systems depend on boundary conditions and how the scaling can be improved by passive modulation of morphogens or active transport in the system. We also analyse scaling of morphogenetic signal caused by two opposing gradients and consider scaling properties of patterns forming in activator-inhibitor systems. We conclude with a few possible mechanisms which allow scaling of morphogenetic patterns. PMID:27255960

  11. Nonlinear stability in reaction-diffusion systems via optimal Lyapunov functions

    NASA Astrophysics Data System (ADS)

    Lombardo, S.; Mulone, G.; Trovato, M.

    2008-06-01

    We define optimal Lyapunov functions to study nonlinear stability of constant solutions to reaction-diffusion systems. A computable and finite radius of attraction for the initial data is obtained. Applications are given to the well-known Brusselator model and a three-species model for the spatial spread of rabies among foxes.

  12. Nuclemeter: A Reaction-Diffusion Column for Quantifying Nucleic Acids Undergoing Enzymatic Amplification

    NASA Astrophysics Data System (ADS)

    Bau, Haim; Liu, Changchun; Killawala, Chitvan; Sadik, Mohamed; Mauk, Michael

    2014-11-01

    Real-time amplification and quantification of specific nucleic acid sequences plays a major role in many medical and biotechnological applications. In the case of infectious diseases, quantification of the pathogen-load in patient specimens is critical to assessing disease progression, effectiveness of drug therapy, and emergence of drug-resistance. Typically, nucleic acid quantification requires sophisticated and expensive instruments, such as real-time PCR machines, which are not appropriate for on-site use and for low resource settings. We describe a simple, low-cost, reactiondiffusion based method for end-point quantification of target nucleic acids undergoing enzymatic amplification. The number of target molecules is inferred from the position of the reaction-diffusion front, analogous to reading temperature in a mercury thermometer. We model the process with the Fisher Kolmogoroff Petrovskii Piscounoff (FKPP) Equation and compare theoretical predictions with experimental observations. The proposed method is suitable for nucleic acid quantification at the point of care, compatible with multiplexing and high-throughput processing, and can function instrument-free. C.L. was supported by NIH/NIAID K25AI099160; M.S. was supported by the Pennsylvania Ben Franklin Technology Development Authority; C.K. and H.B. were funded, in part, by NIH/NIAID 1R41AI104418-01A1.

  13. Bogdanov-Takens Bifurcation of a Class of Delayed Reaction-Diffusion System

    NASA Astrophysics Data System (ADS)

    Cao, Jianzhi; Wang, Peiguang; Yuan, Rong; Mei, Yingying

    2015-06-01

    In this paper, a class of reaction-diffusion system with Neumann boundary condition is considered. By analyzing the generalized eigenvector associated with zero eigenvalue, an equivalent condition for the determination of Bogdonov-Takens (B-T) singularity is obtained. Next, by using center manifold theorem and normal form method, we have a two-dimension ordinary differential system on its center manifold. Finally, two examples show that the given algorithm is effective.

  14. Global Existence of Renormalized Solutions to Entropy-Dissipating Reaction-Diffusion Systems

    NASA Astrophysics Data System (ADS)

    Fischer, J.

    2015-10-01

    In the present work we introduce the notion of a renormalized solution for reaction-diffusion systems with entropy-dissipating reactions. We establish the global existence of renormalized solutions. In the case of integrable reaction terms our notion of a renormalized solution reduces to the usual notion of a weak solution. Our existence result in particular covers all reaction-diffusion systems involving a single reversible reaction with mass-action kinetics and (possibly species-dependent) Fick-law diffusion; more generally, it covers the case of systems of reversible reactions with mass-action kinetics which satisfy the detailed balance condition. For such equations the existence of any kind of solution in general was an open problem, thereby motivating the study of renormalized solutions.

  15. Differential diffusivity of Nodal and Lefty underlies a reaction-diffusion patterning system

    PubMed Central

    Müller, Patrick; Rogers, Katherine W.; Jordan, Ben M.; Lee, Joon S.; Robson, Drew; Ramanathan, Sharad; Schier, Alexander F.

    2012-01-01

    Biological systems involving short-range activators and long-range inhibitors can generate complex patterns. Reaction-diffusion models postulate that differences in signaling range are caused by differential diffusivity of inhibitor and activator. Other models suggest that differential clearance underlies different signaling ranges. To test these models, we measured the biophysical properties of the Nodal/Lefty activator/inhibitor system during zebrafish embryogenesis. Analysis of Nodal and Lefty gradients reveals that Nodals have a shorter range than Lefty proteins. Pulse-labelinganalysis indicates that Nodals and Leftys have similar clearance kinetics, whereas fluorescence recovery assays reveal that Leftys have a higher effective diffusion coefficient than Nodals. These results indicate that differential diffusivity is the major determinant of the differences in Nodal/Lefty range and provide biophysical support for reaction-diffusion models of activator/inhibitor-mediated patterning. PMID:22499809

  16. Primal-mixed formulations for reaction-diffusion systems on deforming domains

    NASA Astrophysics Data System (ADS)

    Ruiz-Baier, Ricardo

    2015-10-01

    We propose a finite element formulation for a coupled elasticity-reaction-diffusion system written in a fully Lagrangian form and governing the spatio-temporal interaction of species inside an elastic, or hyper-elastic body. A primal weak formulation is the baseline model for the reaction-diffusion system written in the deformed domain, and a finite element method with piecewise linear approximations is employed for its spatial discretization. On the other hand, the strain is introduced as mixed variable in the equations of elastodynamics, which in turn acts as coupling field needed to update the diffusion tensor of the modified reaction-diffusion system written in a deformed domain. The discrete mechanical problem yields a mixed finite element scheme based on row-wise Raviart-Thomas elements for stresses, Brezzi-Douglas-Marini elements for displacements, and piecewise constant pressure approximations. The application of the present framework in the study of several coupled biological systems on deforming geometries in two and three spatial dimensions is discussed, and some illustrative examples are provided and extensively analyzed.

  17. An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Padgett, Jill M. A.; Ilie, Silvana

    2016-03-01

    Stochastic modelling is critical for studying many biochemical processes in a cell, in particular when some reacting species have low population numbers. For many such cellular processes the spatial distribution of the molecular species plays a key role. The evolution of spatially heterogeneous biochemical systems with some species in low amounts is accurately described by the mesoscopic model of the Reaction-Diffusion Master Equation. The Inhomogeneous Stochastic Simulation Algorithm provides an exact strategy to numerically solve this model, but it is computationally very expensive on realistic applications. We propose a novel adaptive time-stepping scheme for the tau-leaping method for approximating the solution of the Reaction-Diffusion Master Equation. This technique combines effective strategies for variable time-stepping with path preservation to reduce the computational cost, while maintaining the desired accuracy. The numerical tests on various examples arising in applications show the improved efficiency achieved by the new adaptive method.

  18. Nonlinear Waves in Reaction Diffusion Systems: The Effect of Transport Memory

    SciTech Connect

    HURD,ALAN J.; KENKRE,V.M.; MANNE,K.K.

    1999-11-04

    Motivated by the problem of determining stress distributions in granular materials, we study the effect of finite transport correlation times on the propagation of nonlinear wavefronts in reaction diffusion systems. We obtain new results such as the possibility of spatial oscillations in the wavefront shape for certain values of the system parameters and high enough wavefront speeds. We also generalize earlier known results concerning the minimum wavefront speed and shape-speed relationships stemming from the finiteness of the correlation times. Analytic investigations are made possible by a piece-wise linear representation of the nonlinearity.

  19. Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK

    PubMed Central

    2014-01-01

    Background Investigation of the nonlinear pattern dynamics of a reaction-diffusion system almost always requires numerical solution of the system’s set of defining differential equations. Traditionally, this would be done by selecting an appropriate differential equation solver from a library of such solvers, then writing computer codes (in a programming language such as C or Matlab) to access the selected solver and display the integrated results as a function of space and time. This “code-based” approach is flexible and powerful, but requires a certain level of programming sophistication. A modern alternative is to use a graphical programming interface such as Simulink to construct a data-flow diagram by assembling and linking appropriate code blocks drawn from a library. The result is a visual representation of the inter-relationships between the state variables whose output can be made completely equivalent to the code-based solution. Results As a tutorial introduction, we first demonstrate application of the Simulink data-flow technique to the classical van der Pol nonlinear oscillator, and compare Matlab and Simulink coding approaches to solving the van der Pol ordinary differential equations. We then show how to introduce space (in one and two dimensions) by solving numerically the partial differential equations for two different reaction-diffusion systems: the well-known Brusselator chemical reactor, and a continuum model for a two-dimensional sheet of human cortex whose neurons are linked by both chemical and electrical (diffusive) synapses. We compare the relative performances of the Matlab and Simulink implementations. Conclusions The pattern simulations by Simulink are in good agreement with theoretical predictions. Compared with traditional coding approaches, the Simulink block-diagram paradigm reduces the time and programming burden required to implement a solution for reaction-diffusion systems of equations. Construction of the block

  20. Square Turing patterns in reaction-diffusion systems with coupled layers

    SciTech Connect

    Li, Jing; Wang, Hongli E-mail: qi@pku.edu.cn; Ouyang, Qi E-mail: qi@pku.edu.cn

    2014-06-15

    Square Turing patterns are usually unstable in reaction-diffusion systems and are rarely observed in corresponding experiments and simulations. We report here an example of spontaneous formation of square Turing patterns with the Lengyel-Epstein model of two coupled layers. The squares are found to be a result of the resonance between two supercritical Turing modes with an appropriate ratio. Besides, the spatiotemporal resonance of Turing modes resembles to the mode-locking phenomenon. Analysis of the general amplitude equations for square patterns reveals that the fixed point corresponding to square Turing patterns is stationary when the parameters adopt appropriate values.

  1. Formation of Somitogenesis-like Pattern in a Reaction-Diffusion System

    NASA Astrophysics Data System (ADS)

    Sakamoto, Fumitaka; Miyakawa, Kenji

    2008-08-01

    The Belousov-Zhabotinsky reaction system showing stationary patterns is realized on the basis of water-in-oil microemulsions with the surfactant sodium bis(2-ethylhexyl)sulfosuccinate. We experimentally demonstrate the formation of somitogenesis-like pattern in which chemical waves arising from spontaneous bulk oscillations are successively arrested and then stacked. The experimental results are qualitatively reproduced by numerical simulations using the two-variable oregonator model. These show that a somitogenesis can be accounted for by the genuine reaction-diffusion model.

  2. Pattern formation in the iodate-sulfite-thiosulfate reaction-diffusion system.

    PubMed

    Liu, Haimiao; Pojman, John A; Zhao, Yuemin; Pan, Changwei; Zheng, Juhua; Yuan, Ling; Horváth, Attila K; Gao, Qingyu

    2012-01-01

    Sodium polyacrylate-induced pH pattern formation and starch-induced iodine pattern formation were investigated in the iodate-sulfite-thiosulfate (IST) reaction in a one-side fed disc gel reactor (OSFR). As binding agents of the autocatalyst of hydrogen ions or iodide ions, different content of sodium polyacrylate or starch has induced various types of pattern formation. We observed pH pulses, striped patterns, mixed spots and stripes, and hexagonal spots upon increasing the content of sodium polyacrylate and observed iodine pulses, branched patterns, and labyrinthine patterns upon increasing the starch content in the system. Coexistence of a pH front and an iodine front was also studied in a batch IST reaction-diffusion system. Both pH and iodine front instabilities were observed in the presence of sodium polyacrylate, i.e., cellular fronts and transient Turing structures resulting from the decrease in diffusion coefficients of activators. The mechanism of multiple feedback may explain the different patterns in the IST reaction-diffusion system. PMID:22068976

  3. Self-similar fast-reaction limits for reaction-diffusion systems on unbounded domains

    NASA Astrophysics Data System (ADS)

    Crooks, E. C. M.; Hilhorst, D.

    2016-08-01

    We present a unified approach to characterising fast-reaction limits of systems of either two reaction-diffusion equations, or one reaction-diffusion equation and one ordinary differential equation, on unbounded domains, motivated by models of fast chemical reactions where either one or both reactant(s) is/are mobile. For appropriate initial data, solutions of four classes of problems each converge in the fast-reaction limit k → ∞ to a self-similar limit profile that has one of four forms, depending on how many components diffuse and whether the spatial domain is a half or whole line. For fixed k, long-time convergence to these same self-similar profiles is also established, thanks to a scaling argument of Kamin. Our results generalise earlier work of Hilhorst, van der Hout and Peletier to a much wider class of problems, and provide a quantitative description of the penetration of one substance into another in both the fast-reaction and long-time regimes.

  4. Spatiotemporal patterns in reaction-diffusion system and in a vibrated granular bed

    SciTech Connect

    Swinney, H.L.; Lee, K.J.; McCormick, W.D.

    1995-12-31

    Experiments on a quasi-two-dimensional reaction-diffusion system reveal transitions from a uniform state to stationary hexagonal, striped, and rhombic spatial patterns. For other reactor conditions lamellae and self-replicating spot patterns are observed. These patterns form in continuously fed thin gel reactors that can be maintained indefinitely in well-defined nonequilibrium states. Reaction-diffusion models with two chemical species yield patterns similar to those observed in the experiments. Pattern formation is also being examined in vertically oscillated thin granular layers (typically 3-30 particle diameters deep). For small acceleration amplitudes, a granular layer is flat, but above a well-defined critical acceleration amplitude, spatial patterns spontaneously form. Disordered time-dependent granular patterns are observed as well as regular patterns of squares, stripes, and hexagons. A one-dimensional model consisting of a completely inelastic ball colliding with a sinusoidally oscillating platform provides a semi-quantitative description of most of the observed bifurcations between the different spatiotemporal regimes.

  5. Chemical activity induces dynamical force with global structure in a reaction-diffusion-convection system.

    PubMed

    Mahara, Hitoshi; Okada, Koichi; Nomura, Atsushi; Miike, Hidetoshi; Sakurai, Tatsunari

    2009-07-01

    We found a rotating global structure induced by the dynamical force of local chemical activity in a thin solution layer of excitable Belousov-Zhabotinsky reaction coupled with diffusion. The surface flow and deformation associated with chemical spiral waves (wavelength about 1 mm) represents a global unidirectional structure and a global tilt in the entire Petri dish (100 mm in diameter), respectively. For these observations, we scanned the condition of hierarchal pattern selection. From this result, the bromomalonic acid has an important role to induce the rotating global structure. An interaction between a reaction-diffusion process and a surface-tension-driven effect leads to such hierarchal pattern with different scales. PMID:19658764

  6. Transition to Spatio-Temporal Chaos with Increasing Length in the Reaction-Diffusion System

    NASA Astrophysics Data System (ADS)

    Trail, Collin; Tomlin, Brett; Olsen, Thomas; Wiener, Richard J.

    2003-11-01

    Calculations based up the Reaction-Diffusion model (H. Riecke and H.-G. Paap, Europhys. Lett. 14), 1235 (1991).have proven to be suggestive for a wide variety of pattern forming systems, including Taylor-Couette flow with hourglass geometry(Richard J. Wiener et al), Phys. Rev. E 55, 5489 (1997).. Seeking insight to guide experimental investigations, we extend these calculations. Previous calculations indicated that in smaller systems, only temporal chaos, located in a small region, would be observed, while in longer systems instabilities would form over a wide region. Our simulations explore this transition from purely temporal chaos to spatio-temporal chaos as the length of the system is increased.

  7. Global existence and asymptotic stability of equilibria to reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Wang, Rong-Nian; Tang, Zhong Wei

    2009-06-01

    In this paper, we study weakly coupled reaction-diffusion systems in unbounded domains of {\\bb R}^2 or {\\bb R}^3 , where the reaction terms are sums of quasimonotone nondecreasing and nonincreasing functions. Such systems are more complicated than those in many previous publications and little is known about them. A comparison principle and global existence, and boundedness theorems for solutions to these systems are established. Sufficient conditions on the nonlinearities, ensuring the positively Ljapunov stability of the zero solution with respect to H2-perturbations, are also obtained. As samples of applications, these results are applied to an autocatalytic chemical model and a concrete problem, whose nonlinearities are nonquasimonotone. Our results are novel. In particular, we present a solution to an open problem posed by Escher and Yin (2005 J. Nonlinear Anal. Theory Methods Appl. 60 1065-84).

  8. A gradient structure for systems coupling reaction-diffusion effects in bulk and interfaces

    NASA Astrophysics Data System (ADS)

    Glitzky, Annegret; Mielke, Alexander

    2013-02-01

    We derive gradient-flow formulations for systems describing drift-diffusion processes of a finite number of species which undergo mass-action type reversible reactions. Our investigations cover heterostructures, where material parameter may depend in a nonsmooth way on the space variable. The main results concern a gradient-flow formulation for electro-reaction-diffusion systems with active interfaces permitting drift-diffusion processes and reactions of species living on the interface and transfer mechanisms allowing bulk species to jump into an interface or to pass through interfaces. The gradient flows are formulated in terms of two functionals: the free energy and the dissipation potential. Both functionals consist of a bulk and an interface integral. The interface integrals determine the interface dynamics as well as the self-consistent coupling to the model in the bulk. The advantage of the gradient structure is that it automatically generates thermodynamically consistent models.

  9. Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics

    SciTech Connect

    Strehl, Robert; Ilie, Silvana

    2015-12-21

    In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency.

  10. An ADI extrapolated Crank-Nicolson orthogonal spline collocation method for nonlinear reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Fernandes, Ryan I.; Fairweather, Graeme

    2012-08-01

    An alternating direction implicit (ADI) orthogonal spline collocation (OSC) method is described for the approximate solution of a class of nonlinear reaction-diffusion systems. Its efficacy is demonstrated on the solution of well-known examples of such systems, specifically the Brusselator, Gray-Scott, Gierer-Meinhardt and Schnakenberg models, and comparisons are made with other numerical techniques considered in the literature. The new ADI method is based on an extrapolated Crank-Nicolson OSC method and is algebraically linear. It is efficient, requiring at each time level only O(N) operations where N is the number of unknowns. Moreover, it is shown to produce approximations which are of optimal global accuracy in various norms, and to possess superconvergence properties.

  11. Spatial propagation for a two component reaction-diffusion system arising in population dynamics

    NASA Astrophysics Data System (ADS)

    Ducrot, Arnaud

    2016-06-01

    In this work a two component epidemic reaction-diffusion system posed on the whole space RN is considered. Uniform boundedness of the solutions is proved using suitable local Lp-estimates. The spatial invasion of a localized introduced amount of infective is studied yielding to the derivation of the asymptotic speed of spread for the infection. This part is achieved using uniform persistence ideas. The state of the population after the epidemic is further investigated using different Lyapunov like arguments. The solution is shown to converge the endemic equilibrium point behind the front in the equi-diffusional case. For general diffusion coefficient unique ergodicity of the tail of invasion is obtained by constructing a suitable sub-harmonic map.

  12. Signaling gradients in cascades of two-state reaction-diffusion systems.

    PubMed

    Berezhkovskii, Alexander M; Coppey, Mathieu; Shvartsman, Stanislav Y

    2009-01-27

    Biological networks frequently use cascades, generally defined as chain-like arrangements of similar modules. Spatially lumped cascades can serve as noise filters, time-delay, or thresholding elements. The operation and functional capabilities of spatially distributed cascades are much less understood. Motivated by studies of pattern formation in the early Drosophila embryo, we analyze cascades of 2-state reaction-diffusion systems. At each stage within such as a cascade, a diffusible particle is reversibly bound by immobile traps and can be annihilated in both mobile and immobile states. When trapped, these particles drive the next stage by converting mobile particles of a different type from a passive to active form. The cascade initiated by injection of mobile particles into the first stage. We derive analytical expressions for the steady-state concentration profiles of mobile and immobile particles and analyze how the output of a cascade is controlled by properties of the constituent stages. PMID:19147842

  13. A Robust and Efficient Method for Steady State Patterns in Reaction-Diffusion Systems

    PubMed Central

    Lo, Wing-Cheong; Chen, Long; Wang, Ming; Nie, Qing

    2012-01-01

    An inhomogeneous steady state pattern of nonlinear reaction-diffusion equations with no-flux boundary conditions is usually computed by solving the corresponding time-dependent reaction-diffusion equations using temporal schemes. Nonlinear solvers (e.g., Newton’s method) take less CPU time in direct computation for the steady state; however, their convergence is sensitive to the initial guess, often leading to divergence or convergence to spatially homogeneous solution. Systematically numerical exploration of spatial patterns of reaction-diffusion equations under different parameter regimes requires that the numerical method be efficient and robust to initial condition or initial guess, with better likelihood of convergence to an inhomogeneous pattern. Here, a new approach that combines the advantages of temporal schemes in robustness and Newton’s method in fast convergence in solving steady states of reaction-diffusion equations is proposed. In particular, an adaptive implicit Euler with inexact solver (AIIE) method is found to be much more efficient than temporal schemes and more robust in convergence than typical nonlinear solvers (e.g., Newton’s method) in finding the inhomogeneous pattern. Application of this new approach to two reaction-diffusion equations in one, two, and three spatial dimensions, along with direct comparisons to several other existing methods, demonstrates that AIIE is a more desirable method for searching inhomogeneous spatial patterns of reaction-diffusion equations in a large parameter space. PMID:22773849

  14. The dynamics of localized spot patterns for reaction-diffusion systems on the sphere

    NASA Astrophysics Data System (ADS)

    Trinh, Philippe H.; Ward, Michael J.

    2016-03-01

    In the singularly perturbed limit corresponding to a large diffusivity ratio between two components in a reaction-diffusion (RD) system, quasi-equilibrium spot patterns are often admitted, producing a solution that concentrates at a discrete set of points in the domain. In this paper, we derive and study the differential algebraic equation (DAE) that characterizes the slow dynamics for such spot patterns for the Brusselator RD model on the surface of a sphere. Asymptotic and numerical solutions are presented for the system governing the spot strengths, and we describe the complex bifurcation structure and demonstrate the occurrence of imperfection sensitivity due to higher order effects. Localized spot patterns can undergo a fast time instability and we derive the conditions for this phenomena, which depend on the spatial configuration of the spots and the parameters in the system. In the absence of these instabilities, our numerical solutions of the DAE system for N  =  2 to N  =  8 spots suggest a large basin of attraction to a small set of possible steady-state configurations. We discuss the connections between our results and the study of point vortices on the sphere, as well as the problem of determining a set of elliptic Fekete points, which correspond to globally minimizing the discrete logarithmic energy for N points on the sphere.

  15. Bursting regimes in a reaction-diffusion system with action potential-dependent equilibrium.

    PubMed

    Meier, Stephen R; Lancaster, Jarrett L; Starobin, Joseph M

    2015-01-01

    The equilibrium Nernst potential plays a critical role in neural cell dynamics. A common approximation used in studying electrical dynamics of excitable cells is that the ionic concentrations inside and outside the cell membranes act as charge reservoirs and remain effectively constant during excitation events. Research into brain electrical activity suggests that relaxing this assumption may provide a better understanding of normal and pathophysiological functioning of the brain. In this paper we explore time-dependent ionic concentrations by allowing the ion-specific Nernst potentials to vary with developing transmembrane potential. As a specific implementation, we incorporate the potential-dependent Nernst shift into a one-dimensional Morris-Lecar reaction-diffusion model. Our main findings result from a region in parameter space where self-sustaining oscillations occur without external forcing. Studying the system close to the bifurcation boundary, we explore the vulnerability of the system with respect to external stimulations which disrupt these oscillations and send the system to a stable equilibrium. We also present results for an extended, one-dimensional cable of excitable tissue tuned to this parameter regime and stimulated, giving rise to complex spatiotemporal pattern formation. Potential applications to the emergence of neuronal bursting in similar two-variable systems and to pathophysiological seizure-like activity are discussed. PMID:25823018

  16. Bursting Regimes in a Reaction-Diffusion System with Action Potential-Dependent Equilibrium

    PubMed Central

    Meier, Stephen R.; Lancaster, Jarrett L.; Starobin, Joseph M.

    2015-01-01

    The equilibrium Nernst potential plays a critical role in neural cell dynamics. A common approximation used in studying electrical dynamics of excitable cells is that the ionic concentrations inside and outside the cell membranes act as charge reservoirs and remain effectively constant during excitation events. Research into brain electrical activity suggests that relaxing this assumption may provide a better understanding of normal and pathophysiological functioning of the brain. In this paper we explore time-dependent ionic concentrations by allowing the ion-specific Nernst potentials to vary with developing transmembrane potential. As a specific implementation, we incorporate the potential-dependent Nernst shift into a one-dimensional Morris-Lecar reaction-diffusion model. Our main findings result from a region in parameter space where self-sustaining oscillations occur without external forcing. Studying the system close to the bifurcation boundary, we explore the vulnerability of the system with respect to external stimulations which disrupt these oscillations and send the system to a stable equilibrium. We also present results for an extended, one-dimensional cable of excitable tissue tuned to this parameter regime and stimulated, giving rise to complex spatiotemporal pattern formation. Potential applications to the emergence of neuronal bursting in similar two-variable systems and to pathophysiological seizure-like activity are discussed. PMID:25823018

  17. Hopping Conduction and Bacteria: Transport Properties of Disordered Reaction-Diffusion Systems

    NASA Astrophysics Data System (ADS)

    Missel, Andrew; Dahmen, Karin

    2008-03-01

    Reaction-diffusion (RD) systems are used to model everything from the formation of animal coat patterns to the spread of genes in a population to the seasonal variation of plankton density in the ocean. In all of these problems, disorder plays a large role, but determining its effects on transport properties in RD systems has been a challenge. We present here both analytical and numerical studies of a particular disordered RD system consisting of particles which are allowed to diffuse and compete for resources (2A->A) with spatially homogeneous rates, reproduce (A->2A) in certain areas (``oases''), and die (A->0) everywhere else (the ``desert''). In the low oasis density regime, transport is mediated through rare ``hopping events'' in which a small number of particles diffuse through the desert from one oasis to another; the situation is mathematically analogous to hopping conduction in doped semiconductors, and this analogy, along with some ideas from first passage percolation theory, allows us to make some quantitative predictions about the transport properties of the system on a large scale.

  18. Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems

    PubMed Central

    D'Agostino, Daniele; Pasquale, Giulia; Clematis, Andrea; Maj, Carlo; Mosca, Ettore; Milanesi, Luciano; Merelli, Ivan

    2014-01-01

    There is an increasing awareness of the pivotal role of noise in biochemical processes and of the effect of molecular crowding on the dynamics of biochemical systems. This necessity has given rise to a strong need for suitable and sophisticated algorithms for the simulation of biological phenomena taking into account both spatial effects and noise. However, the high computational effort characterizing simulation approaches, coupled with the necessity to simulate the models several times to achieve statistically relevant information on the model behaviours, makes such kind of algorithms very time-consuming for studying real systems. So far, different parallelization approaches have been deployed to reduce the computational time required to simulate the temporal dynamics of biochemical systems using stochastic algorithms. In this work we discuss these aspects for the spatial TAU-leaping in crowded compartments (STAUCC) simulator, a voxel-based method for the stochastic simulation of reaction-diffusion processes which relies on the Sτ-DPP algorithm. In particular we present how the characteristics of the algorithm can be exploited for an effective parallelization on the present heterogeneous HPC architectures. PMID:25045716

  19. Parallel solutions for voxel-based simulations of reaction-diffusion systems.

    PubMed

    D'Agostino, Daniele; Pasquale, Giulia; Clematis, Andrea; Maj, Carlo; Mosca, Ettore; Milanesi, Luciano; Merelli, Ivan

    2014-01-01

    There is an increasing awareness of the pivotal role of noise in biochemical processes and of the effect of molecular crowding on the dynamics of biochemical systems. This necessity has given rise to a strong need for suitable and sophisticated algorithms for the simulation of biological phenomena taking into account both spatial effects and noise. However, the high computational effort characterizing simulation approaches, coupled with the necessity to simulate the models several times to achieve statistically relevant information on the model behaviours, makes such kind of algorithms very time-consuming for studying real systems. So far, different parallelization approaches have been deployed to reduce the computational time required to simulate the temporal dynamics of biochemical systems using stochastic algorithms. In this work we discuss these aspects for the spatial TAU-leaping in crowded compartments (STAUCC) simulator, a voxel-based method for the stochastic simulation of reaction-diffusion processes which relies on the Sτ-DPP algorithm. In particular we present how the characteristics of the algorithm can be exploited for an effective parallelization on the present heterogeneous HPC architectures. PMID:25045716

  20. Chemical morphogenesis: recent experimental advances in reaction-diffusion system design and control.

    PubMed

    Szalai, István; Cuiñas, Daniel; Takács, Nándor; Horváth, Judit; De Kepper, Patrick

    2012-08-01

    In his seminal 1952 paper, Alan Turing predicted that diffusion could spontaneously drive an initially uniform solution of reacting chemicals to develop stable spatially periodic concentration patterns. It took nearly 40 years before the first two unquestionable experimental demonstrations of such reaction-diffusion patterns could be made in isothermal single phase reaction systems. The number of these examples stagnated for nearly 20 years. We recently proposed a design method that made their number increase to six in less than 3 years. In this report, we formally justify our original semi-empirical method and support the approach with numerical simulations based on a simple but realistic kinetic model. To retain a number of basic properties of real spatial reactors but keep calculations to a minimal complexity, we introduce a new way to collapse the confined spatial direction of these reactors. Contrary to similar reduced descriptions, we take into account the effect of the geometric size in the confinement direction and the influence of the differences in the diffusion coefficient on exchange rates of species with their feed environment. We experimentally support the method by the observation of stationary patterns in red-ox reactions not based on oxihalogen chemistry. Emphasis is also brought on how one of these new systems can process different initial conditions and memorize them in the form of localized patterns of different geometries. PMID:23919126

  1. Stability of periodic traveling waves in the Aliev-Panfilov reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Gani, M. Osman; Ogawa, Toshiyuki

    2016-04-01

    We study the two-component Aliev-Panfilov reaction-diffusion system of cardiac excitation. It is known that the model exhibits spiral wave instability in two-dimensional spatial domains. In order to describe the spiral wave instability, it is important to understand periodic traveling wave instability resulting from the model. We determine the existence and stability of periodic traveling waves in the model. In addition, we calculate the stability boundary between stable and unstable periodic traveling waves in a two-dimensional parameter plane. It is observed that the periodic traveling waves express instability by a stability change of Eckhaus type. As a result, a stable wave bifurcates to an oscillating periodic traveling wave. We describe these phenomena by calculating the essential spectra of the waves. Furthermore, we study the stability of the waves as a function of the gaps between two nullclines. In two dimensions, we determine the spiral wave instability based on the stability boundary of the periodic traveling waves.

  2. A transition in the spatially integrated reaction rate of bimolecular reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Arshadi, Masoud; Rajaram, Harihar

    2015-09-01

    Numerical simulations of diffusion with bimolecular reaction demonstrate a transition in the spatially integrated reaction rate—increasing with time initially, and transitioning to a decrease with time. In previous work, this reaction-diffusion problem has been analyzed as a Stefan problem involving a distinct moving boundary (reaction front), leading to predictions that front motion scales as √t, and correspondingly the spatially integrated reaction rate decreases as the square root of time 1/√t. We present a general nondimensionalization of the problem and a perturbation analysis to show that there is an early time regime where the spatially integrated reaction rate scales as √t rather than 1/√t. The duration of this early time regime (where the spatially integrated reaction rate is kinetically rather than diffusion controlled) is shown to depend on the kinetic rate parameters, diffusion coefficients, and initial concentrations of the two species. Numerical simulation results confirm the theoretical estimates of the transition time. We present illustrative calculations in the context of in situ chemical oxidation for remediation of fractured rock systems where contaminants are largely dissolved in the rock matrix. We consider different contaminants of concern (COCs), including TCE, PCE, MTBE, and RDX. While the early time regime is very short lived for TCE, it can persist over months to years for MTBE and RDX, due to slow oxidation kinetics.

  3. Numerical investigation on oscillatory Turing patterns in a two-layer coupled reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Li, Xin-Zheng; Bai, Zhan-Guo; Li, Yan; Zhao, Kun

    2016-03-01

    In this paper, various kinds of spontaneous dynamic patterns are investigated based on a two-layer nonlinearly coupled Brusselator model. It is found that, when the Hopf mode or supercritical Turing mode respectively plays major role in the short or long wavelength mode layer, the dynamic patterns appear under the action of nonlinearly coupling interactions in the reaction-diffusion system. The stripe pattern can change its symmetrical structure and form other graphics when influenced by small perturbations sourced from other modes. If two supercritical Turing modes are nonlinearly coupled together, the transition from Turing instability to Hopf instability may appear in the short wavelength mode layer, and the twinkling-eye square pattern, traveling and rotating pattern will be obtained in the two subsystems. If Turing mode and subharmonic Turing mode satisfy the three-mode resonance relation, twinkling-eye patterns are generated, and oscillating spots are arranged as square lattice in the two-dimensional space. When the subharmonic Turing mode satisfies the spatio-temporal phase matching condition, the traveling patterns, including the rhombus, hexagon and square patterns are obtained, which presents different moving velocities. It is found that the wave intensity plays an important role in pattern formation and pattern selection.

  4. Brownian-motion based simulation of stochastic reaction-diffusion systems for affinity based sensors

    NASA Astrophysics Data System (ADS)

    Tulzer, Gerhard; Heitzinger, Clemens

    2016-04-01

    In this work, we develop a 2D algorithm for stochastic reaction-diffusion systems describing the binding and unbinding of target molecules at the surfaces of affinity-based sensors. In particular, we simulate the detection of DNA oligomers using silicon-nanowire field-effect biosensors. Since these devices are uniform along the nanowire, two dimensions are sufficient to capture the kinetic effects features. The model combines a stochastic ordinary differential equation for the binding and unbinding of target molecules as well as a diffusion equation for their transport in the liquid. A Brownian-motion based algorithm simulates the diffusion process, which is linked to a stochastic-simulation algorithm for association at and dissociation from the surface. The simulation data show that the shape of the cross section of the sensor yields areas with significantly different target-molecule coverage. Different initial conditions are investigated as well in order to aid rational sensor design. A comparison of the association/hybridization behavior for different receptor densities allows optimization of the functionalization setup depending on the target-molecule density.

  5. Brownian-motion based simulation of stochastic reaction-diffusion systems for affinity based sensors.

    PubMed

    Tulzer, Gerhard; Heitzinger, Clemens

    2016-04-22

    In this work, we develop a 2D algorithm for stochastic reaction-diffusion systems describing the binding and unbinding of target molecules at the surfaces of affinity-based sensors. In particular, we simulate the detection of DNA oligomers using silicon-nanowire field-effect biosensors. Since these devices are uniform along the nanowire, two dimensions are sufficient to capture the kinetic effects features. The model combines a stochastic ordinary differential equation for the binding and unbinding of target molecules as well as a diffusion equation for their transport in the liquid. A Brownian-motion based algorithm simulates the diffusion process, which is linked to a stochastic-simulation algorithm for association at and dissociation from the surface. The simulation data show that the shape of the cross section of the sensor yields areas with significantly different target-molecule coverage. Different initial conditions are investigated as well in order to aid rational sensor design. A comparison of the association/hybridization behavior for different receptor densities allows optimization of the functionalization setup depending on the target-molecule density. PMID:26939610

  6. Interface proliferation and the growth of labyrinths in a reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Goldstein, Raymond E.; Muraki, David J.; Petrich, Dean M.

    1996-04-01

    In the bistable regime of the FitzHugh-Nagumo model of reaction-diffusion systems, spatially homogeneous patterns may be nonlinearly unstable to the formation of compact "localized states." The formation of space-filling patterns from instabilities of such structures is studied in the context of a nonlocal contour dynamics model for the evolution of boundaries between high and low concentrations of the activator. An earlier heuristic derivation [D. M. Petrich and R. E. Goldstein,

    Phys. Rev. Lett. 72, 1120 (1994)
    ] is made more systematic by an asymptotic analysis appropriate to the limits of fast inhibition, sharp activator interfaces, and small asymmetry in the bistable minima. The resulting contour dynamics is temporally local, with the normal component of the velocity involving a local contribution linear in the interface curvature and a nonlocal component having the form of a screened Biot-Savart interaction. The amplitude of the nonlocal interaction is set by the activator-inhibitor coupling and controls the "lateral inhibition" responsible for the destabilization of localized structures such as spots and stripes, and the repulsion of nearby interfaces in the later stages of those instabilities. The phenomenology of pattern formation exhibited by the contour dynamics is consistent with that seen by Lee, McCormick, Ouyang, and Swinney
    [Science 261, 192 (1993)]
    in experiments on the iodide-ferrocyanide-sulfite reaction in a gel reactor. Extensive numerical studies of the underlying partial differential equations are presented and compared in detail with the contour dynamics. The similarity of these phenomena (and their mathematical description) with those observed in amphiphilic monolayers, type I superconductors in the intermediate state, and magnetic fluids in Hele-Shaw geometry is emphasized.

  7. Discrete infinite-dimensional type-K monotone dynamical systems and time-periodic reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Liang, Xing; Jiang, Jifa

    The asymptotic behavior of discrete type-K monotone dynamical systems and reaction-diffusion equations is investigated. The studying content includes the index theory for fixed points, permanence, global stability, convergence everywhere and coexistence. It is shown that the system has a globally asymptotically stable fixed point if every fixed point is locally asymptotically stable with respect to the face it belongs to and at this point the principal eigenvalue of the diagonal partial derivative about any component not belonging to the face is not one. A nice result presented is the sufficient and necessary conditions for the system to have a globally asymptotically stable positive fixed point. It can be used to establish the sufficient conditions for the system to persist uniformly and the convergent result for all orbits. Applications are made to time-periodic Lotka-Volterra systems with diffusion, and sufficient conditions for such systems to have a unique positive periodic solution attracting all positive initial value functions are given. For more general time-periodic type-K monotone reaction-diffusion systems with spatial homogeneity, a simple condition is given to guarantee the convergence of all positive solutions.

  8. Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient.

    PubMed

    Lecca, Paola; Ihekwaba, Adaoha E C; Dematté, Lorenzo; Priami, Corrado

    2010-01-01

    Reaction-diffusion systems are mathematical models that describe how the concentrations of substances distributed in space change under the influence of local chemical reactions, and diffusion which causes the substances to spread out in space. The classical representation of a reaction-diffusion system is given by semi-linear parabolic partial differential equations, whose solution predicts how diffusion causes the concentration field to change with time. This change is proportional to the diffusion coefficient. If the solute moves in a homogeneous system in thermal equilibrium, the diffusion coefficients are constants that do not depend on the local concentration of solvent and solute. However, in nonhomogeneous and structured media the assumption of constant intracellular diffusion coefficient is not necessarily valid, and, consequently, the diffusion coefficient is a function of the local concentration of solvent and solutes. In this paper we propose a stochastic model of reaction-diffusion systems, in which the diffusion coefficients are function of the local concentration, viscosity and frictional forces. We then describe the software tool Redi (REaction-DIffusion simulator) which we have developed in order to implement this model into a Gillespie-like stochastic simulation algorithm. Finally, we show the ability of our model implemented in the Redi tool to reproduce the observed gradient of the bicoid protein in the Drosophila Melanogaster embryo. With Redi, we were able to simulate with an accuracy of 1% the experimental spatio-temporal dynamics of the bicoid protein, as recorded in time-lapse experiments obtained by direct measurements of transgenic bicoidenhanced green fluorescent protein. PMID:21098882

  9. Clustering and Optimal Arrangement of Enzymes in Reaction-Diffusion Systems

    NASA Astrophysics Data System (ADS)

    Buchner, Alexander; Tostevin, Filipe; Gerland, Ulrich

    2013-05-01

    Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion model. The optimal arrangement transitions from a cluster to a distributed profile as a single parameter, which controls the probability of reaction versus diffusive loss of pathway intermediates, is varied. We introduce the concept of enzyme exposure to explain how this transition arises from the stochastic nature of molecular reactions and diffusion.

  10. Cluster geometry and survival probability in systems driven by reaction diffusion dynamics

    NASA Astrophysics Data System (ADS)

    Windus, Alastair; Jensen, Henrik J.

    2008-11-01

    We consider a reaction-diffusion model incorporating the reactions A→phi, A→2A and 2A→3A. Depending on the relative rates for sexual and asexual reproduction of the quantity A, the model exhibits either a continuous or first-order absorbing phase transition to an extinct state. A tricritical point separates the two phase lines. While we comment on this critical behaviour, the main focus of the paper is on the geometry of the population clusters that form. We observe the different cluster structures that arise at criticality for the three different types of critical behaviour and show that there exists a linear relationship for the survival probability against initial cluster size at the tricritical point only.

  11. A geometric approach in the study of traveling waves for some classes of non-monotone reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Huang, Wenzhang

    2016-02-01

    In this paper we further extend a recently developed method to investigate the existence of traveling waves solutions and their minimum wave speed for non-monotone reaction-diffusion systems. Our approach consists of two steps. First we develop a geometrical shooting argument, with the aid of the theorem of homotopy invariance on the fundamental group, to obtain the positive semi-traveling wave solutions for a large class of reaction-diffusion systems, including the models of predator-prey interaction (for both predator-independent/dependent functional responses), the models of combustion, Belousov-Zhabotinskii reaction, SI-type of disease transmission, and the model of biological flow reactor in chemostat. Next, we apply the results obtained from the first step to some models, such as the Beddinton-DeAngelis model and the model of biolocal flow reactor, to show the convergence of these semi-traveling wave solutions to an interior equilibrium point by the construction of a Lyapunov-type function, or the convergence of semi-traveling waves to another boundary equilibrium point by the further analysis of the asymptotical behavior of semi-traveling wave solutions.

  12. Reaction-diffusion waves in biology.

    PubMed

    Volpert, V; Petrovskii, S

    2009-12-01

    The theory of reaction-diffusion waves begins in the 1930s with the works in population dynamics, combustion theory and chemical kinetics. At the present time, it is a well developed area of research which includes qualitative properties of travelling waves for the scalar reaction-diffusion equation and for system of equations, complex nonlinear dynamics, numerous applications in physics, chemistry, biology, medicine. This paper reviews biological applications of reaction-diffusion waves. PMID:20416847

  13. Simulations of the Reaction-Diffusion System demonstrating the Transition from Purely Temporal to Spatio-Temporal Chaos

    NASA Astrophysics Data System (ADS)

    Olsen, Thomas; Hou, Yu; Trail, Collin; Wiener, Richard

    2004-11-01

    The Reaction-Diffusion model (H. Riecke and H.-G. Paap, Europhys. Lett. 14), 1235 (1991).has been applied to a wide variety of pattern forming systems. It correctly predicted a period doubling cascade to chaos in Taylor-Couette flow with hourglass geometry(Richard J. Wiener et al), Phys. Rev. E 55, 5489 (1997).. We have conducted a series of such simulations, varying the length of the system. This has enabled us to study the transition from a purely temporal chaos of the formation of new pairs of Taylor Vortices at a single location, to a spatio-temporal chaos of formation across a range of locations. Application to anticipated experiments will be discussed.

  14. Localized stationary and traveling reaction-diffusion patterns in a two-layer A +B → oscillator system

    NASA Astrophysics Data System (ADS)

    Budroni, M. A.; De Wit, A.

    2016-06-01

    When two solutions containing separate reactants A and B of an oscillating reaction are put in contact in a gel, localized spatiotemporal patterns can develop around the contact zone thanks to the interplay of reaction and diffusion processes. Using the Brusselator model, we explore analytically the deployment in space and time of the bifurcation diagram of such an A +B → oscillator system. We provide a parametric classification of possible instabilities as a function of the ratio of the initial reactant concentrations and of the reaction intermediate species diffusion coefficients. Related one-dimensional reaction-diffusion dynamics are studied numerically. We find that the system can spatially localize waves and Turing patterns as well as induce more complex dynamics such as zigzag spatiotemporal waves when Hopf and Turing modes interact.

  15. Reaction-Diffusion Model Simulations relevant to Modified Taylor-Couette Flow in Systems of Varying Length

    NASA Astrophysics Data System (ADS)

    Halmstad, Andrew; Olsen, Thomas; Wiener, Richard

    2006-11-01

    Previously, we have observed a period-doubling cascade to chaos in Modified Taylor-Couette Flow with Hourglass Geometry. Such behavior had been predicted by The Reaction-Diffusion model simulations. The chaotic formation of Taylor-Vortex pair formation was restricted to a very narrow band about the waist of the hourglass. It was suggested that with increasing lengths of systems, the chaotic region would expand. We present a battery of simulations to determine the variation of the size of the chaotic region with length, seeking the transition to spatio- temporal chaos. Richard J. Wiener et al, Phys. Rev. E 55, 5489 (1997). H. Riecke and H.-G. Paap, Europhys. Lett. 14, 1235 (1991).

  16. Modeling the role of diffusion coefficients on Turing instability in a reaction-diffusion prey-predator system.

    PubMed

    Mukhopadhyay, B; Bhattacharyya, R

    2006-02-01

    The paper is concerned with the effect of variable dispersal rates on Turing instability of a non-Lotka-Volterra reaction-diffusion system. In ecological applications, the dispersal rates of different species tends to oscillate in time. This oscillation is modeled by temporal variation in the diffusion coefficient with large as well as small periodicity. The case of large periodicity is analyzed using the theory of Floquet multipliers and that of the small periodicity by using Hill's equation. The effect of such variation on the resulting Turing space is studied. A comparative analysis of the Turing spaces with constant diffusivity and variable diffusivities is performed. Numerical simulations are carried out to support analytical findings. PMID:16794932

  17. Switch and template pattern formation in a discrete reaction-diffusion system inspired by the Drosophila eye

    PubMed Central

    Pennington, Matthew W.; Lubensky, David K.

    2011-01-01

    We examine a spatially discrete reaction diffusion model based on the interactions that create a periodic pattern in the Drosophila eye imaginal disc. This model is known to be capable of generating a regular hexagonal pattern of gene expression behind a moving front, as observed in the fly system. In order to better understand the novel “switch and template” mechanism behind this pattern formation, we present here a detailed study of the model's behavior in one dimension, using a combination of analytic methods and numerical searches of parameter space. We find that patterns are created robustly provided that there is an appropriate separation of timescales and that self-activation is sufficiently strong, and we derive expressions in this limit for the front speed and the pattern wavelength. Moving fronts in pattern-forming systems near an initial linear instability generically select a unique pattern, but our model operates in a strongly nonlinear regime where the final pattern depends on the initial conditions as well as on parameter values. Our work highlights the important role that cellularization and cell-autonomous feedback can play in biological pattern formation. PMID:20862598

  18. Two- and three-dimensional standing waves in a reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Bánsági, Tamás, Jr.; Vanag, Vladimir K.; Epstein, Irving R.

    2012-10-01

    We observe standing waves of chemical concentration in thin layers [quasi-two-dimensional (2D)] and capillaries [three-dimensional (3D)] containing the aqueous Belousov-Zhabotinsky reaction in a reverse microemulsion stabilized by the ionic surfactant sodium bis-2-ethylhexyl sulfosuccinate (AOT) and with cyclo-octane as the continuous phase. The 3D structures are oscillatory lamellae or square-packed cylinders at high and low volume fractions, respectively, of aqueous droplets. These patterns correspond to oscillatory labyrinthine stripes and square-packed spots in the 2D configuration. Computer simulations, as well as observations in E. coli, give qualitative agreement with the observed patterns and suggest that, in contrast to Turing patterns, the structures are sensitive to the size and shape of the system.

  19. Two- and three-dimensional standing waves in a reaction-diffusion system.

    PubMed

    Bánsági, Tamás; Vanag, Vladimir K; Epstein, Irving R

    2012-10-01

    We observe standing waves of chemical concentration in thin layers [quasi-two-dimensional (2D)] and capillaries [three-dimensional (3D)] containing the aqueous Belousov-Zhabotinsky reaction in a reverse microemulsion stabilized by the ionic surfactant sodium bis-2-ethylhexyl sulfosuccinate (AOT) and with cyclo-octane as the continuous phase. The 3D structures are oscillatory lamellae or square-packed cylinders at high and low volume fractions, respectively, of aqueous droplets. These patterns correspond to oscillatory labyrinthine stripes and square-packed spots in the 2D configuration. Computer simulations, as well as observations in E. coli, give qualitative agreement with the observed patterns and suggest that, in contrast to Turing patterns, the structures are sensitive to the size and shape of the system. PMID:23214640

  20. REVIEWS OF TOPICAL PROBLEMS: Waves and patterns in reaction-diffusion systems. Belousov-Zhabotinsky reaction in water-in-oil microemulsions

    NASA Astrophysics Data System (ADS)

    Vanag, Vladimir K.

    2004-09-01

    Advances in nonequilibrium pattern formation in reaction-diffusion systems are reviewed. Special emphasis is placed on patterns found in the spatially extended Belousov-Zhabotinsky reaction dispersed in aerosol OT water-in-oil microemulsions (BZ-AOT system): Turing patterns, packet and standing waves, antispirals and segmented spirals, and accelerating waves and oscillons. All experimental results are explained theoretically and reproduced in computer simulations.

  1. Logarithmic Expansions and the Stability of Periodic Patterns of Localized Spots for Reaction-Diffusion Systems in

    NASA Astrophysics Data System (ADS)

    Iron, David; Rumsey, John; Ward, Michael J.; Wei, Juncheng

    2014-10-01

    The linear stability of steady-state periodic patterns of localized spots in for the two-component Gierer-Meinhardt (GM) and Schnakenberg reaction-diffusion models is analyzed in the semi-strong interaction limit corresponding to an asymptotically small diffusion coefficient of the activator concentration. In the limit , localized spots in the activator are centered at the lattice points of a Bravais lattice with constant area . To leading order in , the linearization of the steady-state periodic spot pattern has a zero eigenvalue when the inhibitor diffusivity satisfies for some independent of the lattice and the Bloch wavevector . From a combination of the method of matched asymptotic expansions, Floquet-Bloch theory, and the rigorous study of certain nonlocal eigenvalue problems, an explicit analytical formula for the continuous band of spectrum that lies within an neighborhood of the origin in the spectral plane is derived when , where is a detuning parameter. The periodic pattern is linearly stable when is chosen small enough so that this continuous band is in the stable left half-plane for all . Moreover, for both the Schnakenberg and GM models, our analysis identifies a model-dependent objective function, involving the regular part of the Bloch Green's function, that must be maximized in order to determine the specific periodic arrangement of localized spots that constitutes a linearly stable steady-state pattern for the largest value of . From a numerical computation, based on an Ewald-type algorithm, of the regular part of the Bloch Green's function that defines the objective function, it is shown within the class of oblique Bravais lattices that a regular hexagonal lattice arrangement of spots is optimal for maximizing the stability threshold in.

  2. Modelling non-homogeneous stochastic reaction-diffusion systems: the case study of gemcitabine-treated non-small cell lung cancer growth

    PubMed Central

    2012-01-01

    Background Reaction-diffusion based models have been widely used in the literature for modeling the growth of solid tumors. Many of the current models treat both diffusion/consumption of nutrients and cell proliferation. The majority of these models use classical transport/mass conservation equations for describing the distribution of molecular species in tumor spheroids, and the Fick's law for describing the flux of uncharged molecules (i.e oxygen, glucose). Commonly, the equations for the cell movement and proliferation are first order differential equations describing the rate of change of the velocity of the cells with respect to the spatial coordinates as a function of the nutrient's gradient. Several modifications of these equations have been developed in the last decade to explicitly indicate that the tumor includes cells, interstitial fluids and extracellular matrix: these variants provided a model of tumor as a multiphase material with these as the different phases. Most of the current reaction-diffusion tumor models are deterministic and do not model the diffusion as a local state-dependent process in a non-homogeneous medium at the micro- and meso-scale of the intra- and inter-cellular processes, respectively. Furthermore, a stochastic reaction-diffusion model in which diffusive transport of the molecular species of nutrients and chemotherapy drugs as well as the interactions of the tumor cells with these species is a novel approach. The application of this approach to he scase of non-small cell lung cancer treated with gemcitabine is also novel. Methods We present a stochastic reaction-diffusion model of non-small cell lung cancer growth in the specification formalism of the tool Redi, we recently developed for simulating reaction-diffusion systems. We also describe how a spatial gradient of nutrients and oncological drugs affects the tumor progression. Our model is based on a generalization of the Fick's first diffusion law that allows to model

  3. Numerical studies of the thermal design sensitivity calculation for a reaction-diffusion system with discontinuous derivatives

    NASA Technical Reports Server (NTRS)

    Hou, Jean W.; Sheen, Jeen S.

    1987-01-01

    The aim of this study is to find a reliable numerical algorithm to calculate thermal design sensitivities of a transient problem with discontinuous derivatives. The thermal system of interest is a transient heat conduction problem related to the curing process of a composite laminate. A logical function which can smoothly approximate the discontinuity is introduced to modify the system equation. Two commonly used methods, the adjoint variable method and the direct differentiation method, are then applied to find the design derivatives of the modified system. The comparisons of numerical results obtained by these two methods demonstrate that the direct differentiation method is a better choice to be used in calculating thermal design sensitivity.

  4. Free-Propagator Reweighting Integrator for Single-Particle Dynamics in Reaction-Diffusion Models of Heterogeneous Protein-Protein Interaction Systems

    NASA Astrophysics Data System (ADS)

    Johnson, Margaret E.; Hummer, Gerhard

    2014-07-01

    We present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine the use of the exact Green's function for a pair of reacting particles with the approximate free-diffusion propagator for position updates to particles. Trajectory reweighting in our free-propagator reweighting (FPR) method recovers the exact association rates for a pair of interacting particles at all times. FPR simulations of many-body systems accurately reproduce the theoretically known dynamic behavior for a variety of different reaction types. FPR does not suffer from the loss of efficiency common to other path-reweighting schemes, first, because corrections apply only in the immediate vicinity of reacting particles and, second, because by construction the average weight factor equals one upon leaving this reaction zone. FPR applications include the modeling of pathways and networks of protein-driven processes where reaction rates can vary widely and thousands of proteins may participate in the formation of large assemblies. With a limited amount of bookkeeping necessary to ensure proper association rates for each reactant pair, FPR can account for changes to reaction rates or diffusion constants as a result of reaction events. Importantly, FPR can also be extended to physical descriptions of protein interactions with long-range forces, as we demonstrate here for Coulombic interactions.

  5. Chiral selection and frequency response of spiral waves in reaction-diffusion systems under a chiral electric field.

    PubMed

    Li, Bing-Wei; Cai, Mei-Chun; Zhang, Hong; Panfilov, Alexander V; Dierckx, Hans

    2014-05-14

    Chirality is one of the most fundamental properties of many physical, chemical, and biological systems. However, the mechanisms underlying the onset and control of chiral symmetry are largely understudied. We investigate possibility of chirality control in a chemical excitable system (the Belousov-Zhabotinsky reaction) by application of a chiral (rotating) electric field using the Oregonator model. We find that unlike previous findings, we can achieve the chirality control not only in the field rotation direction, but also opposite to it, depending on the field rotation frequency. To unravel the mechanism, we further develop a comprehensive theory of frequency synchronization based on the response function approach. We find that this problem can be described by the Adler equation and show phase-locking phenomena, known as the Arnold tongue. Our theoretical predictions are in good quantitative agreement with the numerical simulations and provide a solid basis for chirality control in excitable media. PMID:24832300

  6. Chiral selection and frequency response of spiral waves in reaction-diffusion systems under a chiral electric field

    NASA Astrophysics Data System (ADS)

    Li, Bing-Wei; Cai, Mei-Chun; Zhang, Hong; Panfilov, Alexander V.; Dierckx, Hans

    2014-05-01

    Chirality is one of the most fundamental properties of many physical, chemical, and biological systems. However, the mechanisms underlying the onset and control of chiral symmetry are largely understudied. We investigate possibility of chirality control in a chemical excitable system (the Belousov-Zhabotinsky reaction) by application of a chiral (rotating) electric field using the Oregonator model. We find that unlike previous findings, we can achieve the chirality control not only in the field rotation direction, but also opposite to it, depending on the field rotation frequency. To unravel the mechanism, we further develop a comprehensive theory of frequency synchronization based on the response function approach. We find that this problem can be described by the Adler equation and show phase-locking phenomena, known as the Arnold tongue. Our theoretical predictions are in good quantitative agreement with the numerical simulations and provide a solid basis for chirality control in excitable media.

  7. Transition from spiral waves to defect-mediated turbulence induced by gradient effects in a reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Zhang, Chunxia; Zhang, Hong; Ouyang, Qi; Hu, Bambi; Gunaratne, Gemunu H.

    2003-09-01

    The transition from spiral waves to defect-mediated turbulence was studied in a spatial open reactor using Belousov-Zhabotinsky reaction. The experimental results show a new mechanism of the transition from spirals to spatiotemporal chaos, in which the gradient effects in the three-dimensional system are essential. The transition scenario consists of two stages: first, the effects of gradients in the third dimension cause a splitting of the spiral tip and a deletion of certain wave segments, generating new wave sources; second, the waves sent by the new wave sources undergo a backfire instability, and the back waves are laterally unstable. As a result, defects are automatically generated and fill all over the system. The result of numerical simulation using the FitzHugh-Nagumo model essentially agrees with the experimental observation.

  8. Reaction-diffusion systems for spatio-temporal intracellular protein networks: A beginner's guide with two examples.

    PubMed

    Eliaš, Ján; Clairambault, Jean

    2014-06-01

    Spatio-temporal dynamics of a variety of proteins is, among other things, regulated by post-translational modifications of these proteins. Such modifications can thus influence stability and biochemical activities of the proteins, activity and stability of their upstream targets within specific signalling pathways. Commonly used mathematical tools for such protein-protein (and/or protein-mRNA) interactions in single cells, namely, Michaelis-Menten and Hill kinetics, yielding a system of ordinary differential equations, are extended here into (non-linear) partial differential equations by taking into account a more realistic spatial representation of the environment where these reactions occur. In the modelling framework under consideration, all interactions occur in a cell divided into two compartments, the nucleus and the cytoplasm, connected by the semipermeable nuclear membrane and bounded by the impermeable cell membrane. Passive transport mechanism, modelled by the so-called Kedem-Katchalsky boundary conditions, is used here to represent migration of species throughout the nuclear membrane. Nonlinear systems of partial differential equations are solved by the semi-implicit Rothe method. Examples of two spatial oscillators are shown. Namely, these are the circadian rhythm for concentration of the FRQ protein in Neurospora crassa and oscillatory dynamics observed in the activation and regulation of the p53 protein following DNA damage in mammalian cells. PMID:25210594

  9. Remodelling of cellular excitation (reaction) and intercellular coupling (diffusion) by chronic atrial fibrillation represented by a reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Zhang, Henggui; Garratt, Clifford J.; Kharche, Sanjay; Holden, Arun V.

    2009-06-01

    Human atrial tissue is an excitable system, in which myocytes are excitable elements, and cell-to-cell electrotonic interactions are via diffusive interactions of cell membrane potentials. We developed a family of excitable system models for human atrium at cellular, tissue and anatomical levels for both normal and chronic atrial fibrillation (AF) conditions. The effects of AF-induced remodelling of cell membrane ionic channels (reaction kinetics) and intercellular gap junctional coupling (diffusion) on atrial excitability, conduction of excitation waves and dynamics of re-entrant excitation waves are quantified. Both ionic channel and gap junctional coupling remodelling have rate dependent effects on atrial propagation. Membrane channel conductance remodelling allows the propagation of activity at higher rates than those sustained in normal tissue or in tissue with gap junctional remodelling alone. Membrane channel conductance remodelling is essential for the propagation of activity at rates higher than 300/min as seen in AF. Spatially heterogeneous gap junction coupling remodelling increased the risk of conduction block, an essential factor for the genesis of re-entry. In 2D and 3D anatomical models, the dynamical behaviours of re-entrant excitation waves are also altered by membrane channel modelling. This study provides insights to understand the pro-arrhythmic effects of AF-induced reaction and diffusion remodelling in atrial tissue.

  10. Accounting for Diffusion in Agent Based Models of Reaction-Diffusion Systems with Application to Cytoskeletal Diffusion

    PubMed Central

    Azimi, Mohammad; Jamali, Yousef; Mofrad, Mohammad R. K.

    2011-01-01

    Diffusion plays a key role in many biochemical reaction systems seen in nature. Scenarios where diffusion behavior is critical can be seen in the cell and subcellular compartments where molecular crowding limits the interaction between particles. We investigate the application of a computational method for modeling the diffusion of molecules and macromolecules in three-dimensional solutions using agent based modeling. This method allows for realistic modeling of a system of particles with different properties such as size, diffusion coefficients, and affinity as well as the environment properties such as viscosity and geometry. Simulations using these movement probabilities yield behavior that mimics natural diffusion. Using this modeling framework, we simulate the effects of molecular crowding on effective diffusion and have validated the results of our model using Langevin dynamics simulations and note that they are in good agreement with previous experimental data. Furthermore, we investigate an extension of this framework where single discrete cells can contain multiple particles of varying size in an effort to highlight errors that can arise from discretization that lead to the unnatural behavior of particles undergoing diffusion. Subsequently, we explore various algorithms that differ in how they handle the movement of multiple particles per cell and suggest an algorithm that properly accommodates multiple particles of various sizes per cell that can replicate the natural behavior of these particles diffusing. Finally, we use the present modeling framework to investigate the effect of structural geometry on the directionality of diffusion in the cell cytoskeleton with the observation that parallel orientation in the structural geometry of actin filaments of filopodia and the branched structure of lamellipodia can give directionality to diffusion at the filopodia-lamellipodia interface. PMID:21966493

  11. A Lattice Boltzmann Model for Oscillating Reaction-Diffusion

    NASA Astrophysics Data System (ADS)

    Rodríguez-Romo, Suemi; Ibañez-Orozco, Oscar; Sosa-Herrera, Antonio

    2016-07-01

    A computational algorithm based on the lattice Boltzmann method (LBM) is proposed to model reaction-diffusion systems. In this paper, we focus on how nonlinear chemical oscillators like Belousov-Zhabotinsky (BZ) and the chlorite-iodide-malonic acid (CIMA) reactions can be modeled by LBM and provide with new insight into the nature and applications of oscillating reactions. We use Gaussian pulse initial concentrations of sulfuric acid in different places of a bidimensional reactor and nondiffusive boundary walls. We clearly show how these systems evolve to a chaotic attractor and produce specific pattern images that are portrayed in the reactions trajectory to the corresponding chaotic attractor and can be used in robotic control.

  12. Physarum machines: encapsulating reaction-diffusion to compute spanning tree

    NASA Astrophysics Data System (ADS)

    Adamatzky, Andrew

    2007-12-01

    The Physarum machine is a biological computing device, which employs plasmodium of Physarum polycephalum as an unconventional computing substrate. A reaction-diffusion computer is a chemical computing device that computes by propagating diffusive or excitation wave fronts. Reaction-diffusion computers, despite being computationally universal machines, are unable to construct certain classes of proximity graphs without the assistance of an external computing device. I demonstrate that the problem can be solved if the reaction-diffusion system is enclosed in a membrane with few ‘growth points’, sites guiding the pattern propagation. Experimental approximation of spanning trees by P. polycephalum slime mold demonstrates the feasibility of the approach. Findings provided advance theory of reaction-diffusion computation by enriching it with ideas of slime mold computation.

  13. Laser Spot Detection Based on Reaction Diffusion

    PubMed Central

    Vázquez-Otero, Alejandro; Khikhlukha, Danila; Solano-Altamirano, J. M.; Dormido, Raquel; Duro, Natividad

    2016-01-01

    Center-location of a laser spot is a problem of interest when the laser is used for processing and performing measurements. Measurement quality depends on correctly determining the location of the laser spot. Hence, improving and proposing algorithms for the correct location of the spots are fundamental issues in laser-based measurements. In this paper we introduce a Reaction Diffusion (RD) system as the main computational framework for robustly finding laser spot centers. The method presented is compared with a conventional approach for locating laser spots, and the experimental results indicate that RD-based computation generates reliable and precise solutions. These results confirm the flexibility of the new computational paradigm based on RD systems for addressing problems that can be reduced to a set of geometric operations. PMID:26938537

  14. Laser Spot Detection Based on Reaction Diffusion.

    PubMed

    Vázquez-Otero, Alejandro; Khikhlukha, Danila; Solano-Altamirano, J M; Dormido, Raquel; Duro, Natividad

    2016-01-01

    Center-location of a laser spot is a problem of interest when the laser is used for processing and performing measurements. Measurement quality depends on correctly determining the location of the laser spot. Hence, improving and proposing algorithms for the correct location of the spots are fundamental issues in laser-based measurements. In this paper we introduce a Reaction Diffusion (RD) system as the main computational framework for robustly finding laser spot centers. The method presented is compared with a conventional approach for locating laser spots, and the experimental results indicate that RD-based computation generates reliable and precise solutions. These results confirm the flexibility of the new computational paradigm based on RD systems for addressing problems that can be reduced to a set of geometric operations. PMID:26938537

  15. Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion

    SciTech Connect

    Del Razo, Mauricio; Pan, Wenxiao; Qian, Hong; Lin, Guang

    2014-05-30

    The currently existing theory of fluorescence correlation spectroscopy (FCS) is based on the linear fluctuation theory originally developed by Einstein, Onsager, Lax, and others as a phenomenological approach to equilibrium fluctuations in bulk solutions. For mesoscopic reaction-diffusion systems with nonlinear chemical reactions among a small number of molecules, a situation often encountered in single-cell biochemistry, it is expected that FCS time correlation functions of a reaction-diffusion system can deviate from the classic results of Elson and Magde [Biopolymers (1974) 13:1-27]. We first discuss this nonlinear effect for reaction systems without diffusion. For nonlinear stochastic reaction-diffusion systems there are no closed solutions; therefore, stochastic Monte-Carlo simulations are carried out. We show that the deviation is small for a simple bimolecular reaction; the most significant deviations occur when the number of molecules is small and of the same order. Extending Delbrück-Gillespie’s theory for stochastic nonlinear reactions with rapidly stirring to reaction-diffusion systems provides a mesoscopic model for chemical and biochemical reactions at nanometric and mesoscopic level such as a single biological cell.

  16. Application of Bogolyubov's theory of weakly nonideal Bose gases to the A+A, A+B, B+B reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Konkoli, Zoran

    2004-01-01

    Theoretical methods for dealing with diffusion-controlled reactions inevitably rely on some kind of approximation, and to find the one that works on a particular problem is not always easy. Here the approximation used by Bogolyubov to study a weakly nonideal Bose gas, referred to as the weakly nonideal Bose gas approximation (WBGA), is applied in the analysis of three reaction-diffusion models: (i) A+A→Ø, (ii) A+B→Ø, and (iii) A+A,B+B,A+B→Ø (the ABBA model). Two types of WBGA are considered, the simpler WBGA-I and the more complicated WBGA-II. All models are defined on the lattice to facilitate comparison with computer experiment (simulation). It is found that the WBGA describes the A+B reaction well, it reproduces the correct d/4 density decay exponent. However, it fails in the case of the A+A reaction and the ABBA model. (To cure the deficiency of WBGA in dealing with the A+A model, a hybrid of the WBGA and Kirkwood superposition approximations is suggested.) It is shown that the WBGA-I is identical to the dressed-tree calculation suggested by Lee [J. Phys. A 27, 2633 (1994)], and that the dressed-tree calculation does not lead to the d/2 density decay exponent when applied to the A+A reaction, as normally believed, but it predicts the d/4 decay exponent. Last, the usage of the small n0 approximation suggested by Mattis and Glasser [Rev. Mod. Phys. 70, 979 (1998)] is questioned if used beyond the A+B reaction-diffusion model.

  17. Reaction-Diffusion Processes in Ultrathin Films of Photoresist

    NASA Astrophysics Data System (ADS)

    Perera, Ginusha; Stein, Gila

    2011-03-01

    Projection lithography is the primary technology used for patterning semiconductor devices. High-throughput manufacturing requires imaging materials (resists) that are highly sensitive to radiation, and this demand is satisfied through a process termed chemical amplification (CA). CA resists are comprised of a polymer resin (reactant) and photoacid generator (catalyst); a coupled reaction-diffusion mechanism drives image formation, where image resolution is limited by slow diffusion of the acid catalyst. There is evidence that thin film reaction rates deviate from the bulk behavior, and current models for image formation do not capture such effects. We demonstrate that X-Ray Diffraction can measure spatial extent-of-reaction in ultrathin films of a nanopatterned poly(4-hydroxystyrene-co-tertbutylacrylate) CA resist. The feedback acquired is used to construct predictive models for the coupled reaction-diffusion processes that incorporate the physics of confined polymers. Funded by NSF ECCS 0927147.

  18. Transient spatiotemporal chaos in reaction-diffusion networks

    NASA Astrophysics Data System (ADS)

    Wackerbauer, Renate

    2010-03-01

    Complex transient dynamics is reported in various extended systems, including transient turbulence in shear flows, transient spatiotemporal chaos in reaction- diffusion models, and non-chaotic irregular transient dynamics in neural networks. The asymptotic stability is difficult to determine since the transient lifetime typically increases exponentially with the system size. Our studies show that transient spatiotemporal chaos is extensive in various reaction- diffusion systems; the Lyapunov dimension increases linearly with the network size. A master stability analysis provides insight into the asymptotic stability in the Baer- Eiswirth and the Gray-Scott systems. The asymptotic state is characterized by negative transverse Lyapunov exponents on the attractor of the invariant synchronization manifold. The average lifetime depends on the number of transverse directions that are unstable along a typical excitation cycle.

  19. Nonlocalized modulation of periodic reaction diffusion waves: The Whitham equation

    NASA Astrophysics Data System (ADS)

    Johnson, Mathew A.; Noble, Pascal; Rodrigues, L. Miguel; Zumbrun, Kevin

    2013-02-01

    In a companion paper, we established nonlinear stability with detailed diffusive rates of decay of spectrally stable periodic traveling-wave solutions of reaction diffusion systems under small perturbations consisting of a nonlocalized modulation plus a localized ( L 1) perturbation. Here, we determine time-asymptotic behavior under such perturbations, showing that solutions consist of a leading order of a modulation whose parameter evolution is governed by an associated Whitham averaged equation.

  20. Cohabitation reaction-diffusion model for virus focal infections

    NASA Astrophysics Data System (ADS)

    Amor, Daniel R.; Fort, Joaquim

    2014-12-01

    The propagation of virus infection fronts has been typically modeled using a set of classical (noncohabitation) reaction-diffusion equations for interacting species. However, for some single-species systems it has been recently shown that noncohabitation reaction-diffusion equations may lead to unrealistic descriptions. We argue that previous virus infection models also have this limitation, because they assume that a virion can simultaneously reproduce inside a cell and diffuse away from it. For this reason, we build a several-species cohabitation model that does not have this limitation. Furthermore, we perform a sensitivity analysis for the most relevant parameters of the model, and we compare the predicted infection speed with observed data for two different strains of the T7 virus.

  1. Reaction diffusion equation with spatio-temporal delay

    NASA Astrophysics Data System (ADS)

    Zhao, Zhihong; Rong, Erhua

    2014-07-01

    We investigate reaction-diffusion equation with spatio-temporal delays, the global existence, uniqueness and asymptotic behavior of solutions for which in relation to constant steady-state solution, included in the region of attraction of a stable steady solution. It is shown that if the delay reaction function satisfies some conditions and the system possesses a pair of upper and lower solutions then there exists a unique global solution. In terms of the maximal and minimal constant solutions of the corresponding steady-state problem, we get the asymptotic stability of reaction-diffusion equation with spatio-temporal delay. Applying this theory to Lotka-Volterra model with spatio-temporal delay, we get the global solution asymptotically tend to the steady-state problem's steady-state solution.

  2. Reaction-diffusion processes at the nano- and microscales

    NASA Astrophysics Data System (ADS)

    Epstein, Irving R.; Xu, Bing

    2016-04-01

    The bottom-up fabrication of nano- and microscale structures from primary building blocks (molecules, colloidal particles) has made remarkable progress over the past two decades, but most research has focused on structural aspects, leaving our understanding of the dynamic and spatiotemporal aspects at a relatively primitive stage. In this Review, we draw inspiration from living cells to argue that it is now time to move beyond the generation of structures and explore dynamic processes at the nanoscale. We first introduce nanoscale self-assembly, self-organization and reaction-diffusion processes as essential features of cells. Then, we highlight recent progress towards designing and controlling these fundamental features of life in abiological systems. Specifically, we discuss examples of reaction-diffusion processes that lead to such outcomes as self-assembly, self-organization, unique nanostructures, chemical waves and dynamic order to illustrate their ubiquity within a unifying context of dynamic oscillations and energy dissipation. Finally, we suggest future directions for research on reaction-diffusion processes at the nano- and microscales that we find hold particular promise for a new understanding of science at the nanoscale and the development of new kinds of nanotechnologies for chemical transport, chemical communication and integration with living systems.

  3. Programming reaction-diffusion: From theory to micro- and nanofabrication

    NASA Astrophysics Data System (ADS)

    Campbell, Christopher James

    Nature often uses reaction-diffusion(RD) as a means of making structures and materials of unique properties or morphologies on scales from macro- (e.g., stripes in zebras, tigers, and seashells, and formations in trees, agates, and rocks) to microscopic (e.g., cellular growth, chemotaxis and biological waves). However, reaction-diffusion phenomena have not yet been applied in modern materials science and micro-/nanotechnology. In this context, RD systems are particularly promising for micropatterning of surfaces. Unlike conventional micropatterning techniques that modify the properties of the substrate only at the locations to which a modifying agent - be it a chemical or radiation - is delivered, RD can, in principle, evolve chemicals delivered onto a surface into structures of characteristic dimensions significantly smaller than those of the original pattern. In this Dissertation, I describe how reaction-diffusions are programmed and executed via a new micropatterning technique called Wet Stamping to (i) transform microscopic patterns of chemicals delivered onto thin films of dry gelatin into regular arrays of lines of submicrometer thicknesses, multicolor arrays on the micrometer scale, or three-dimensional microstructured surfaces; (ii) modify the properties of a surface by precisely delivering an oxidant to change hydrophilicity or deliver silanes or thiols to build a self-assembling monolayer; or (iii) cut into a metal, glass, or crystal surface by delivery of an etchant to form binary and curvilinear three-dimensional microstructures. This technique has allowed for a fundamental understanding and control of reaction-diffusion processes down to the nanoscale. In addition, this platform has allowed for the development of a range of applications on the micro- and nanoscale, including microlenses, microfluidic devices, and templates for studying cell motility and cancer metastasis.

  4. Reaction rates for a generalized reaction-diffusion master equation

    PubMed Central

    Hellander, Stefan; Petzold, Linda

    2016-01-01

    It has been established that there is an inherent limit to the accuracy of the reaction-diffusion master equation. Specifically, there exists a fundamental lower bound on the mesh size, below which the accuracy deteriorates as the mesh is refined further. In this paper we extend the standard reaction-diffusion master equation to allow molecules occupying neighboring voxels to react, in contrast to the traditional approach in which molecules react only when occupying the same voxel. We derive reaction rates, in two dimensions as well as three dimensions, to obtain an optimal match to the more fine-grained Smoluchowski model, and show in two numerical examples that the extended algorithm is accurate for a wide range of mesh sizes, allowing us to simulate systems that are intractable with the standard reaction-diffusion master equation. In addition, we show that for mesh sizes above the fundamental lower limit of the standard algorithm, the generalized algorithm reduces to the standard algorithm. We derive a lower limit for the generalized algorithm which, in both two dimensions and three dimensions, is on the order of the reaction radius of a reacting pair of molecules. PMID:26871190

  5. Reaction rates for a generalized reaction-diffusion master equation

    NASA Astrophysics Data System (ADS)

    Hellander, Stefan; Petzold, Linda

    2016-01-01

    It has been established that there is an inherent limit to the accuracy of the reaction-diffusion master equation. Specifically, there exists a fundamental lower bound on the mesh size, below which the accuracy deteriorates as the mesh is refined further. In this paper we extend the standard reaction-diffusion master equation to allow molecules occupying neighboring voxels to react, in contrast to the traditional approach, in which molecules react only when occupying the same voxel. We derive reaction rates, in two dimensions as well as three dimensions, to obtain an optimal match to the more fine-grained Smoluchowski model and show in two numerical examples that the extended algorithm is accurate for a wide range of mesh sizes, allowing us to simulate systems that are intractable with the standard reaction-diffusion master equation. In addition, we show that for mesh sizes above the fundamental lower limit of the standard algorithm, the generalized algorithm reduces to the standard algorithm. We derive a lower limit for the generalized algorithm which, in both two dimensions and three dimensions, is of the order of the reaction radius of a reacting pair of molecules.

  6. Synthesis of Programmable Reaction-Diffusion Fronts Using DNA Catalyzers

    NASA Astrophysics Data System (ADS)

    Zadorin, Anton S.; Rondelez, Yannick; Galas, Jean-Christophe; Estevez-Torres, André

    2015-02-01

    We introduce a DNA-based reaction-diffusion (RD) system in which reaction and diffusion terms can be precisely and independently controlled. The effective diffusion coefficient of an individual reaction component, as we demonstrate on a traveling wave, can be reduced up to 2.7-fold using a self-assembled hydrodynamic drag. The intrinsic programmability of this RD system allows us to engineer, for the first time, orthogonal autocatalysts that counterpropagate with minimal interaction. Our results are in excellent quantitative agreement with predictions of the Fisher-Kolmogorov-Petrovskii-Piscunov model. These advances open the way for the rational engineering of pattern formation in pure chemical RD systems.

  7. Reaction-diffusion in the NEURON simulator

    PubMed Central

    McDougal, Robert A.; Hines, Michael L.; Lytton, William W.

    2013-01-01

    In order to support research on the role of cell biological principles (genomics, proteomics, signaling cascades and reaction dynamics) on the dynamics of neuronal response in health and disease, NEURON's Reaction-Diffusion (rxd) module in Python provides specification and simulation for these dynamics, coupled with the electrophysiological dynamics of the cell membrane. Arithmetic operations on species and parameters are overloaded, allowing arbitrary reaction formulas to be specified using Python syntax. These expressions are then transparently compiled into bytecode that uses NumPy for fast vectorized calculations. At each time step, rxd combines NEURON's integrators with SciPy's sparse linear algebra library. PMID:24298253

  8. Reaction-diffusion in the NEURON simulator.

    PubMed

    McDougal, Robert A; Hines, Michael L; Lytton, William W

    2013-01-01

    In order to support research on the role of cell biological principles (genomics, proteomics, signaling cascades and reaction dynamics) on the dynamics of neuronal response in health and disease, NEURON's Reaction-Diffusion (rxd) module in Python provides specification and simulation for these dynamics, coupled with the electrophysiological dynamics of the cell membrane. Arithmetic operations on species and parameters are overloaded, allowing arbitrary reaction formulas to be specified using Python syntax. These expressions are then transparently compiled into bytecode that uses NumPy for fast vectorized calculations. At each time step, rxd combines NEURON's integrators with SciPy's sparse linear algebra library. PMID:24298253

  9. Exact solutions for logistic reaction-diffusion equations in biology

    NASA Astrophysics Data System (ADS)

    Broadbridge, P.; Bradshaw-Hajek, B. H.

    2016-08-01

    Reaction-diffusion equations with a nonlinear source have been widely used to model various systems, with particular application to biology. Here, we provide a solution technique for these types of equations in N-dimensions. The nonclassical symmetry method leads to a single relationship between the nonlinear diffusion coefficient and the nonlinear reaction term; the subsequent solutions for the Kirchhoff variable are exponential in time (either growth or decay) and satisfy the linear Helmholtz equation in space. Example solutions are given in two dimensions for particular parameter sets for both quadratic and cubic reaction terms.

  10. Reactive radical facilitated reaction-diffusion modeling for holographic photopolymerization

    SciTech Connect

    Liu Jianhua; Pu Haihui; Gao Bin; Gao Hongyue; Yin Dejin; Dai Haitao

    2010-02-08

    A phenomenological concentration of reactive radical is proposed to take the role of curing light intensity in explicit proportion to the reaction rate for the conventional reaction-diffusion model. This revision rationally eliminates the theoretical defect of null reaction rate in modeling of the postcuring process, and facilitates the applicability of the model in the whole process of holographic photopolymerizations in photocurable monomer and nematic liquid crystal blend system. Excellent consistencies are obtained in both curing and postcuring processes between simulated and experimentally measured evolutions of the first order diffraction efficiency of the formed composite Bragg gratings.

  11. Bosonic reaction-diffusion processes on scale-free networks

    NASA Astrophysics Data System (ADS)

    Baronchelli, Andrea; Catanzaro, Michele; Pastor-Satorras, Romualdo

    2008-07-01

    Reaction-diffusion processes can be adopted to model a large number of dynamics on complex networks, such as transport processes or epidemic outbreaks. In most cases, however, they have been studied from a fermionic perspective, in which each vertex can be occupied by at most one particle. While still useful, this approach suffers from some drawbacks, the most important probably being the difficulty to implement reactions involving more than two particles simultaneously. Here we develop a general framework for the study of bosonic reaction-diffusion processes on complex networks, in which there is no restriction on the number of interacting particles that a vertex can host. We describe these processes theoretically by means of continuous-time heterogeneous mean-field theory and divide them into two main classes: steady-state and monotonously decaying processes. We analyze specific examples of both behaviors within the class of one-species processes, comparing the results (whenever possible) with the corresponding fermionic counterparts. We find that the time evolution and critical properties of the particle density are independent of the fermionic or bosonic nature of the process, while differences exist in the functional form of the density of occupied vertices in a given degree class k . We implement a continuous-time Monte Carlo algorithm, well suited for general bosonic simulations, which allows us to confirm the analytical predictions formulated within mean-field theory. Our results, at both the theoretical and numerical levels, can be easily generalized to tackle more complex, multispecies, reaction-diffusion processes and open a promising path for a general study and classification of this kind of dynamical systems on complex networks.

  12. Chemical computing with reaction-diffusion processes.

    PubMed

    Gorecki, J; Gizynski, K; Guzowski, J; Gorecka, J N; Garstecki, P; Gruenert, G; Dittrich, P

    2015-07-28

    Chemical reactions are responsible for information processing in living organisms. It is believed that the basic features of biological computing activity are reflected by a reaction-diffusion medium. We illustrate the ideas of chemical information processing considering the Belousov-Zhabotinsky (BZ) reaction and its photosensitive variant. The computational universality of information processing is demonstrated. For different methods of information coding constructions of the simplest signal processing devices are described. The function performed by a particular device is determined by the geometrical structure of oscillatory (or of excitable) and non-excitable regions of the medium. In a living organism, the brain is created as a self-grown structure of interacting nonlinear elements and reaches its functionality as the result of learning. We discuss whether such a strategy can be adopted for generation of chemical information processing devices. Recent studies have shown that lipid-covered droplets containing solution of reagents of BZ reaction can be transported by a flowing oil. Therefore, structures of droplets can be spontaneously formed at specific non-equilibrium conditions, for example forced by flows in a microfluidic reactor. We describe how to introduce information to a droplet structure, track the information flow inside it and optimize medium evolution to achieve the maximum reliability. Applications of droplet structures for classification tasks are discussed. PMID:26078345

  13. Cox process representation and inference for stochastic reaction-diffusion processes

    NASA Astrophysics Data System (ADS)

    Schnoerr, David; Grima, Ramon; Sanguinetti, Guido

    2016-05-01

    Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to the social sciences, yet they are notoriously difficult to simulate and calibrate to observational data. Here we use ideas from statistical physics and machine learning to provide a solution to the inverse problem of learning a stochastic reaction-diffusion process from data. Our solution relies on a non-trivial connection between stochastic reaction-diffusion processes and spatio-temporal Cox processes, a well-studied class of models from computational statistics. This connection leads to an efficient and flexible algorithm for parameter inference and model selection. Our approach shows excellent accuracy on numeric and real data examples from systems biology and epidemiology. Our work provides both insights into spatio-temporal stochastic systems, and a practical solution to a long-standing problem in computational modelling.

  14. Guiding brine shrimp through mazes by solving reaction diffusion equations

    NASA Astrophysics Data System (ADS)

    Singal, Krishma; Fenton, Flavio

    Excitable systems driven by reaction diffusion equations have been shown to not only find solutions to mazes but to also to find the shortest path between the beginning and the end of the maze. In this talk we describe how we can use the Fitzhugh-Nagumo model, a generic model for excitable media, to solve a maze by varying the basin of attraction of its two fixed points. We demonstrate how two dimensional mazes are solved numerically using a Java Applet and then accelerated to run in real time by using graphic processors (GPUs). An application of this work is shown by guiding phototactic brine shrimp through a maze solved by the algorithm. Once the path is obtained, an Arduino directs the shrimp through the maze using lights from LEDs placed at the floor of the Maze. This method running in real time could be eventually used for guiding robots and cars through traffic.

  15. Field theory of propagating reaction-diffusion fronts

    SciTech Connect

    Escudero, C.

    2004-10-01

    The problem of velocity selection of reaction-diffusion fronts has been widely investigated. While the mean-field limit results are well known theoretically, there is a lack of analytic progress in those cases in which fluctuations are to be taken into account. Here, we construct an analytic theory connecting the first principles of the reaction-diffusion process to an effective equation of motion via field-theoretic arguments, and we arrive at results already confirmed by numerical simulations.

  16. Generation of diversity in a reaction-diffusion-based controller.

    PubMed

    Zahadat, Payam; Schmickl, Thomas

    2014-01-01

    A controller of biological or artificial organism (e.g., in bio-inspired cellular robots) consists of a number of processes that drive its dynamics. For a system of processes to perform as a successful controller, different properties can be mentioned. One of the desirable properties of such a system is the capability of generating sufficiently diverse patterns of outputs and behaviors. A system with such a capability is potentially adaptable to perform complicated tasks with proper parameterizations and may successfully reach the solution space of behaviors from the point of view of search and evolutionary algorithms. This article aims to take an early step toward exploring this capability at the levels of individuals and populations by introducing measures of diversity generation and by evaluating the influence of different types of processes on diversity generation. A reaction-diffusion-based controller called the artificial homeostatic hormone system (AHHS) is studied as a system consisting of different processes with various domains of functioning (e.g., internal or external to the control unit). Various combinations of these processes are investigated in terms of diversity generation at levels of both individuals and populations, and the effects of the processes are discussed representing different influences for the processes. A case study of evolving a multimodular AHHS controller with all the various process combinations is also investigated, representing the relevance of the diversity generation measures and practical scenarios. PMID:24730765

  17. Reaction diffusion Voronoi diagrams: from sensors data to computing.

    PubMed

    Vázquez-Otero, Alejandro; Faigl, Jan; Dormido, Raquel; Duro, Natividad

    2015-01-01

    In this paper, a new method to solve computational problems using reaction diffusion (RD) systems is presented. The novelty relies on the use of a model configuration that tailors its spatiotemporal dynamics to develop Voronoi diagrams (VD) as a part of the system's natural evolution. The proposed framework is deployed in a solution of related robotic problems, where the generalized VD are used to identify topological places in a grid map of the environment that is created from sensor measurements. The ability of the RD-based computation to integrate external information, like a grid map representing the environment in the model computational grid, permits a direct integration of sensor data into the model dynamics. The experimental results indicate that this method exhibits significantly less sensitivity to noisy data than the standard algorithms for determining VD in a grid. In addition, previous drawbacks of the computational algorithms based on RD models, like the generation of volatile solutions by means of excitable waves, are now overcome by final stable states. PMID:26035349

  18. Adaptive mesh refinement for stochastic reaction-diffusion processes

    SciTech Connect

    Bayati, Basil; Chatelain, Philippe; Koumoutsakos, Petros

    2011-01-01

    We present an algorithm for adaptive mesh refinement applied to mesoscopic stochastic simulations of spatially evolving reaction-diffusion processes. The transition rates for the diffusion process are derived on adaptive, locally refined structured meshes. Convergence of the diffusion process is presented and the fluctuations of the stochastic process are verified. Furthermore, a refinement criterion is proposed for the evolution of the adaptive mesh. The method is validated in simulations of reaction-diffusion processes as described by the Fisher-Kolmogorov and Gray-Scott equations.

  19. Modeling mammary gland morphogenesis as a reaction-diffusion process.

    PubMed

    Grant, Mark R; Hunt, C Anthony; Xia, Lan; Fata, Jimmie E; Bissell, Mina J

    2004-01-01

    Mammary ducts are formed through a process of branching morphogenesis. We present results of experiments using a simulation model of this process, and discuss their implications for understanding mammary duct extension and bifurcation. The model is a cellular automaton approximation of a reaction-diffusion process in which matrix metalloproteinases represent the activator, inhibitors of matrix metalloproteinases represent the inhibitor, and growth factors serve as a substrate. We compare results from the simulation model with those from in-vivo experiments as part of an assessment of whether duct extension and bifurcation during morphogenesis may be a consequence of a reaction-diffusion mechanism mediated by MMPs and TIMPs. PMID:17271768

  20. Transient spatiotemporal chaos is extensive in three reaction-diffusion networks

    NASA Astrophysics Data System (ADS)

    Stahlke, Dan; Wackerbauer, Renate

    2009-11-01

    Extensive (asymptotic) spatiotemporal chaos is comprised of statistically similar subsystems that interact only weakly. A systematic study of transient spatiotemporal chaos reveals extensive system behavior in all three reaction-diffusion networks for various boundary conditions. The Lyapunov dimension, the sum of positive Lyapunov exponents, and the logarithm of the transient lifetime grow linearly with the system size. The unstable manifold of the chaotic saddle has nearly the same dimension as the saddle itself, and the stable manifold is nearly space filling.

  1. Analysis of some identification problems for the reaction-diffusion-convection equation

    NASA Astrophysics Data System (ADS)

    Alekseev, G. V.; Mashkov, D. V.; Yashenko, E. N.

    2016-04-01

    Identification problems for a linear stationary reaction-diffusion-convection model, considered in the bounded domain under Dirichlet boundary condition, are studied. Using an optimization method these problems are reduced to respective control problems. The reaction coefficient and the volume density of substance source play the role of controls in this control problem. The solvability of the direct and control problems is proved, the optimality system, which describes the necessary optimality conditions, is derived and the numerical algorithm is developed.

  2. Cox process representation and inference for stochastic reaction-diffusion processes.

    PubMed

    Schnoerr, David; Grima, Ramon; Sanguinetti, Guido

    2016-01-01

    Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to the social sciences, yet they are notoriously difficult to simulate and calibrate to observational data. Here we use ideas from statistical physics and machine learning to provide a solution to the inverse problem of learning a stochastic reaction-diffusion process from data. Our solution relies on a non-trivial connection between stochastic reaction-diffusion processes and spatio-temporal Cox processes, a well-studied class of models from computational statistics. This connection leads to an efficient and flexible algorithm for parameter inference and model selection. Our approach shows excellent accuracy on numeric and real data examples from systems biology and epidemiology. Our work provides both insights into spatio-temporal stochastic systems, and a practical solution to a long-standing problem in computational modelling. PMID:27222432

  3. Kidney Tumor Growth Prediction by Coupling Reaction-Diffusion and Biomechanical Model

    PubMed Central

    Chen, Xinjian; Summers, Ronald M.; Yao, Jianhua

    2014-01-01

    It is desirable to predict the tumor growth rate so that appropriate treatment can be planned in the early stage. Previously, we proposed a finite element method (FEM)-based 3D kidney tumor growth prediction system using longitudinal images. A reaction-diffusion model was applied as the tumor growth model. In this paper, we not only improve the tumor growth model by coupling the reaction-diffusion model with a biomechanical model, but also take the surrounding tissues into account. Different diffusion and biomechanical properties are applied for different tissue types. FEM is employed to simulate the coupled tumor growth model. Model parameters are estimated by optimizing an objective function of overlap accuracy using a hybrid optimization parallel search package (HOPSPACK). The proposed method was tested with kidney CT images of eight tumors from five patients with seven time points. The experimental results showed the performance of the proposed method improved greatly compared to our previous work. PMID:23047857

  4. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings.

    PubMed

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-29

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization. PMID:27176541

  5. Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings

    NASA Astrophysics Data System (ADS)

    Maucher, Fabian; Sutcliffe, Paul

    2016-04-01

    We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.

  6. Field theory for a reaction-diffusion model of quasispecies dynamics.

    PubMed

    Pastor-Satorras, R; Solé, R V

    2001-11-01

    RNA viruses are known to replicate with extremely high mutation rates. These rates are actually close to the so-called error threshold. This threshold is in fact a critical point beyond which genetic information is lost through a second-order phase transition, which has been dubbed as the "error catastrophe." Here we explore this phenomenon using a field theory approximation to the spatially extended Swetina-Schuster quasispecies model [J. Swetina and P. Schuster, Biophys. Chem. 16, 329 (1982)], a single-sharp-peak landscape. In analogy with standard absorbing-state phase transitions, we develop a reaction-diffusion model whose discrete rules mimic the Swetina-Schuster model. The field theory representation of the reaction-diffusion system is constructed. The proposed field theory belongs to the same universality class as a conserved reaction-diffusion model previously proposed [F. van Wijland et al., Physica A 251, 179 (1998)]. From the field theory, we obtain the full set of exponents that characterize the critical behavior at the error threshold. Our results present the error catastrophe from a different point of view and suggest that spatial degrees of freedom can modify several mean-field predictions previously considered, leading to the definition of characteristic exponents that could be experimentally measurable. PMID:11735970

  7. Anomalous Impact in Reaction-Diffusion Financial Models

    NASA Astrophysics Data System (ADS)

    Mastromatteo, I.; Tóth, B.; Bouchaud, J.-P.

    2014-12-01

    We generalize the reaction-diffusion model A +B → /0 in order to study the impact of an excess of A (or B ) at the reaction front. We provide an exact solution of the model, which shows that the linear response breaks down: the average displacement of the reaction front grows as the square root of the imbalance. We argue that this model provides a highly simplified but generic framework to understand the square-root impact of large orders in financial markets.

  8. Reaction-diffusion modelling of bacterial colony patterns

    NASA Astrophysics Data System (ADS)

    Mimura, Masayasu; Sakaguchi, Hideo; Matsushita, Mitsugu

    2000-07-01

    It is well known from experiments that bacterial species Bacillus subtilis exhibit various colony patterns. These are essentially classified into five types in the morphological diagram, depending on the substrate softness and nutrient concentration. (A) diffusion-limited aggregation-like; (B) Eden-like; (C) concentric ring-like; (D) disk-like; and (E) dense branching morphology-like. There arises the naive question of whether the diversity of colony patterns observed in experiments is caused by different effects or governed by the same underlying principles. Our research has led us to propose reaction-diffusion models to describe the morphological diversity of colony patterns except for Eden-like ones.

  9. A reaction-diffusion model of CO2 influx into an oocyte.

    PubMed

    Somersalo, Erkki; Occhipinti, Rossana; Boron, Walter F; Calvetti, Daniela

    2012-09-21

    We have developed and implemented a novel mathematical model for simulating transients in surface pH (pH(S)) and intracellular pH (pH(i)) caused by the influx of carbon dioxide (CO(2)) into a Xenopus oocyte. These transients are important tools for studying gas channels. We assume that the oocyte is a sphere surrounded by a thin layer of unstirred fluid, the extracellular unconvected fluid (EUF), which is in turn surrounded by the well-stirred bulk extracellular fluid (BECF) that represents an infinite reservoir for all solutes. Here, we assume that the oocyte plasma membrane is permeable only to CO(2). In both the EUF and intracellular space, solute concentrations can change because of diffusion and reactions. The reactions are the slow equilibration of the CO(2) hydration-dehydration reactions and competing equilibria among carbonic acid (H(2)CO(3))/bicarbonate (HCO(3)(-)) and a multitude of non-CO(2)/HCO(3)(-) buffers. Mathematically, the model is described by a coupled system of reaction-diffusion equations that-assuming spherical radial symmetry-we solved using the method of lines with appropriate stiff solvers. In agreement with experimental data [Musa-Aziz et al. 2009, PNAS 106 5406-5411], the model predicts that exposing the cell to extracellular 1.5% CO(2)/10 mM HCO(3)(-) (pH 7.50) causes pH(i) to fall and pH(S) to rise rapidly to a peak and then decay. Moreover, the model provides insights into the competition between diffusion and reaction processes when we change the width of the EUF, membrane permeability to CO(2), native extra- and intracellular carbonic anhydrase-like activities, the non-CO(2)/HCO(3)(-) (intrinsic) intracellular buffering power, or mobility of intrinsic intracellular buffers. PMID:22728674

  10. Reaction-diffusion patterns: From observations in halogene chemistry to a test for implication in mitosis

    NASA Astrophysics Data System (ADS)

    Dulos, E.; Hunding, A.; Boissonade, J.; de Kepper, P.

    Since the seminal paper "The chemical basis of morphogenesis" by Alan Turing, the temporal and spatial self-organization phenomena produced in chemically reacting and diffusing systems are often thought as paradigms for biological development. The basic theoretical principles on which the development of stationary concentration patterns (Turing structures) rely on are briefly presented. We review different aspects of our contribution to the experimental observation of reaction-diffusion patterns in iodine-oxychlorine systems. The experimental techniques are emphasized. Phase diagrams gathering different standing and travelling patterns are presented, analyzed and modeled. A special attention is also given to some peculiar pattern growth dynamics (spot division, finger splitting).

  11. Transient spatiotemporal chaos is extensive in three reaction-diffusion networks.

    PubMed

    Stahlke, Dan; Wackerbauer, Renate

    2009-11-01

    Extensive (asymptotic) spatiotemporal chaos is comprised of statistically similar subsystems that interact only weakly. A systematic study of transient spatiotemporal chaos reveals extensive system behavior in all three reaction-diffusion networks for various boundary conditions. The Lyapunov dimension, the sum of positive Lyapunov exponents, and the logarithm of the transient lifetime grow linearly with the system size. The unstable manifold of the chaotic saddle has nearly the same dimension as the saddle itself, and the stable manifold is nearly space filling. PMID:20365064

  12. Small-scale properties of a stochastic cubic-autocatalytic reaction-diffusion model

    NASA Astrophysics Data System (ADS)

    Gagnon, Jean-Sébastien; Hochberg, David; Pérez-Mercader, Juan

    2015-10-01

    We investigate the small-scale properties of a stochastic cubic-autocatalytic reaction-diffusion (CARD) model using renormalization techniques. We renormalize noise-induced ultraviolet divergences and obtain β functions for the decay rate and coupling at one loop. Assuming colored (power-law) noise, our results show that the behavior of both decay rate and coupling with scale depends crucially on the noise exponent. Interpreting the CARD model as a proxy for a (very simple) living system, our results suggest that power-law correlations in environmental fluctuations can both decrease or increase the growth of structures at smaller scales.

  13. Breakdown of the reaction-diffusion master equation with nonelementary rates

    NASA Astrophysics Data System (ADS)

    Smith, Stephen; Grima, Ramon

    2016-05-01

    The chemical master equation (CME) is the exact mathematical formulation of chemical reactions occurring in a dilute and well-mixed volume. The reaction-diffusion master equation (RDME) is a stochastic description of reaction-diffusion processes on a spatial lattice, assuming well mixing only on the length scale of the lattice. It is clear that, for the sake of consistency, the solution of the RDME of a chemical system should converge to the solution of the CME of the same system in the limit of fast diffusion: Indeed, this has been tacitly assumed in most literature concerning the RDME. We show that, in the limit of fast diffusion, the RDME indeed converges to a master equation but not necessarily the CME. We introduce a class of propensity functions, such that if the RDME has propensities exclusively of this class, then the RDME converges to the CME of the same system, whereas if the RDME has propensities not in this class, then convergence is not guaranteed. These are revealed to be elementary and nonelementary propensities, respectively. We also show that independent of the type of propensity, the RDME converges to the CME in the simultaneous limit of fast diffusion and large volumes. We illustrate our results with some simple example systems and argue that the RDME cannot generally be an accurate description of systems with nonelementary rates.

  14. Turing instability in reaction-diffusion models on complex networks

    NASA Astrophysics Data System (ADS)

    Ide, Yusuke; Izuhara, Hirofumi; Machida, Takuya

    2016-09-01

    In this paper, the Turing instability in reaction-diffusion models defined on complex networks is studied. Here, we focus on three types of models which generate complex networks, i.e. the Erdős-Rényi, the Watts-Strogatz, and the threshold network models. From analysis of the Laplacian matrices of graphs generated by these models, we numerically reveal that stable and unstable regions of a homogeneous steady state on the parameter space of two diffusion coefficients completely differ, depending on the network architecture. In addition, we theoretically discuss the stable and unstable regions in the cases of regular enhanced ring lattices which include regular circles, and networks generated by the threshold network model when the number of vertices is large enough.

  15. Derivation of an Analytical Solution to a Reaction-Diffusion Model for Autocatalytic Degradation and Erosion in Polymer Microspheres

    PubMed Central

    Ford Versypt, Ashlee N.; Arendt, Paul D.; Pack, Daniel W.; Braatz, Richard D.

    2015-01-01

    A mathematical reaction-diffusion model is defined to describe the gradual decomposition of polymer microspheres composed of poly(D,L-lactic-co-glycolic acid) (PLGA) that are used for pharmaceutical drug delivery over extended periods of time. The partial differential equation (PDE) model treats simultaneous first-order generation due to chemical reaction and diffusion of reaction products in spherical geometry to capture the microsphere-size-dependent effects of autocatalysis on PLGA erosion that occurs when the microspheres are exposed to aqueous media such as biological fluids. The model is solved analytically for the concentration of the autocatalytic carboxylic acid end groups of the polymer chains that comprise the microspheres as a function of radial position and time. The analytical solution for the reaction and transport of the autocatalytic chemical species is useful for predicting the conditions under which drug release from PLGA microspheres transitions from diffusion-controlled to erosion-controlled release, for understanding the dynamic coupling between the PLGA degradation and erosion mechanisms, and for designing drug release particles. The model is the first to provide an analytical prediction for the dynamics and spatial heterogeneities of PLGA degradation and erosion within a spherical particle. The analytical solution is applicable to other spherical systems with simultaneous diffusive transport and first-order generation by reaction. PMID:26284787

  16. Derivation of an Analytical Solution to a Reaction-Diffusion Model for Autocatalytic Degradation and Erosion in Polymer Microspheres.

    PubMed

    Ford Versypt, Ashlee N; Arendt, Paul D; Pack, Daniel W; Braatz, Richard D

    2015-01-01

    A mathematical reaction-diffusion model is defined to describe the gradual decomposition of polymer microspheres composed of poly(D,L-lactic-co-glycolic acid) (PLGA) that are used for pharmaceutical drug delivery over extended periods of time. The partial differential equation (PDE) model treats simultaneous first-order generation due to chemical reaction and diffusion of reaction products in spherical geometry to capture the microsphere-size-dependent effects of autocatalysis on PLGA erosion that occurs when the microspheres are exposed to aqueous media such as biological fluids. The model is solved analytically for the concentration of the autocatalytic carboxylic acid end groups of the polymer chains that comprise the microspheres as a function of radial position and time. The analytical solution for the reaction and transport of the autocatalytic chemical species is useful for predicting the conditions under which drug release from PLGA microspheres transitions from diffusion-controlled to erosion-controlled release, for understanding the dynamic coupling between the PLGA degradation and erosion mechanisms, and for designing drug release particles. The model is the first to provide an analytical prediction for the dynamics and spatial heterogeneities of PLGA degradation and erosion within a spherical particle. The analytical solution is applicable to other spherical systems with simultaneous diffusive transport and first-order generation by reaction. PMID:26284787

  17. A minimally-resolved immersed boundary model for reaction-diffusion problems.

    PubMed

    Bhalla, Amneet Pal Singh; Griffith, Boyce E; Patankar, Neelesh A; Donev, Aleksandar

    2013-12-01

    We develop an immersed boundary approach to modeling reaction-diffusion processes in dispersions of reactive spherical particles, from the diffusion-limited to the reaction-limited setting. We represent each reactive particle with a minimally-resolved "blob" using many fewer degrees of freedom per particle than standard discretization approaches. More complicated or more highly resolved particle shapes can be built out of a collection of reactive blobs. We demonstrate numerically that the blob model can provide an accurate representation at low to moderate packing densities of the reactive particles, at a cost not much larger than solving a Poisson equation in the same domain. Unlike multipole expansion methods, our method does not require analytically computed Green's functions, but rather, computes regularized discrete Green's functions on the fly by using a standard grid-based discretization of the Poisson equation. This allows for great flexibility in implementing different boundary conditions, coupling to fluid flow or thermal transport, and the inclusion of other effects such as temporal evolution and even nonlinearities. We develop multigrid-based preconditioners for solving the linear systems that arise when using implicit temporal discretizations or studying steady states. In the diffusion-limited case the resulting linear system is a saddle-point problem, the efficient solution of which remains a challenge for suspensions of many particles. We validate our method by comparing to published results on reaction-diffusion in ordered and disordered suspensions of reactive spheres. PMID:24320369

  18. A Local, Self-Organizing Reaction-Diffusion Model Can Explain Somite Patterning in Embryos.

    PubMed

    Cotterell, James; Robert-Moreno, Alexandre; Sharpe, James

    2015-10-28

    During somitogenesis in embryos, a posteriorly moving differentiation front arrests the oscillations of "segmentation clock" genes, leaving behind a frozen, periodic pattern of expression stripes. Both mathematical theories and experimental observations have invoked a "clock and wavefront" model to explain this phenomenon, in which long-range molecular gradients control the movement of the front and therefore the placement of the stripes in the embryo. Here, we develop a fundamentally different model-a progressive oscillatory reaction-diffusion (PORD) system driven by short-range interactions. In this model, posterior movement of the front is a local, emergent phenomenon that, in contrast to the clock and wavefront model, is not controlled by global positional information. The PORD model explains important features of somitogenesis, such as size regulation, that previous reaction-diffusion models could not explain. Moreover, the PORD and clock and wavefront models make different predictions about the results of FGF-inhibition and tissue-cutting experiments, and we demonstrate that the results of these experiments favor the PORD model. PMID:27136055

  19. A deterministic particle method for one-dimensional reaction-diffusion equations

    NASA Technical Reports Server (NTRS)

    Mascagni, Michael

    1995-01-01

    We derive a deterministic particle method for the solution of nonlinear reaction-diffusion equations in one spatial dimension. This deterministic method is an analog of a Monte Carlo method for the solution of these problems that has been previously investigated by the author. The deterministic method leads to the consideration of a system of ordinary differential equations for the positions of suitably defined particles. We then consider the time explicit and implicit methods for this system of ordinary differential equations and we study a Picard and Newton iteration for the solution of the implicit system. Next we solve numerically this system and study the discretization error both analytically and numerically. Numerical computation shows that this deterministic method is automatically adaptive to large gradients in the solution.

  20. Reaction Diffusion Modeling of Calcium Dynamics with Realistic ER Geometry

    PubMed Central

    Means, Shawn; Smith, Alexander J.; Shepherd, Jason; Shadid, John; Fowler, John; Wojcikiewicz, Richard J. H.; Mazel, Tomas; Smith, Gregory D.; Wilson, Bridget S.

    2006-01-01

    We describe a finite-element model of mast cell calcium dynamics that incorporates the endoplasmic reticulum's complex geometry. The model is built upon a three-dimensional reconstruction of the endoplasmic reticulum (ER) from an electron tomographic tilt series. Tetrahedral meshes provide volumetric representations of the ER lumen, ER membrane, cytoplasm, and plasma membrane. The reaction-diffusion model simultaneously tracks changes in cytoplasmic and ER intraluminal calcium concentrations and includes luminal and cytoplasmic protein buffers. Transport fluxes via PMCA, SERCA, ER leakage, and Type II IP3 receptors are also represented. Unique features of the model include stochastic behavior of IP3 receptor calcium channels and comparisons of channel open times when diffusely distributed or aggregated in clusters on the ER surface. Simulations show that IP3R channels in close proximity modulate activity of their neighbors through local Ca2+ feedback effects. Cytoplasmic calcium levels rise higher, and ER luminal calcium concentrations drop lower, after IP3-mediated release from receptors in the diffuse configuration. Simulation results also suggest that the buffering capacity of the ER, and not restricted diffusion, is the predominant factor influencing average luminal calcium concentrations. PMID:16617072

  1. A Reaction-Diffusion Model of Cholinergic Retinal Waves

    PubMed Central

    Lansdell, Benjamin; Ford, Kevin; Kutz, J. Nathan

    2014-01-01

    Prior to receiving visual stimuli, spontaneous, correlated activity in the retina, called retinal waves, drives activity-dependent developmental programs. Early-stage waves mediated by acetylcholine (ACh) manifest as slow, spreading bursts of action potentials. They are believed to be initiated by the spontaneous firing of Starburst Amacrine Cells (SACs), whose dense, recurrent connectivity then propagates this activity laterally. Their inter-wave interval and shifting wave boundaries are the result of the slow after-hyperpolarization of the SACs creating an evolving mosaic of recruitable and refractory cells, which can and cannot participate in waves, respectively. Recent evidence suggests that cholinergic waves may be modulated by the extracellular concentration of ACh. Here, we construct a simplified, biophysically consistent, reaction-diffusion model of cholinergic retinal waves capable of recapitulating wave dynamics observed in mice retina recordings. The dense, recurrent connectivity of SACs is modeled through local, excitatory coupling occurring via the volume release and diffusion of ACh. In addition to simulation, we are thus able to use non-linear wave theory to connect wave features to underlying physiological parameters, making the model useful in determining appropriate pharmacological manipulations to experimentally produce waves of a prescribed spatiotemporal character. The model is used to determine how ACh mediated connectivity may modulate wave activity, and how parameters such as the spontaneous activation rate and sAHP refractory period contribute to critical wave size variability. PMID:25474327

  2. Spatiotemporal patterns in a reaction-diffusion model with the Degn-Harrison reaction scheme

    NASA Astrophysics Data System (ADS)

    Peng, Rui; Yi, Feng-qi; Zhao, Xiao-qiang

    Spatial and temporal patterns generated in ecological and chemical systems have become a central object of research in recent decades. In this work, we are concerned with a reaction-diffusion model with the Degn-Harrison reaction scheme, which accounts for the qualitative feature of the respiratory process in a Klebsiella aerogenes bacterial culture. We study the global stability of the constant steady state, existence and nonexistence of nonconstant steady states as well as the Hopf and steady state bifurcations. In particular, our results show the existence of Turing patterns and inhomogeneous periodic oscillatory patterns while the system parameters are all spatially homogeneous. These results also exhibit the critical role of the system parameters in leading to the formation of spatiotemporal patterns.

  3. Taylor-Couette Flow with Hourglass Geometry of Varying Lengths Simulated by Reaction-Diffusion

    NASA Astrophysics Data System (ADS)

    Zhao, Yunjie; Halmstad, Andrew; Olsen, Thomas; Wiener, Richard

    2008-11-01

    Previously, we have observed chaotic formation of Taylor-Vortex pairs in Modified Taylor- Couette Flow with Hourglass Geometry. In the experiment, the chaotic formation in a shorter system has been restricted to a narrow band about the waist of the hourglass. Such behavior has been modeled by The Reaction-Diffusion equation, which has been previously studied, by Riecke and Paap. Their calculation suggested that quadrupling length of the system would lead to spatial chaos in the vortex formation. We present a careful recreation of this result and consider an intermediate length. We demonstrate that doubling the length should be sufficient to observe spatially chaotic behavior. Richard J. Wiener et al, Phys. Rev. E 55, 5489 (1997). H. Riecke and H.-G. Paap, Europhys. Lett. 14, 1235 (1991).

  4. Link between alginate reaction front propagation and general reaction diffusion theory.

    PubMed

    Braschler, Thomas; Valero, Ana; Colella, Ludovica; Pataky, Kristopher; Brugger, Jürgen; Renaud, Philippe

    2011-03-15

    We provide a common theoretical framework reuniting specific models for the Ca(2+)-alginate system and general reaction diffusion theory along with experimental validation on a microfluidic chip. As a starting point, we use a set of nonlinear, partial differential equations that are traditionally solved numerically: the Mikkelsen-Elgsaeter model. Applying the traveling-wave hypothesis as a major simplification, we obtain an analytical solution. The solution indicates that the fundamental properties of the alginate reaction front are governed by a single dimensionless parameter λ. For small λ values, a large depletion zone accompanies the reaction front. For large λ values, the alginate reacts before having the time to diffuse significantly. We show that the λ parameter is of general importance beyond the alginate model system, as it can be used to classify known solutions for second-order reaction diffusion schemes, along with the novel solution presented here. For experimental validation, we develop a microchip model system, in which the alginate gel formation can be carried out in a highly controlled, essentially 1D environment. The use of a filter barrier enables us to rapidly renew the CaCl(2) solution, while maintaining flow speeds lower than 1 μm/s for the alginate compartment. This allows one to impose an exactly known bulk CaCl(2) concentration and diffusion resistance. This experimental model system, taken together with the theoretical development, enables the determination of the entire set of physicochemical parameters governing the alginate reaction front in a single experiment. PMID:21351747

  5. Hybrid approaches for multiple-species stochastic reaction-diffusion models

    NASA Astrophysics Data System (ADS)

    Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

    2015-10-01

    Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

  6. An adaptive algorithm for simulation of stochastic reaction-diffusion processes

    SciTech Connect

    Ferm, Lars Hellander, Andreas Loetstedt, Per

    2010-01-20

    We propose an adaptive hybrid method suitable for stochastic simulation of diffusion dominated reaction-diffusion processes. For such systems, simulation of the diffusion requires the predominant part of the computing time. In order to reduce the computational work, the diffusion in parts of the domain is treated macroscopically, in other parts with the tau-leap method and in the remaining parts with Gillespie's stochastic simulation algorithm (SSA) as implemented in the next subvolume method (NSM). The chemical reactions are handled by SSA everywhere in the computational domain. A trajectory of the process is advanced in time by an operator splitting technique and the timesteps are chosen adaptively. The spatial adaptation is based on estimates of the errors in the tau-leap method and the macroscopic diffusion. The accuracy and efficiency of the method are demonstrated in examples from molecular biology where the domain is discretized by unstructured meshes.

  7. Scalable implicit methods for reaction-diffusion equations in two and three space dimensions

    SciTech Connect

    Veronese, S.V.; Othmer, H.G.

    1996-12-31

    This paper describes the implementation of a solver for systems of semi-linear parabolic partial differential equations in two and three space dimensions. The solver is based on a parallel implementation of a non-linear Alternating Direction Implicit (ADI) scheme which uses a Cartesian grid in space and an implicit time-stepping algorithm. Various reordering strategies for the linearized equations are used to reduce the stride and improve the overall effectiveness of the parallel implementation. We have successfully used this solver for large-scale reaction-diffusion problems in computational biology and medicine in which the desired solution is a traveling wave that may contain rapid transitions. A number of examples that illustrate the efficiency and accuracy of the method are given here; the theoretical analysis will be presented.

  8. Spread of infectious diseases in a hyperbolic reaction-diffusion susceptible-infected-removed model

    NASA Astrophysics Data System (ADS)

    Barbera, Elvira; Consolo, Giancarlo; Valenti, Giovanna

    2013-11-01

    A one-dimensional hyperbolic reaction-diffusion model of epidemics is developed to describe the dynamics of diseases spread occurring in an environment where three kinds of individuals mutually interact: the susceptibles, the infectives, and the removed. It is assumed that the disease is transmitted from the infected population to the susceptible one according to a nonlinear convex incidence rate. The model, based upon the framework of extended thermodynamics, removes the unphysical feature of instantaneous diffusive effects, which is typical of parabolic models. Linear stability analyses are performed to study the nature of the equilibrium states against uniform and nonuniform perturbations. Emphasis is given to the occurrence of Hopf and Turing bifurcations, which break the temporal and the spatial symmetry of the system, respectively. The existence of traveling wave solutions connecting two steady states is also discussed. The governing equations are also integrated numerically to validate the analytical results and to characterize the spatiotemporal evolution of diseases.

  9. Symmetry breaking in a bulk-surface reaction-diffusion model for signalling networks

    NASA Astrophysics Data System (ADS)

    Rätz, Andreas; Röger, Matthias

    2014-08-01

    Signalling molecules play an important role for many cellular functions. We investigate here a general system of two membrane reaction-diffusion equations coupled to a diffusion equation inside the cell by a Robin-type boundary condition and a flux term in the membrane equations. A specific model of this form was recently proposed by the authors for the GTPase cycle in cells. We investigate here a putative role of diffusive instabilities in cell polarization. By a linearized stability analysis, we identify two different mechanisms. The first resembles a classical Turing instability for the membrane subsystem and requires (unrealistically) large differences in the lateral diffusion of activator and substrate. On the other hand, the second possibility is induced by the difference in cytosolic and lateral diffusion and appears much more realistic. We complement our theoretical analysis by numerical simulations that confirm the new stability mechanism and allow us to investigate the evolution beyond the regime where the linearization applies.

  10. The Spatial Chemical Langevin and Reaction Diffusion Master Equations: Moments and Qualitative Solutions

    NASA Astrophysics Data System (ADS)

    Ghosh, Atiyo; Leier, Andre; Marquez-Lago, Tatiana

    2014-03-01

    Spatial stochastic effects are prevalent in many biological systems spanning a variety of scales, from intracellular (e.g. gene expression) to ecological (plankton aggregation). The most common ways of simulating such systems involve drawing sample paths from either the Reaction Diffusion Master Equation (RDME) or the Smoluchowski Equation, using methods such as Gillespie's Simulation Algorithm, Green's Function Reaction Dynamics and Single Particle Tracking. The simulation times of such techniques scale with the number of simulated particles, leading to much computational expense when considering large systems. The Spatial Chemical Langevin Equation (SCLE) can be simulated with fixed time intervals, independent of the number of particles, and can thus provide significant computational savings. However, very little work has been done to investigate the behavior of the SCLE. In this talk we summarize our findings on comparing the SCLE to the well-studied RDME. We use both analytical and numerical procedures to show when one should expect the moments of the SCLE to be close to the RDME, and also when they should differ.

  11. Metastable dynamics of internal interfaces for a convection-reaction-diffusion equation

    NASA Astrophysics Data System (ADS)

    Strani, Marta

    2015-12-01

    We study the one-dimensional metastable dynamics of internal interfaces for the initial boundary value problem for the following convection-reaction-diffusion equation Metastable behaviour appears when the time-dependent solution develops into a layered function in a relatively short time, and subsequently approaches its steady state in a very long time interval. A rigorous analysis is used to study such behaviour by means of the construction of a one-parameter family {{≤ft\\{{{U}\\varepsilon}≤ft(x;ξ \\right)\\right\\}}ξ} of approximate stationary solutions and of a linearisation of the original system around an element of this family. We obtain a system consisting of an ODE for the parameter ξ, describing the position of the interface coupled with a PDE for the perturbation v and defined as the difference v:=u-{{U}\\varepsilon} . The key of our analysis are the spectral properties of the linearised operator around an element of the family ≤ft\\{{{U}\\varepsilon}\\right\\} : the presence of a first eigenvalue, small with respect to ε, leads to metastable behaviour when \\varepsilon \\ll 1 .

  12. Local Perturbation Analysis: A Computational Tool for Biophysical Reaction-Diffusion Models

    PubMed Central

    Holmes, William R.; Mata, May Anne; Edelstein-Keshet, Leah

    2015-01-01

    Diffusion and interaction of molecular regulators in cells is often modeled using reaction-diffusion partial differential equations. Analysis of such models and exploration of their parameter space is challenging, particularly for systems of high dimensionality. Here, we present a relatively simple and straightforward analysis, the local perturbation analysis, that reveals how parameter variations affect model behavior. This computational tool, which greatly aids exploration of the behavior of a model, exploits a structural feature common to many cellular regulatory systems: regulators are typically either bound to a membrane or freely diffusing in the interior of the cell. Using well-documented, readily available bifurcation software, the local perturbation analysis tracks the approximate early evolution of an arbitrarily large perturbation of a homogeneous steady state. In doing so, it provides a bifurcation diagram that concisely describes various regimes of the model’s behavior, reducing the need for exhaustive simulations to explore parameter space. We explain the method and provide detailed step-by-step guides to its use and application. PMID:25606671

  13. tiReaction Diffusion Voronoi Diagrams: From Sensors Data to Computing

    PubMed Central

    Vázquez-Otero, Alejandro; Faigl, Jan; Dormido, Raquel; Duro, Natividad

    2015-01-01

    In this paper, a new method to solve computational problems using reaction diffusion (RD) systems is presented. The novelty relies on the use of a model configuration that tailors its spatiotemporal dynamics to develop Voronoi diagrams (VD) as a part of the system's natural evolution. The proposed framework is deployed in a solution of related robotic problems, where the generalized VD are used to identify topological places in a grid map of the environment that is created from sensor measurements. The ability of the RD-based computation to integrate external information, like a grid map representing the environment in the model computational grid, permits a direct integration of sensor data into the model dynamics. The experimental results indicate that this method exhibits significantly less sensitivity to noisy data than the standard algorithms for determining VD in a grid. In addition, previous drawbacks of the computational algorithms based on RD models, like the generation of volatile solutions by means of excitable waves, are now overcome by final stable states. PMID:26035349

  14. Modelling Population Dynamics in Realistic Landscapes with Linear Elements: A Mechanistic-Statistical Reaction-Diffusion Approach.

    PubMed

    Roques, Lionel; Bonnefon, Olivier

    2016-01-01

    We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid "2D/1D model", i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature. PMID:26986201

  15. Modelling Population Dynamics in Realistic Landscapes with Linear Elements: A Mechanistic-Statistical Reaction-Diffusion Approach

    PubMed Central

    2016-01-01

    We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid “2D/1D model”, i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature. PMID:26986201

  16. Reaction-diffusion waves in neuronal tissue and the window of cortical excitability

    NASA Astrophysics Data System (ADS)

    Dahlem, M. A.; Müller, S. C.

    2004-07-01

    Spreading depression (SD) is a dynamic wave phenomenon occurring in all gray matter regions of the central nervous systems (CNS). It is characterized by a sudden breakdown of neuronal activity and accompanied by a massive influx and efflux of ions across the membrane of neurons. The retina is a constituent of the CNS in which one can easily observe the dynamic behavior of the SD wave fronts, because SD changes the optical properties of the tissue. There is ample evidence that SD belongs to the self-organization processes due to the coupling of reaction with diffusion in excitable medium. It is assumed that the occurrence of SD is associated with some neurological symptoms of migraine with aura. A frequently reported aura symptom is a traveling visual blind region (scotoma) with a preceding figure of scintillating line segments. The characteristic form and development of the scotoma suggests that the underlying phenomenon is a wave propagating through the primary visual cortex, most likely the cortical spreading depression. In this article we discuss similarities between SD waves and the migraine aura on the basis of properties of reaction-diffusion waves known from other excitable media. In particular, the propagation velocities, the shape and the dynamics of the waves are compared with each other. We find that the assumption of the neuronal tissue to be in a state of only weak excitability explains some properties of the migraine aura, such as the confined appearance and its propagation with a stable velocity.

  17. Discrete-continuous reaction-diffusion model with mobile point-like sources and sinks.

    PubMed

    Kondrat, Svyatoslav; Zimmermann, Olav; Wiechert, Wolfgang; von Lieres, Eric

    2016-01-01

    In many applications in soft and biological physics, there are multiple time and length scales involved but often with a distinct separation between them. For instance, in enzyme kinetics, enzymes are relatively large, move slowly and their copy numbers are typically small, while the metabolites (being transformed by these enzymes) are often present in abundance, are small in size and diffuse fast. It seems thus natural to apply different techniques to different time and length levels and couple them. Here we explore this possibility by constructing a stochastic-deterministic discrete-continuous reaction-diffusion model with mobile sources and sinks. Such an approach allows in particular to separate different sources of stochasticity. We demonstrate its application by modelling enzyme-catalysed reactions with freely diffusing enzymes and a heterogeneous source of metabolites. Our calculations suggest that using a higher amount of less active enzymes, as compared to fewer more active enzymes, reduces the metabolite pool size and correspondingly the lag time, giving rise to a faster response to external stimuli. The methodology presented can be extended to more complex systems and offers exciting possibilities for studying problems where spatial heterogeneities, stochasticity or discreteness play a role. PMID:26830760

  18. Bifurcation analysis of brown tide by reaction-diffusion equation using finite element method

    SciTech Connect

    Kawahara, Mutsuto; Ding, Yan

    1997-03-01

    In this paper, we analyze the bifurcation of a biodynamics system in a two-dimensional domain by virtue of reaction-diffusion equations. The discretization method in space is the finite element method. The computational algorithm for an eigenspectrum is described in detail. On the basis of an analysis of eigenspectra according to Helmholtz`s equation, the discrete spectra in regards to the physical variables are numerically obtained in two-dimensional space. In order to investigate this mathematical model in regards to its practical use, we analyzed the stability of two cases, i.e., hydranth regeneration in the marine hydroid Tubularia and a brown tide in a harbor in Japan. By evaluating the stability according to the linearized stability definition, the critical parameters for outbreaks of brown tide can be theoretically determined. In addition, results for the linear combination of eigenspectrum coincide with the distribution of the observed brown tide. Its periodic characteristic was also verified. 10 refs., 8 figs., 5 tabs.

  19. Local error estimates for adaptive simulation of the reaction-diffusion master equation via operator splitting

    NASA Astrophysics Data System (ADS)

    Hellander, Andreas; Lawson, Michael J.; Drawert, Brian; Petzold, Linda

    2014-06-01

    The efficiency of exact simulation methods for the reaction-diffusion master equation (RDME) is severely limited by the large number of diffusion events if the mesh is fine or if diffusion constants are large. Furthermore, inherent properties of exact kinetic-Monte Carlo simulation methods limit the efficiency of parallel implementations. Several approximate and hybrid methods have appeared that enable more efficient simulation of the RDME. A common feature to most of them is that they rely on splitting the system into its reaction and diffusion parts and updating them sequentially over a discrete timestep. This use of operator splitting enables more efficient simulation but it comes at the price of a temporal discretization error that depends on the size of the timestep. So far, existing methods have not attempted to estimate or control this error in a systematic manner. This makes the solvers hard to use for practitioners since they must guess an appropriate timestep. It also makes the solvers potentially less efficient than if the timesteps were adapted to control the error. Here, we derive estimates of the local error and propose a strategy to adaptively select the timestep when the RDME is simulated via a first order operator splitting. While the strategy is general and applicable to a wide range of approximate and hybrid methods, we exemplify it here by extending a previously published approximate method, the diffusive finite-state projection (DFSP) method, to incorporate temporal adaptivity.

  20. Dynamical Behavior of Delayed Reaction-Diffusion Hopfield Neural Networks Driven by Infinite Dimensional Wiener Processes.

    PubMed

    Liang, Xiao; Wang, Linshan; Wang, Yangfan; Wang, Ruili

    2016-09-01

    In this paper, we focus on the long time behavior of the mild solution to delayed reaction-diffusion Hopfield neural networks (DRDHNNs) driven by infinite dimensional Wiener processes. We analyze the existence, uniqueness, and stability of this system under the local Lipschitz function by constructing an appropriate Lyapunov-Krasovskii function and utilizing the semigroup theory. Some easy-to-test criteria affecting the well-posedness and stability of the networks, such as infinite dimensional noise and diffusion effect, are obtained. The criteria can be used as theoretic guidance to stabilize DRDHNNs in practical applications when infinite dimensional noise is taken into consideration. Meanwhile, considering the fact that the standard Brownian motion is a special case of infinite dimensional Wiener process, we undertake an analysis of the local Lipschitz condition, which has a wider range than the global Lipschitz condition. Two samples are given to examine the availability of the results in this paper. Simulations are also given using the MATLAB. PMID:26259224

  1. A Turing Reaction-Diffusion Model for Human Cortical Folding Patterns and Cortical Pattern Malformations

    NASA Astrophysics Data System (ADS)

    Hurdal, Monica K.; Striegel, Deborah A.

    2011-11-01

    Modeling and understanding cortical folding pattern formation is important for quantifying cortical development. We present a biomathematical model for cortical folding pattern formation in the human brain and apply this model to study diseases involving cortical pattern malformations associated with neural migration disorders. Polymicrogyria is a cortical malformation disease resulting in an excessive number of small gyri. Our mathematical model uses a Turing reaction-diffusion system to model cortical folding. The lateral ventricle (LV) and ventricular zone (VZ) of the brain are critical components in the formation of cortical patterning. In early cortical development the shape of the LV can be modeled with a prolate spheroid and the VZ with a prolate spheroid surface. We use our model to study how global cortex characteristics, such as size and shape of the LV, affect cortical pattern formation. We demonstrate increasing domain scale can increase the number of gyri and sulci formed. Changes in LV shape can account for sulcus directionality. By incorporating LV size and shape, our model is able to elucidate which parameters can lead to excessive cortical folding.

  2. Dissipation and displacement of hotspots in reaction-diffusion models of crime.

    PubMed

    Short, Martin B; Brantingham, P Jeffrey; Bertozzi, Andrea L; Tita, George E

    2010-03-01

    The mechanisms driving the nucleation, spread, and dissipation of crime hotspots are poorly understood. As a consequence, the ability of law enforcement agencies to use mapped crime patterns to design crime prevention strategies is severely hampered. We also lack robust expectations about how different policing interventions should impact crime. Here we present a mathematical framework based on reaction-diffusion partial differential equations for studying the dynamics of crime hotspots. The system of equations is based on empirical evidence for how offenders move and mix with potential victims or targets. Analysis shows that crime hotspots form when the enhanced risk of repeat crimes diffuses locally, but not so far as to bind distant crime together. Crime hotspots may form as either supercritical or subcritical bifurcations, the latter the result of large spikes in crime that override linearly stable, uniform crime distributions. Our mathematical methods show that subcritical crime hotspots may be permanently eradicated with police suppression, whereas supercritical hotspots are displaced following a characteristic spatial pattern. Our results thus provide a mechanistic explanation for recent failures to observe crime displacement in experimental field tests of hotspot policing. PMID:20176972

  3. Synchronization criteria for generalized reaction-diffusion neural networks via periodically intermittent control

    NASA Astrophysics Data System (ADS)

    Gan, Qintao; Lv, Tianshi; Fu, Zhenhua

    2016-04-01

    In this paper, the synchronization problem for a class of generalized neural networks with time-varying delays and reaction-diffusion terms is investigated concerning Neumann boundary conditions in terms of p-norm. The proposed generalized neural networks model includes reaction-diffusion local field neural networks and reaction-diffusion static neural networks as its special cases. By establishing a new inequality, some simple and useful conditions are obtained analytically to guarantee the global exponential synchronization of the addressed neural networks under the periodically intermittent control. According to the theoretical results, the influences of diffusion coefficients, diffusion space, and control rate on synchronization are analyzed. Finally, the feasibility and effectiveness of the proposed methods are shown by simulation examples, and by choosing different diffusion coefficients, diffusion spaces, and control rates, different controlled synchronization states can be obtained.

  4. Synchronization criteria for generalized reaction-diffusion neural networks via periodically intermittent control.

    PubMed

    Gan, Qintao; Lv, Tianshi; Fu, Zhenhua

    2016-04-01

    In this paper, the synchronization problem for a class of generalized neural networks with time-varying delays and reaction-diffusion terms is investigated concerning Neumann boundary conditions in terms of p-norm. The proposed generalized neural networks model includes reaction-diffusion local field neural networks and reaction-diffusion static neural networks as its special cases. By establishing a new inequality, some simple and useful conditions are obtained analytically to guarantee the global exponential synchronization of the addressed neural networks under the periodically intermittent control. According to the theoretical results, the influences of diffusion coefficients, diffusion space, and control rate on synchronization are analyzed. Finally, the feasibility and effectiveness of the proposed methods are shown by simulation examples, and by choosing different diffusion coefficients, diffusion spaces, and control rates, different controlled synchronization states can be obtained. PMID:27131492

  5. Isometric graphing and multidimensional scaling for reaction-diffusion modeling on regular and fractal surfaces with spatiotemporal pattern recognition

    NASA Astrophysics Data System (ADS)

    Kuriakose, Jainy; Ghosh, Anandamohan; Ravi Kumar, V.; Kulkarni, B. D.

    2004-03-01

    Heterogeneous surface reactions exhibiting complex spatiotemporal dynamics and patterns can be studied as processes involving reaction-diffusion mechanisms. In many realistic situations, the surface has fractal characteristics. This situation is studied by isometric graphing and multidimensional scaling (IGMDS) of fractal surfaces for extracting geodesic distances (i.e., shortest scaled distances that obtain edges of neighboring surface nodes and their interconnections) and the results obtained used to model effects of surface diffusion with nonlinear reactions. Further analysis of evolved spatiotemporal patterns may be carried out by IGMDS because high-dimensional snapshot data can be efficiently projected to a transformed subspace with reduced dimensions. Validation of the IGMDS methodology is carried out by comparing results with reduction capabilities of conventional principal component analysis for simple situations of reaction and diffusion on surfaces. The usefulness of the IGMDS methodology is shown for analysis of complex patterns formed on both regular and fractal surfaces, and using generic nonlinear reaction-diffusion systems following FitzHugh Nagumo and cubic reaction kinetics. The studies of these systems with nonlinear kinetics and noise show that effects of surface disorder due to fractality can become very relevant. The relevance is shown by studying properties of dynamical invariants in IGMDS component space, viz., the Lyapunov exponents and the KS entropy for interesting situations of spiral formation and turbulent patterns.

  6. Reaction-diffusion processes on interconnected scale-free networks

    NASA Astrophysics Data System (ADS)

    Garas, Antonios

    2015-08-01

    We study the two-particle annihilation reaction A +B →∅ on interconnected scale-free networks, using different interconnecting strategies. We explore how the mixing of particles and the process evolution are influenced by the number of interconnecting links, by their functional properties, and by the interconnectivity strategies in use. We show that the reaction rates on this system are faster than what was observed in other topologies, due to the better particle mixing that suppresses the segregation effect, in line with previous studies performed on single scale-free networks.

  7. Flexible single molecule simulation of reaction-diffusion processes

    SciTech Connect

    Hellander, Stefan; Loetstedt, Per

    2011-05-10

    An algorithm is developed for simulation of the motion and reactions of single molecules at a microscopic level. The molecules diffuse in a solvent and react with each other or a polymer and molecules can dissociate. Such simulations are of interest e.g. in molecular biology. The algorithm is similar to the Green's function reaction dynamics (GFRD) algorithm by van Zon and ten Wolde where longer time steps can be taken by computing the probability density functions (PDFs) and then sample from the distribution functions. Our computation of the PDFs is much less complicated than GFRD and more flexible. The solution of the partial differential equation for the PDF is split into two steps to simplify the calculations. The sampling is without splitting error in two of the coordinate directions for a pair of molecules and a molecule-polymer interaction and is approximate in the third direction. The PDF is obtained either from an analytical solution or a numerical discretization. The errors due to the operator splitting, the partitioning of the system, and the numerical approximations are analyzed. The method is applied to three different systems involving up to four reactions. Comparisons with other mesoscopic and macroscopic models show excellent agreement.

  8. A new Sumudu transform iterative method for time-fractional Cauchy reaction-diffusion equation.

    PubMed

    Wang, Kangle; Liu, Sanyang

    2016-01-01

    In this paper, a new Sumudu transform iterative method is established and successfully applied to find the approximate analytical solutions for time-fractional Cauchy reaction-diffusion equations. The approach is easy to implement and understand. The numerical results show that the proposed method is very simple and efficient. PMID:27386314

  9. Nonplanar traveling fronts in reaction-diffusion equations with combustion and degenerate Fisher-KPP nonlinearities

    NASA Astrophysics Data System (ADS)

    Wang, Zhi-Cheng; Bu, Zhen-Hui

    2016-04-01

    This paper is concerned with nonplanar traveling fronts in reaction-diffusion equations with combustion nonlinearity and degenerate Fisher-KPP nonlinearity. Our study contains two parts: in the first part we establish the existence of traveling fronts of pyramidal shape in R3, and in the second part we establish the existence and stability of V-shaped traveling fronts in R2.

  10. Stability and bifurcations in a nonlocal delayed reaction-diffusion population model

    NASA Astrophysics Data System (ADS)

    Chen, Shanshan; Yu, Jianshe

    2016-01-01

    A nonlocal delayed reaction-diffusion equation with Dirichlet boundary condition is considered in this paper. It is shown that a positive spatially nonhomogeneous equilibrium bifurcates from the trivial equilibrium. The stability/instability of the bifurcated positive equilibrium and associated Hopf bifurcation are investigated, providing us with a complete picture of the dynamics.

  11. Stability and bifurcation in a reaction-diffusion model with nonlocal delay effect

    NASA Astrophysics Data System (ADS)

    Guo, Shangjiang

    2015-08-01

    In this paper, the existence, stability, and multiplicity of spatially nonhomogeneous steady-state solution and periodic solutions for a reaction-diffusion model with nonlocal delay effect and Dirichlet boundary condition are investigated by using Lyapunov-Schmidt reduction. Moreover, we illustrate our general results by applications to models with a single delay and one-dimensional spatial domain.

  12. Wavelet-Based Spatial Scaling of Coupled Reaction-Diffusion Fields

    SciTech Connect

    Mishra, Sudib; Muralidharan, Krishna; Deymier, Pierre; Frantziskonis, G.; Pannala, Sreekanth; Simunovic, Srdjan

    2008-01-01

    Multiscale schemes for transferring information from fine to coarse scales are typically based on homogenization techniques. Such schemes smooth the fine scale features of the underlying fields, often resulting in the inability to accurately retain the fine scale correlations. In addition, higher-order statistical moments (beyond mean) of the relevant field variables are not necessarily preserved. As a superior alternative to averaging homogenization methods, a wavelet-based scheme for the exchange of information between a reactive and diffusive field in the context of multiscale reaction-diffusion problems is proposed and analyzed. The scheme is shown to be efficient in passing information along scales, from fine to coarse, i.e., upscaling as well as from coarse to fine, i.e., downscaling. It incorporates fine scale statistics (higher-order moments beyond mean), mainly due to the capability of wavelets to represent fields hierarchically. Critical to the success of the scheme is the identification of dominant scales containing the majority of the useful information. The dominant scales in effect specify the coarsest resolution possible. The scheme is applied in detail to the analysis of a diffusive system with a chemically reacting boundary. Reactions are simulated using kinetic Monte Carlo (kMC) and diffusion is solved by finite differences (FDs). Spatial scale differences are present at the interface of the kMC sites and the diffusion grid. The computational efficiency of the scheme is compared to results obtained by averaging homogenization, and to results from a benchmark scheme that ensures spatial scale parity between kMC and FD.

  13. Reaction-diffusion-advection approach to spatially localized treadmilling aggregates of molecular motors

    NASA Astrophysics Data System (ADS)

    Yochelis, Arik; Bar-On, Tomer; Gov, Nir S.

    2016-04-01

    Unconventional myosins belong to a class of molecular motors that walk processively inside cellular protrusions towards the tips, on top of actin filament. Surprisingly, in addition, they also form retrograde moving self-organized aggregates. The qualitative properties of these aggregates are recapitulated by a mass conserving reaction-diffusion-advection model and admit two distinct families of modes: traveling waves and pulse trains. Unlike the traveling waves that are generated by a linear instability, pulses are nonlinear structures that propagate on top of linearly stable uniform backgrounds. Asymptotic analysis of isolated pulses via a simplified reaction-diffusion-advection variant on large periodic domains, allows to draw qualitative trends for pulse properties, such as the amplitude, width, and propagation speed. The results agree well with numerical integrations and are related to available empirical observations.

  14. Fokas method for a multi-domain linear reaction-diffusion equation with discontinuous diffusivity

    NASA Astrophysics Data System (ADS)

    Asvestas, M.; Sifalakis, A. G.; Papadopoulou, E. P.; Saridakis, Y. G.

    2014-03-01

    Motivated by proliferation-diffusion mathematical models for studying highly diffusive brain tumors, that also take into account the heterogeneity of the brain tissue, in the present work we consider a multi-domain linear reaction-diffusion equation with a discontinuous diffusion coefficient. For the solution of the problem at hand we implement Fokas transform method by directly following, and extending in this way, our recent work for a white-gray-white matter brain model pertaining to high grade gliomas. Fokas's novel approach for the solution of linear PDE problems, yields novel integral representations of the solution in the complex plane that, for appropriately chosen integration contours, decay exponentially fast and converge uniformly at the boundaries. Combining these method-inherent advantages with simple numerical quadrature rules, we produce an efficient method, with fast decaying error properties, for the solution of the discontinuous reaction-diffusion problem.

  15. Long-term behavior of reaction-diffusion equations with nonlocal boundary conditions on rough domains

    NASA Astrophysics Data System (ADS)

    Gal, Ciprian G.; Warma, Mahamadi

    2016-08-01

    We investigate the long term behavior in terms of finite dimensional global and exponential attractors, as time goes to infinity, of solutions to a semilinear reaction-diffusion equation on non-smooth domains subject to nonlocal Robin boundary conditions, characterized by the presence of fractional diffusion on the boundary. Our results are of general character and apply to a large class of irregular domains, including domains whose boundary is Hölder continuous and domains which have fractal-like geometry. In addition to recovering most of the existing results on existence, regularity, uniqueness, stability, attractor existence, and dimension, for the well-known reaction-diffusion equation in smooth domains, the framework we develop also makes possible a number of new results for all diffusion models in other non-smooth settings.

  16. Delay-induced Turing-like waves for one-species reaction-diffusion model on a network

    NASA Astrophysics Data System (ADS)

    Petit, Julien; Carletti, Timoteo; Asllani, Malbor; Fanelli, Duccio

    2015-09-01

    A one-species time-delay reaction-diffusion system defined on a complex network is studied. Traveling waves are predicted to occur following a symmetry-breaking instability of a homogeneous stationary stable solution, subject to an external nonhomogeneous perturbation. These are generalized Turing-like waves that materialize in a single-species populations dynamics model, as the unexpected byproduct of the imposed delay in the diffusion part. Sufficient conditions for the onset of the instability are mathematically provided by performing a linear stability analysis adapted to time-delayed differential equations. The method here developed exploits the properties of the Lambert W-function. The prediction of the theory are confirmed by direct numerical simulation carried out for a modified version of the classical Fisher model, defined on a Watts-Strogatz network and with the inclusion of the delay.

  17. Notch-mediated lateral inhibition regulates proneural wave propagation when combined with EGF-mediated reaction diffusion.

    PubMed

    Sato, Makoto; Yasugi, Tetsuo; Minami, Yoshiaki; Miura, Takashi; Nagayama, Masaharu

    2016-08-30

    Notch-mediated lateral inhibition regulates binary cell fate choice, resulting in salt and pepper patterns during various developmental processes. However, how Notch signaling behaves in combination with other signaling systems remains elusive. The wave of differentiation in the Drosophila visual center or "proneural wave" accompanies Notch activity that is propagated without the formation of a salt and pepper pattern, implying that Notch does not form a feedback loop of lateral inhibition during this process. However, mathematical modeling and genetic analysis clearly showed that Notch-mediated lateral inhibition is implemented within the proneural wave. Because partial reduction in EGF signaling causes the formation of the salt and pepper pattern, it is most likely that EGF diffusion cancels salt and pepper pattern formation in silico and in vivo. Moreover, the combination of Notch-mediated lateral inhibition and EGF-mediated reaction diffusion enables a function of Notch signaling that regulates propagation of the wave of differentiation. PMID:27535937

  18. Internal layers in the one-dimensional reaction-diffusion equation with a discontinuous reactive term

    NASA Astrophysics Data System (ADS)

    Nefedov, N. N.; Ni, Minkang

    2015-12-01

    A singularly perturbed boundary value problem for a second-order ordinary differential equation known in applications as a stationary reaction-diffusion equation is studied. A new class of problems is considered, namely, problems with nonlinearity having discontinuities localized in some domains, which leads to the formation of sharp transition layers in these domains. The existence of solutions with an internal transition layer is proved, and their asymptotic expansion is constructed.

  19. Contribution to an effective design method for stationary reaction-diffusion patterns.

    PubMed

    Szalai, István; Horváth, Judit; De Kepper, Patrick

    2015-06-01

    The British mathematician Alan Turing predicted, in his seminal 1952 publication, that stationary reaction-diffusion patterns could spontaneously develop in reacting chemical or biochemical solutions. The first two clear experimental demonstrations of such a phenomenon were not made before the early 1990s when the design of new chemical oscillatory reactions and appropriate open spatial chemical reactors had been invented. Yet, the number of pattern producing reactions had not grown until 2009 when we developed an operational design method, which takes into account the feeding conditions and other specificities of real open spatial reactors. Since then, on the basis of this method, five additional reactions were shown to produce stationary reaction-diffusion patterns. To gain a clearer view on where our methodical approach on the patterning capacity of a reaction stands, numerical studies in conditions that mimic true open spatial reactors were made. In these numerical experiments, we explored the patterning capacity of Rabai's model for pH driven Landolt type reactions as a function of experimentally attainable parameters that control the main time and length scales. Because of the straightforward reversible binding of protons to carboxylate carrying polymer chains, this class of reaction is at the base of the chemistry leading to most of the stationary reaction-diffusion patterns presently observed. We compare our model predictions with experimental observations and comment on agreements and differences. PMID:26117122

  20. Contribution to an effective design method for stationary reaction-diffusion patterns

    NASA Astrophysics Data System (ADS)

    Szalai, István; Horváth, Judit; De Kepper, Patrick

    2015-06-01

    The British mathematician Alan Turing predicted, in his seminal 1952 publication, that stationary reaction-diffusion patterns could spontaneously develop in reacting chemical or biochemical solutions. The first two clear experimental demonstrations of such a phenomenon were not made before the early 1990s when the design of new chemical oscillatory reactions and appropriate open spatial chemical reactors had been invented. Yet, the number of pattern producing reactions had not grown until 2009 when we developed an operational design method, which takes into account the feeding conditions and other specificities of real open spatial reactors. Since then, on the basis of this method, five additional reactions were shown to produce stationary reaction-diffusion patterns. To gain a clearer view on where our methodical approach on the patterning capacity of a reaction stands, numerical studies in conditions that mimic true open spatial reactors were made. In these numerical experiments, we explored the patterning capacity of Rabai's model for pH driven Landolt type reactions as a function of experimentally attainable parameters that control the main time and length scales. Because of the straightforward reversible binding of protons to carboxylate carrying polymer chains, this class of reaction is at the base of the chemistry leading to most of the stationary reaction-diffusion patterns presently observed. We compare our model predictions with experimental observations and comment on agreements and differences.

  1. Contribution to an effective design method for stationary reaction-diffusion patterns

    SciTech Connect

    Szalai, István; Horváth, Judit; De Kepper, Patrick

    2015-06-15

    The British mathematician Alan Turing predicted, in his seminal 1952 publication, that stationary reaction-diffusion patterns could spontaneously develop in reacting chemical or biochemical solutions. The first two clear experimental demonstrations of such a phenomenon were not made before the early 1990s when the design of new chemical oscillatory reactions and appropriate open spatial chemical reactors had been invented. Yet, the number of pattern producing reactions had not grown until 2009 when we developed an operational design method, which takes into account the feeding conditions and other specificities of real open spatial reactors. Since then, on the basis of this method, five additional reactions were shown to produce stationary reaction-diffusion patterns. To gain a clearer view on where our methodical approach on the patterning capacity of a reaction stands, numerical studies in conditions that mimic true open spatial reactors were made. In these numerical experiments, we explored the patterning capacity of Rabai's model for pH driven Landolt type reactions as a function of experimentally attainable parameters that control the main time and length scales. Because of the straightforward reversible binding of protons to carboxylate carrying polymer chains, this class of reaction is at the base of the chemistry leading to most of the stationary reaction-diffusion patterns presently observed. We compare our model predictions with experimental observations and comment on agreements and differences.

  2. A Luenberger observer for reaction-diffusion models with front position data

    NASA Astrophysics Data System (ADS)

    Collin, Annabelle; Chapelle, Dominique; Moireau, Philippe

    2015-11-01

    We propose a Luenberger observer for reaction-diffusion models with propagating front features, and for data associated with the location of the front over time. Such models are considered in various application fields, such as electrophysiology, wild-land fire propagation and tumor growth modeling. Drawing our inspiration from image processing methods, we start by proposing an observer for the eikonal-curvature equation that can be derived from the reaction-diffusion model by an asymptotic expansion. We then carry over this observer to the underlying reaction-diffusion equation by an "inverse asymptotic analysis", and we show that the associated correction in the dynamics has a stabilizing effect for the linearized estimation error. We also discuss the extension to joint state-parameter estimation by using the earlier-proposed ROUKF strategy. We then illustrate and assess our proposed observer method with test problems pertaining to electrophysiology modeling, including with a realistic model of cardiac atria. Our numerical trials show that state estimation is directly very effective with the proposed Luenberger observer, while specific strategies are needed to accurately perform parameter estimation - as is usual with Kalman filtering used in a nonlinear setting - and we demonstrate two such successful strategies.

  3. Characteristics of the probability function for three random-walk models of reaction-diffusion processes

    NASA Astrophysics Data System (ADS)

    Musho, Matthew K.; Kozak, John J.

    1984-10-01

    A method is presented for calculating exactly the relative width (σ2)1/2/, the skewness γ1, and the kurtosis γ2 characterizing the probability distribution function for three random-walk models of diffusion-controlled processes. For processes in which a diffusing coreactant A reacts irreversibly with a target molecule B situated at a reaction center, three models are considered. The first is the traditional one of an unbiased, nearest-neighbor random walk on a d-dimensional periodic/confining lattice with traps; the second involves the consideration of unbiased, non-nearest-neigh bor (i.e., variable-step length) walks on the same d-dimensional lattice; and, the third deals with the case of a biased, nearest-neighbor walk on a d-dimensional lattice (wherein a walker experiences a potential centered at the deep trap site of the lattice). Our method, which has been described in detail elsewhere [P.A. Politowicz and J. J. Kozak, Phys. Rev. B 28, 5549 (1983)] is based on the use of group theoretic arguments within the framework of the theory of finite Markov processes. The approach allows the separate effects of geometry (system size N, dimensionality d, and valency ν), of the governing potential and of the medium temperature to be assessed and their respective influence on (σ2)1/2/, γ1, and γ2 to be studied quantitatively. We determine the classes of potential functions and the regimes of temperature for which allowing variable-length jumps or admitting a bias in the site-to-site trajectory of the walker produces results which are significantly different (both quantitatively and qualitatively) from those calculated assuming only unbiased, nearest-neighbor random walks. Finally, we demonstrate that the approach provides a method for determining a continuous probability (density) distribution function consistent with the numerical data on (σ2)1/2/, γ1, and γ2 for the processes described above. In particular we show that the first of the above reaction-diffusion

  4. Threshold dynamics of a time periodic reaction-diffusion epidemic model with latent period

    NASA Astrophysics Data System (ADS)

    Zhang, Liang; Wang, Zhi-Cheng; Zhao, Xiao-Qiang

    2015-05-01

    In this paper, we first propose a time-periodic reaction-diffusion epidemic model which incorporates simple demographic structure and the latent period of infectious disease. Then we introduce the basic reproduction number R0 for this model and prove that the sign of R0 - 1 determines the local stability of the disease-free periodic solution. By using the comparison arguments and persistence theory, we further show that the disease-free periodic solution is globally attractive if R0 < 1, while there is an endemic periodic solution and the disease is uniformly persistent if R0 > 1.

  5. Reaction-diffusion analysis for one-step plasma etching and bonding of microfluidic devices

    SciTech Connect

    Rosso, Michel; Steijn, Volkert van; Smet, Louis C. P. M. de; Sudhoelter, Ernst J. R.; Kreutzer, Michiel T.; Kleijn, Chris R.

    2011-04-25

    A self-similar reaction front develops in reactive ion etching when the ions penetrate channels of shallow height h. This relates to the patterning of microchannels using a single-step etching and bonding, as described by Rhee et al. [Lab Chip 5, 102 (2005)]. Experimentally, we report that the front location scales as x{sub f{approx}}ht{sup 1/2} and the width is time-invariant and scales as {delta}{approx}h. Mean-field reaction-diffusion theory and Knudsen diffusion give a semiquantitative understanding of these observations and allow optimization of etching times in relation to bonding requirements.

  6. Hopf bifurcations in a reaction-diffusion population model with delay effect

    NASA Astrophysics Data System (ADS)

    Su, Ying; Wei, Junjie; Shi, Junping

    A reaction-diffusion population model with a general time-delayed growth rate per capita is considered. The growth rate per capita can be logistic or weak Allee effect type. From a careful analysis of the characteristic equation, the stability of the positive steady state solution and the existence of forward Hopf bifurcation from the positive steady state solution are obtained via the implicit function theorem, where the time delay is used as the bifurcation parameter. The general results are applied to a "food-limited" population model with diffusion and delay effects as well as a weak Allee effect population model.

  7. Conservation Laws of a Family of Reaction-Diffusion-Convection Equations

    NASA Astrophysics Data System (ADS)

    Bruzón, M. S.; Gandarias, M. L.; de la Rosa, R.

    Ibragimov introduced the concept of nonlinear self-adjoint equations. This definition generalizes the concept of self-adjoint and quasi-self-adjoint equations. Gandarias defined the concept of weak self-adjoint. In this paper, we found a class of nonlinear self-adjoint nonlinear reaction-diffusion-convection equations which are neither self-adjoint nor quasi-self-adjoint nor weak self-adjoint. From a general theorem on conservation laws proved by Ibragimov we obtain conservation laws for these equations.

  8. Reaction-Diffusion Processes on Random and Scale-Free Networks

    NASA Astrophysics Data System (ADS)

    Banerjee, Subhasis; Mallick, Shrestha Basu; Bose, Indrani

    We study the discrete Gierer-Meinhardt model of reaction-diffusion on three different types of networks: regular, random and scale-free. The model dynamics lead to the formation of stationary Turing patterns in the steady state in certain parameter regions. Some general features of the patterns are studied through numerical simulation. The results for the random and scale-free networks show a marked difference from those in the case of the regular network. The difference may be ascribed to the small world character of the first two types of networks.

  9. A reaction-diffusion SIS epidemic model in an almost periodic environment

    NASA Astrophysics Data System (ADS)

    Wang, Bin-Guo; Li, Wan-Tong; Wang, Zhi-Cheng

    2015-12-01

    A susceptible-infected-susceptible almost periodic reaction-diffusion epidemic model is studied by means of establishing the theories and properties of the basic reproduction ratio {R0}. Particularly, the asymptotic behaviors of {R0} with respect to the diffusion rate {DI} of the infected individuals are obtained. Furthermore, the uniform persistence, extinction and global attractivity are presented in terms of {R0}. Our results indicate that the interaction of spatial heterogeneity and temporal almost periodicity tends to enhance the persistence of the disease.

  10. Extension of Newman's method to electrochemical reaction-diffusion in a fuel cell catalyst layer

    NASA Astrophysics Data System (ADS)

    Duan, Tianping; Weidner, John W.; White, Ralph E.

    A numerical technique is developed for solving coupled electrochemical reaction-diffusion equations. Through analyzing the nonlinearity of the problem, a trial and error iterating procedure is constructed. The coefficient matrix is arranged as a tridiagonal form with elements of block matrix and is decomposed to LU form. A compact forward and backward substitution algorithm based on the shift of inversing block matrix by Gauss-Jordan full pivoting is developed. A large number of node points is required to converge the calculation. Computation experiences show that the iteration converges very quickly. The effects of inner diffusion on the electrochemical reaction are analyzed by numerical solutions.

  11. Analysis of discrete reaction-diffusion equations for autocatalysis and continuum diffusion equations for transport

    SciTech Connect

    Wang, Chi-Jen

    2013-01-01

    In this thesis, we analyze both the spatiotemporal behavior of: (A) non-linear “reaction” models utilizing (discrete) reaction-diffusion equations; and (B) spatial transport problems on surfaces and in nanopores utilizing the relevant (continuum) diffusion or Fokker-Planck equations. Thus, there are some common themes in these studies, as they all involve partial differential equations or their discrete analogues which incorporate a description of diffusion-type processes. However, there are also some qualitative differences, as shall be discussed below.

  12. Positional information and reaction-diffusion: two big ideas in developmental biology combine.

    PubMed

    Green, Jeremy B A; Sharpe, James

    2015-04-01

    One of the most fundamental questions in biology is that of biological pattern: how do the structures and shapes of organisms arise? Undoubtedly, the two most influential ideas in this area are those of Alan Turing's 'reaction-diffusion' and Lewis Wolpert's 'positional information'. Much has been written about these two concepts but some confusion still remains, in particular about the relationship between them. Here, we address this relationship and propose a scheme of three distinct ways in which these two ideas work together to shape biological form. PMID:25804733

  13. Self-assembly and plasticity of synaptic domains through a reaction-diffusion mechanism

    NASA Astrophysics Data System (ADS)

    Haselwandter, Christoph A.; Kardar, Mehran; Triller, Antoine; da Silveira, Rava Azeredo

    2015-09-01

    Signal transmission across chemical synapses relies crucially on neurotransmitter receptor molecules, concentrated in postsynaptic membrane domains along with scaffold and other postsynaptic molecules. The strength of the transmitted signal depends on the number of receptor molecules in postsynaptic domains, and activity-induced variation in the receptor number is one of the mechanisms of postsynaptic plasticity. Recent experiments have demonstrated that the reaction and diffusion properties of receptors and scaffolds at the membrane, alone, yield spontaneous formation of receptor-scaffold domains of the stable characteristic size observed in neurons. On the basis of these experiments we develop a model describing synaptic receptor domains in terms of the underlying reaction-diffusion processes. Our model predicts that the spontaneous formation of receptor-scaffold domains of the stable characteristic size observed in experiments depends on a few key reactions between receptors and scaffolds. Furthermore, our model suggests novel mechanisms for the alignment of pre- and postsynaptic domains and for short-term postsynaptic plasticity in receptor number. We predict that synaptic receptor domains localize in membrane regions with an increased receptor diffusion coefficient or a decreased scaffold diffusion coefficient. Similarly, we find that activity-dependent increases or decreases in receptor or scaffold diffusion yield a transient increase in the number of receptor molecules concentrated in postsynaptic domains. Thus, the proposed reaction-diffusion model puts forth a coherent set of biophysical mechanisms for the formation, stability, and plasticity of molecular domains on the postsynaptic membrane.

  14. Turing-Hopf bifurcation in the reaction-diffusion equations and its applications

    NASA Astrophysics Data System (ADS)

    Song, Yongli; Zhang, Tonghua; Peng, Yahong

    2016-04-01

    In this paper, we consider the Turing-Hopf bifurcation arising from the reaction-diffusion equations. It is a degenerate case and where the characteristic equation has a pair of simple purely imaginary roots and a simple zero root. First, the normal form theory for partial differential equations (PDEs) with delays developed by Faria is adopted to this degenerate case so that it can be easily applied to Turing-Hopf bifurcation. Then, we present a rigorous procedure for calculating the normal form associated with the Turing-Hopf bifurcation of PDEs. We show that the reduced dynamics associated with Turing-Hopf bifurcation is exactly the dynamics of codimension-two ordinary differential equations (ODE), which implies the ODE techniques can be employed to classify the reduced dynamics by the unfolding parameters. Finally, we apply our theoretical results to an autocatalysis model governed by reaction-diffusion equations; for such model, the dynamics in the neighbourhood of this bifurcation point can be divided into six categories, each of which is exactly demonstrated by the numerical simulations; and then according to this dynamical classification, a stable spatially inhomogeneous periodic solution has been found.

  15. 3D choroid neovascularization growth prediction based on reaction-diffusion model

    NASA Astrophysics Data System (ADS)

    Zhu, Shuxia; Chen, Xinjian; Shi, Fei; Xiang, Dehui; Zhu, Weifang; Chen, Haoyu

    2016-03-01

    Choroid neovascularization (CNV) is a kind of pathology from the choroid and CNV-related disease is one important cause of vision loss. It is desirable to predict the CNV growth rate so that appropriate treatment can be planned. In this paper, we seek to find a method to predict the growth of CNV based on 3D longitudinal Optical Coherence Tomography (OCT) images. A reaction-diffusion model is proposed for prediction. The method consists of four phases: pre-processing, meshing, CNV growth modeling and prediction. We not only apply the reaction-diffusion model to the disease region, but also take the surrounding tissues into consideration including outer retinal layer, inner retinal layer and choroid layer. The diffusion in these tissues is considered as isotropic. The finite-element-method (FEM) is used to solve the partial differential equations (PDE) in the diffusion model. The curve of CNV growth with treatment are fitted and then we can predict the CNV status in a future time point. The preliminary results demonstrated that our proposed method is accurate and the validity and feasibility of our model is obvious.

  16. Reaction-diffusion equation for quark-hadron transition in heavy-ion collisions

    NASA Astrophysics Data System (ADS)

    Bagchi, Partha; Das, Arpan; Sengupta, Srikumar; Srivastava, Ajit M.

    2015-09-01

    Reaction-diffusion equations with suitable boundary conditions have special propagating solutions which very closely resemble the moving interfaces in a first-order transition. We show that the dynamics of the chiral order parameter for the chiral symmetry breaking transition in heavy-ion collisions, with dissipative dynamics, is governed by one such equation; specifically, the Newell-Whitehead equation. Furthermore, required boundary conditions are automatically satisfied due to the geometry of the collision. The chiral transition is, therefore, completed by a propagating interface, exactly as for a first-order transition, even though the transition actually is a crossover for relativistic heavy-ion collisions. The same thing also happens when we consider the initial confinement-deconfinement transition with the Polyakov loop order parameter. The resulting equation, again with dissipative dynamics, can then be identified with the reaction-diffusion equation known as the FitzHugh-Nagumo equation which is used in population genetics. Observational constraints imply that the entire phase conversion cannot be achieved by such slow moving fronts, and some alternate faster dynamics needs also to be invoked; for example, involving fluctuations. We discuss the implications of these results for heavy-ion collisions. We also discuss possible extensions for the case of the early universe.

  17. Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations

    PubMed Central

    Hallock, Michael J.; Stone, John E.; Roberts, Elijah; Fry, Corey; Luthey-Schulten, Zaida

    2014-01-01

    Simulation of in vivo cellular processes with the reaction-diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time scales using the MPD-RDME method on a single GPU. Simulations of larger eukaryotic systems exceed the on-board memory capacity of individual GPUs, and long time simulations of modest-sized cells such as yeast are impractical on a single GPU. We present a new multi-GPU parallel implementation of the MPD-RDME method based on a spatial decomposition approach that supports dynamic load balancing for workstations containing GPUs of varying performance and memory capacity. We take advantage of high-performance features of CUDA for peer-to-peer GPU memory transfers and evaluate the performance of our algorithms on state-of-the-art GPU devices. We present parallel e ciency and performance results for simulations using multiple GPUs as system size, particle counts, and number of reactions grow. We also demonstrate multi-GPU performance in simulations of the Min protein system in E. coli. Moreover, our multi-GPU decomposition and load balancing approach can be generalized to other lattice-based problems. PMID:24882911

  18. Quantitative macroscopic treatment of the spatiotemporal properties of spin crossover solids based on a reaction diffusion equation

    NASA Astrophysics Data System (ADS)

    Paez-Espejo, Miguel; Sy, Mouhamadou; Varret, François; Boukheddaden, Kamel

    2014-01-01

    We propose here a new theoretical treatment of the spatiotemporal properties in spin-crosser solids, based on the expansion of the free energy taking into account the spatial fluctuations of the high-spin (HS) fraction. This leads to an equation of motion on the HS fraction following a reaction diffusion equation (RDE), in which most of the parameters can be derived from the experiments. This equation involves the true temporal and spatial scales at variance from the previous stochastic microscopic models, which were based on a homogeneous treatment of the crystal's properties. We have illustrated this new treatment for a two-dimensional rectangularly shaped system with a square symmetry and we could reproduce quantitatively the process of nucleation, growth, and propagation of the HS fraction inside the thermal hysteresis loop, accompanying a first-order transition. The computed spatiotemporal evolution of the system allowed one to follow the propagation of a well-defined macroscopic HS:LS interface, which was found in excellent quantitative agreement with the experimental observations of optical microscopy on the switchable spin crossover crystal [{Fe(NCSe)(py)2}2(m-bpypz)]. The RDE treatment should generate predictive models for novel spatiotemporal effects in spin crossover solids and more generally for all kinds of switchable molecular solids.

  19. A reaction-diffusion-based coding rate control mechanism for camera sensor networks.

    PubMed

    Yamamoto, Hiroshi; Hyodo, Katsuya; Wakamiya, Naoki; Murata, Masayuki

    2010-01-01

    A wireless camera sensor network is useful for surveillance and monitoring for its visibility and easy deployment. However, it suffers from the limited capacity of wireless communication and a network is easily overflown with a considerable amount of video traffic. In this paper, we propose an autonomous video coding rate control mechanism where each camera sensor node can autonomously determine its coding rate in accordance with the location and velocity of target objects. For this purpose, we adopted a biological model, i.e., reaction-diffusion model, inspired by the similarity of biological spatial patterns and the spatial distribution of video coding rate. Through simulation and practical experiments, we verify the effectiveness of our proposal. PMID:22163620

  20. Reaction-diffusion-like formalism for plastic neural networks reveals dissipative solitons at criticality

    NASA Astrophysics Data System (ADS)

    Grytskyy, Dmytro; Diesmann, Markus; Helias, Moritz

    2016-06-01

    Self-organized structures in networks with spike-timing dependent synaptic plasticity (STDP) are likely to play a central role for information processing in the brain. In the present study we derive a reaction-diffusion-like formalism for plastic feed-forward networks of nonlinear rate-based model neurons with a correlation sensitive learning rule inspired by and being qualitatively similar to STDP. After obtaining equations that describe the change of the spatial shape of the signal from layer to layer, we derive a criterion for the nonlinearity necessary to obtain stable dynamics for arbitrary input. We classify the possible scenarios of signal evolution and find that close to the transition to the unstable regime metastable solutions appear. The form of these dissipative solitons is determined analytically and the evolution and interaction of several such coexistent objects is investigated.

  1. The dilution wave in polymer crystallization is described by Fisher's reaction-diffusion equation

    NASA Astrophysics Data System (ADS)

    Higgs, Paul G.; Ungar, Goran

    2001-04-01

    Monodisperse long-chain alkanes such as C198H398 form lamellar crystals in both extended- and folded-chain forms. Folded-chain crystals are in a meta-stable equilibrium with polymer solution at a concentration CF. The crystal growth rate is virtually zero at this point, due to the self-poisoning phenomenon. If extended-chain crystallization is initiated from this state, a wave of crystallization proceeds through the solution, termed the dilution wave. The solution concentration falls as the wave passes, until a value CE is reached that is in equilibrium with the extended-chain crystal phase. We write down a reaction-diffusion equation to describe the dilution wave, and show that this is equivalent to Fisher's equation, which has previously been used to describe many other traveling wave phenomena. Numerical solutions of the equation are used to show examples of the wave shape.

  2. The Hirota Method for Reaction-Diffusion Equations with Three Distinct Roots

    SciTech Connect

    Tanoglu, Gamze; Pashaev, Oktay

    2004-10-04

    The Hirota Method, with modified background is applied to construct exact analytical solutions of nonlinear reaction-diffusion equations of two types. The first equation has only nonlinear reaction part, while the second one has in addition the nonlinear transport term. For both cases, the reaction part has the form of the third order polynomial with three distinct roots. We found analytic one-soliton solutions and the relationships between three simple roots and the wave speed of the soliton. For the first case, if one of the roots is the mean value of other two roots, the soliton is static. We show that the restriction on three distinct roots to obtain moving soliton is removed in the second case by, adding nonlinear transport term to the first equation.

  3. Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations.

    PubMed

    Hepburn, I; Chen, W; De Schutter, E

    2016-08-01

    Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification. PMID:27497550

  4. Accurate reaction-diffusion operator splitting on tetrahedral meshes for parallel stochastic molecular simulations

    NASA Astrophysics Data System (ADS)

    Hepburn, I.; Chen, W.; De Schutter, E.

    2016-08-01

    Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.

  5. A Reaction-Diffusion-Based Coding Rate Control Mechanism for Camera Sensor Networks

    PubMed Central

    Yamamoto, Hiroshi; Hyodo, Katsuya; Wakamiya, Naoki; Murata, Masayuki

    2010-01-01

    A wireless camera sensor network is useful for surveillance and monitoring for its visibility and easy deployment. However, it suffers from the limited capacity of wireless communication and a network is easily overflown with a considerable amount of video traffic. In this paper, we propose an autonomous video coding rate control mechanism where each camera sensor node can autonomously determine its coding rate in accordance with the location and velocity of target objects. For this purpose, we adopted a biological model, i.e., reaction-diffusion model, inspired by the similarity of biological spatial patterns and the spatial distribution of video coding rate. Through simulation and practical experiments, we verify the effectiveness of our proposal. PMID:22163620

  6. Extremal equilibria for reaction-diffusion equations in bounded domains and applications

    NASA Astrophysics Data System (ADS)

    Rodríguez-Bernal, Aníbal; Vidal-López, Alejandro

    We show the existence of two special equilibria, the extremal ones, for a wide class of reaction-diffusion equations in bounded domains with several boundary conditions, including non-linear ones. They give bounds for the asymptotic dynamics and so for the attractor. Some results on the existence and/or uniqueness of positive solutions are also obtained. As a consequence, several well-known results on the existence and/or uniqueness of solutions for elliptic equations are revisited in a unified way obtaining, in addition, information on the dynamics of the associated parabolic problem. Finally, we ilustrate the use of the general results by applying them to the case of logistic equations. In fact, we obtain a detailed picture of the positive dynamics depending on the parameters appearing in the equation.

  7. Using adaptive proper orthogonal decomposition to solve the reaction-diffusion equation

    SciTech Connect

    Singer, M A; Green, W H

    2007-12-03

    We introduce an adaptive POD method to reduce the computational cost of reacting flow simulations. The scheme is coupled with an operator-splitting algorithm to solve the reaction-diffusion equation. For the reaction sub-steps, locally valid basis vectors, obtained via POD and the method of snapshots, are used to project the minor species mass fractions onto a reduced dimensional space thereby decreasing the number of equations that govern combustion chemistry. The method is applied to a one-dimensional laminar premixed CH{sub 4}-air flame using GRImech 3.0; with errors less than 0:25%, a speed-up factor of 3:5 is observed. The speed-up results from fewer source term evaluations required to compute the Jacobian matrices.

  8. Modified Taylor-Couette Flow in Multiply-Waisted Hourglass Geometries Simulations based upon Reaction-Diffusion Models

    NASA Astrophysics Data System (ADS)

    Olsen, Thomas; Hou, Yu; Kowalski, Adam; Wiener, Richard

    2006-05-01

    The Reaction-Diffusion model predicted a period doubling cascade to chaos in a situation analagous Taylor- Couette flow with hourglass geometry. This cascade to chaos was discovered in the actual fluid flow experiments. We model Taylor-Couette flow in a cylindrical geometry with multiple waists of super-critical flow connected by regions of barely super-critical flow by corresponding Reaction-Diffusion models. We compare our results to the findings of an ongoing experimental program. H. Riecke and H.-G. Paap, Europhys. Lett. 14, 1235 (1991). Richard J. Wiener et al, Phys. Rev. E 55, 5489 (1997).

  9. Possibility of formation of a disoriented chiral condensate in p p collisions at energies available at the CERN Large Hadron Collider via the reaction-diffusion equation

    NASA Astrophysics Data System (ADS)

    Bagchi, Partha; Das, Arpan; Sengupta, Srikumar; Srivastava, Ajit M.

    2016-02-01

    There are indications of formation of a thermalized medium in high multiplicity p p collisions at energies available at the CERN Large Hadron Collider. It is possible that such a medium may reach high enough energy density and temperature that a transient stage of quark-gluon plasma, where chiral symmetry is restored, may be achieved. Due to rapid three-dimensional expansion, the system will quickly cool, undergoing a spontaneous chiral symmetry breaking transition. We study the dynamics of the chiral field, after the symmetry breaking transition, for such an event using a reaction-diffusion equation approach which we have recently applied for studying QCD transitions in relativistic heavy-ion collisions. We show that the interior of such a rapidly expanding system is likely to lead to the formation of a single large domain of disoriented chiral condensate (DCC), which has been a subject of intensive search in earlier experiments. We argue that large multiplicity p p collisions naturally give rise to required boundary conditions for the existence of slowly propagating front solutions of the reaction-diffusion equation with resulting dynamics of the chiral field leading to the formation of a large DCC domain.

  10. Instability mechanisms in a low-Mach-number reacting flow from coupled convection-reaction-diffusion equations

    NASA Astrophysics Data System (ADS)

    Pulikkottil, V. V.; Sujith, R. I.

    2015-07-01

    In this paper, instability mechanisms in a low Mach number reacting flow are investigated. Here, the emphasis is on the growth or decay of acoustic oscillations which arise from the acoustic-hydrodynamic interaction in a low Mach number reacting flow. Motivated by the studies in magnetohydrodynamics and atmospheric flows, we propose to investigate the acoustic-hydrodynamic coupling as a system of wave-mean flow interaction. For example, a comparison with the heat fluctuation modified hydrodynamics associated with magnetohydrodynamics is useful in understanding this coupling. The wavelike acoustic disturbance is introduced here as a compressibility correction to the mean flow. Accounting for the multiple scales introduced by the weak compressibility, we derive a set of equations governing wave-mean flow interaction in a reacting low Mach number flow. Sources such as volume expansion (which, in atmospheric flows arises due to the density variation with altitude) occur in reacting flows due to the heat release rate. This heat release rate, when coupled with the acoustic field, often leads to self-sustained thermo-acoustic oscillations. In the study of such oscillations, we discover a relation between the acoustic pressure and second order thermal fluctuations. Further, using this relation, we discover the nonlinear coupling mechanism that would lead to self-sustained oscillations in a reacting low Mach number flow. This mechanism, represented by a coupled convection reaction diffusion system, is presented here for the first time. In addition to the acoustic pressure and temperature fields, we also discover the role of acoustic velocity field in the acoustic-hydrodynamic interaction through a convective and lift-up mechanism.

  11. Computation and visualization of spreading depression based on reaction-diffusion equation with recovery

    NASA Astrophysics Data System (ADS)

    Ding, Hongxia; Chen, Shangbin; Zeng, Shuai; Zeng, Shaoqun; Liu, Qian; Luo, Qingming

    2008-12-01

    Spreading depression (SD) shows as propagating suppression of electrical activity, which relates with migraine and focal cerebral ischaemia. The putative mechanism of SD is the reaction-diffusion hypothesis involving potassium ions. In part inspired by optical imaging of two SD waves collision, we aimed to show the merged and large wavefront but not annihilation during collision by experimental and computational study. This paper modified Reggia et al established bistable equation with recovery to compute and visualize SD. Firstly, the media tissue of SD was assumed as one-dimensional continuum. The Crank-Nicholson method was used to solve the modified equations with recovery term. Then, the computation results were extended to two-dimensional space by symmetry. One individual SD was visualized as a concentric wave initiating from the stimulation point. The mergence but not annihilation of two colliding waves of SD was demonstrated. In addition, the dynamics of SD depending on the parameters was studied and presented. The results allied SD with the emerging concepts of volume transmission. This work not only supplied a paradigm to compute and visualize SD but also became a tool to explore the mechanisms of SD.

  12. Competing computational approaches to reaction-diffusion equations in clusters of cells

    NASA Astrophysics Data System (ADS)

    Stella, Sabrina; Chignola, Roberto; Milotti, Edoardo

    2014-03-01

    We have developed a numerical model that simulates the growth of small avascular solid tumors. At its core lies a set of partial differential equations that describe diffusion processes as well as transport and reaction mechanisms of a selected number of nutrients. Although the model relies on a restricted subset of molecular pathways, it compares well with experiments, and its emergent properties have recently led us to uncover a metabolic scaling law that stresses the common mechanisms that drive tumor growth. Now we plan to expand the biochemical model at the basis of the simulator to extend its reach. However, the introduction of additional molecular pathways requires an extensive revision of the reaction-diffusion part of the C++ code to make it more modular and to boost performance. To this end, we developed a novel computational abstract model where the individual molecular species represent the basic computational building blocks. Using a simple two-dimensional toy model to benchmark the new code, we find that the new implementation produces a more modular code without affecting performance. Preliminary results also show that a factor 2 speedup can be achieved with OpenMP multithreading, and other very preliminary results indicate that at least an order-of-magnitude speedup can be obtained using an NVidia Fermi GPU with CUDA code.

  13. Lie symmetry properties of nonlinear reaction-diffusion equations with gradient-dependent diffusivity

    NASA Astrophysics Data System (ADS)

    Cherniha, Roman; King, John R.; Kovalenko, Sergii

    2016-07-01

    Complete descriptions of the Lie symmetries of a class of nonlinear reaction-diffusion equations with gradient-dependent diffusivity in one and two space dimensions are obtained. A surprisingly rich set of Lie symmetry algebras depending on the form of diffusivity and source (sink) in the equations is derived. It is established that there exists a subclass in 1-D space admitting an infinite-dimensional Lie algebra of invariance so that it is linearisable. A special power-law diffusivity with a fixed exponent, which leads to wider Lie invariance of the equations in question in 2-D space, is also derived. However, it is shown that the diffusion equation without a source term (which often arises in applications and is sometimes called the Perona-Malik equation) possesses no rich variety of Lie symmetries depending on the form of gradient-dependent diffusivity. The results of the Lie symmetry classification for the reduction to lower dimensionality, and a search for exact solutions of the nonlinear 2-D equation with power-law diffusivity, also are included.

  14. A nonlocal and periodic reaction-diffusion-advection model of a single phytoplankton species.

    PubMed

    Peng, Rui; Zhao, Xiao-Qiang

    2016-02-01

    In this article, we are concerned with a nonlocal reaction-diffusion-advection model which describes the evolution of a single phytoplankton species in a eutrophic vertical water column where the species relies solely on light for its metabolism. The new feature of our modeling equation lies in that the incident light intensity and the death rate are assumed to be time periodic with a common period. We first establish a threshold type result on the global dynamics of this model in terms of the basic reproduction number R0. Then we derive various characterizations of R0 with respect to the vertical turbulent diffusion rate, the sinking or buoyant rate and the water column depth, respectively, which in turn give rather precise conditions to determine whether the phytoplankton persist or become extinct. Our theoretical results not only extend the existing ones for the time-independent case, but also reveal new interesting effects of the modeling parameters and the time-periodic heterogeneous environment on persistence and extinction of the phytoplankton species, and thereby suggest important implications for phytoplankton growth control. PMID:26063527

  15. Local traps as nanoscale reaction-diffusion probes: B clustering in c-Si

    SciTech Connect

    Pawlak, B. J.; Cowern, N. E. B.; Ahn, C.; Vandervorst, W.; Gwilliam, R.; Berkum, J. G. M. van

    2014-12-01

    A series of B implantation experiments into initially amorphized and not fully recrystallized Si, i.e., into an existing a/c-Si bi-layer material, have been conducted. We varied B dose, energy, and temperature during implantation process itself. Significant B migration has been observed within c-Si part near the a/c-interface and near the end-of-range region before any activation annealing. We propose a general concept of local trapping sites as experimental probes of nanoscale reaction-diffusion processes. Here, the a/c-Si interface acts as a trap, and the process itself is explored as the migration and clustering of mobile BI point defects in nearby c-Si during implantation at temperatures from 77 to 573 K. We find that at room temperature—even at B concentrations as high as 1.6 atomic %, the key B-B pairing step requires diffusion lengths of several nm owing to a small, ∼0.1 eV, pairing energy barrier. Thus, in nanostructures doped by ion implantation, the implant distribution can be strongly influenced by thermal migration to nearby impurities, defects, and interfaces.

  16. A reaction-diffusion model of the Darien Gap Sterile Insect Release Method

    NASA Astrophysics Data System (ADS)

    Alford, John G.

    2015-05-01

    The Sterile Insect Release Method (SIRM) is used as a biological control for invasive insect species. SIRM involves introducing large quantities of sterilized male insects into a wild population of invading insects. A fertile/sterile mating produces offspring that are not viable and the wild insect population will eventually be eradicated. A U.S. government program maintains a permanent sterile fly barrier zone in the Darien Gap between Panama and Columbia to control the screwworm fly (Cochliomyia Hominivorax), an insect that feeds off of living tissue in mammals and has devastating effects on livestock. This barrier zone is maintained by regular releases of massive quantities of sterilized male screwworm flies from aircraft. We analyze a reaction-diffusion model of the Darien Gap barrier zone. Simulations of the model equations yield two types of spatially inhomogeneous steady-state solutions representing a sterile fly barrier that does not prevent invasion and a barrier that does prevent invasion. We investigate steady-state solutions using both phase plane methods and monotone iteration methods and describe how barrier width and the sterile fly release rate affects steady-state behavior.

  17. Revisited reaction-diffusion model of thermal desorption spectroscopy experiments on hydrogen retention in material

    SciTech Connect

    Guterl, Jerome Smirnov, R. D.; Krasheninnikov, S. I.

    2015-07-28

    Desorption phase of thermal desorption spectroscopy (TDS) experiments performed on tungsten samples exposed to flux of hydrogen isotopes in fusion relevant conditions is analyzed using a reaction-diffusion model describing hydrogen retention in material bulk. Two regimes of hydrogen desorption are identified depending on whether hydrogen trapping rate is faster than hydrogen diffusion rate in material during TDS experiments. In both regimes, a majority of hydrogen released from material defects is immediately outgassed instead of diffusing deeply in material bulk when the evolution of hydrogen concentration in material is quasi-static, which is the case during TDS experiments performed with tungsten samples exposed to flux of hydrogen isotopes in fusion related conditions. In this context, analytical expressions of the hydrogen outgassing flux as a function of the material temperature are obtained with sufficient accuracy to describe main features of thermal desorption spectra (TDSP). These expressions are then used to highlight how characteristic temperatures of TDSP depend on hydrogen retention parameters, such as trap concentration or activation energy of detrapping processes. The use of Arrhenius plots to characterize retention processes is then revisited when hydrogen trapping takes place during TDS experiments. Retention processes are also characterized using the shape of desorption peaks in TDSP, and it is shown that diffusion of hydrogen in material during TDS experiment can induce long desorption tails visible aside desorption peaks at high temperature in TDSP. These desorption tails can be used to estimate activation energy of diffusion of hydrogen in material.

  18. A simulation and time series analysis of reaction- diffusion equations in biological pattern formation

    NASA Astrophysics Data System (ADS)

    Cooper, Crystal Diane

    A computer program was modified to model the dynamics of morphogen concentrations in a developing eye of a Xenopus laevis frog. The dynamics were modelled because it is believed that the behavior of the morphogen concentrations determine how the developing eye maps to the brain. The eye in the xenophus grows as a series of rings, and thus this is the model used. The basis for the simulation are experiments done by Sullivan et al. Following the experiment, aIl eye ring is 'split' in half, inverted, and then 'pasted' onto a donor half. The purpose of the program is to replicate and analyze the results that were found experimentally: a graft made on a north to south axis (dorsal to ventral) produces a change in vision along the east to west axis (anterior to posterior). Four modified Gierer-Meinhardt reaction- diffusion equations are used to simulate the operation. In the second part of the research, the program was further modified and a time series analysis was done on the results. It was found that the modified Gierer- Meinhardt equations demonstrated chaotic behavior under certain conditions. The dynamics included fixed points, limit cycles, transient chaos, intermittent chaos, and strange attractors. The creation and destruction of fractal torii was found.

  19. Bifurcation analysis of a delay reaction-diffusion malware propagation model with feedback control

    NASA Astrophysics Data System (ADS)

    Zhu, Linhe; Zhao, Hongyong; Wang, Xiaoming

    2015-05-01

    With the rapid development of network information technology, information networks security has become a very critical issue in our work and daily life. This paper attempts to develop a delay reaction-diffusion model with a state feedback controller to describe the process of malware propagation in mobile wireless sensor networks (MWSNs). By analyzing the stability and Hopf bifurcation, we show that the state feedback method can successfully be used to control unstable steady states or periodic oscillations. Moreover, formulas for determining the properties of the bifurcating periodic oscillations are derived by applying the normal form method and center manifold theorem. Finally, we conduct extensive simulations on large-scale MWSNs to evaluate the proposed model. Numerical evidences show that the linear term of the controller is enough to delay the onset of the Hopf bifurcation and the properties of the bifurcation can be regulated to achieve some desirable behaviors by choosing the appropriate higher terms of the controller. Furthermore, we obtain that the spatial-temporal dynamic characteristics of malware propagation are closely related to the rate constant for nodes leaving the infective class for recovered class and the mobile behavior of nodes.

  20. Quantitative modeling of the reaction/diffusion kinetics of two-chemistry photopolymers

    NASA Astrophysics Data System (ADS)

    Kowalski, Benjamin Andrew

    Optically driven diffusion in photopolymers is an appealing material platform for a broad range of applications, in which the recorded refractive index patterns serve either as images (e.g. data storage, display holography) or as optical elements (e.g. custom GRIN components, integrated optical devices). A quantitative understanding of the reaction/diffusion kinetics is difficult to obtain directly, but is nevertheless necessary in order to fully exploit the wide array of design freedoms in these materials. A general strategy for characterizing these kinetics is proposed, in which key processes are decoupled and independently measured. This strategy enables prediction of a material's potential refractive index change, solely on the basis of its chemical components. The degree to which a material does not reach this potential reveals the fraction of monomer that has participated in unwanted reactions, reducing spatial resolution and dynamic range. This approach is demonstrated for a model material similar to commercial media, achieving quantitative predictions of index response over three orders of exposure dose (~1 to ~103 mJ cm-2) and three orders of feature size (0.35 to 500 microns). The resulting insights enable guided, rational design of new material formulations with demonstrated performance improvement.

  1. Local traps as nanoscale reaction-diffusion probes: B clustering in c-Si

    NASA Astrophysics Data System (ADS)

    Pawlak, B. J.; Cowern, N. E. B.; Ahn, C.; Vandervorst, W.; Gwilliam, R.; van Berkum, J. G. M.

    2014-12-01

    A series of B implantation experiments into initially amorphized and not fully recrystallized Si, i.e., into an existing a/c-Si bi-layer material, have been conducted. We varied B dose, energy, and temperature during implantation process itself. Significant B migration has been observed within c-Si part near the a/c-interface and near the end-of-range region before any activation annealing. We propose a general concept of local trapping sites as experimental probes of nanoscale reaction-diffusion processes. Here, the a/c-Si interface acts as a trap, and the process itself is explored as the migration and clustering of mobile BI point defects in nearby c-Si during implantation at temperatures from 77 to 573 K. We find that at room temperature—even at B concentrations as high as 1.6 atomic %, the key B-B pairing step requires diffusion lengths of several nm owing to a small, ˜0.1 eV, pairing energy barrier. Thus, in nanostructures doped by ion implantation, the implant distribution can be strongly influenced by thermal migration to nearby impurities, defects, and interfaces.

  2. Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations

    NASA Astrophysics Data System (ADS)

    Flegg, Mark B.; Hellander, Stefan; Erban, Radek

    2015-05-01

    In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is called the ghost cell method (GCM), since it works by constructing a "ghost cell" in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step Δt (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter h, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: Δt → 0 and h is fixed; Δt → 0 and h → 0 such that √{ Δt } / h is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model.

  3. Tumor growth prediction with reaction-diffusion and hyperelastic biomechanical model by physiological data fusion.

    PubMed

    Wong, Ken C L; Summers, Ronald M; Kebebew, Electron; Yao, Jianhua

    2015-10-01

    The goal of tumor growth prediction is to model the tumor growth process, which can be achieved by physiological modeling and model personalization from clinical measurements. Although image-driven frameworks have been proposed with promising results, several issues such as infinitesimal strain assumptions, complicated personalization procedures, and the lack of functional information, may limit their prediction accuracy. In view of these issues, we propose a framework for pancreatic neuroendocrine tumor growth prediction, which comprises a FEM-based tumor growth model with coupled reaction-diffusion equation and nonlinear biomechanics. Physiological data fusion of structural and functional images is used to improve the subject-specificity of model personalization, and a derivative-free global optimization algorithm is adopted to facilitate the complicated model and accommodate flexible choices of objective functions. With this flexibility, we propose an objective function accounting for both the tumor volume difference and the root-mean-squared error of intracellular volume fractions. Experiments were performed on synthetic and clinical data to verify the parameter estimation capability and the prediction performance. Comparisons of using different biomechanical models and objective functions were also performed. From the experimental results of eight patient data sets, the average recall, precision, Dice coefficient, and relative volume difference between predicted and measured tumor volumes were 84.5 ± 6.9%, 85.8 ± 8.2%, 84.6 ± 1.7%, and 14.2 ± 8.4%, respectively. PMID:25962846

  4. Cubic autocatalysis in a reaction-diffusion annulus: semi-analytical solutions

    NASA Astrophysics Data System (ADS)

    Alharthi, M. R.; Marchant, T. R.; Nelson, M. I.

    2016-06-01

    Semi-analytical solutions for cubic autocatalytic reactions are considered in a circularly symmetric reaction-diffusion annulus. The Galerkin method is used to approximate the spatial structure of the reactant and autocatalyst concentrations. Ordinary differential equations are then obtained as an approximation to the governing partial differential equations and analyzed to obtain semi-analytical results for this novel geometry. Singularity theory is used to determine the regions of parameter space in which the different types of steady-state diagram occur. The region of parameter space, in which Hopf bifurcations can occur, is found using a degenerate Hopf bifurcation analysis. A novel feature of this geometry is the effect, of varying the width of the annulus, on the static and dynamic multiplicity. The results show that for a thicker annulus, Hopf bifurcations and multiple steady-state solutions occur in a larger portion of parameter space. The usefulness and accuracy of the semi-analytical results are confirmed by comparison with numerical solutions of the governing partial differential equations.

  5. Analysis and Dynamically Consistent Numerical Schemes for the SIS Model and Related Reaction Diffusion Equation

    NASA Astrophysics Data System (ADS)

    Lubuma, J. M.-S.; Mureithi, E.; Terefe, Y. A.

    2011-11-01

    The classical SIS epidemiological model is extended in two directions: (a) The number of adequate contacts per infective in unit time is assumed to be a function of the total population in such a way that this number grows less rapidly as the total population increases; (b) A diffusion term is added to the SIS model and this leads to a reaction diffusion equation, which governs the spatial spread of the disease. With the parameter R0 representing the basic reproduction number, it is shown that R0 = 1 is a forward bifurcation for the model (a), with the disease-free equilibrium being globally asymptotic stable when R0 is less than 1. In the case when R0 is greater than 1, traveling wave solutions are found for the model (b). Nonstandard finite difference (NSFD) schemes that replicate the dynamics of the continuous models are presented. In particular, for the model (a), a nonstandard version of the Runge-Kutta method having high order of convergence is investigated. Numerical experiments that support the theory are provided.

  6. Evolutionary distributions and competition by way of reaction-diffusion and by way of convolution.

    PubMed

    Cohen, Yosef; Galiano, Gonzalo

    2013-12-01

    Evolution by natural selection is the most ubiquitous and well understood process of evolution. We say distribution instead of the distribution of the density of populations of phenotypes across the values of their adaptive traits. A phenotype refers to an organism that exhibits a set of values of adaptive traits. An adaptive trait is a trait that a phenotype exhibits where the trait is subject to natural selection. Natural selection is a process by which populations of different phenotypes decline at different rates. An evolutionary distribution (ED) encapsulates the dynamics of evolution by natural selection. The main results are: (i) ED are derived by way of PDE of reaction-diffusion type and by way of integro-differential equations. The latter capture mutations through convolution of a kernel with the rate of growth of a population. The kernel controls the size and rate of mutations. (ii) The numerical solution of a logistic-like ED driven by competition corresponds to a bounded traveling wave solution of population models based on the logistic. (iii) Competition leads to increase in diversity of phenotypes on a single ED. Diversity refers to change in the number of local maxima (minima) within the bounds of values of adaptive traits. (iv) The principle of competitive exclusion in the context of evolution depends, smoothly, on the size and rate of mutations. (v) We identify the sensitivity—with respect to survival—of phenotypes to changes in values of adaptive traits to be an important parameter: increase in the value of this parameter results in decrease in evolutionary-based diversity. (vi) Stable ED corresponds to Evolutionary Stable Strategy; the latter refers to the outcome of a game of evolution. PMID:24122397

  7. Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations

    PubMed Central

    Flegga, Mark B.; Hellander, Stefan; Erban, Radek

    2015-01-01

    In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is called the ghost cell method (GCM), since it works by constructing a “ghost cell” in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step Δt (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter h, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: (i) Δt → 0 and h is fixed; (ii) Δt → 0 and h → 0 such that √Δt/h is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model. PMID:26568640

  8. Manifolds and front propagation barriers in advection-reaction-diffusion systems

    NASA Astrophysics Data System (ADS)

    Solomon, Tom

    2015-03-01

    We present experiments on the propagation of reaction fronts in laminar, vortex-dominated flows. The fronts are produced by the excitable Belousov-Zhabotinsky chemical reaction. The flows studied are driven by magnetohydrodynamic forcing techniques and are composed of a single vortex, chains or arrays of vortices, or spatially-disordered flows. In all of these cases, one-way barriers appear that either inhibit front propagation or, in some cases, pin the reactions fronts. We analyze this behavior with a recent theory of burning invariant manifolds (BIMs) that are a generalization of the theory of invariant manifolds developed in the past to characterize chaotic mixing and transport of passive impurities. We demonstrate that the BIMs are responsible for the reaction barriers observed experimentally, and we discuss the applicability of this BIM formalism to a range of flows: time-independent, time-periodic and time-aperiodic. Supported by NSF Grants DMR-1004744, DMR-1361881 and PHY-1156964.

  9. Reaction diffusion in the nickel-chromium-aluminum and cobalt-chromium-aluminum systems

    NASA Technical Reports Server (NTRS)

    Levine, S. R.

    1977-01-01

    The effects of MCrAl coating-substrate interdiffusion on oxidation life and the general mutliphase, multicomponent diffusion problem were examined. Semi-infinite diffusion couples that had sources representing coatings and sinks representing gas turbine alloys were annealed at 1,000, 1,095, 1,150, or 1,205 C for as long as 500 hours. The source and sink aluminum and chromium contents and the base metal (cobalt or nickel) determined the parabolic diffusion rate constants of the couples and predicted finite coating lives. The beta source strength concept provided a method (1) for correlating beta recession rate constants with composition; (2) for determining reliable average total, diffusion, and constitutional activation energies; and (3) for calculating interdiffusion coefficients.

  10. Reaction-diffusion systems in natural sciences and new technology transfer

    NASA Astrophysics Data System (ADS)

    Keller, André A.

    2012-12-01

    Diffusion mechanisms in natural sciences and innovation management involve partial differential equations (PDEs). This is due to their spatio-temporal dimensions. Functional semi-discretized PDEs (with lattice spatial structures or time delays) may be even more adapted to real world problems. In the modeling process, PDEs can also formalize behaviors, such as the logistic growth of populations with migration, and the adopters’ dynamics of new products in innovation models. In biology, these events are related to variations in the environment, population densities and overcrowding, migration and spreading of humans, animals, plants and other cells and organisms. In chemical reactions, molecules of different species interact locally and diffuse. In the management of new technologies, the diffusion processes of innovations in the marketplace (e.g., the mobile phone) are a major subject. These innovation diffusion models refer mainly to epidemic models. This contribution introduces that modeling process by using PDEs and reviews the essential features of the dynamics and control in biological, chemical and new technology transfer. This paper is essentially user-oriented with basic nonlinear evolution equations, delay PDEs, several analytical and numerical methods for solving, different solutions, and with the use of mathematical packages, notebooks and codes. The computations are carried out by using the software Wolfram Mathematica®7, and C++ codes.

  11. Analysis of reaction-diffusion systems for flame capturing in type IA supernova simulations

    NASA Astrophysics Data System (ADS)

    Zhyglo, Andriy V.

    2009-06-01

    We present a study of numerical behavior of a thickened flame used in Flame Capturing (FC, Khokhlov (1995)) for tracking thin physical flames in deflagration simulations. This technique, used extensively in astrophysics, utilizes artificial flame variable to evolve flame region, width of which is resolved in simulations, with physically motivated propagation speed. We develop a steady-state procedure for calibrating flame model used in FC, and test it against analytical results. Original flame model is properly calibrated with taking matter expansion into consideration and keeping artificial flame width at predetermined value regardless of expansion. We observe numerical noises generated by original realization of the technique. Alternative artificial burning rates are discussed, which produce acceptably quiet flames (relative dispersion in propagation speed within 0.1% at physically interesting ratios of fuel and ash densities). Two new quiet models are calibrated to yield required "flame" speed and width, and further studied in 2D and 3D setting. Landau-Darrieus type instabilities of the flames are observed. One model also shows significantly anisotropic propagation speed on the grid, both effects increasingly pronounced at larger matter expansion as a result of burning; these 2D/3D effects make that model unacceptable for use in type Ia supernova simulations at fuel densities below about 100 tons per cubic centimeter. Another model, first presented here, looks promising for use in flame capturing at fuel to ash density ratio of order 3 and below, the interval of most interest for astrophysical applications. No model was found to significantly inhibit LD instability development at larger expansions without increasing flame width. The model we propose, "Model B", yields flames completely localized within a region 6 cells wide at any expansion. We study Markstein effect (speed of the flame dependence on its curvature) for flame models described, through direct numerical simulations and through quasi- steady technique developed. By comparing results obtained by the 2 approaches we demonstrate that Markstein effect dominates instability effects on curved flame speed for Model B in 2D simulations for fuel to ash density of about 2.5 and below. We find critical wavelength of LD instability by direct simulations of perturbed nearly planar flames; these agree with analytical predictions with Markstein number values found in this work. We conclude that the behavior of model B is well understood, and optimal for FC applications among all flame models proposed to date.

  12. Experimental studies of coherent structures in an advection-reaction-diffusion system.

    PubMed

    Gowen, Savannah; Solomon, Tom

    2015-08-01

    We present experimental studies of reaction front propagation in a single vortex flow with an imposed external wind. The fronts are produced by the excitable, ferroin-catalyzed Belousov-Zhabotinsky chemical reaction. The flow is generated using an electromagnetic forcing technique: an almost-radial electrical current interacts with a magnetic field from a magnet below the fluid layer to produce the vortex. The magnet is mounted on crossed translation stages allowing for movement of the vortex through the flow. Reaction fronts triggered in or in front of the moving vortex form persistent structures that are seen experimentally for time-independent (constant motion), time-periodic, and time-aperiodic flows. These results are examined with the use of burning invariant manifolds that act as one-way barriers to front motion in the flows. We also explore the usefulness of finite-time Lyapunov exponent fields as an instrument for analyzing front propagation behavior in a fluid flow. PMID:26328574

  13. GPU accelerated solver for nonlinear reaction-diffusion systems. Application to the electrophysiology problem

    NASA Astrophysics Data System (ADS)

    Mena, Andres; Ferrero, Jose M.; Rodriguez Matas, Jose F.

    2015-11-01

    Solving the electric activity of the heart possess a big challenge, not only because of the structural complexities inherent to the heart tissue, but also because of the complex electric behaviour of the cardiac cells. The multi-scale nature of the electrophysiology problem makes difficult its numerical solution, requiring temporal and spatial resolutions of 0.1 ms and 0.2 mm respectively for accurate simulations, leading to models with millions degrees of freedom that need to be solved for thousand time steps. Solution of this problem requires the use of algorithms with higher level of parallelism in multi-core platforms. In this regard the newer programmable graphic processing units (GPU) has become a valid alternative due to their tremendous computational horsepower. This paper presents results obtained with a novel electrophysiology simulation software entirely developed in Compute Unified Device Architecture (CUDA). The software implements fully explicit and semi-implicit solvers for the monodomain model, using operator splitting. Performance is compared with classical multi-core MPI based solvers operating on dedicated high-performance computer clusters. Results obtained with the GPU based solver show enormous potential for this technology with accelerations over 50 × for three-dimensional problems.

  14. Simulating Stochastic Reaction-Diffusion Systems on and within Moving Boundaries

    PubMed Central

    Ghosh, Atiyo; Marquez-Lago, Tatiana T.

    2015-01-01

    Chemical reactions inside cells are generally considered to happen within fixed-size compartments. However, cells and their compartments are highly dynamic. Thus, such stringent geometrical assumptions may not reflect biophysical reality, and can highly bias conclusions from simulation studies. In this work, we present an intuitive algorithm for particle-based diffusion in and on moving boundaries, for both point particles and spherical particles. We first benchmark our proposed stochastic method against solutions of partial differential equations in appropriate scenarios, and further demonstrate that moving boundaries can give rise to super-diffusive motion as well as time-inhomogeneous reaction rates. Finally, we conduct a numerical experiment representing photobleaching of diffusing fluorescent proteins in dividing Saccharomyces cerevisiae cells to demonstrate that moving boundaries might cause important effects neglected in previously published studies of cell compartmentalization. PMID:26230406

  15. Experimental studies of coherent structures in an advection-reaction-diffusion system

    NASA Astrophysics Data System (ADS)

    Gowen, Savannah; Solomon, Tom

    2015-08-01

    We present experimental studies of reaction front propagation in a single vortex flow with an imposed external wind. The fronts are produced by the excitable, ferroin-catalyzed Belousov-Zhabotinsky chemical reaction. The flow is generated using an electromagnetic forcing technique: an almost-radial electrical current interacts with a magnetic field from a magnet below the fluid layer to produce the vortex. The magnet is mounted on crossed translation stages allowing for movement of the vortex through the flow. Reaction fronts triggered in or in front of the moving vortex form persistent structures that are seen experimentally for time-independent (constant motion), time-periodic, and time-aperiodic flows. These results are examined with the use of burning invariant manifolds that act as one-way barriers to front motion in the flows. We also explore the usefulness of finite-time Lyapunov exponent fields as an instrument for analyzing front propagation behavior in a fluid flow.

  16. Finite-scale singularity in the renormalization group flow of a reaction-diffusion system.

    PubMed

    Gredat, Damien; Chaté, Hugues; Delamotte, Bertrand; Dornic, Ivan

    2014-01-01

    We study the nonequilibrium critical behavior of the pair contact process with diffusion (PCPD) by means of nonperturbative functional renormalization group techniques. We show that usual perturbation theory fails because the effective potential develops a nonanalyticity at a finite length scale: Perturbatively forbidden terms are dynamically generated and the flow can be continued once they are taken into account. Our results suggest that the critical behavior of PCPD can be either in the directed percolation or in a different (conjugated) universality class. PMID:24580152

  17. The Time Dependent Propensity Function for Acceleration of Spatial Stochastic Simulation of Reaction-Diffusion Systems

    PubMed Central

    Wu, Sheng; Li, Hong; Petzold, Linda R.

    2015-01-01

    The inhomogeneous stochastic simulation algorithm (ISSA) is a fundamental method for spatial stochastic simulation. However, when diffusion events occur more frequently than reaction events, simulating the diffusion events by ISSA is quite costly. To reduce this cost, we propose to use the time dependent propensity function in each step. In this way we can avoid simulating individual diffusion events, and use the time interval between two adjacent reaction events as the simulation stepsize. We demonstrate that the new algorithm can achieve orders of magnitude efficiency gains over widely-used exact algorithms, scales well with increasing grid resolution, and maintains a high level of accuracy. PMID:26609185

  18. Spreading speeds and uniqueness of traveling waves for a reaction diffusion equation with spatio-temporal delays

    NASA Astrophysics Data System (ADS)

    Xu, Zhaoquan; Xiao, Dongmei

    2016-01-01

    A class of reaction diffusion equation with spatio-temporal delays is systematically investigated. When the reaction function of this equation is nonlinear without monotonicity, it is shown that there exists a spreading speed c* > 0 for this equation such that c* is linearly determinate and coincides with the minimal wave speed of traveling waves, and that this equation admits a unique traveling wave (up to translation) with speed c >c* and no traveling wave with c

  19. Predicting in vivo glioma growth with the reaction diffusion equation constrained by quantitative magnetic resonance imaging data

    NASA Astrophysics Data System (ADS)

    Hormuth, David A., II; Weis, Jared A.; Barnes, Stephanie L.; Miga, Michael I.; Rericha, Erin C.; Quaranta, Vito; Yankeelov, Thomas E.

    2015-07-01

    Reaction-diffusion models have been widely used to model glioma growth. However, it has not been shown how accurately this model can predict future tumor status using model parameters (i.e., tumor cell diffusion and proliferation) estimated from quantitative in vivo imaging data. To this end, we used in silico studies to develop the methods needed to accurately estimate tumor specific reaction-diffusion model parameters, and then tested the accuracy with which these parameters can predict future growth. The analogous study was then performed in a murine model of glioma growth. The parameter estimation approach was tested using an in silico tumor ‘grown’ for ten days as dictated by the reaction-diffusion equation. Parameters were estimated from early time points and used to predict subsequent growth. Prediction accuracy was assessed at global (total volume and Dice value) and local (concordance correlation coefficient, CCC) levels. Guided by the in silico study, rats (n = 9) with C6 gliomas, imaged with diffusion weighted magnetic resonance imaging, were used to evaluate the model’s accuracy for predicting in vivo tumor growth. The in silico study resulted in low global (tumor volume error <8.8%, Dice >0.92) and local (CCC values >0.80) level errors for predictions up to six days into the future. The in vivo study showed higher global (tumor volume error >11.7%, Dice <0.81) and higher local (CCC <0.33) level errors over the same time period. The in silico study shows that model parameters can be accurately estimated and used to accurately predict future tumor growth at both the global and local scale. However, the poor predictive accuracy in the experimental study suggests the reaction-diffusion equation is an incomplete description of in vivo C6 glioma biology and may require further modeling of intra-tumor interactions including segmentation of (for example) proliferative and necrotic regions.

  20. MINIATURE ACID CONDENSATION SYSTEM: DESIGN AND OPERATION

    EPA Science Inventory

    An extractive source sampling system was designed and constructed. The sampling system measures gaseous sulfuric acid and sulfur dioxide in combustion emissions. The miniature acid condensation system (MACS) includes a high-temperature quartz probe and quartz-filter holder. Since...

  1. Neutron Reflectivity Characterization of the Photoacid Reaction-Diffusion Latent and Developed Images of Molecular Resists for Extreme Ultraviolet Lithography

    SciTech Connect

    Prabhu, Vivek M.; Kang, Shuhui; Sha, Jing; Bonnesen, Peter V; Satija, Sushil K.; Wu, Wen-li; Ober, Christoper K.

    2012-01-01

    Lithographic feature size requirements have approached a few radius of gyration of photoresist polymers used in thin-film patterning. Furthermore, the feature dimensions are commensurate with the photoacid diffusion length that defines the underlying latent image. Smaller imaging building blocks may enable reduced feature sizes; however, resolution limits are also dependent upon the spatial extent of the photoacid-catalyzed reaction diffusion front and subsequent dissolution mechanism. The reaction-diffusion front was characterized by neutron reflectivity for ccc stereoisomer-purified, deuterium-labeled tert-butoxycarbonyloxy calix[4]resorcinarene molecular resists. The spatial extent of the reaction front exceeds the size of the molecular resist with an effective diffusion constant of (0.13 0.06) nm2/s for reaction times longer than 60 s, with the maximum at shorter times. Comparison to a mean-field reaction-diffusion model shows that a photoacid trapping process provides bounds to the spatial and extent of reaction via a reaction-limited mechanism whereas the ratio of the reaction rate to trapping rate constants recovers the effective diffusion peak. Under the ideal step-exposure conditions, surface roughness was observed after either positive- or negative-tone development. However, negative-tone development follows a surface restructuring mechanism rather than etch-like dissolution in positive-tone development.

  2. Gene drive through a landscape: Reaction-diffusion models of population suppression and elimination by a sex ratio distorter.

    PubMed

    Beaghton, Andrea; Beaghton, Pantelis John; Burt, Austin

    2016-04-01

    Some genes or gene complexes are transmitted from parents to offspring at a greater-than-Mendelian rate, and can spread and persist in populations even if they cause some harm to the individuals carrying them. Such genes may be useful for controlling populations or species that are harmful. Driving-Y chromosomes may be particularly potent in this regard, as they produce a male-biased sex ratio that, if sufficiently extreme, can lead to population elimination. To better understand the potential of such genes to spread over a landscape, we have developed a series of reaction-diffusion models of a driving-Y chromosome in 1-D and radially-symmetric 2-D unbounded domains. The wild-type system at carrying capacity is found to be unstable to the introduction of driving-Y males for all models investigated. Numerical solutions exhibit travelling wave pulses and fronts, and analytical and semi-analytical solutions for the asymptotic wave speed under bounded initial conditions are derived. The driving-Y male invades the wild-type equilibrium state at the front of the wave and completely replaces the wild-type males, leaving behind, at the tail of the wave, a reduced- or zero-population state of females and driving-Y males only. In our simplest model of a population with one life stage and density-dependent mortality, wave speed depends on the strength of drive and the diffusion rate of Y-drive males, and is independent of the population dynamic consequences (suppression or elimination). Incorporating an immobile juvenile stage of fixed duration into the model reduces wave speed approximately in proportion to the relative time spent as a juvenile. If females mate just once in their life, storing sperm for subsequent reproduction, then wave speed depends on the movement of mated females as well as Y-drive males, and may be faster or slower than in the multiple-mating model, depending on the relative duration of juvenile and adult life stages. Numerical solutions are shown for

  3. Reaction diffusion dynamics and the Schryer-Walker solution for domain walls of the Landau-Lifshitz-Gilbert equation

    NASA Astrophysics Data System (ADS)

    Benguria, R. D.; Depassier, M. C.

    2016-04-01

    We study the dynamics of the equation obtained by Schryer and Walker for the motion of domain walls. The reduced equation is a reaction diffusion equation for the angle between the applied field and the magnetization vector. If the hard-axis anisotropy Kd is much larger than the easy-axis anisotropy Ku, there is a range of applied fields where the dynamics does not select the Schryer-Walker solution. We give an analytic expression for the speed of the domain wall in this regime and the conditions for its existence.

  4. 21 CFR 862.1450 - Lactic acid test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Lactic acid test system. 862.1450 Section 862.1450....1450 Lactic acid test system. (a) Identification. A lactic acid test system is a device intended to measure lactic acid in whole blood and plasma. Lactic acid measurements that evaluate the acid-base...

  5. 21 CFR 862.1450 - Lactic acid test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ....1450 Lactic acid test system. (a) Identification. A lactic acid test system is a device intended to measure lactic acid in whole blood and plasma. Lactic acid measurements that evaluate the acid-base status... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Lactic acid test system. 862.1450 Section...

  6. 21 CFR 862.1450 - Lactic acid test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Lactic acid test system. 862.1450 Section 862.1450....1450 Lactic acid test system. (a) Identification. A lactic acid test system is a device intended to measure lactic acid in whole blood and plasma. Lactic acid measurements that evaluate the acid-base...

  7. Exact Solutions of Linear Reaction-Diffusion Processes on a Uniformly Growing Domain: Criteria for Successful Colonization

    PubMed Central

    Simpson, Matthew J

    2015-01-01

    Many processes during embryonic development involve transport and reaction of molecules, or transport and proliferation of cells, within growing tissues. Mathematical models of such processes usually take the form of a reaction-diffusion partial differential equation (PDE) on a growing domain. Previous analyses of such models have mainly involved solving the PDEs numerically. Here, we present a framework for calculating the exact solution of a linear reaction-diffusion PDE on a growing domain. We derive an exact solution for a general class of one-dimensional linear reaction—diffusion process on 0

  8. Micro-electro-mechanical systems phosphoric acid fuel cell

    DOEpatents

    Sopchak, David A.; Morse, Jeffrey D.; Upadhye, Ravindra S.; Kotovsky, Jack; Graff, Robert T.

    2010-08-17

    A phosphoric acid fuel cell system comprising a porous electrolyte support, a phosphoric acid electrolyte in the porous electrolyte support, a cathode electrode contacting the phosphoric acid electrolyte, and an anode electrode contacting the phosphoric acid electrolyte.

  9. Micro-electro-mechanical systems phosphoric acid fuel cell

    DOEpatents

    Sopchak, David A.; Morse, Jeffrey D.; Upadhye, Ravindra S.; Kotovsky, Jack; Graff, Robert T.

    2010-12-21

    A phosphoric acid fuel cell system comprising a porous electrolyte support, a phosphoric acid electrolyte in the porous electrolyte support, a cathode electrode contacting the phosphoric acid electrolyte, and an anode electrode contacting the phosphoric acid electrolyte.

  10. Sulfuric acid thermoelectrochemical system and method

    DOEpatents

    Ludwig, Frank A.

    1989-01-01

    A thermoelectrochemical system in which an electrical current is generated between a cathode immersed in a concentrated sulfuric acid solution and an anode immersed in an aqueous buffer solution of sodium bisulfate and sodium sulfate. Reactants consumed at the electrodes during the electrochemical reaction are thermochemically regenerated and recycled to the electrodes to provide continuous operation of the system.

  11. 21 CFR 862.1290 - Fatty acids test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Fatty acids test system. 862.1290 Section 862.1290....1290 Fatty acids test system. (a) Identification. A fatty acids test system is a device intended to measure fatty acids in plasma and serum. Measurements of fatty acids are used in the diagnosis...

  12. Propagation Behaviors of an Acid Wavefront Through a Microchannel Junction.

    PubMed

    Nabika, Hideki; Hasegawa, Takahiko; Unoura, Kei

    2015-07-30

    Waves in reaction-diffusion systems yield a wealth of dynamic self-assembling phenomena in nature. Recent studies have been devoted to utilizing these active waves in conjunction with microscale technology. To provide a compass for controlling reaction-diffusion waves in microspaces, we have investigated the propagation behavior of one specific variety of the reaction-diffusion wave: an acid wave that utilizes an autocatalytic proton-production reaction. Furthermore, the acid wave that we have investigated occurs in a microchannel with a junction connecting circular and straight regions. The obtained results were compared with a neutralization wave that involves only a neutralization reaction. The acid wave was ignited by the addition of the appropriate amount of H2SO4 into the circular region that was filled with a substrate solution, where proton-consuming and proton-producing reactions followed a rapid neutralization reaction. At this stage, the wave penetrated and propagated into the channel region. Comparison between the acid and the neutralization waves clarified that the acid wave required a minimum threshold of H2SO4 concentration in order to be ignited and that the propagation of the acid wave was temporarily delayed because of the presence of intermediate chemical reaction steps. Furthermore, the propagation dynamics was found to be tuned through the configuration of the microchannel. The importance of microchannel configuration, especially for systems with a junction connecting different shapes, is discussed in terms of Fick's law and in terms of the proton flux from the circular to the straight regions. PMID:26132891

  13. Finite difference/spectral approximations for the distributed order time fractional reaction-diffusion equation on an unbounded domain

    NASA Astrophysics Data System (ADS)

    Chen, Hu; Lü, Shujuan; Chen, Wenping

    2016-06-01

    The numerical approximation of the distributed order time fractional reaction-diffusion equation on a semi-infinite spatial domain is discussed in this paper. A fully discrete scheme based on finite difference method in time and spectral approximation using Laguerre functions in space is proposed. The scheme is unconditionally stable and convergent with order O (τ2 + Δα2 +N (1 - m) / 2), where τ, Δα, N, and m are the time-step size, step size in distributed-order variable, polynomial degree, and regularity in the space variable of the exact solution, respectively. A pseudospectral scheme is also proposed and analyzed. Some numerical examples are presented to demonstrate the efficiency of the proposed scheme.

  14. One-Dimensional Reaction-Diffusion Simulation of Cu Migration in Polycrystalline CdTe Solar Cells

    SciTech Connect

    Guo, Da; Akis, Richard; Brinkman, Daniel; Sankin, Igor; Fang, Tian; Vasileska, Dragica; Ringhofer, Christain

    2014-06-13

    In this work, we report on developing 1D reaction-diffusion solver to understand the kinetics of p-type doping formation in CdTe absorbers and to shine some light on underlying causes of metastabilities observed in CdTe PV devices. Evolution of intrinsic and Cu-related defects in CdTe solar cell has been studied in time-space domain self-consistently with free carrier transport and Poisson equation. Resulting device performance was simulated as a function of Cu diffusion anneal time showing pronounced effect the evolution of associated acceptor and donor states can cause on device characteristics. Although 1D simulation has intrinsic limitations when applied to poly-crystalline films, the results suggest strong potential of the approach in better understanding of the performance and metastabilities of CdTe photovoltaic device.

  15. Global bifurcation and stability of steady states for a reaction-diffusion-chemotaxis model with volume-filling effect

    NASA Astrophysics Data System (ADS)

    Ma, Manjun; Wang, Zhi-An

    2015-08-01

    This paper is devoted to studying a reaction-diffusion-chemotaxis model with a volume-filling effect in a bounded domain with Neumann boundary conditions. We first establish the global existence of classical solutions bounded uniformly in time. Then applying the asymptotic analysis and bifurcation theory, we obtain both the local and global structure of steady states bifurcating from the homogeneous steady states in one dimension by treating the chemotactic coefficient as a bifurcation parameter. Moveover we find the stability criterion of the bifurcating steady states and give a sufficient condition for the stability of steady states with small amplitude. The pattern formation of the model is numerically shown and the stability criterion is verified by our numerical simulations.

  16. A mechanically coupled reaction-diffusion model for predicting the response of breast tumors to neoadjuvant chemotherapy

    NASA Astrophysics Data System (ADS)

    Weis, Jared A.; Miga, Michael I.; Arlinghaus, Lori R.; Li, Xia; Bapsi Chakravarthy, A.; Abramson, Vandana; Farley, Jaime; Yankeelov, Thomas E.

    2013-09-01

    There is currently a paucity of reliable techniques for predicting the response of breast tumors to neoadjuvant chemotherapy. The standard approach is to monitor gross changes in tumor size as measured by physical exam and/or conventional imaging, but these methods generally do not show whether a tumor is responding until the patient has received many treatment cycles. One promising approach to address this clinical need is to integrate quantitative in vivo imaging data into biomathematical models of tumor growth in order to predict eventual response based on early measurements during therapy. In this work, we illustrate a novel biomechanical mathematical modeling approach in which contrast enhanced and diffusion weighted magnetic resonance imaging data acquired before and after the first cycle of neoadjuvant therapy are used to calibrate a patient-specific response model which subsequently is used to predict patient outcome at the conclusion of therapy. We present a modification of the reaction-diffusion tumor growth model whereby mechanical coupling to the surrounding tissue stiffness is incorporated via restricted cell diffusion. We use simulations and experimental data to illustrate how incorporating tissue mechanical properties leads to qualitatively and quantitatively different tumor growth patterns than when such properties are ignored. We apply the approach to patient data in a preliminary dataset of eight patients exhibiting a varying degree of responsiveness to neoadjuvant therapy, and we show that the mechanically coupled reaction-diffusion tumor growth model, when projected forward, more accurately predicts residual tumor burden at the conclusion of therapy than the non-mechanically coupled model. The mechanically coupled model predictions exhibit a significant correlation with data observations (PCC = 0.84, p < 0.01), and show a statistically significant >4 fold reduction in model/data error (p = 0.02) as compared to the non-mechanically coupled model.

  17. Threshold effect with stochastic fluctuation in bacteria-colony-like proliferation dynamics as analyzed through a comparative study of reaction-diffusion equations and cellular automata

    NASA Astrophysics Data System (ADS)

    Odagiri, Kenta; Takatsuka, Kazuo

    2009-02-01

    We report a comparative study on pattern formation between the methods of cellular automata (CA) and reaction-diffusion equations (RD) applying to a morphology of bacterial colony formation. To do so, we began the study with setting an extremely simple model, which was designed to realize autocatalytic proliferation of bacteria (denoted as X ) fed with nutrition (N) and their inactive state (prespore state) P1 due to starvation: X+N→2X and X→P1 , respectively. It was found numerically that while the CA could successfully generate rich patterns ranging from the circular fat structure to the viscous-finger-like complicated one, the naive RD reproduced only the circular pattern but failed to give a finger structure. Augmenting the RD equations by adding two physical factors, (i) a threshold effect in the dynamics of X+N→2X (breaking the continuity limit of RD) and (ii) internal noise with onset threshold (breaking the inherent symmetry of RD), we have found that the viscous-finger-like realistic patterns are indeed recovered by thus modified RD. This highlights the important difference between CA and RD, and at the same time, clarifies the necessary factors for the complicated patterns to emerge in such a surprisingly simple model system.

  18. 21 CFR 862.1509 - Methylmalonic acid (nonquantitative) test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Methylmalonic acid (nonquantitative) test system... Test Systems § 862.1509 Methylmalonic acid (nonquantitative) test system. (a) Identification. A methylmalonic acid (nonquantitative) test system is a device intended to identify methylmalonic acid in...

  19. 21 CFR 862.1509 - Methylmalonic acid (nonquantitative) test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Methylmalonic acid (nonquantitative) test system... Test Systems § 862.1509 Methylmalonic acid (nonquantitative) test system. (a) Identification. A methylmalonic acid (nonquantitative) test system is a device intended to identify methylmalonic acid in...

  20. 21 CFR 862.1509 - Methylmalonic acid (nonquantitative) test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Methylmalonic acid (nonquantitative) test system... Test Systems § 862.1509 Methylmalonic acid (nonquantitative) test system. (a) Identification. A methylmalonic acid (nonquantitative) test system is a device intended to identify methylmalonic acid in...

  1. 21 CFR 862.1509 - Methylmalonic acid (nonquantitative) test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Methylmalonic acid (nonquantitative) test system... Test Systems § 862.1509 Methylmalonic acid (nonquantitative) test system. (a) Identification. A methylmalonic acid (nonquantitative) test system is a device intended to identify methylmalonic acid in...

  2. 21 CFR 862.1795 - Vanilmandelic acid test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Vanilmandelic acid test system. 862.1795 Section... Systems § 862.1795 Vanilmandelic acid test system. (a) Identification. A vanilmandelic acid test system is a device intended to measure vanilmandelic acid in urine. Measurements of vanilmandelic...

  3. 21 CFR 862.1795 - Vanilmandelic acid test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Vanilmandelic acid test system. 862.1795 Section... Systems § 862.1795 Vanilmandelic acid test system. (a) Identification. A vanilmandelic acid test system is a device intended to measure vanilmandelic acid in urine. Measurements of vanilmandelic...

  4. Acid mine water aeration and treatment system

    DOEpatents

    Ackman, Terry E.; Place, John M.

    1987-01-01

    An in-line system is provided for treating acid mine drainage which basically comprises the combination of a jet pump (or pumps) and a static mixer. The jet pump entrains air into the acid waste water using a Venturi effect so as to provide aeration of the waste water while further aeration is provided by the helical vanes of the static mixer. A neutralizing agent is injected into the suction chamber of the jet pump and the static mixer is formed by plural sections offset by 90 degrees.

  5. Phase transitions in a reaction-diffusion model on a line with boundaries

    SciTech Connect

    Khorrami, Mohammad Aghamohammadi, Amir

    2014-03-15

    A one-dimensional model on a line of length L is investigated, which involves particle diffusion as well as single particle annihilation. There are also creation and annihilation at the boundaries. The static and dynamical behaviors of the system are studied. It is seen that the system could exhibit a dynamical phase transition. For small drift velocities, the relaxation time does not depend on the absorption rates at the boundaries. This is the fast phase. For large velocities, the smaller of the absorption rates at boundaries enter the relaxation rate and makes it longer. This is the slow phase. Finally, the effect of a random particle creation in the bulk is also investigated.

  6. Docosahexaenoic acid in neural signaling systems.

    PubMed

    Crawford, Michael A

    2006-01-01

    Docosahexaenoic acid has been conserved in neural signalling systems in the cephalopods, fish, amphibian, reptiles, birds, mammals, primates and humans. This extreme conservation, despite wide genomic changes over 500 million years, testifies to a uniqueness of this molecule in the brain. The brain selectively incorporates docosahexaenoic acid and its rate of incorporation into the developing brain has been shown to be greater than ten times more efficient than its synthesis from the omega 3 fatty acids of land plant origin. Data has now been published demonstrating a significant influence of dietary omega 3 fatty acids on neural gene expression. As docosahexaenoic acid is the only omega 3 fatty acid in the brain, it is likely that it is the ligand involved. The selective uptake, requirement for function and stimulation of gene expression would have conferred an advantage to a primate which separated from the chimpanzees in the forests and woodlands and sought a different ecological niche. In view of the paucity of docosahexaenoic acid in the land food chain it is likely that the advantage would have been gained from a lacustrine or marine coastal habitat with access to food rich in docosahexaenoic acid and the accessory micronutrients, such as iodine, zinc, copper, manganese and selenium, of importance in brain development and protection against peroxidation. Land agricultural development has, in recent time, come to dominate the human food chain. The decline in use and availability of aquatic resources is not considered important by Langdon (2006) as he considers the resource was not needed for human evolution and can be replaced from the terrestrial food chain. This notion is not supported by the biochemistry nor the molecular biology. He misses the point that the shoreline hypothesis is not just dependent on docosahexaenoic acid but also on the other accessory nutrients specifically required by the brain. Moreover he neglects the basic principle of Darwinian

  7. 21 CFR 862.1775 - Uric acid test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Uric acid test system. 862.1775 Section 862.1775....1775 Uric acid test system. (a) Identification. A uric acid test system is a device intended to measure uric acid in serum, plasma, and urine. Measurements obtained by this device are used in the...

  8. Tomography of reaction-diffusion microemulsions reveals three-dimensional Turing patterns.

    PubMed

    Bánsági, Tamás; Vanag, Vladimir K; Epstein, Irving R

    2011-03-11

    Spatially periodic, temporally stationary patterns that emerge from instability of a homogeneous steady state were proposed by Alan Turing in 1952 as a mechanism for morphogenesis in living systems and have attracted increasing attention in biology, chemistry, and physics. Patterns found to date have been confined to one or two spatial dimensions. We used tomography to study the Belousov-Zhabotinsky reaction in a microemulsion in which the polar reactants are confined to aqueous nanodroplets much smaller than the scale of the stationary patterns. We demonstrate the existence of Turing patterns that can exist only in three dimensions, including curved surfaces, hexagonally packed cylinders, spots, and labyrinthine and lamellar patterns. PMID:21310963

  9. A Refined Reaction-Diffusion Model of Tau-Microtubule Dynamics and Its Application in FDAP Analysis

    PubMed Central

    Igaev, Maxim; Janning, Dennis; Sündermann, Frederik; Niewidok, Benedikt; Brandt, Roland; Junge, Wolfgang

    2014-01-01

    Fluorescence decay after photoactivation (FDAP) and fluorescence recovery after photobleaching (FRAP) are well established approaches for studying the interaction of the microtubule (MT)-associated protein tau with MTs in neuronal cells. Previous interpretations of FDAP/FRAP data have revealed dwell times of tau on MTs in the range of several seconds. However, this is difficult to reconcile with a dwell time recently measured by single-molecule analysis in neuronal processes that was shorter by two orders of magnitude. Questioning the validity of previously used phenomenological interpretations of FDAP/FRAP data, we have generalized the standard two-state reaction-diffusion equations by 1), accounting for the parallel and discrete arrangement of MTs in cell processes (i.e., homogeneous versus heterogeneous distribution of tau-binding sites); and 2), explicitly considering both active (diffusion upon MTs) and passive (piggybacking upon MTs at rates of slow axonal transport) motion of bound tau. For some idealized cases, analytical solutions were derived. By comparing them with the full numerical solution and Monte Carlo simulations, the respective validity domains were mapped. Interpretation of our FDAP data (from processes of neuronally differentiated PC12 cells) in light of the heterogeneous formalism yielded independent estimates for the association (∼2 ms) and dwell (∼100 ms) times of tau to/on a single MT rather than in an MT array. The dwell time was shorter by orders of magnitude than that in a previous report where a homogeneous topology of MTs was assumed. We found that the diffusion of bound tau was negligible in vivo, in contrast to an earlier report that tau diffuses along the MT lattice in vitro. Methodologically, our results demonstrate that the heterogeneity of binding sites cannot be ignored when dealing with reaction-diffusion of cytoskeleton-associated proteins. Physiologically, the results reveal the behavior of tau in cellular processes

  10. Reaction-diffusion waves of reversible actin filament assembly drive cell oscillations and locomotion

    NASA Astrophysics Data System (ADS)

    Vicker, Michael G.

    Excitation waves of actin filament (F-actin) polymerization and depolymerization have been visualized in fixed and in living Dictyostelium cells by confocal and fluorescence resonance energy transfer (FRET) microscopy. F-actin waves generate supramolecular F-actin patterns, typical of chemical wave systems. Scroll waves distinguishable as sphere, ring and spiral patterns propagate up to several micrometres in diameter in a few seconds at wavefront speeds measured at up to 25 µm/min. These newly identified nonlinear F-actin dynamics drive eukaryotic cell locomotion. F-actin autowaves also induce oscillatory modi of temporally variable frequency and amplitude as cell surface projections, including pseudopodia and lamellipodia, which may traverse the cell surface as waves. F-actin waves may also govern a range of cell functions and behaviours, including phagocytosis, chemotaxis, cell surface receptor activity and biological rhythms.

  11. Neutrality condition and response law for nonlinear reaction-diffusion equations, with application to population genetics

    NASA Astrophysics Data System (ADS)

    Vlad, Marcel Ovidiu; Moran, Federico; Tsuchiya, Masa; Cavalli-Sforza, L. Luca; Oefner, Peter J.; Ross, John

    2002-06-01

    We study a general class of nonlinear macroscopic evolution equations with ``transport'' and ``reaction'' terms which describe the dynamics of a species of moving individuals (atoms, molecules, quasiparticles, organisms, etc.). We consider that two types of individuals exist, ``not marked'' and ``marked,'' respectively. We assume that the concentrations of both types of individuals are measurable and that they obey a neutrality condition, that is, the kinetic and transport properties of the ``not marked'' and ``marked'' individuals are identical. We suggest a response experiment, which consists in varying the fraction of ``marked'' individuals with the preservation of total fluxes, and show that the response of the system can be represented by a linear superposition law even though the underlying dynamics of the system is in general highly nonlinear. The linear response law is valid even for large perturbations and is not the result of a linearization procedure but rather a necessary consequence of the neutrality condition. First, we apply the response theorem to chemical kinetics, where the ``marked species'' is a molecule labeled with a radioactive isotope and there is no kinetic isotope effect. The susceptibility function of the response law can be related to the reaction mechanism of the process. Secondly we study the geographical distribution of the nonrecurrent, nonreversible neutral mutations of the nonrecombining portion of the Y chromosome from human populations and show that the fraction of mutants at a given point in space and time obeys a linear response law of the type introduced in this paper. The theory may be used for evaluating the geographic position and the moment in time where and when a mutation originated.

  12. Fast simulation of solid tumors thermal ablation treatments with a 3D reaction diffusion model.

    PubMed

    Bertaccini, Daniele; Calvetti, Daniela

    2007-08-01

    An efficient computational method for near real-time simulation of thermal ablation of tumors via radio frequencies is proposed. Model simulations of the temperature field in a 3D portion of tissue containing the tumoral mass for different patterns of source heating can be used to design the ablation procedure. The availability of a very efficient computational scheme makes it possible to update the predicted outcome of the procedure in real time. In the algorithms proposed here a discretization in space of the governing equations is followed by an adaptive time integration based on implicit multistep formulas. A modification of the ode15s MATLAB function which uses Krylov space iterative methods for the solution of the linear systems arising at each integration step makes it possible to perform the simulations on standard desktop for much finer grids than using the built-in ode15s. The proposed algorithm can be applied to a wide class of nonlinear parabolic differential equations. PMID:17173888

  13. Pursuit-and-Evasion Reaction-Diffusion Waves in Microreactors with Tailored Geometry.

    PubMed

    Zambrano, A; Zadorin, A S; Rondelez, Y; Estévez-Torres, A; Galas, J-C

    2015-04-30

    Out-of-equilibrium chemical systems may self-organize into structures displaying spatiotemporal order, such as traveling waves and Turing patterns. Because of its predictable chemistry, DNA has recently appeared as an interesting candidate to engineer these spatiotemporal structures. However, in addition to the intrinsic chemical parameters, initial and boundary conditions have a major impact on the final structure. Here we take advantage of microfluidics to design controlled reactors and investigate pursuit-and-evasion chemical waves generated by a DNA-based reaction network with Predator-Prey dynamics. We first propose two complementary microfabrication strategies to either control the initial condition or the two-dimensional geometry of the reactor where the waves develop. We subsequently use them to investigate the effect of curvature in wave propagation. We finally show that DNA-based waves can compute the optimal path within a maze. We thus suggest that coupling configurable microfluidics to programmable DNA-based dissipative reaction networks is a powerful route to investigate spatiotemporal order formation in chemistry. PMID:25839240

  14. FAST SIMULATION OF SOLID TUMORS THERMAL ABLATION TREATMENTS WITH A 3D REACTION DIFFUSION MODEL *

    PubMed Central

    BERTACCINI, DANIELE; CALVETTI, DANIELA

    2007-01-01

    An efficient computational method for near real-time simulation of thermal ablation of tumors via radio frequencies is proposed. Model simulations of the temperature field in a 3D portion of tissue containing the tumoral mass for different patterns of source heating can be used to design the ablation procedure. The availability of a very efficient computational scheme makes it possible update the predicted outcome of the procedure in real time. In the algorithms proposed here a discretization in space of the governing equations is followed by an adaptive time integration based on implicit multistep formulas. A modification of the ode15s MATLAB function which uses Krylov space iterative methods for the solution of for the linear systems arising at each integration step makes it possible to perform the simulations on standard desktop for much finer grids than using the built-in ode15s. The proposed algorithm can be applied to a wide class of nonlinear parabolic differential equations. PMID:17173888

  15. A Splitting Scheme for Solving Reaction-Diffusion Equations Modeling Dislocation Dynamics in Materials Subjected to Cyclic Loading

    NASA Astrophysics Data System (ADS)

    Pontes, J.; Walgraef, D.; Christov, C. I.

    2010-11-01

    Strain localization and dislocation pattern formation are typical features of plastic deformation in metals and alloys. Glide and climb dislocation motion along with accompanying production/annihilation processes of dislocations lead to the occurrence of instabilities of initially uniform dislocation distributions. These instabilities result into the development of various types of dislocation micro-structures, such as dislocation cells, slip and kink bands, persistent slip bands, labyrinth structures, etc., depending on the externally applied loading and the intrinsic lattice constraints. The Walgraef-Aifantis (WA) (Walgraef and Aifanits, J. Appl. Phys., 58, 668, 1985) model is an example of a reaction-diffusion model of coupled nonlinear equations which describe 0 formation of forest (immobile) and gliding (mobile) dislocation densities in the presence of cyclic loading. This paper discuss two versions of the WA model and focus on a finite difference, second order in time 1-Nicolson semi-implicit scheme, with internal iterations at each time step and a spatial splitting using the Stabilizing, Correction (Christov and Pontes, Mathematical and Computer Modelling, 35, 87, 2002) for solving the model evolution equations in two dimensions. The results of two simulations are presented. More complete results will appear in a forthcoming paper.

  16. The existence of uniform attractors for non-autonomous reaction-diffusion equations on the whole space

    NASA Astrophysics Data System (ADS)

    Xie, Yongqin; Zhu, Kaixuan; Sun, Chunyou

    2012-08-01

    In this paper, we introduce a new class of functions satisfying spacial absolutely continuous (see Definition 3.1), denoted by L2_{sac}({R};{R}n), which are translation bounded but not normal (see [S. S. Lu, H. Q. Wu, and C. K. Zhong, "Attractors for non-autonomous 2D Navier-Stokes equations with normal external forces," Discrete Contin. Dyn. Syst. A 13(3), 701-719 (2005)], 10.3934/dcds.2005.13.701 and Definition 3.1) in L2_{loc}({R};{R}n). Then the asymptotic a priori estimate is applied to some nonlinear reaction-diffusion equations with external forces g(x,s)in L2_{sac}({R};{R}n). We obtain the existence of uniform attractor together with its structure in the bi-spaces (L2({R}n), L2({R}n)) and (L2({R}n), Lp({R}n))(p>2) without any restriction on the growing order of the nonlinear term.

  17. Revisiting reaction-diffusion model of thermal desorption spectroscopy experiments on hydrogen retention in material for fusion applications

    NASA Astrophysics Data System (ADS)

    Guterl, Jerome; Smirnov, Roman; Krasheninnikov, Sergei

    2015-11-01

    Plasma-material interactions may strongly influence plasma performance and life-time of future magnetic fusion devices. Understanding the multifaceted physics of hydrogen retention in plasma-facing components (PFC) is thus crucial, but remains challenging due to the wide spectrum of retention processes on PFC surface and in PFC bulk induced by long-time exposure of PFC to high flux of energy and particles. We revisit here some aspects of reaction-diffusion models used to investigate hydrogen retention in material. We focus on analysis of thermal desorption spectroscopy (TDS) experiment considering only one type of traps in material and first neglecting surface effects. We show that solute hydrogen concentration in retention region usually remains in equilibrium during TDS experiments. In this regime, analytic description of thermal desorption spectra indicates that trapping of solute hydrogen during TDS cannot be ignored. Main features of thermal desorption are then analytically described and refined interpretation of Arrhenius plots is proposed. Effects of surface processes on hydrogen outgassing during TDS experiments are then introduced and surface-limited outgassing regimes are discussed.

  18. Algal morphogenesis: modelling interspecific variation in Micrasterias with reaction--diffusion patterned catalysis of cell surface growth

    PubMed Central

    Holloway, D. M.

    1999-01-01

    Semi-cell morphogenesis in unicellular desmid algae of the genus Micrasterias generates a stellar shape by repeated dichotomous branching of growing tips of the cell surface. The numerous species of the genus display variations of the branching pattern that differ markedly in number of branchings, lobe width and lobe length. We have modelled this morphogenesis, following previous work by D. M. Harrison and M. Kolar (1988), on the assumptions that patterning occurs by chemical reaction-diffusion activity within the plasma membrane, leading to morphological expression by patterned catalysis of the extension of the cell surface. The latter has been simulated in simplified form by two-dimensional computations. Our results indicate that for generation of repeated branchings and for the control of diverse species-specific shapes, the loss of patterning activity and of rapid growth in regions separating the active growing tips is an essential feature. We believe this conclusion to be much more general than the specific details of our model. We discuss the limitations of the model especially in terms of what extra features might be addressed in three-dimensional computation.

  19. Functional constraints method for constructing exact solutions to delay reaction-diffusion equations and more complex nonlinear equations

    NASA Astrophysics Data System (ADS)

    Polyanin, Andrei D.; Zhurov, Alexei I.

    2014-03-01

    We propose a new method for constructing exact solutions to nonlinear delay reaction-diffusion equations of the form ut=kuxx+F(u,w), where u=u(x,t),w=u(x,t-τ), and τ is the delay time. The method is based on searching for solutions in the form u=∑n=1Nξn(x)ηn(t), where the functions ξn(x) and ηn(t) are determined from additional functional constraints (which are difference or functional equations) and the original delay partial differential equation. All of the equations considered contain one or two arbitrary functions of a single argument. We describe a considerable number of new exact generalized separable solutions and a few more complex solutions representing a nonlinear superposition of generalized separable and traveling wave solutions. All solutions involve free parameters (in some cases, infinitely many parameters) and so can be suitable for solving certain problems and testing approximate analytical and numerical methods for nonlinear delay PDEs. The results are extended to a wide class of nonlinear partial differential-difference equations involving arbitrary linear differential operators of any order with respect to the independent variables x and t (in particular, this class includes the nonlinear delay Klein-Gordon equation) as well as to some partial functional differential equations with time-varying delay.

  20. Nucleic acid detection systems for enteroviruses.

    PubMed Central

    Rotbart, H A

    1991-01-01

    The enteroviruses comprise nearly 70 human pathogens responsible for a wide array of diseases including poliomyelitis, meningitis, myocarditis, and neonatal sepsis. Current diagnostic tests for the enteroviruses are limited in their use by the slow growth, or failure to grow, of certain serotypes in culture, the antigenic diversity among the serotypes, and the low titer of virus in certain clinical specimens. Within the past 6 years, applications of molecular cloning techniques, in vitro transcription vectors, automated nucleic acid synthesis, and the polymerase chain reaction have resulted in significant progress toward nucleic acid-based detection systems for the enteroviruses that take advantage of conserved genomic sequences across many, if not all, serotypes. Similar approaches to the study of enteroviral pathogenesis have already produced dramatic advances in our understanding of how these important viruses cause their diverse clinical spectra. PMID:1649002

  1. Fatty acid oxidation: systems analysis and applications.

    PubMed

    Cintolesi, Angela; Rodríguez-Moyá, María; Gonzalez, Ramon

    2013-01-01

    Fatty acids (FAs) are essential components of cellular structure and energy-generating routes in living organisms. They exist in a variety of chemical configurations and functionalities and are catabolized by different oxidative routes, according to their structure. α- and ω-Oxidation are minor routes that occur only in eukaryotes, while β-oxidation is the major degradation route in eukaroytes and prokaryotes. These pathways have been characterized and engineered from different perspectives for industrial and biomedical applications. The severity of FA oxidation disorders in humans initially guided the study of FA metabolism at a molecular-level. On the other hand, recent advances in metabolic engineering and systems biology have powered the study of FA biosynthetic and catabolic routes in microorganisms at a systems-level. Several studies have proposed these pathways as platforms for the production of fuels and chemicals from biorenewable sources. The lower complexity of microbial systems has allowed a more comprehensive study of FA metabolism and has opened opportunities for a wider range of applications. Still, there is a need for techniques that facilitate the translation of high-throughput data from microorganisms to more complex eukaryotic systems in order to aid the development of diagnostic and treatment strategies for FA oxidation disorders. In addition, further systems biology analyses on human systems could also provide valuable insights on oxidation disorders. This article presents a comparison of the three main FA oxidative routes, systems biology analyses that have been used to study FA metabolism, and engineering efforts performed on microbial systems. PMID:23661533

  2. Lysophosphatidic Acid signaling in the nervous system.

    PubMed

    Yung, Yun C; Stoddard, Nicole C; Mirendil, Hope; Chun, Jerold

    2015-02-18

    The brain is composed of many lipids with varied forms that serve not only as structural components but also as essential signaling molecules. Lysophosphatidic acid (LPA) is an important bioactive lipid species that is part of the lysophospholipid (LP) family. LPA is primarily derived from membrane phospholipids and signals through six cognate G protein-coupled receptors (GPCRs), LPA1-6. These receptors are expressed on most cell types within central and peripheral nervous tissues and have been functionally linked to many neural processes and pathways. This Review covers a current understanding of LPA signaling in the nervous system, with particular focus on the relevance of LPA to both physiological and diseased states. PMID:25695267

  3. Retinoic Acid in the Immune System

    PubMed Central

    Pino-Lagos, Karina; Benson, Micah J.; Noelle, Randolph J.

    2013-01-01

    On occasion, emerging scientific fields intersect and great discoveries result. In the last decade, the discovery of regulatory T cells (Treg) in immunity has revolutionized our understanding of how the immune system is controlled. Intersecting the rapidly emerging field of Treg function, has been the discovery that retinoic acid (RA) controls both the homing and differentiation of Treg. Instantly, the wealth and breadth of knowledge of the molecular basis for RA action, its receptors, and how it controls cellular differentiation can and will be exploited to understand its profound effects on Treg. Historically, vitamin A deprivation and repletion and RA agonists have been shown to profoundly affect immunity. Now these findings can be interpreted in light of the revelations that RA controls leukocyte homing and Treg function. PMID:19076350

  4. Hydroxybenzoic acid isomers and the cardiovascular system

    PubMed Central

    2014-01-01

    Today we are beginning to understand how phytochemicals can influence metabolism, cellular signaling and gene expression. The hydroxybenzoic acids are related to salicylic acid and salicin, the first compounds isolated that have a pharmacological activity. In this review we examine how a number of hydroxyphenolics have the potential to ameliorate cardiovascular problems related to aging such as hypertension, atherosclerosis and dyslipidemia. The compounds focused upon include 2,3-dihydroxybenzoic acid (Pyrocatechuic acid), 2,5-dihydroxybenzoic acid (Gentisic acid), 3,4-dihydroxybenzoic acid (Protocatechuic acid), 3,5-dihydroxybenzoic acid (α-Resorcylic acid) and 3-monohydroxybenzoic acid. The latter two compounds activate the hydroxycarboxylic acid receptors with a consequence there is a reduction in adipocyte lipolysis with potential improvements of blood lipid profiles. Several of the other compounds can activate the Nrf2 signaling pathway that increases the expression of antioxidant enzymes, thereby decreasing oxidative stress and associated problems such as endothelial dysfunction that leads to hypertension as well as decreasing generalized inflammation that can lead to problems such as atherosclerosis. It has been known for many years that increased consumption of fruits and vegetables promotes health. We are beginning to understand how specific phytochemicals are responsible for such therapeutic effects. Hippocrates’ dictum of ‘Let food be your medicine and medicine your food’ can now be experimentally tested and the results of such experiments will enhance the ability of nutritionists to devise specific health-promoting diets. PMID:24943896

  5. 21 CFR 862.1295 - Folic acid test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Folic acid test system. 862.1295 Section 862.1295 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1295 Folic acid test system. (a)...

  6. 21 CFR 862.1450 - Lactic acid test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Lactic acid test system. 862.1450 Section 862.1450 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1450 Lactic acid test system....

  7. 21 CFR 862.1775 - Uric acid test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Uric acid test system. 862.1775 Section 862.1775 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1775 Uric acid test system. (a) Identification....

  8. 21 CFR 862.1450 - Lactic acid test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Lactic acid test system. 862.1450 Section 862.1450 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1450 Lactic acid test system....

  9. Amino acid isotopic analysis in agricultural systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A relatively new approach to stable isotopic analysis—referred to as compound-specific isotopic analysis (CSIA)—has emerged, centering on the measurement of 15N:14N ratios in amino acids (glutamic acid and phenylalanine). CSIA has recently been used to generate trophic position estimates among anima...

  10. Tested Demonstrations: Color Oscillations in the Formic Acid-Nitric Acid-Sulfuric Acid System.

    ERIC Educational Resources Information Center

    Raw, C. J. G.; And Others

    1983-01-01

    Presented are procedures for demonstrating the production of color oscillations when nitric acid is added to a formic acid/concentrated sulfuric acid mixture. Because of safety considerations, "Super-8" home movie of the color changes was found to be satisfactory for demonstration purposes. (JN)

  11. Mathematical modeling of microbially induced crown corrosion in wastewater collection systems and laboratory investigation and modeling of sulfuric acid corrosion of concrete

    NASA Astrophysics Data System (ADS)

    Jahani, Fereidoun

    In the model for microbially induced crown corrosion, the diffusion of sulfide inside the concrete pores, its biological conversion to sulfuric acid, and the corrosion of calcium carbonate aggregates are represented. The corrosion front is modeled as a moving boundary. The location of the interface between the corrosion layer and the concrete is determined as part of the solution to the model equations. This model consisted of a system of one dimensional reaction-diffusion equations coupled to an equation describing the movement of the corrosion front. The equations were solved numerically using finite element Galerkin approximation. The concentration profiles of sulfide in the air and the liquid phases, the pH as a function of concrete depth, and the position of the corrosion front. A new equation for the corrosion rate was also derived. A more specific model for the degradation of a concrete specimen exposed to a sulfuric acid solution was also studied. In this model, diffusion of hydrogen ions and their reaction with alkaline components of concrete were expressed using Fick's Law of diffusion. The model equations described the moving boundary, the dissolution rate of alkaline components in the concrete, volume increase of sulfuric acid solution over the concrete specimen, and the boundary conditions on the surface of the concrete. An apparatus was designed and experiments were performed to measure pH changes on the surface of concrete. The data were used to calculate the dissolution rate of the concrete and, with the model, to determine the diffusion rate of sulfuric acid in the corrosion layer and corrosion layer thickness. Electrochemical Impedance Spectroscopy (EIS) was used to study the corrosion rate of iron pins embedded in the concrete sample. The open circuit potential (OCP) determined the onset of corrosion on the surface of the pins. Visual observation of the corrosion layer thickness was in good agreement with the simulation results.

  12. Continuous-flow free acid monitoring method and system

    DOEpatents

    Strain, J.E.; Ross, H.H.

    1980-01-11

    A free acid monitoring method and apparatus is provided for continuously measuring the excess acid present in a process stream. The disclosed monitoring system and method is based on the relationship of the partial pressure ratio of water and acid in equilibrium with an acid solution at constant temperature. A portion of the process stream is pumped into and flows through the monitor under the influence of gravity and back to the process stream. A continuous flowing sample is vaporized at a constant temperature and the vapor is subsequently condensed. Conductivity measurements of the condensate produces a nonlinear response function from which the free acid molarity of the sample process stream is determined.

  13. Continuous-flow free acid monitoring method and system

    DOEpatents

    Strain, James E.; Ross, Harley H.

    1981-01-01

    A free acid monitoring method and apparatus is provided for continuously measuring the excess acid present in a process stream. The disclosed monitoring system and method is based on the relationship of the partial pressure ratio of water and acid in equilibrium with an acid solution at constant temperature. A portion of the process stream is pumped into and flows through the monitor under the influence of gravity and back to the process stream. A continuous flowing sample is vaporized at a constant temperature and the vapor is subsequently condensed. Conductivity measurements of the condensate produces a nonlinear response function from which the free acid molarity of the sample process stream is determined.

  14. Nucleic acid detection system and method for detecting influenza

    SciTech Connect

    Cai, Hong; Song, Jian

    2015-03-17

    The invention provides a rapid, sensitive and specific nucleic acid detection system which utilizes isothermal nucleic acid amplification in combination with a lateral flow chromatographic device, or DNA dipstick, for DNA-hybridization detection. The system of the invention requires no complex instrumentation or electronic hardware, and provides a low cost nucleic acid detection system suitable for highly sensitive pathogen detection. Hybridization to single-stranded DNA amplification products using the system of the invention provides a sensitive and specific means by which assays can be multiplexed for the detection of multiple target sequences.

  15. System for agitating the acid in a lead-acid battery

    DOEpatents

    Weintraub, Alvin; MacCormack, Robert S.

    1987-01-01

    A system and method for agitating the acid in a large lead-sulfuric acid storage battery of the calcium type. An air-lift is utilized to provide the agitation. The air fed to the air-lift is humidified prior to being delivered to the air-lift.

  16. Amino Acid Synthesis in a Supercritical Carbon Dioxide - Water System

    PubMed Central

    Fujioka, Kouki; Futamura, Yasuhiro; Shiohara, Tomoo; Hoshino, Akiyoshi; Kanaya, Fumihide; Manome, Yoshinobu; Yamamoto, Kenji

    2009-01-01

    Mars is a CO2-abundant planet, whereas early Earth is thought to be also CO2-abundant. In addition, water was also discovered on Mars in 2008. From the facts and theory, we assumed that soda fountains were present on both planets, and this affected amino acid synthesis. Here, using a supercritical CO2/liquid H2O (10:1) system which mimicked crust soda fountains, we demonstrate production of amino acids from hydroxylamine (nitrogen source) and keto acids (oxylic acid sources). In this research, several amino acids were detected with an amino acid analyzer. Moreover, alanine polymers were detected with LC-MS. Our research lights up a new pathway in the study of life’s origin. PMID:19582225

  17. 300 Area waste acid treatment system closure plan. Revision 1

    SciTech Connect

    1996-03-01

    This section provides a description of the Hanford Site, identifies the proposed method of 300 Area Waste Acid Treatment System (WATS) closure, and briefly summarizes the contents of each chapter of this plan.

  18. Acid-base homeostasis in the human system

    NASA Technical Reports Server (NTRS)

    White, R. J.

    1974-01-01

    Acid-base regulation is a cooperative phenomena in vivo with body fluids, extracellular and intracellular buffers, lungs, and kidneys all playing important roles. The present account is much too brief to be considered a review of present knowledge of these regulatory systems, and should be viewed, instead, as a guide to the elements necessary to construct a simple model of the mutual interactions of the acid-base regulatory systems of the body.

  19. A computational method for the coupled solution of reaction-diffusion equations on evolving domains and manifolds: Application to a model of cell migration and chemotaxis

    NASA Astrophysics Data System (ADS)

    MacDonald, G.; Mackenzie, J. A.; Nolan, M.; Insall, R. H.

    2016-03-01

    In this paper, we devise a moving mesh finite element method for the approximate solution of coupled bulk-surface reaction-diffusion equations on an evolving two dimensional domain. Fundamental to the success of the method is the robust generation of bulk and surface meshes. For this purpose, we use a novel moving mesh partial differential equation (MMPDE) approach. The developed method is applied to model problems with known analytical solutions; these experiments indicate second-order spatial and temporal accuracy. Coupled bulk-surface problems occur frequently in many areas; in particular, in the modelling of eukaryotic cell migration and chemotaxis. We apply the method to a model of the two-way interaction of a migrating cell in a chemotactic field, where the bulk region corresponds to the extracellular region and the surface to the cell membrane.

  20. Computed phase diagrams for the system: Sodium hydroxide-uric acid-hydrochloric acid-water

    NASA Astrophysics Data System (ADS)

    Brown, W. E.; Gregory, T. M.; Füredi-Milhofer, H.

    1987-07-01

    Renal stone formation is made complex by the variety of solid phases that are formed, by the number of components in the aqueous phase, and by the multiplicity of ionic dissociation and association processes that are involved. In the present work we apply phase diagrams calculated by the use of equilibrium constants from the ternary system sodium hydroxide-uric acid-water to simplify and make more rigorous the understanding of the factors governing dissolution and precipitation of uric acid (anhydrous and dihydrate) and sodium urate monohydrate. The system is then examined in terms of four components. Finally, procedures are described for fluids containing more than four components. The isotherms, singular points, and fields of supersaturation and undersaturation are shown in various forms of phase diagrams. This system has two notable features: (1) in the coordinates -log[H 2U] versus -log[NaOH], the solubility isotherms for anhydrous uric acid and uric acid dihydrate approximate straight lines with slopes equal to +1 over a wide range of concentrations. As a result, substantial quantities of sodium acid urate monohydrate can precipitate from solution or dissolve without changing the degree of saturation of uric acid significantly. (2) The solubility isotherm for NaHU·H 2O has a deltoid shape with the low-pH branch having a slope of infinity. As a result of the vertical slope of this isotherm, substantial quantities of uric acid can dissolve or precipitate without changing the degree of saturation of sodium acid urate monohydrate significantly. The H 2U-NaOH singular point has a pH of 6.87 at 310 K in the ternary system.

  1. 21 CFR 862.1095 - Ascorbic acid test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Ascorbic acid test system. 862.1095 Section 862.1095 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  2. 21 CFR 862.1290 - Fatty acids test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Fatty acids test system. 862.1290 Section 862.1290 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  3. 21 CFR 862.1290 - Fatty acids test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Fatty acids test system. 862.1290 Section 862.1290 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  4. 21 CFR 862.1095 - Ascorbic acid test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Ascorbic acid test system. 862.1095 Section 862.1095 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  5. 21 CFR 862.1320 - Gastric acidity test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Gastric acidity test system. 862.1320 Section 862.1320 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  6. 21 CFR 862.1295 - Folic acid test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Folic acid test system. 862.1295 Section 862.1295 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  7. 21 CFR 862.1320 - Gastric acidity test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Gastric acidity test system. 862.1320 Section 862.1320 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  8. 21 CFR 862.1095 - Ascorbic acid test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Ascorbic acid test system. 862.1095 Section 862.1095 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  9. 21 CFR 862.1290 - Fatty acids test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Fatty acids test system. 862.1290 Section 862.1290 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  10. 21 CFR 862.1295 - Folic acid test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Folic acid test system. 862.1295 Section 862.1295 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  11. 21 CFR 862.1095 - Ascorbic acid test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Ascorbic acid test system. 862.1095 Section 862.1095 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  12. 21 CFR 862.1295 - Folic acid test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Folic acid test system. 862.1295 Section 862.1295 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  13. 21 CFR 862.1290 - Fatty acids test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Fatty acids test system. 862.1290 Section 862.1290 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  14. 21 CFR 862.1095 - Ascorbic acid test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Ascorbic acid test system. 862.1095 Section 862.1095 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  15. 21 CFR 862.1295 - Folic acid test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Folic acid test system. 862.1295 Section 862.1295 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  16. 21 CFR 862.1320 - Gastric acidity test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Gastric acidity test system. 862.1320 Section 862.1320 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  17. 21 CFR 862.1320 - Gastric acidity test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Gastric acidity test system. 862.1320 Section 862.1320 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  18. 21 CFR 862.1320 - Gastric acidity test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Gastric acidity test system. 862.1320 Section 862.1320 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems §...

  19. 21 CFR 862.1509 - Methylmalonic acid (nonquantitative) test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Methylmalonic acid (nonquantitative) test system. 862.1509 Section 862.1509 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1509...

  20. Jasmonic acid and salicylic acid activate a common defense system in rice

    PubMed Central

    Tamaoki, Daisuke; Seo, Shigemi; Yamada, Shoko; Kano, Akihito; Miyamoto, Ayumi; Shishido, Hodaka; Miyoshi, Seika; Taniguchi, Shiduku; Akimitsu, Kazuya; Gomi, Kenji

    2013-01-01

    Jasmonic acid (JA) and salicylic acid (SA) play important roles in plant defense systems. JA and SA signaling pathways interact antagonistically in dicotyledonous plants, but, the status of crosstalk between JA and SA signaling is unknown in monocots. Our rice microarray analysis showed that more than half of the genes upregulated by the SA analog BTH are also upregulated by JA, suggesting that a major portion of the SA-upregulated genes are regulated by JA-dependent signaling in rice. A common defense system that is activated by both JA and SA is thus proposed which plays an important role in pathogen defense responses in rice. PMID:23518581

  1. Dissolution state of cellulose in aqueous systems. 2. Acidic solvents.

    PubMed

    Alves, Luis; Medronho, Bruno; Antunes, Filipe E; Topgaard, Daniel; Lindman, Björn

    2016-10-20

    Cellulose is insoluble in water but can be dissolved in strong acidic or alkaline conditions. How well dissolved cellulose is in solution and how it organizes are key questions often neglected in literature. The typical low pH required for dissolving cellulose in acidic solvents limits the use of typical characterization techniques. In this respect, Polarization Transfer Solid State NMR (PT ssNMR) emerges as a reliable alternative. In this work, combining PT ssNMR, microscopic techniques and X-ray diffraction, a set of different acidic systems (phosphoric acid/water, sulfuric acid/glycerol and zinc chloride/water) is investigated. The studied solvent systems are capable to efficiently dissolve cellulose, although degradation occurs to some extent. PT ssNMR is capable to identify the liquid and solid fractions of cellulose, the degradation products and it is also sensitive to gelation. The materials regenerated from the acidic dopes were found to be highly sensitive to the solvent system and to the presence of amphiphilic additives in solution. PMID:27474617

  2. IUPAC-NIST Solubility Data Series. 90. Hydroxybenzoic Acid Derivatives in Binary and Ternary Systems. Part II. Hydroxybenzoic Acids, Hydroxybenzoates, and Hydroxybenzoic Acid Salts in Nonaqueous Systems

    NASA Astrophysics Data System (ADS)

    Goto, Ayako; Miyamoto, Hiroshi; Salomon, Mark; Goto, Rensuke; Fukuda, Hiroshi; Königsberger, Erich; Königsberger, Lan-Chi; Scharlin, Pirketta

    2011-06-01

    The solid-liquid solubility data for well defined nonaqueous binary and ternary systems are reviewed. One component includes hydroxybenzoic acid, hydroxybenzoate, and hydroxybenzoic acid salt, and another component includes a variety of organic compounds (hydrocarbons, alcohols, halogenated hydrocarbons, carboxylic acids, esters, et al.) and carbon dioxide. The ternary systems include mixtures of organic substances of various classes and carbon dioxide. The total number of compilation sheets is 270 for six types of system. Almost all data are expressed as mass percent and mole fraction as well as the originally reported units, while some data are expressed as molar concentration. Critical evaluation was carried out for the binary nonaqueous systems of 2-, 3-, and 4-hydroxybenzoic acids and hydroxybenzoates (methylparaben, ethylparaben, propylparaben, and butylparaben) in alcohols, 1-heptane, and benzene.

  3. Phase diagram of a system of adipic, glutaric, and sebacic acids

    NASA Astrophysics Data System (ADS)

    Kolyado, A. V.; Alenova, S. M.; Garkushin, I. K.

    2016-06-01

    Adipic acid-glutaric acid, glutaric acid-sebacic acid, and adipic acid-sebacic acid binary systems are studied, along with an adipic acid-glutaric acid-sebacic acid ternary system. It is shown all of these systems are eutectic. Phase equilibria for the diagram elements of the binary systems and the ternary system are described. It is concluded that the above low-melting compounds can be recommended for use as working bodies in heat accumulators, and for preparing electrolytes used in the thin-layer anodic oxidation of aluminum alloys.

  4. The influence of receptor-mediated interactions on reaction-diffusion mechanisms of cellular self-organisation.

    PubMed

    Klika, Václav; Baker, Ruth E; Headon, Denis; Gaffney, Eamonn A

    2012-04-01

    Understanding the mechanisms governing and regulating self-organisation in the developing embryo is a key challenge that has puzzled and fascinated scientists for decades. Since its conception in 1952 the Turing model has been a paradigm for pattern formation, motivating numerous theoretical and experimental studies, though its verification at the molecular level in biological systems has remained elusive. In this work, we consider the influence of receptor-mediated dynamics within the framework of Turing models, showing how non-diffusing species impact the conditions for the emergence of self-organisation. We illustrate our results within the framework of hair follicle pre-patterning, showing how receptor interaction structures can be constrained by the requirement for patterning, without the need for detailed knowledge of the network dynamics. Finally, in the light of our results, we discuss the ability of such systems to pattern outside the classical limits of the Turing model, and the inherent dangers involved in model reduction. PMID:22072186

  5. Bile acid nuclear receptor FXR and digestive system diseases

    PubMed Central

    Ding, Lili; Yang, Li; Wang, Zhengtao; Huang, Wendong

    2015-01-01

    Bile acids (BAs) are not only digestive surfactants but also important cell signaling molecules, which stimulate several signaling pathways to regulate some important biological processes. The bile-acid-activated nuclear receptor, farnesoid X receptor (FXR), plays a pivotal role in regulating bile acid, lipid and glucose homeostasis as well as in regulating the inflammatory responses, barrier function and prevention of bacterial translocation in the intestinal tract. As expected, FXR is involved in the pathophysiology of a wide range of diseases of gastrointestinal tract, including inflammatory bowel disease, colorectal cancer and type 2 diabetes. In this review, we discuss current knowledge of the roles of FXR in physiology of the digestive system and the related diseases. Better understanding of the roles of FXR in digestive system will accelerate the development of FXR ligands/modulators for the treatment of digestive system diseases. PMID:26579439

  6. 300 Area waste acid treatment system closure plan

    SciTech Connect

    LUKE, S.N.

    1999-05-17

    The Hanford Facility Dangerous Waste Permit Application is considered to be a single application organized into a General Information Portion (document number DOERL-91-28) and a Unit-Specific Portion. The scope of the Unit-Specific Portion includes closure plan documentation submitted for individual, treatment, storage, and/or disposal units undergoing closure, such as the 300 Area Waste Acid Treatment System. Documentation contained in the General Information Portion is broader in nature and could be used by multiple treatment, storage, and/or disposal units (e.g., the glossary provided in the General Information Portion). Whenever appropriate, 300 Area Waste Acid Treatment System documentation makes cross-reference to the General Information Portion, rather than duplicating text. This 300 Area Waste Acid Treatment System Closure Plan (Revision 2) includes a Hanford Facility Dangerous Waste Permit Application, Part A, Form 3. Information provided in this closure plan is current as of April 1999.

  7. Bile acid nuclear receptor FXR and digestive system diseases.

    PubMed

    Ding, Lili; Yang, Li; Wang, Zhengtao; Huang, Wendong

    2015-03-01

    Bile acids (BAs) are not only digestive surfactants but also important cell signaling molecules, which stimulate several signaling pathways to regulate some important biological processes. The bile-acid-activated nuclear receptor, farnesoid X receptor (FXR), plays a pivotal role in regulating bile acid, lipid and glucose homeostasis as well as in regulating the inflammatory responses, barrier function and prevention of bacterial translocation in the intestinal tract. As expected, FXR is involved in the pathophysiology of a wide range of diseases of gastrointestinal tract, including inflammatory bowel disease, colorectal cancer and type 2 diabetes. In this review, we discuss current knowledge of the roles of FXR in physiology of the digestive system and the related diseases. Better understanding of the roles of FXR in digestive system will accelerate the development of FXR ligands/modulators for the treatment of digestive system diseases. PMID:26579439

  8. Gas dilution system results and application to acid rain utilities

    SciTech Connect

    Jolley-Souders, K.; Geib, R.; Dunn, C.

    1997-12-31

    In 1997, the United States EPA will remove restrictions preventing acid rain utilities from using gas dilution systems for calibration or linearity studies for continuous emissions monitoring, Test Method 205 in 40CFR51 requires that a gas dilution system must produce calibration gases whose measured values are within {+-}2% of predicted values. This paper presents the evaluation of the Environics/CalMat 2020 Dilution System for use in calibration studies. Internal studies show that concentrations generated by this unit are within {+-}0.5% of predicted values. Studies are being conducted by several acid rain utilities to evaluate the Environics/CalMat system using single minor component calibration standards. In addition, an internally generated study is being performed to demonstrate the system`s accuracy using a multi-component gas mixture. Data from these tests will be presented in the final version of the paper.

  9. Reaction-diffusion based co-synthesis of stable α- and β-cobalt hydroxide in bio-organic gels

    NASA Astrophysics Data System (ADS)

    Al-Ghoul, Mazen; El-Rassy, Houssam; Coradin, Thibaud; Mokalled, Tharwat

    2010-03-01

    We report the preparation, dynamics of formation and extensive characterization of a stable two-phase system of crystalline α- and β-Co(OH) 2. The method is based on the reaction and diffusion of hydroxide ions into a biopolymer gel (agar, gelatin) containing Co(II). The spatio-temporal dynamics leading to the formation and coexistence of two polymorphs exhibit a complicated and rich pattern whereby the system proceeds as a propagating Ostwald ripening front that continuously transforms blue/green α-Co(OH) 2 to crystalline β-Co(OH) 2. Depending on the nature of the gel, the system might further exhibit fascinating Liesegang bands. The coexisting polymorphs were characterized using XRD, FTIR, UV-vis, TGA, SEM and TEM, and EPR. The FTIR spectra reveal the intercalation of water molecules and chloride ions between the hydroxyl layers in the case of α-Co(OH) 2. X-ray diffraction and electronic microscopy investigations confirm the aforementioned Ostwald ripening process during the phase transformation whereby almost-amorphous α-Co(OH) 2 dissolves to form crystalline β-Co(OH) 2 5 μm in length. The UV-vis reflectance spectra reveal that the origin of the blue/green color in the α-polymorph is due to the tetrahedrally coordinated Co(II) ions existing within the octahedral Co(II) layers. The reorganization of these tetrahedral Co(II) ions in the α-polymorph to form octahedral Co(II) in the β-polymorph is shown to take place in seconds without induction time. α-Co(OH) 2 was found to be mesoporous while the β-polymorph is microporous with low nitrogen adsorption capacities. Due to dipole-dipole broadening, no EPR spectrum was obtained for the β-polymorphs even at low temperature. In contrast, the obtained EPR spectrum of the α-polymorph was consistent with that of Co(II) in various materials.

  10. Status of commercial phosphoric acid fuel cell system development

    NASA Technical Reports Server (NTRS)

    Warshay, M.; Prokopius, P. R.; Simons, S. N.; King, R. B.

    1981-01-01

    A review of the current commercial phosphoric acid fuel cell system development efforts is presented. In both the electric utility and on-site integrated energy system applications, reducing cost and increasing reliability are important. The barrier to the attainment of these goals has been materials. The differences in approach among the three major participants are their technological features, including electrodes, matrices, intercell cooling, bipolar/separator plates, electrolyte management, fuel selection and system design philosophy.

  11. Phorbic Acid Biosynthesis in the Latex Vessel System of Euphorbia

    PubMed Central

    Nordal, Arnold; Benson, A. A.

    1969-01-01

    Evidence is presented that phorbic acid is formed in the latex producing cell system, rather than in photosynthetic or chlorophyll-free tissues of Euphorbia resinifera Berg. When a branch of the plant was kept first in a 14CO2 atmosphere with 12 hr light-dark periods for 2 days and then left under natural conditions in the air outside for at least 2 to 3 days, radioactive phorbic acid was found in the latex. Phorbic acid synthesis appeared to be independent of the photosynthetic and respiratory activities of the plant. Besides phorbic acid 2 other major radioactive compounds were recognized in the latex, a glycoside or oligosaccharide, and a lipid belonging to the group of triterpenoid compounds characteristic of the latex in several species of Euphorbia. Images PMID:16657036

  12. ACID PRECIPITATION IN NORTH AMERICA: 1984 ANNUAL DATA SUMMARY FROM ACID DEPOSITION SYSTEM DATA BASE

    EPA Science Inventory

    The report gives a summary of 1984 wet deposition precipitation chemistry data collected in North America and available in the Acid Deposition System (ADS) data base. North American wet deposition monitoring networks with data in ADS are NADP/NTN, CANSAP, APN, UAPSP, MAP3S/PCN, W...

  13. ACID PRECIPITATION IN NORTH AMERICA: 1983 ANNUAL DATA SUMMARY FROM ACID DEPOSITION SYSTEM DATA BASE

    EPA Science Inventory

    The report gives a summary of 1983 wet deposition precipitation chemistry data collected in North America and available in the Acid Deposition System (ADS) data base. North American wet deposition monitoring networks with data in ADS are NADP/NTN, CANSAP, APN, UAPSP, MAP3S/PCN, W...

  14. Lead/acid batteries in systems to improve power quality

    NASA Astrophysics Data System (ADS)

    Taylor, P.; Butler, P.; Nerbun, W.

    Increasing dependence on computer technology is driving needs for extremely high-quality power to prevent loss of information, material, and workers' time that represent billions of dollars annually. This cost has motivated commercial and Federal research and development of energy storage systems that detect and respond to power-quality failures in milliseconds. Electrochemical batteries are among the storage media under investigation for these systems. Battery energy storage systems that employ either flooded lead/acid or valve-regulated lead/acid battery technologies are becoming commercially available to capture a share of this emerging market. Cooperative research and development between the US Department of Energy and private industry have led to installations of lead/acid-based battery energy storage systems to improve power quality at utility and industrial sites and commercial development of fully integrated, modular battery energy storage system products for power quality. One such system by AC Battery Corporation, called the PQ2000, is installed at a test site at Pacific Gas and Electric Company (San Ramon, CA, USA) and at a customer site at Oglethorpe Power Corporation (Tucker, GA, USA). The PQ2000 employs off-the-shelf power electronics in an integrated methodology to control the factors that affect the performance and service life of production-model, low-maintenance, flooded lead/acid batteries. This system, and other members of this first generation of lead/acid-based energy storage systems, will need to compete vigorously for a share of an expanding, yet very aggressive, power quality market.

  15. Microtubule self-organisation by reaction-diffusion processes causes collective transport and organisation of cellular particles

    PubMed Central

    Glade, Nicolas; Demongeot, Jacques; Tabony, James

    2004-01-01

    Background The transport of intra-cellular particles by microtubules is a major biological function. Under appropriate in vitro conditions, microtubule preparations behave as a 'complex' system and show 'emergent' phenomena. In particular, they form dissipative structures that self-organise over macroscopic distances by a combination of reaction and diffusion. Results Here, we show that self-organisation also gives rise to a collective transport of colloidal particles along a specific direction. Particles, such as polystyrene beads, chromosomes, nuclei, and vesicles are carried at speeds of several microns per minute. The process also results in the macroscopic self-organisation of these particles. After self-organisation is completed, they show the same pattern of organisation as the microtubules. Numerical simulations of a population of growing and shrinking microtubules, incorporating experimentally realistic reaction dynamics, predict self-organisation. They forecast that during self-organisation, macroscopic parallel arrays of oriented microtubules form which cross the reaction space in successive waves. Such travelling waves are capable of transporting colloidal particles. The fact that in the simulations, the aligned arrays move along the same direction and at the same speed as the particles move, suggest that this process forms the underlying mechanism for the observed transport properties. Conclusions This process constitutes a novel physical chemical mechanism by which chemical energy is converted into collective transport of colloidal particles along a given direction. Self-organisation of this type provides a new mechanism by which intra cellular particles such as chromosomes and vesicles can be displaced and simultaneously organised by microtubules. It is plausible that processes of this type occur in vivo. PMID:15176973

  16. High Level Waste System Impacts from Acid Dissolution of Sludge

    SciTech Connect

    KETUSKY, EDWARD

    2006-04-20

    This research evaluates the ability of OLI{copyright} equilibrium based software to forecast Savannah River Site High Level Waste system impacts from oxalic acid dissolution of Tank 1-15 sludge heels. Without further laboratory and field testing, only the use of oxalic acid can be considered plausible to support sludge heel dissolution on multiple tanks. Using OLI{copyright} and available test results, a dissolution model is constructed and validated. Material and energy balances, coupled with the model, identify potential safety concerns. Overpressurization and overheating are shown to be unlikely. Corrosion induced hydrogen could, however, overwhelm the tank ventilation. While pH adjustment can restore the minimal hydrogen generation, resultant precipitates will notably increase the sludge volume. OLI{copyright} is used to develop a flowsheet such that additional sludge vitrification canisters and other negative system impacts are minimized. Sensitivity analyses are used to assess the processability impacts from variations in the sludge/quantities of acids.

  17. 21 CFR 862.3580 - Lysergic acid diethylamide (LSD) test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Lysergic acid diethylamide (LSD) test system. 862... Test Systems § 862.3580 Lysergic acid diethylamide (LSD) test system. (a) Identification. A lysergic acid diethylamide (LSD) test system is a device intended to measure lysergic acid diethylamide,...

  18. 21 CFR 862.3580 - Lysergic acid diethylamide (LSD) test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Lysergic acid diethylamide (LSD) test system. 862... Test Systems § 862.3580 Lysergic acid diethylamide (LSD) test system. (a) Identification. A lysergic acid diethylamide (LSD) test system is a device intended to measure lysergic acid diethylamide,...

  19. 21 CFR 862.3580 - Lysergic acid diethylamide (LSD) test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Lysergic acid diethylamide (LSD) test system. 862... Test Systems § 862.3580 Lysergic acid diethylamide (LSD) test system. (a) Identification. A lysergic acid diethylamide (LSD) test system is a device intended to measure lysergic acid diethylamide,...

  20. 21 CFR 862.3580 - Lysergic acid diethylamide (LSD) test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Lysergic acid diethylamide (LSD) test system. 862... Test Systems § 862.3580 Lysergic acid diethylamide (LSD) test system. (a) Identification. A lysergic acid diethylamide (LSD) test system is a device intended to measure lysergic acid diethylamide,...

  1. 21 CFR 862.3580 - Lysergic acid diethylamide (LSD) test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Lysergic acid diethylamide (LSD) test system. 862... Test Systems § 862.3580 Lysergic acid diethylamide (LSD) test system. (a) Identification. A lysergic acid diethylamide (LSD) test system is a device intended to measure lysergic acid diethylamide,...

  2. Implementation and efficiency analysis of an adaptive hp-finite element method for solving boundary value problems for the stationary reaction-diffusion equation

    NASA Astrophysics Data System (ADS)

    Zolotareva, N. D.; Nikolaev, E. S.

    2016-05-01

    An iterative process implementing an adaptive hp-version of the finite element method (FEM) previously proposed by the authors for the approximate solution of boundary value problems for the stationary reaction-diffusion equation is described. The method relies on piecewise polynomial basis functions and makes use of an adaptive strategy for constructing a sequence of finite-dimensional subspaces based on the computation of correction indicators. Singularly perturbed boundary value test problems with smooth and not very smooth solutions are used to analyze the efficiency of the method in the situation when an approximate solution has to be found with high accuracy. The convergence of the approximate solution to the exact one is investigated depending on the value of the small parameter multiplying the highest derivative, on the family of basis functions and the quadrature formulas used, and on the internal parameters of the method. The method is compared with an adaptive h-version of FEM that also relies on correction indicators and with its nonadaptive variant based on the bisection of grid intervals.

  3. 21 CFR 862.1305 - Formiminoglutamic acid (FIGLU) test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Formiminoglutamic acid (FIGLU) test system. 862.1305 Section 862.1305 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical...

  4. 21 CFR 862.1305 - Formiminoglutamic acid (FIGLU) test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Formiminoglutamic acid (FIGLU) test system. 862.1305 Section 862.1305 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical...

  5. 21 CFR 862.1305 - Formiminoglutamic acid (FIGLU) test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Formiminoglutamic acid (FIGLU) test system. 862.1305 Section 862.1305 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical...

  6. ACID EXTRACTION TREATMENT SYSTEM FOR TREATMENT OF METAL CONTAMINATED SOILS

    EPA Science Inventory

    The Acid Extraction Treatment System (AETS) reduces the concentrations and/or leachability of heavy metals in contaminated soils so the soil can be returned to the site from which it originated. he objective of the project was to determine the effectiveness and commercial viabili...

  7. Skin delivery of ferulic acid from different vesicular systems.

    PubMed

    Chen, Ming; Liu, Xiangli; Fahr, Alfred

    2010-10-01

    The aim of the present research is to evaluate the skin delivery capabilities of different vesicular systems, including conventional liposomes (CL), Tween 80-based deformable liposomes (DL), invasomes (INS) and ethosomes bearing ferulic acid (FA) being an antioxidant exhibiting a wide range of therapeutic effects against various diseases. All of the test formulations were characterized for particle size distribution, zeta-potential, vesicular shape and surface morphology, in vitro human skin permeation and skin deposition. Dynamic Light Scattering (DLS) and Transmission Electron Microscopy (TEM) defined that all of liposomal vesicles were almost spherical, displaying unilamellar structures with low polydispersity (PDI < 0.2) and nanometric size range (z-average no more than 150 nm). In addition, all the vesicular systems except conventional liposomes were negatively charged to a certain extent. In vitro skin permeation and skin deposition experiments demonstrated that the permeation profile of ferulic acid through human stratum corneum epidermis membrane (SCE) and the drug deposition in skin were both improved significantly using these vesicular liposomal systems. Permeation and skin deposition enhancing effect was highlighted by the ethosomal system containing 18.0 mg/ml of ferulic acid with an significantly (P < 0.01) enhanced skin flux (267.8 +/- 16.77 microg/cm2/h) and skin drug deposition (51.67 +/- 1.94 microg/cm2), which was 75 times and 7.3 times higher than those of ferulic acid from saturated PBS (pH 7.4) solution, respectively. This study demonstrated that ethosomes are promising vesicular carriers for delivering ferulic acid into or across the skin. PMID:21329050

  8. Erythrocyte Saturated Fatty Acids and Systemic Inflammation in Adults

    PubMed Central

    Mu, Lin; Mukamal, Kenneth J.; Naqvi, Asghar Z.

    2014-01-01

    Objective The role of saturated fatty acids (SFAs) in chronic disease remains controversial; inflammation is one pathway by which SFAs influence the risk of chronic disease. We aim to investigate the associations between red blood cell (RBC) phospholipid SFAs and systemic inflammation. Methods As part of a randomized controlled trial, we measured RBC phospholipid FA composition among 55 generally healthy adults twice at three-month intervals. We estimated associations of RBC total SFAs and two major SFA subtypes, palmitic and stearic acids, with C-reactive protein (CRP), interleukin-6 (IL-6), white blood count (WBC), and a composite inflammation measure using generalized estimating equations in multivariable FA substitution models. Results Mean (±SD) SFA level across both visits was 45±3% of the total RBC FAs, mainly palmitic (21±1%) and stearic (17±3%) acids. In models adjusted for age, sex, race, smoking, BMI, statin use, aspirin use, transunsaturated FAs, and ω3FAs, SFAs were significantly associated with IL-6 (20% increase per 1 SD increment; 95% CI: 0.03%, 43%; P=0.05) and the composite inflammation measure (P=0.05) and marginally associated with CRP (34% increase; − 1%, 81%; P=0.06), but not associated with WBC. Stearic acid was positively associated with CRP (35% increase; 2%, 79%; P=0.04). Palmitic acid was marginally associated with the composite inflammation measure (P=0.06) and, upon additional ω6FA adjustment, significantly associated with IL-6 (15% increase; 0.4%, 27%; P=0.006). Conclusions RBC SFAs, which represent longer-term dietary intake, are positively associated with inflammation. In particular, palmitic acid was associated with IL-6, and stearic acid was associated with CRP after multivariable adjustment. PMID:25280420

  9. Commercial phosphoric acid fuel cell system technology development

    NASA Technical Reports Server (NTRS)

    Prokopius, P. R.; Warshay, M.; Simons, S. N.; King, R. B.

    1979-01-01

    A review of the current commercial phosphoric acid fuel cell system technology development efforts is presented. In both the electric utility and on-site integrated energy system applications, reducing cost and increasing reliability are the technology drivers at this time. The longstanding barrier to the attainment of these goals, which manifests itself in a number of ways, has been materials. The differences in approach among the three major participants (United Technologies Corporation (UTC), Westinghouse Electric Corporation/Energy Research Corporation (ERC), and Engelhard Industries) and their unique technological features, including electrodes, matrices, intercell cooling, bipolar/separator plates, electrolyte management, fuel selection and system design philosophy are discussed.

  10. Systems solutions by lactic acid bacteria: from paradigms to practice

    PubMed Central

    2011-01-01

    Lactic acid bacteria are among the powerhouses of the food industry, colonize the surfaces of plants and animals, and contribute to our health and well-being. The genomic characterization of LAB has rocketed and presently over 100 complete or nearly complete genomes are available, many of which serve as scientific paradigms. Moreover, functional and comparative metagenomic studies are taking off and provide a wealth of insight in the activity of lactic acid bacteria used in a variety of applications, ranging from starters in complex fermentations to their marketing as probiotics. In this new era of high throughput analysis, biology has become big science. Hence, there is a need to systematically store the generated information, apply this in an intelligent way, and provide modalities for constructing self-learning systems that can be used for future improvements. This review addresses these systems solutions with a state of the art overview of the present paradigms that relate to the use of lactic acid bacteria in industrial applications. Moreover, an outlook is presented of the future developments that include the transition into practice as well as the use of lactic acid bacteria in synthetic biology and other next generation applications. PMID:21995776

  11. Systems solutions by lactic acid bacteria: from paradigms to practice.

    PubMed

    de Vos, Willem M

    2011-08-30

    Lactic acid bacteria are among the powerhouses of the food industry, colonize the surfaces of plants and animals, and contribute to our health and well-being. The genomic characterization of LAB has rocketed and presently over 100 complete or nearly complete genomes are available, many of which serve as scientific paradigms. Moreover, functional and comparative metagenomic studies are taking off and provide a wealth of insight in the activity of lactic acid bacteria used in a variety of applications, ranging from starters in complex fermentations to their marketing as probiotics. In this new era of high throughput analysis, biology has become big science. Hence, there is a need to systematically store the generated information, apply this in an intelligent way, and provide modalities for constructing self-learning systems that can be used for future improvements. This review addresses these systems solutions with a state of the art overview of the present paradigms that relate to the use of lactic acid bacteria in industrial applications. Moreover, an outlook is presented of the future developments that include the transition into practice as well as the use of lactic acid bacteria in synthetic biology and other next generation applications. PMID:21995776

  12. Amino acids as cryoprotectants for liposomal delivery systems.

    PubMed

    Mohammed, Afzal R; Coombes, Allan G A; Perrie, Yvonne

    2007-04-01

    Liposomes provide an efficient delivery system for solubilisation and delivery of both small and macro molecules. However, they suffer from the disadvantage of instability when stored as aqueous dispersions. Cryoprotection of the liposomal systems provides an effective approach to overcome poor stability whilst maintaining formulation characteristics, although, the formulation of a freeze-dried product requires the consideration of not only the selection of an appropriate cryoprotectant, but also needs careful consideration of the processing parameters including pre-freezing conditions, primary and secondary drying protocols along with optimisation of cryoprotectant concentration. This current work investigates the application of amino acids as potential cryoprotectants for the stabilisation of liposomes, and results indicate that amino acids show biphasic nature of stabilisation with 4 mol of cryoprotectant per mole of the lipid exhibiting optimum cryoprotection. The investigations of process parameters showed that the pre-freezing temperatures below the glass transition of the amino acids followed by drying for over 6h resulted in stable formulations. Studies investigating the efficiency of drug retention showed that the cryoprotection offered by lysine was similar to that shown by trehalose, suggesting that amino acids act as effective stabilizers. ESEM analysis was carried out to monitor morphology of the rehydrated liposomes. PMID:17317117

  13. Hepatic Fatty Acid Oxidation Restrains Systemic Catabolism during Starvation.

    PubMed

    Lee, Jieun; Choi, Joseph; Scafidi, Susanna; Wolfgang, Michael J

    2016-06-28

    The liver is critical for maintaining systemic energy balance during starvation. To understand the role of hepatic fatty acid β-oxidation on this process, we generated mice with a liver-specific knockout of carnitine palmitoyltransferase 2 (Cpt2(L-/-)), an obligate step in mitochondrial long-chain fatty acid β-oxidation. Fasting induced hepatic steatosis and serum dyslipidemia with an absence of circulating ketones, while blood glucose remained normal. Systemic energy homeostasis was largely maintained in fasting Cpt2(L-/-) mice by adaptations in hepatic and systemic oxidative gene expression mediated in part by Pparα target genes including procatabolic hepatokines Fgf21, Gdf15, and Igfbp1. Feeding a ketogenic diet to Cpt2(L-/-) mice resulted in severe hepatomegaly, liver damage, and death with a complete absence of adipose triglyceride stores. These data show that hepatic fatty acid oxidation is not required for survival during acute food deprivation but essential for constraining adipocyte lipolysis and regulating systemic catabolism when glucose is limiting. PMID:27320917

  14. IR-UV photochemistry of protein-nucleic acid systems

    SciTech Connect

    Kozub, J.; Edwards, G.

    1995-12-31

    UV light has often been used to induce the formation of covalent bonds between DNA (or RNA) and tightly-bound protein molecules. However, the internal photoreactions of nucleic acids and proteins limit the yield and complicate the analysis of intermolecular crosslinks. In an ongoing search for improved reaction specificity or new photoreactions in these systems, we have employed UV photons from a Nd:YAG-pumped dye laser and mid-IR photons from the Vanderbilt FEL. Having crosslinked several protein-nucleic acid systems with nanosecond UV laser pulses, we are currently studying the effect of various IR wavelengths on a model system (gene 32 protein and poly[dT]). We have found that irradiation with sufficiently intense FEL macropulses creates an altered form of gene 32 protein which was not observed with UV-only irradiation. The electrophoretic nobility of the product is consistent with the formation of a specific protein-protein crosslink. No evidence of the non-specific protein damage typically induced by UV light is found. The yield of the new photoproduct is apparently enhanced by exposure to FEL macropulses which are synchronized with UV laser pulses. With ideal exposure parameters, the two-color reaction effectively competes with UV-only reactions. Experiments designed to determine the reaction mechanism and to demonstrate FEL-induced reactions in other protein-nucleic acid systems are currently underway.

  15. Shaken and Stirred: A Combined Reaction-Diffusion and Random Rate Model for the Temporal Evolution and Earthquake-induced Hydrodynamics of Silicate Mineral Weathering

    NASA Astrophysics Data System (ADS)

    Evaristo, J. A.; Willenbring, J.

    2013-12-01

    The time dependency of silicate mineral weathering has been explored in the literature in terms of processes and features that are intrinsic and extrinsic to the mineral [1]. However, although the advent of sophisticated reactive transport models has allowed for coupling increasingly complex reaction and transport processes [2,3], a simple and fundamental understanding of the temporal evolution of weathering is lacking. Here, we propose that a purely deterministic approach may not be sufficient given the inherent differences in reactivity over space and time. Therefore, we explore how a combined reaction-diffusion and random rate model - informed by a stochastic distribution of weathering rates K (T-1) - might be able to explain not only the temporal evolution but also the hydrodynamics of weathering during earthquakes; the latter being purportedly described by time-dependent property permeability (L2). Preliminary model results show that (1) an increase in dimensionless quantity βrp, where β is the diffusion length (L-1) and rp is the distance between pores (L), leads to a decrease in minimum reaction rate with time from the relation Kmin ∝ e-βrp/rp ; (2) at a given porosity, a time-dependent decrease in reactivity arises as permeability decreases due to decreasing pore size (and therefore increasing rp), which in turn may be related to the time-dependent feedback between dissolution and precipitation; (3) while permeability is lower in older soils, transient stresses as during earthquakes [4], may induce more efficient "declogging" of pores in these soils than in younger soils due to higher hydrodynamic viscous shear stress, thereby, resulting in a coseismic change in stream discharge Q; and (4) subsequent weathering beyond t~Kmin-1 exhibits a fall in rates, marking the cessation of logarithmic decay possibly due to dissolution-precipitation feedback. [1] White and Brantley (2003), Chem. Geol. 202, 479. [2] Lichtner P.C. (1996), Mineralogical Society of

  16. Superabsorbent biphasic system based on poly(lactic acid) and poly(acrylic acid)

    NASA Astrophysics Data System (ADS)

    Sartore, Luciana; Pandini, Stefano; Baldi, Francesco; Bignotti, Fabio

    2016-05-01

    In this research work, biocomposites based on crosslinked particles of poly(acrylic acid), commonly used as superabsorbent polymer (SAP), and poly-L-lactic acid (PLLA) were developed to elucidate the role of the filler (i.e., polymeric crosslinked particles) on the overall physico-mechanical behavior and to obtain superabsorbent thermoplastic products. Samples prepared by melt-blending of components in different ratios showed a biphasic system with a regular distribution of particles, with diameter ranging from 5 to 10 μm, within the PLLA polymeric matrix. The polymeric biphasic system, coded PLASA i.e. superabsorbent poly(lactic acid), showed excellent swelling properties, demonstrating that cross-linked particles retain their superabsorbent ability, as in their free counterparts, even if distributed in a thermoplastic polymeric matrix. The thermal characteristics of the biocomposites evidence enhanced thermal stability in comparison with neat PLLA and also mechanical properties are markedly modified by addition of crosslinked particles which induce regular stiffening effect. Furthermore, in aqueous environments the particles swell and are leached from PLLA matrix generating very high porosity. These new open-pore PLLA foams, produced in absence of organic solvents and chemical foaming agents, with good physico-mechanical properties appear very promising for several applications, for instance in tissue engineering for scaffold production.

  17. Quasi-steady state reduction for compartmental systems

    NASA Astrophysics Data System (ADS)

    Goeke, Alexandra; Lax, Christian

    2016-07-01

    We present a method to determine an asymptotic reduction (in the sense of Tikhonov and Fenichel) for singularly perturbed compartmental systems in the presence of slow transport. It turns out that the reduction can be derived from the individual interaction terms alone. We apply the result to spatially discretized reaction-diffusion systems and obtain (based on the reduced discretized systems) a heuristic to reduce reaction-diffusion systems in presence of slow diffusion.

  18. Effects of organic acids, amino acids and ethanol on the radio-degradation of patulin in an aqueous model system

    NASA Astrophysics Data System (ADS)

    Yun, Hyejeong; Lim, Sangyong; Jo, Cheorun; Chung, Jinwoo; Kim, Soohyun; Kwon, Joong-Ho; Kim, Dongho

    2008-06-01

    The effects of organic acids, amino acids, and ethanol on the radio-degradation of patulin by gamma irradiation in an aqueous model system were investigated. The patulin, dissolved in distilled water at a concentration of 50 ppm, was practically degraded by the gamma irradiation at the dose of 1.0 kGy, while 33% of the patulin remained in apple juice. In the aqueous model system, the radio-degradation of patulin was partially inhibited by the addition of organic acids, amino acids, and ethanol. The proportions of remaining patulin after irradiation with the dose of 1.0 kGy in the 1% solution of malic acid, citric acid, lactic acid, acetic acid, ascorbic acid, and ethanol were 31.4%, 2.3%, 31.2%, 6.1%, 50.8%, and 12.5%, respectively. During 30 days of storage, the remaining patulin was reduced gradually in the solution of ascorbic acid and malic acid compared to being stable in other samples. The amino acids, serine, threonine, and histidine, inhibited the radio-degradation of patulin. In conclusion, it was suggested that 1 kGy of gamma irradiation (recommended radiation doses for radicidation and/or quarantine in fruits) is effective for the reduction of patulin, but the nutritional elements should be considered because the radio-degradation effects are environment dependent.

  19. Delivery Systems for In Vivo Use of Nucleic Acid Drugs

    PubMed Central

    Resende, R.R; Torres, H.A.M; Yuahasi, K.K; Majumder, P; Ulrich, H

    2007-01-01

    The notorious biotechnological advance of the last few decades has allowed the development of experimental methods for understanding molecular mechanisms of genes and new therapeutic approaches. Gene therapy is maturing into a viable, practical method with the potential to cure a variety of human illnesses. Some nucleic-acid-based drugs are now available for controlling the progression of genetic diseases by inhibiting gene expression or the activity of their gene products. New therapeutic strategies employ a wide range of molecular tools such as bacterial plasmids containing transgenic inserts, RNA interference and aptamers. A nucleic-acid based constitution confers a lower immunogenic potential and as result of the high stringency selection of large molecular variety, these drugs have high affinity and selectivity for their targets. However, nucleic acids have poor biostability thus requiring chemical modifications and delivery systems to maintain their activity and ease their cellular internalization. This review discusses some of the mechanisms of action and the application of therapies based on nucleic acids such as aptamers and RNA interference as well as platforms for cellular uptake and intracellular delivery of therapeutic oligonucleotides and their trade-offs. PMID:21901073

  20. System for portable nucleic acid testing in low resource settings

    NASA Astrophysics Data System (ADS)

    Lu, Hsiang-Wei; Roskos, Kristina; Hickerson, Anna I.; Carey, Thomas; Niemz, Angelika

    2013-03-01

    Our overall goal is to enable timely diagnosis of infectious diseases through nucleic acid testing at the point-of-care and in low resource settings, via a compact system that integrates nucleic acid sample preparation, isothermal DNA amplification, and nucleic acid lateral flow (NALF) detection. We herein present an interim milestone, the design of the amplification and detection subsystem, and the characterization of thermal and fluidic control and assay execution within this system. Using an earlier prototype of the amplification and detection unit, comprised of a disposable cartridge containing flexible pouches, passive valves, and electrolysis-driven pumps, in conjunction with a small heater, we have demonstrated successful execution of an established and clinically validated isothermal loop-mediated amplification (LAMP) reaction targeting Mycobacterium tuberculosis (M.tb) DNA, coupled to NALF detection. The refined design presented herein incorporates miniaturized and integrated electrolytic pumps, novel passive valves, overall design changes to facilitate integration with an upstream sample preparation unit, and a refined instrument design that automates pumping, heating, and timing. Nucleic acid amplification occurs in a two-layer pouch that facilitates fluid handling and appropriate thermal control. The disposable cartridge is manufactured using low-cost and scalable techniques and forms a closed system to prevent workplace contamination by amplicons. In a parallel effort, we are developing a sample preparation unit based on similar design principles, which performs mechanical lysis of mycobacteria and DNA extraction from liquefied and disinfected sputum. Our next step is to combine sample preparation, amplification, and detection in a final integrated cartridge and device, to enable fully automated sample-in to answer-out diagnosis of active tuberculosis in primary care facilities of low-resource and high-burden countries.

  1. 21 CFR 862.1390 - 5-Hydroxyindole acetic acid/serotonin test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false 5-Hydroxyindole acetic acid/serotonin test system... Test Systems § 862.1390 5-Hydroxyindole acetic acid/serotonin test system. (a) Identification. A 5-hydroxyindole acetic acid/serotonin test system is a device intended to measure 5-hydroxyindole acetic...

  2. 21 CFR 862.1390 - 5-Hydroxyindole acetic acid/serotonin test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false 5-Hydroxyindole acetic acid/serotonin test system... Test Systems § 862.1390 5-Hydroxyindole acetic acid/serotonin test system. (a) Identification. A 5-hydroxyindole acetic acid/serotonin test system is a device intended to measure 5-hydroxyindole acetic...

  3. 21 CFR 862.1390 - 5-Hydroxyindole acetic acid/serotonin test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false 5-Hydroxyindole acetic acid/serotonin test system... Test Systems § 862.1390 5-Hydroxyindole acetic acid/serotonin test system. (a) Identification. A 5-hydroxyindole acetic acid/serotonin test system is a device intended to measure 5-hydroxyindole acetic...

  4. KLM's Boric Acid Reclamation System (BARS): An update

    SciTech Connect

    Schuelke, D.; Kniazewycz, B.G.; Markind, J.; Brossart, M.A.; Choi, R.C.

    1987-02-01

    KLM Technologies has implemented its Department of Energy Phase II Small Business Innovative Research (SBIR) demonstration program for a radioactive waste Boric Acid Reclamation System (BARS). Preliminary performance indicates enhanced treatment by the BARS technique over state of the art process methods for selective removal of silica and other impurities from borated water matrices. At optimal system recovery of 96 to 97%, BARS removes nominal levels of boric acid while achieving significant rejection for soluble silica and selective radioisotopes. This is indicative of superior performance compared to existing data governing standard boric acid process treatment in the presence of silica and other contaminants. Conventional technologies have also proven to be relatively expensive, utilizing costly chemically treated disposable resins for primary waste removal. The overall BARS program indicates substantial savings regarding off-site disposal costs based on reduced waste generation. Optimization of the BARS technology could have potential impact on conventional process technologies that are essentially non-selective in removal capacities. 2 figs.

  5. Bioluminescence regenerative cycle (BRC) system for nucleic acid quantification assays

    NASA Astrophysics Data System (ADS)

    Hassibi, Arjang; Lee, Thomas H.; Davis, Ronald W.; Pourmand, Nader

    2003-07-01

    A new label-free methodology for nucleic acid quantification has been developed where the number of pyrophosphate molecules (PPi) released during polymerization of the target nucleic acid is counted and correlated to DNA copy number. The technique uses the enzymatic complex of ATP-sulfurylase and firefly luciferase to generate photons from PPi. An enzymatic unity gain positive feedback is also implemented to regenerate the photon generation process and compensate any decay in light intensity by self regulation. Due to this positive feedback, the total number of photons generated by the bioluminescence regenerative cycle (BRC) can potentially be orders of magnitude higher than typical chemiluminescent processes. A system level kinetic model that incorporates the effects of contaminations and detector noise was used to show that the photon generation process is in fact steady and also proportional to the nucleic acid quantity. Here we show that BRC is capable of detecting quantities of DNA as low as 1 amol (10-18 mole) in 40μlit aqueous solutions, and this enzymatic assay has a controllable dynamic range of 5 orders of magnitude. The sensitivity of this technology, due to the excess number of photons generated by the regenerative cycle, is not constrained by detector performance, but rather by possible PPi or ATP (adenosine triphosphate) contamination, or background bioluminescence of the enzymatic complex.

  6. Dietary amino acid-induced systemic lupus erythematosus.

    PubMed

    Montanaro, A; Bardana, E J

    1991-05-01

    The effects of dietary manipulations on autoimmune disease are understood poorly. In this article, we detail our experience with a human subject who developed autoimmune hemolytic anemia while participating in a research study that required the ingestion of alfalfa seeds. Subsequent experimental studies in primates ingesting alfalfa sprout seeds and L-canavanine (a prominent amino acid constituent of alfalfa) is presented. The results of these studies indicate a potential toxic and immunoregulatory role of L-canavanine in the induction of a systemic lupus-like disease in primates. PMID:1862241

  7. Results of electric-vehicle propulsion system performance on three lead-acid battery systems

    NASA Technical Reports Server (NTRS)

    Ewashinka, J. G.

    1984-01-01

    Three types of state of the art 6 V lead acid batteries were tested. The cycle life of lead acid batteries as a function of the electric vehicle propulsion system design was determined. Cycle life, degradation rate and failure modes with different battery types (baseline versus state of the art tubular and thin plate batteries) were compared. The effects of testing strings of three versus six series connected batteries on overall performance were investigated. All three types do not seem to have an economically feasible battery system for the propulsion systems. The tubular plate batteries on the load leveled profile attained 235 cycles with no signs of degradation and minimal capacity loss.

  8. Results of electric-vehicle propulsion system performance on three lead-acid battery systems

    NASA Technical Reports Server (NTRS)

    Ewashinka, J. G.

    1984-01-01

    Three types of state of the art 6 V lead acid batteries were tested. The cycle life of lead acid batteries as a function of the electric vehicle propulsion system design was determined. Cycle life, degradation rate and failure modes with different battery types (baseline versus state of the art tubular and thin plate batteries were compared. The effects of testing strings of three versus six series connected batteries on overall performance were investigated. All three types do not seem to have an economically feasible battery system for the propulsion systems. The tubular plate batteries on the load leveled profile attained 235 cycles with no signs of degradation and minimal capacity loss.

  9. 21 CFR 862.1187 - Conjugated sulfolithocholic acid (SLCG) test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1187 Conjugated sulfolithocholic acid (SLCG) test system. (a) Identification....

  10. 21 CFR 862.1187 - Conjugated sulfolithocholic acid (SLCG) test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1187 Conjugated sulfolithocholic acid (SLCG) test system. (a) Identification....

  11. 21 CFR 862.1187 - Conjugated sulfolithocholic acid (SLCG) test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1187 Conjugated sulfolithocholic acid (SLCG) test system. (a) Identification....

  12. 21 CFR 862.1187 - Conjugated sulfolithocholic acid (SLCG) test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1187 Conjugated sulfolithocholic acid (SLCG) test system. (a) Identification....

  13. 21 CFR 862.1187 - Conjugated sulfolithocholic acid (SLCG) test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1187 Conjugated sulfolithocholic acid (SLCG) test system. (a) Identification....

  14. Preparation and evaluation of microemulsion systems containing salicylic acid.

    PubMed

    Badawi, Alia A; Nour, Samia A; Sakran, Wedad S; El-Mancy, Shereen Mohamed Sameh

    2009-01-01

    Microemulsions (MEs) are clear, thermodynamically stable systems. They were used to solubilize drugs and to improve topical drug availability. Salicylic acid (SA) is a keratolytic agent used in topical products with antimicrobial actions. The objective of this work was to prepare and evaluate SA ME systems. Different concentrations of SA were incorporated in an ME base composed of isopropyl myristate, water, and Tween 80: propylene glycol in the ratio of 15:1. Three ME systems were prepared: S2%, S5%, and S10% which contain 2%, 5%, and 10% of SA, respectively. Evaluation by examination under cross-polarizing microscope, measuring of percent transmittance, pH measurement, determination of the specific gravity, assessment of rheological properties, and accelerated stability study were carried out. The data showed that the addition of SA markedly affected the physical properties of the base. All systems were not affected by accelerated stability tests. Stability study for 6 months under ambient conditions was carried out for S10%. No remarkable changes were recorded except a decrease in the viscosity value after 1 month. The results suggested that ME could be a suitable vehicle for topical application of different concentrations of SA. PMID:19757081

  15. Molecular cloning of mouse amino acid transport system B0, a neutral amino acid transporter related to Hartnup disorder.

    PubMed

    Bröer, Angelika; Klingel, Karin; Kowalczuk, Sonja; Rasko, John E J; Cavanaugh, Juleen; Bröer, Stefan

    2004-06-01

    Resorption of amino acids in kidney and intestine is mediated by transporters, which prefer groups of amino acids with similar physico-chemical properties. It is generally assumed that most neutral amino acids are transported across the apical membrane of epithelial cells by system B(0). Here we have characterized a novel member of the Na(+)-dependent neurotransmitter transporter family (B(0)AT1) isolated from mouse kidney, which shows all properties of system B(0). Flux experiments showed that the transporter is Na(+)-dependent, electrogenic, and actively transports most neutral amino acids but not anionic or cationic amino acids. Superfusion of mB(0)AT1-expressing oocytes with neutral amino acids generated inward currents, which were proportional to the fluxes observed with labeled amino acids. In situ hybridization showed strong expression in intestinal microvilli and in the proximal tubule of the kidney. Expression of mouse B(0)AT1 was restricted to kidney, intestine, and skin. It is generally assumed that mutations of the system B(0) transporter underlie autosomal recessive Hartnup disorder. In support of this notion mB(0)AT1 is located on mouse chromosome 13 in a region syntenic to human chromosome 5p15, the locus of Hartnup disorder. Thus, the human homologue of this transporter is an excellent functional and positional candidate for Hartnup disorder. PMID:15044460

  16. ACID DEPOSITION SYSTEM (ADS) FOR STATISTICAL REPORTING: SYSTEM DESIGN AND USER'S CODE MANUAL

    EPA Science Inventory

    This document is a general purpose description of the ADS data management system. It explains to acid precipitation monitoring network managers how their data is being merged with that from other networks. For the researcher, this document defines what information is available in...

  17. Genotype, production system and sex effects on fatty acid composition of meat from goat kids.

    PubMed

    Özcan, Mustafa; Demirel, Gulcan; Yakan, Akın; Ekiz, Bülent; Tölü, Cemil; Savaş, Türker

    2015-02-01

    Two trials were performed to assess the meat fatty acid profile of goat kids from different genotypes, production systems and sex. In the first trial, genotype effect was determined in 24 suckling male kids from Turkish Saanen, Maltese and Gokceada breeds. In the second trial, male and female Gokceada Goat kids were used to compare the effect of extensive and semi-intensive production systems on fatty acid composition of meat. Significant genotype effect was observed in the percentages of myristic acid (C14:0), palmitic acid (C16:0), oleic acid (C18:1 n-9), linolenic acid (C18:3 n-3), arachidonic acid (C20:4 n-6) and docosahexaenoic acid (C22:6 n-3), despite no differences on the ratios of polyunsaturated fatty acids to saturated fatty acids (PUFA/SFA) and n-6/n-3 (P > 0.05). The effect of production system had also significant effects on fatty acids, but sex only influenced significantly stearic acid (C18:0), C18:1 n-9 and C18:3 n-3 fatty acids and total PUFA level and PUFA/SFA ratio. This study confirms that dairy breeds are prone to produce higher levels of unsaturated fatty acids in their muscle. Meanwhile, meat from Gokceada goat kids, which is one of the indigenous breeds in Turkey, had similar PUFA/SFA and n-6/n-3 ratios to Turkish Saanen and Maltase. PMID:25186278

  18. Phase equilibria and distribution constants of metal ions in diantipyryl alkane-organic acid-hydrochloric acid-water systems

    NASA Astrophysics Data System (ADS)

    Degtev, M. I.; Popova, O. N.; Yuminova, A. A.

    2014-08-01

    The ability of antipyrine and its derivatives (diantipyryl alkanes) to form separating systems in the presence of salicylic (sulfosalicylic) acid and hydrochloric acid and water is studied. The optimum volume of the organic phase, the composition of complexes, and the mechanism for the distribution of metal ions are determined, depending on the concentrations of the main components and the salting-out agent. The complex distribution and extraction constants are calculated.

  19. Self-powered switch-controlled nucleic acid extraction system.

    PubMed

    Han, Kyungsup; Yoon, Yong-Jin; Shin, Yong; Park, Mi Kyoung

    2016-01-01

    Over the past few decades, lab-on-a-chip (LOC) technologies have played a great role in revolutionizing the way in vitro medical diagnostics are conducted and transforming bulky and expensive laboratory instruments and labour-intensive tests into easy to use, cost-effective miniaturized systems with faster analysis time, which can be used for near-patient or point-of-care (POC) tests. Fluidic pumps and valves are among the key components for LOC systems; however, they often require on-line electrical power or batteries and make the whole system bulky and complex, therefore limiting its application to POC testing especially in low-resource setting. This is particularly problematic for molecular diagnostics where multi-step sample processing (e.g. lysing, washing, elution) is necessary. In this work, we have developed a self-powered switch-controlled nucleic acid extraction system (SSNES). The main components of SSNES are a powerless vacuum actuator using two disposable syringes and a switchgear made of PMMA blocks and an O-ring. In the vacuum actuator, an opened syringe and a blocked syringe are bound together and act as a working syringe and an actuating syringe, respectively. The negative pressure in the opened syringe is generated by a restoring force of the compressed air inside the blocked syringe and utilized as the vacuum source. The Venus symbol shape of the switchgear provides multiple functions including being a reagent reservoir, a push-button for the vacuum actuator, and an on-off valve. The SSNES consists of three sets of vacuum actuators, switchgears and microfluidic components. The entire system can be easily fabricated and is fully disposable. We have successfully demonstrated DNA extraction from a urine sample using a dimethyl adipimidate (DMA)-based extraction method and the performance of the DNA extraction has been confirmed by genetic (HRAS) analysis of DNA biomarkers from the extracted DNAs using the SSNES. Therefore, the SSNES can be widely

  20. [Study of antioxidant and membrane activity of rosmarinic acid using different model systems].

    PubMed

    Popov, A M; Osipov, A N; Korepanova, E A; Krivoshapko, O N; Artiukov, A A

    2013-01-01

    Rosmarinic acid is found in many species of different families of higher plants and its chemical structure is phenol propanoid with various biological activity. In this paper, we conducted a comparative study of antioxidant (radical-scavenging) properties of rosmarinic acid in systems of 2,2'-azo-bis(2-methylpropionamidin)dihydrochloride-luminol and hemoglobin-hydrogen peroxide-lu- minol, determined its protective potential in preventing peroxidation of linoleic acid, and evaluated the effect on the permeability of planar bilayer lipid membranes. Linoleic acid peroxidation was assessed by iron-thiocyanate method. In these studies, trolox was used as a reference antioxidant, and ascorbic acid, and dihydroquercetin were taken as standards. Rosmarinic acid is significantly superior to trolox, ascorbic acid and dihydroquercetin in the tests for antioxidant activity in the systems studied, as well as in inhibition of linoleic acid peroxidation. According to their activity the investigated substances can be arranged in the following order: rosmarinic acid > dihydroquercetin trolox > ascorbic acid. Rosmarinic acid does not cause significant changes in the permeability of planar bilayer membranes in a dose range of 0.5 to 10 mkg/mL. Antioxidant activity of rosmarinic acid is due to the neutralization of reactive oxygen species and/or luminol radicals generated in model systems. The observed features of the antioxidant and membrane activity of rosmarinic acid, which may underlie the previously mentioned pharmacological effects are discussed. PMID:25481945

  1. [Study of antioxidant and membrane activity of rosmarinic acid using different model systems].

    PubMed

    2013-01-01

    Rosmarinic acid is found in many species of different families of higher plants and its chemical structure is phenol propanoid with various biological activity. In this paper, we conducted a comparative study of antioxidant (radical-scavenging) properties of rosmarinic acid in systems of 2,2'-azo-bis(2-methylpropionamidin)dihydrochloride-luminol and hemoglobin-hydrogen peroxide-lu- minol, determined its protective potential in preventing peroxidation of linoleic acid, and evaluated the effect on the permeability of planar bilayer lipid membranes. Linoleic acid peroxidation was assessed by iron-thiocyanate method. In these studies, trolox was used as a reference antioxidant, and ascorbic acid, and dihydroquercetin were taken as standards. Rosmarinic acid is significantly superior to trolox, ascorbic acid and dihydroquercetin in the tests for antioxidant activity in the systems studied, as well as in inhibition of linoleic acid peroxidation. According to their activity the investigated substances can be arranged in the following order: rosmarinic acid > dihydroquercetin trolox > ascorbic acid. Rosmarinic acid does not cause significant changes in the permeability of planar bilayer membranes in a dose range of 0.5 to 10 mkg/mL. Antioxidant activity of rosmarinic acid is due to the neutralization of reactive oxygen species and/or luminol radicals generated in model systems. The observed features of the antioxidant and membrane activity of rosmarinic acid, which may underlie the previously mentioned pharmacological effects are discussed. PMID:25508797

  2. Sialic Acids in the Brain: Gangliosides and Polysialic Acid in Nervous System Development, Stability, Disease, and Regeneration

    PubMed Central

    Gerardy-Schahn, Rita; Hildebrandt, Herbert

    2014-01-01

    Every cell in nature carries a rich surface coat of glycans, its glycocalyx, which constitutes the cell's interface with its environment. In eukaryotes, the glycocalyx is composed of glycolipids, glycoproteins, and proteoglycans, the compositions of which vary among different tissues and cell types. Many of the linear and branched glycans on cell surface glycoproteins and glycolipids of vertebrates are terminated with sialic acids, nine-carbon sugars with a carboxylic acid, a glycerol side-chain, and an N-acyl group that, along with their display at the outmost end of cell surface glycans, provide for varied molecular interactions. Among their functions, sialic acids regulate cell-cell interactions, modulate the activities of their glycoprotein and glycolipid scaffolds as well as other cell surface molecules, and are receptors for pathogens and toxins. In the brain, two families of sialoglycans are of particular interest: gangliosides and polysialic acid. Gangliosides, sialylated glycosphingolipids, are the most abundant sialoglycans of nerve cells. Mouse genetic studies and human disorders of ganglioside metabolism implicate gangliosides in axon-myelin interactions, axon stability, axon regeneration, and the modulation of nerve cell excitability. Polysialic acid is a unique homopolymer that reaches >90 sialic acid residues attached to select glycoproteins, especially the neural cell adhesion molecule in the brain. Molecular, cellular, and genetic studies implicate polysialic acid in the control of cell-cell and cell-matrix interactions, intermolecular interactions at cell surfaces, and interactions with other molecules in the cellular environment. Polysialic acid is essential for appropriate brain development, and polymorphisms in the human genes responsible for polysialic acid biosynthesis are associated with psychiatric disorders including schizophrenia, autism, and bipolar disorder. Polysialic acid also appears to play a role in adult brain plasticity

  3. STANDARDIZING TERMINOLOGY FOR ESTIMATING THE DIET-DEPENDENT NET ACID LOAD TO THE METABOLIC SYSTEM

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Contemporary Western diets contain acid precursors in excess of base precursors, yielding a daily systemic net acid load of varying amounts, depending on the specific composition of the diet. Increasing evidence suggests that differences in daily net acid load, resulting predominantly from differen...

  4. 78 FR 36698 - Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium tuberculosis

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-19

    ... Nucleic Acid-Based Systems for Mycobacterium tuberculosis Complex in Respiratory Specimens AGENCY: Food...) is proposing to reclassify nucleic acid-based in vitro diagnostic devices for the detection of... Controls Guideline: Nucleic Acid-Based In Vitro Diagnostic Devices for the Detection of...

  5. Effect of fatty acids on self-assembly of soybean lecithin systems.

    PubMed

    Godoy, C A; Valiente, M; Pons, R; Montalvo, G

    2015-07-01

    With the increasing interest in natural formulations for drug administration and functional foods, it is desirable a good knowledge of the phase behavior of lecithin/fatty acid formulations. Phase structure and properties of ternary lecithin/fatty acids/water systems are studied at 37°C, making emphasis in regions with relatively low water and fatty acid content. The effect of fatty acid saturation degree on the phase microstructure is studied by comparing a fully saturated (palmitic acid, C16:0), monounsaturated (oleic acid, C18:1), and diunsaturated (linoleic acid, C18:2) fatty acids. Phase determinations are based on a combination of polarized light microscopy and small-angle X-ray scattering measurements. Interestingly, unsaturated (oleic acid and linoleic acid) fatty acid destabilizes the lamellar bilayer. Slight differences are observed between the phase diagrams produced by the unsaturated ones: small lamellar, medium cubic and large hexagonal regions. A narrow isotropic fluid region also appears on the lecithin-fatty acid axis, up to 8wt% water. In contrast, a marked difference in phase microsctructure was observed between unsaturated and saturated systems in which the cubic and isotropic fluid phases are not formed. These differences are, probably, a consequence of the high Krafft point of the C16 saturated chains that imply rather rigid chains. However, unsaturated fatty acids result in more flexible tails. The frequent presence of, at least, one unsaturated chain in phospholipids makes it very likely a better mixing situation than in the case of more rigid chains. This swelling potential favors the formation of reverse hexagonal, cubic, and micellar phases. Both unsaturated fatty acid systems evolve by aging, with a reduction of the extension of reverse hexagonal phase and migration of the cubic phase to lower fatty acid and water contents. The kinetic stability of the systems seems to be controlled by the unsaturation of fatty acids. PMID:25938851

  6. Abscisic Acid: Hidden Architect of Root System Structure

    PubMed Central

    Harris, Jeanne M.

    2015-01-01

    Plants modulate root growth in response to changes in the local environment, guided by intrinsic developmental genetic programs. The hormone Abscisic Acid (ABA) mediates responses to different environmental factors, such as the presence of nitrate in the soil, water stress and salt, shaping the structure of the root system by regulating the production of lateral roots as well as controlling root elongation by modulating cell division and elongation. Curiously, ABA controls different aspects of root architecture in different plant species, perhaps providing some insight into the great diversity of root architecture in different plants, both from different taxa and from different environments. ABA is an ancient signaling pathway, acquired well before the diversification of land plants. Nonetheless, how this ancient signaling module is implemented or interacts within a larger signaling network appears to vary in different species. This review will examine the role of ABA in the control of root architecture, focusing on the regulation of lateral root formation in three plant species, Arabidopsis thaliana, Medicago truncatula and Oryza sativa. We will consider how the implementation of the ABA signaling module might be a target of natural selection, to help contribute to the diversity of root architecture in nature. PMID:27135341

  7. Abscisic Acid: Hidden Architect of Root System Structure.

    PubMed

    Harris, Jeanne M

    2015-01-01

    Plants modulate root growth in response to changes in the local environment, guided by intrinsic developmental genetic programs. The hormone Abscisic Acid (ABA) mediates responses to different environmental factors, such as the presence of nitrate in the soil, water stress and salt, shaping the structure of the root system by regulating the production of lateral roots as well as controlling root elongation by modulating cell division and elongation. Curiously, ABA controls different aspects of root architecture in different plant species, perhaps providing some insight into the great diversity of root architecture in different plants, both from different taxa and from different environments. ABA is an ancient signaling pathway, acquired well before the diversification of land plants. Nonetheless, how this ancient signaling module is implemented or interacts within a larger signaling network appears to vary in different species. This review will examine the role of ABA in the control of root architecture, focusing on the regulation of lateral root formation in three plant species, Arabidopsis thaliana, Medicago truncatula and Oryza sativa. We will consider how the implementation of the ABA signaling module might be a target of natural selection, to help contribute to the diversity of root architecture in nature. PMID:27135341

  8. Influence of pasture-based feeding systems on fatty acids, organic acids and volatile organic flavour compounds in yoghurt.

    PubMed

    Akbaridoust, Ghazal; Plozza, Tim; Trenerry, V Craige; Wales, William J; Auldist, Martin J; Ajlouni, Said

    2015-08-01

    The influence of different pasture-based feeding systems on fatty acids, organic acids and volatile organic flavour compounds in yoghurt was studied. Pasture is the main source of nutrients for dairy cows in many parts of the world, including southeast Australia. Milk and milk products produced in these systems are known to contain a number of compounds with positive effects on human health. In the current study, 260 cows were fed supplementary grain and forage according to one of 3 different systems; Control (a traditional pasture based diet offered to the cows during milking and in paddock), PMR1 (a partial mixed ration which contained the same supplement as Control but was offered to the cows as a partial mixed ration on a feedpad), PMR 2 (a differently formulated partial mixed ration compared to Control and PMR1 which was offered to the cows on a feedpad). Most of the yoghurt fatty acids were influenced by feeding systems; however, those effects were minor on organic acids. The differences in feeding systems did not lead to the formation of different volatile organic flavour compounds in yoghurt. Yet, it did influence the relative abundance of these components. PMID:26143651

  9. Self-assembled nanostructures of fully hydrated monoelaidin-elaidic acid and monoelaidin-oleic acid systems.

    PubMed

    Yaghmur, Anan; Sartori, Barbara; Rappolt, Michael

    2012-07-01

    In recent years, there has been a surge of interest in exploring the effect of trans-fatty acids (TFAs) on biological membrane properties. The research studies are motivated by an increasing body of evidence suggesting that the consumption of TFAs increases the risk of developing negative health effects such as coronary heart disease and cancer. The ultimate goal of studying the lipid-fatty acid interactions at the molecular level is to predict the biological role of fatty acids in cells. In this regard, it is interesting to elucidate the effect of loading TFAs and their counterpart cis-fatty acids (CFAs) on the physical properties of lipid model membranes. Here, the present study focuses on discussing the following: (1) the effect of mixing monoelaidin (ME, TFA-containing lipid) with its counterpart monoolein (MO, CFA-containing lipid) on modulating the fully hydrated self-assembled structure, and (2) the influence of solubilizing oleic acid (OA) and its trans counterpart elaidic acid (EA) on the fully hydrated ME system. The ME model membrane was selected due to its sensitivity to variations in lipid composition and temperature. Synchrotron small-angle X-ray scattering (SAXS) was applied for studying the temperature-dependent structural behavior of the fully hydrated ME/MO-based system prepared with an equal ME/MO weight ratio and also for characterizing the fully hydrated OA- and EA-loaded ME systems. Wide-angle X-ray (WAXS) experiments were also performed for characterizing the formed crystalline lamellar phases at ambient temperatures. The results demonstrate the significant influence of the partial replacement of ME by MO on the phase behavior. The addition of MO induces the lamellar-nonlamellar phase transitions at ambient temperatures and promotes the formation of the inverted type hexagonal (H(2)) phase above 72 °C. The fully hydrated ME/EA and ME/OA systems with their rich polymorphism exhibit an interesting temperature-dependent complex behavior. The

  10. The nomenclature of 1-aminoalkylphosphonic acids and derivatives: evolution of the code system.

    PubMed

    Drabowicz, Józef; Jakubowski, Hieronim; Kudzin, Marcin H; Kudzin, Zbigniew H

    2015-01-01

    The approach for the unification of published proposals for the nomenclature and abbreviations of aminoalkylphosphonic acids and their derivatives is presented. Their modification was made on the basis of the IUPAC-IUB rules concerning the nomenclature and code system of proteinogenic amino acids. Our present proposal formulates the supplementary code and nomenclature system allowing unambiguous description of phosphonic analogs of proteinogenic amino acids, their analogs, homologs, metabolites, and derivatives including phosphonopeptides. PMID:25730210

  11. What is the safe upper intake level of folic acid for the nervous system? Implications for folic acid fortification policies.

    PubMed

    Reynolds, E H

    2016-05-01

    Between 1945 and 1959 it was convincingly documented that folic acid can precipitate or aggravate the neurological and haematological consequences of vitamin B12 deficiency by increasing the demand for vitamin B12. Since then there has been much misunderstanding of the issues, mainly by advocates of folic acid fortification who have been inclined to minimise or even dismiss the risks by misinterpreting the evidence as only a 'masking' of the anaemia of pernicious anaemia. Recent studies in the era of fortification are rediscovering the risks to the nervous system, especially cognitive function, of excess folate in the presence of vitamin B12 deficiency. I have reviewed the Reports of four Expert Advisory Committees in Europe and the USA, which suggest that the safe upper tolerable limit (UL) for folic acid is 1 mg in adults. These reports are unsound and there is already evidence of neurological harm from long-term exposure to doses of folic acid between 0.5 and 1 mg in the presence of vitamin B12 deficiency. There is an urgent need to review the safe UL for folic acid and to consider the addition of vitamin B12 to folic acid fortification policies. PMID:26862004

  12. DimaSense™: A Novel Nucleic Acid Detection System

    SciTech Connect

    Stadler, A.

    2011-05-18

    sensors. These sensors operate with very low concentrations of target, can utilize standard instrumentation, produce detection results rapidly, and are robust enough to function in the presence of many competing genetic targets. Many current genetic target detection products/approaches/technologies rely upon methods (such as qPCR) which are more complicated, cumbersome, and costly to perform, and are not well suited to point-of-care diagnostic applications. Several clinical diagnostic applications, particularly point-of-care (POC) diagnostics for infectious diseases, are possible and appear to be a good fit for the technology. In addition, the advent of personalized medicine will create opportunities for molecular diagnostic companies with the capabilities of rapidly and quantitatively detecting nucleic acid sequences. The global POC market was {approx}$7.7B in 2010, with a recent annual growth rate of {approx}7%. A specific disease or disease-class diagnostic would need to be identified before a more meaningful sub-market value could be stated. Additional validation of the technology to show that it displays appropriate performance parameters for a commercial application on 'real world' samples is required for true commercial readiness. In addition, optimization of sensor design parameters, to effect a 10-fold increase in sensitivity, may be required to produce a commercially ready sensor system. These validation and sensor design optimization are estimated to require 3-4 months and {approx}$75k. For an unregulated product to give this sensor system a distinct competitive advantage, 2-3 years of product development and $1.5-3M are likely required. For regulated markets, time to market (through clinic) and cost would depend upon the product.

  13. Polymerase chain reaction system using magnetic beads for analyzing a sample that includes nucleic acid

    SciTech Connect

    Nasarabadi, Shanavaz

    2011-01-11

    A polymerase chain reaction system for analyzing a sample containing nucleic acid includes providing magnetic beads; providing a flow channel having a polymerase chain reaction chamber, a pre polymerase chain reaction magnet position adjacent the polymerase chain reaction chamber, and a post pre polymerase magnet position adjacent the polymerase chain reaction chamber. The nucleic acid is bound to the magnetic beads. The magnetic beads with the nucleic acid flow to the pre polymerase chain reaction magnet position in the flow channel. The magnetic beads and the nucleic acid are washed with ethanol. The nucleic acid in the polymerase chain reaction chamber is amplified. The magnetic beads and the nucleic acid are separated into a waste stream containing the magnetic beads and a post polymerase chain reaction mix containing the nucleic acid. The reaction mix containing the nucleic acid flows to an analysis unit in the channel for analysis.

  14. Organic acids enhanced decoloration of azo dye in gas phase surface discharge plasma system.

    PubMed

    Wang, Tiecheng; Qu, Guangzhou; Ren, Jingyu; Sun, Qiuhong; Liang, Dongli; Hu, Shibin

    2016-01-25

    A gas phase surface discharge plasma combined with organic acids system was developed to enhance active species mass transfer and dye-containing wastewater treatment efficacy, with Acid Orange II (AO7) as the model pollutant. The effects of discharge voltage and various organic acid additives (acetic acid, lactic acid and nonoic acid) on AO7 decoloration efficiency were evaluated. The experimental results showed that an AO7 decoloration efficiency of approximately 69.0% was obtained within 4 min of discharge plasma treatment without organic acid addition, which was improved to 82.8%, 83.5% and 88.6% within the same treatment time with the addition of acetic acid, lactic acid and nonoic acid, respectively. The enhancement effects on AO7 decoloration efficiency could be attributed to the decrease in aqueous surface tension, improvement in bubble distribution and shape, and increase in ozone equivalent concentration. The AO7 wastewater was biodegradable after discharge plasma treatment with the addition of organic acid. AO7 decomposition intermediates were analyzed by UV-vis spectrometry and GC-MS; 2-naphthol, 1,4-benzoquinone, phthalic anhydride, coumarin, 1,2-naphthoquinone, and 2-formyl-benzoic acid were detected. A possible pathway for AO7 decomposition in this system was proposed. PMID:26444488

  15. Systemic distribution and speciation of diphenylarsinic acid fed to rats

    SciTech Connect

    Naranmandura, Hua Suzuki, Noriyuki; Takano, Juniti; McKnight-Whitford, Tony; Ogra, Yasumitsu; Suzuki, Kazuo T.; Le, X. Chris

    2009-06-01

    Diphenylarsinic acid (DPAA) is an environmental degradation product of diphenylarsine chloride or diphenylarsine cyanide, which were chemical warfare agents produced by Japan during the World War II. DPAA is now considered a dangerous environmental pollutant in Kamisu, Japan, where it is suspected of inducing health effects that include articulation disorders (cerebellar ataxia of the extremities and trunk), involuntary movements (myoclonus and tremor), and sleep disorders. In order to elucidate the toxic mechanism of DPAA, we focused on the distribution and metabolism of DPAA in rats. Systemic distribution of DPAA was determined by administering DPAA orally to rats at a single dose of 5.0 mg As/kg body weight, followed by speciation analysis of selected organs and body fluids. Most of the total arsenic burden was recovered in the urine (23% of the dose) and feces (27%), with the distribution in most other organs/tissues being less than 1%. However, compared with the typical distribution of inorganic dietary arsenic, DPAA administration resulted in elevated levels in the brain, testes and pancreas. In contrast to urine, in which DPAA was found mostly in its unmodified form, the tissues and organs contained arsenic that was mostly bound to non-soluble and soluble high molecular weight proteins. These bound arsenic species could be converted back to DPAA after oxidation with H{sub 2}O{sub 2}, suggesting that the DPAA bound to proteins had been reduced within the body and was in a trivalent oxidation state. Furthermore, we also detected two unknown arsenic metabolites in rat urine, which were assumed to be hydroxylated arsenic metabolites.

  16. Abscisic acid ameliorates the systemic sclerosis fibroblast phenotype in vitro

    SciTech Connect

    Bruzzone, Santina; Battaglia, Florinda; Mannino, Elena; Parodi, Alessia; Fruscione, Floriana; Basile, Giovanna; Salis, Annalisa; Sturla, Laura; Negrini, Simone; Kalli, Francesca; Stringara, Silvia; Filaci, Gilberto; and others

    2012-05-25

    Highlights: Black-Right-Pointing-Pointer ABA is an endogenous hormone in humans, regulating different cell responses. Black-Right-Pointing-Pointer ABA reverts some of the functions altered in SSc fibroblasts to a normal phenotype. Black-Right-Pointing-Pointer UV-B irradiation increases ABA content in SSc cultures. Black-Right-Pointing-Pointer SSc fibroblasts could benefit from exposure to ABA and/or to UV-B. -- Abstract: The phytohormone abscisic acid (ABA) has been recently identified as an endogenous hormone in humans, regulating different cell functions, including inflammatory processes, insulin release and glucose uptake. Systemic sclerosis (SSc) is a chronic inflammatory disease resulting in fibrosis of skin and internal organs. In this study, we investigated the effect of exogenous ABA on fibroblasts obtained from healthy subjects and from SSc patients. Migration of control fibroblasts induced by ABA was comparable to that induced by transforming growth factor-{beta} (TGF-{beta}). Conversely, migration toward ABA, but not toward TGF-{beta}, was impaired in SSc fibroblasts. In addition, ABA increased cell proliferation in fibroblasts from SSc patients, but not from healthy subjects. Most importantly, presence of ABA significantly decreased collagen deposition by SSc fibroblasts, at the same time increasing matrix metalloproteinase-1 activity and decreasing the expression level of tissue inhibitor of metalloproteinase (TIMP-1). Thus, exogenously added ABA appeared to revert some of the functions altered in SSc fibroblasts to a normal phenotype. Interestingly, ABA levels in plasma from SSc patients were found to be significantly lower than in healthy subjects. UV-B irradiation induced an almost 3-fold increase in ABA content in SSc cultures. Altogether, these results suggest that the fibrotic skin lesions in SSc patients could benefit from exposure to high(er) ABA levels.

  17. ACID PRECIPITATION IN NORTH AMERICA: 1987 ANNUAL AND SEASONAL DATA SUMMARIES FROM ACID DEPOSITION SYSTEM DATA BASE

    EPA Science Inventory

    This report summarizes the 1987 wet deposition precipitation chemistry data collected in North America and available in the Acid Deposition System (ADS) data base. nterpretative statistical analyses are not a focus of this report; however, users of the report will learn about maj...

  18. ACID PRECIPITATION IN NORTH AMERICA: 1980, 1981 AND 1982 ANNUAL DATA SUMMARIES FROM ACID DEPOSITION SYSTEM DATA BASE

    EPA Science Inventory

    The Acid Deposition System (ADS) data base for North American wet deposition data is used to provide an overview of the major North American monitoring networks: NADP, CANSAP, APN, MAP3S/PCN, EPRI/SURE, UAPSP and APIOS daily and cumulative. Individual site annual statistical summ...

  19. ACID PRECIPITATION IN NORTH AMERICA: 1985 ANNUAL AND SEASONAL DATA SUMMARIES FROM ACID DEPOSITION SYSTEM DATA BASE

    EPA Science Inventory

    The report gives a summary of 1985 wet deposition precipitation chemistry data collected in North America and available in the Acid Deposition System (ADS) data base. North American wet deposition monitoring networks with data in ADS are NADP/NTN, CANSAP, APN, UAPSP, MAP3S/PCN, W...

  20. Omega-3 fatty acids differentially modulate enzymatic anti-oxidant systems in skeletal muscle cells.

    PubMed

    da Silva, E P; Nachbar, R T; Levada-Pires, A C; Hirabara, S M; Lambertucci, R H

    2016-01-01

    During physical activity, increased reactive oxygen species production occurs, which can lead to cell damage and in a decline of individual's performance and health. The use of omega-3 polyunsaturated fatty acids as a supplement to protect the immune system has been increasing; however, their possible benefit to the anti-oxidant system is not well described. Thus, the aim of this study was to evaluate whether the omega-3 fatty acids (docosahexaenoic acid and eicosapentaenoic acid) can be beneficial to the anti-oxidant system in cultured skeletal muscle cells. C2C12 myocytes were differentiated and treated with either eicosapentaenoic acid or docosahexaenoic acid for 24 h. Superoxide content was quantified using the dihydroethidine oxidation method and superoxide dismutase, catalase, and glutathione peroxidase activity, and expression was quantified. We observed that the docosahexaenoic fatty acids caused an increase in superoxide production. Eicosapentaenoic acid induced catalase activity, while docosahexaenoic acid suppressed superoxide dismutase activity. In addition, we found an increased protein expression of the total manganese superoxide dismutase and catalase enzymes when cells were treated with eicosapentaenoic acid. Taken together, these data indicate that the use of eicosapentaenoic acid may present both acute and chronic benefits; however, the treatment with DHA may not be beneficial to muscle cells. PMID:26386577

  1. 21 CFR 862.1655 - Pyruvic acid test system.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... measure pyruvic acid (an intermediate compound in the metabolism of carbohydrate) in plasma. Measurements obtained by this device are used in the evaluation of electrolyte metabolism and in the diagnosis...

  2. 21 CFR 862.1655 - Pyruvic acid test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... measure pyruvic acid (an intermediate compound in the metabolism of carbohydrate) in plasma. Measurements obtained by this device are used in the evaluation of electrolyte metabolism and in the diagnosis...

  3. 21 CFR 862.1655 - Pyruvic acid test system.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... measure pyruvic acid (an intermediate compound in the metabolism of carbohydrate) in plasma. Measurements obtained by this device are used in the evaluation of electrolyte metabolism and in the diagnosis...

  4. 21 CFR 862.1655 - Pyruvic acid test system.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... measure pyruvic acid (an intermediate compound in the metabolism of carbohydrate) in plasma. Measurements obtained by this device are used in the evaluation of electrolyte metabolism and in the diagnosis...

  5. 21 CFR 862.1655 - Pyruvic acid test system.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... measure pyruvic acid (an intermediate compound in the metabolism of carbohydrate) in plasma. Measurements obtained by this device are used in the evaluation of electrolyte metabolism and in the diagnosis...

  6. Materials characterization of phosphoric acid fuel cell system

    NASA Technical Reports Server (NTRS)

    Venkatesh, Srinivasan

    1986-01-01

    The component materials used in the fabrication of phosphoric acid fuel cells (PAFC) must have mechanical, chemical, and electrochemical stability to withstand the moderately high temperature (200 C) and pressure (500 kPa) and highly oxidizing nature of phosphoric acid. This study discusses the chemical and structural stability, performance and corrosion data on certain catalysts, catalyst supports, and electrode support materials used in PAFC applications.

  7. Metabolic Transformation of Mevalonic Acid by an Enzyme System from Peas 1

    PubMed Central

    Pollard, C. J.; Bonner, J.; Haagen-Smit, A. J.; Nimmo, C. C.

    1966-01-01

    En enzyme system has been found in peas which converts mevalonic acid to isoprenoid compounds. Among the intermediates in such conversion are mevalonic acid-5-phosphate and pyrophosphate, isopentenyl pyrophosphate and dimethylallylpyrophosphate. Among the products formed by the system are the pyrophosphates of geraniol, farnesol, nerolidol and higher isoprenoid alcohols. PMID:16656233

  8. EFFECT OF TRACE METALS AND SULFITE OXIDATION OF ADIPIC ACID DEGRADATION IN FGD SYSTEMS

    EPA Science Inventory

    The report gives results of the measurement of the adipic acid degradation rate in a bench-scale flue gas desulfurization (FGD) system, designed to simulate many of the important aspects of full-scale FGD systems. Results show that the adipic acid degradation rate depends on the ...

  9. Using Acid Number as a Leading Indicator of Refrigeration and Air Conditioning System Performance

    SciTech Connect

    Dennis Cartlidge; Hans Schellhase

    2003-07-31

    This report summarizes a literature review to assess the acidity characteristics of the older mineral oil and newer polyolester (POE) refrigeration systems as well as to evaluate acid measuring techniques used in other non-aqueous systems which may be applicable for refrigeration systems. Failure in the older chlorofluorocarbon/hydrochlorofluorocarbon (CFC/HCFC) / mineral oil systems was primarily due to thermal degradation of the refrigerant which resulted in the formation of hydrochloric and hydrofluoric acids. These are strong mineral acids, which can, over time, severely corrode the system metals and lead to the formation of copper plating on iron surfaces. The oil lubricants used in the older systems were relatively stable and were not prone to hydrolytic degradation due to the low solubility of water in oil. The refrigerants in the newer hydrofluorocarbon (HFC)/POE systems are much more thermally stable than the older CFC/HCFC refrigerants and mineral acid formation is negligible. However, acidity is produced in the new systems by hydrolytic decomposition of the POE lubricants with water to produce the parent organic acids and alcohols used to prepare the POE. The individual acids can therefore vary but they are generally C5 to C9 carboxylic acids. Organic acids are much weaker and far less corrosive to metals than the mineral acids from the older systems but they can, over long time periods, react with metals to form carboxylic metal salts. The salts tend to accumulate in narrow areas such as capillary tubes, particularly if residual hydrocarbon processing chemicals are present in the system, which can lead to plugging. The rate of acid production from POEs varies on a number of factors including chemical structure, moisture levels, temperature, acid concentration and metals. The hydrolysis rate of reaction can be reduced by using driers to reduce the free water concentration and by using scavenging chemicals which react with the system acids. Total acid

  10. Analysis of Natural Buffer Systems and the Impact of Acid Rain

    ERIC Educational Resources Information Center

    Powers, David C.; Yoder, Claude H.; Higgs, Andrew T.; Obley, Matt L.; Hess, Kenneth R.; Leber, Phyllis A.

    2005-01-01

    The environmental significance of acid rain on water systems of different buffer capacities is discussed. The most prevalent natural buffer system is created by the equilibrium between carbonate ions and carbon dioxide.

  11. [Association of fatty acid metabolism with systemic inflammatory response in chronic respiratory diseases].

    PubMed

    Denisenko, Y K; Novgorodtseva, T P; Zhukova, N V; Antonuk, M V; Lobanova, E G; Kalinina, E P

    2016-03-01

    We examined composition of plasma non-esterified fatty acids (NFAs), erythrocyte fatty acids, levels of eicosanoids in patients with asthma and chronic obstructive pulmonary disease (COPD) with different type of the inflammatory response. The results of our study show that asthma and COPD in remission are associated with changes in the composition NFAs of plasma, FA of erythrocytes, level eicosanoid despite the difference in the regulation of immunological mechanisms of systemic inflammation. These changes are characterized by excessive production of arachidonic acid (20:4n-6) and cyclooxygenase and lipoxygenase metabolites (thromboxane B2, leukotriene B4) and deficiency of their functional antagonist, eicosapentaenoic acid (20:5n-3). The recognized association between altered fatty acid composition and disorders of the immune mechanisms of regulation of systemic inflammation in COPD and asthma demonstrated the important role of fatty acids and their metabolites in persistence of inflammatory processes in diseases of the respiratory system in the condition of remission. PMID:27420629

  12. A novel enzyme-based acidizing system: Matrix acidizing and drilling fluid damage removal

    SciTech Connect

    Harris, R.E.; McKay, D.M.; Moses, V.

    1995-12-31

    A novel acidizing process is used to increase the permeability of carbonate rock cores in the laboratory and to remove drilling fluid damage from cores and wafers. Field results show the benefits of the technology as applied both to injector and producer wells.

  13. The solubilization of fatty acids in systems based on block copolymers and nonionic surfactants

    NASA Astrophysics Data System (ADS)

    Mirgorodskaya, A. B.; Yatskevich, E. I.; Zakharova, L. Ya.

    2010-12-01

    The solubilizing action of micellar, microemulsion, and polymer-colloid systems formed on the basis of biologically compatible amphiphilic polymers and nonionic surfactants on capric, lauric, palmitic, and stearic acids was characterized quantitatively. Systems based on micelle forming oxyethyl compounds increased the solubility of fatty acids by more than an order of magnitude. Acid molecules incorporated into micelles increased their size and caused structural changes. Solubilization was accompanied by complete or partial destruction of intrinsic acid associates and an increase in their p K a by 1.5-2 units compared with water.

  14. Arabidopsis ENHANCED DISEASE SUSCEPTIBILITY1 promotes systemic acquired resistance via azelaic acid and its precursor 9-oxo nonanoic acid.

    PubMed

    Wittek, Finni; Hoffmann, Thomas; Kanawati, Basem; Bichlmeier, Marlies; Knappe, Claudia; Wenig, Marion; Schmitt-Kopplin, Philippe; Parker, Jane E; Schwab, Wilfried; Vlot, A Corina

    2014-11-01

    Systemic acquired resistance (SAR) is a form of inducible disease resistance that depends on salicylic acid and its upstream regulator ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1). Although local Arabidopsis thaliana defence responses activated by the Pseudomonas syringae effector protein AvrRpm1 are intact in eds1 mutant plants, SAR signal generation is abolished. Here, the SAR-specific phenotype of the eds1 mutant is utilized to identify metabolites that contribute to SAR. To this end, SAR bioassay-assisted fractionation of extracts from the wild type compared with eds1 mutant plants that conditionally express AvrRpm1 was performed. Using high-performance liquid chromatography followed by mass spectrometry, systemic immunity was associated with the accumulation of 60 metabolites, including the putative SAR signal azelaic acid (AzA) and its precursors 9-hydroperoxy octadecadienoic acid (9-HPOD) and 9-oxo nonanoic acid (ONA). Exogenous ONA induced SAR in systemic untreated leaves when applied at a 4-fold lower concentration than AzA. The data suggest that in planta oxidation of ONA to AzA might be partially responsible for this response and provide further evidence that AzA mobilizes Arabidopsis immunity in a concentration-dependent manner. The AzA fragmentation product pimelic acid did not induce SAR. The results link the C9 lipid peroxidation products ONA and AzA with systemic rather than local resistance and suggest that EDS1 directly or indirectly promotes the accumulation of ONA, AzA, or one or more of their common precursors possibly by activating one or more pathways that either result in the release of these compounds from galactolipids or promote lipid peroxidation. PMID:25114016

  15. Arabidopsis ENHANCED DISEASE SUSCEPTIBILITY1 promotes systemic acquired resistance via azelaic acid and its precursor 9-oxo nonanoic acid

    PubMed Central

    Wittek, Finni; Hoffmann, Thomas; Kanawati, Basem; Bichlmeier, Marlies; Knappe, Claudia; Wenig, Marion; Schmitt-Kopplin, Philippe; Parker, Jane E.; Schwab, Wilfried; Vlot, A. Corina

    2014-01-01

    Systemic acquired resistance (SAR) is a form of inducible disease resistance that depends on salicylic acid and its upstream regulator ENHANCED DISEASE SUSCEPTIBILITY1 (EDS1). Although local Arabidopsis thaliana defence responses activated by the Pseudomonas syringae effector protein AvrRpm1 are intact in eds1 mutant plants, SAR signal generation is abolished. Here, the SAR-specific phenotype of the eds1 mutant is utilized to identify metabolites that contribute to SAR. To this end, SAR bioassay-assisted fractionation of extracts from the wild type compared with eds1 mutant plants that conditionally express AvrRpm1 was performed. Using high-performance liquid chromatography followed by mass spectrometry, systemic immunity was associated with the accumulation of 60 metabolites, including the putative SAR signal azelaic acid (AzA) and its precursors 9-hydroperoxy octadecadienoic acid (9-HPOD) and 9-oxo nonanoic acid (ONA). Exogenous ONA induced SAR in systemic untreated leaves when applied at a 4-fold lower concentration than AzA. The data suggest that in planta oxidation of ONA to AzA might be partially responsible for this response and provide further evidence that AzA mobilizes Arabidopsis immunity in a concentration-dependent manner. The AzA fragmentation product pimelic acid did not induce SAR. The results link the C9 lipid peroxidation products ONA and AzA with systemic rather than local resistance and suggest that EDS1 directly or indirectly promotes the accumulation of ONA, AzA, or one or more of their common precursors possibly by activating one or more pathways that either result in the release of these compounds from galactolipids or promote lipid peroxidation. PMID:25114016

  16. Thermal phase diagram of acetamide-benzoic acid and benzoic acid-phthalimide binary systems for solar thermal applications

    NASA Astrophysics Data System (ADS)

    Kumar, Rohitash; Kumar, Ravindra; Dixit, Ambesh

    2016-05-01

    Thermal properties of Acetamide (AM) - Benzoic acid (BA) and Benzoic acid (BA) - Phthalimide (PM) binary eutectic systems are theoretically calculated using thermodynamic principles. We found that the binary systems of AM-BA at 67.6 : 32.4 molar ratio, BA-PM at 89.7 : 10.3 molar ratio form eutectic mixtures with melting temperatures ~ 54.5 °C and 114.3 °C respectively. Calculated latent heat of fusion for these eutectic mixtures are 191 kJ/kg and 146.5 kJ/kg respectively. These melting temperatures and heat of fusions of these eutectic mixtures make them suitable for thermal energy storage applications in solar water heating and solar cooking systems.

  17. Control of acid mist emissions from FGD systems

    SciTech Connect

    Dahlin, R S; Brown, T D

    1991-01-01

    Improved control of acid mist emissions can be achieved by replacing or augmenting the conventional mist eliminators with a wet electrostatic precipitator (WESP). This paper describes a two-phased study performed to determine the degree of control that can be achieved with this approach. Phase I was a study of the electrical operation of a lab-scale WESP collecting an acid mist from a coal combustion pilot plant equipped with a spray chamber. The results of this study were used to develop and validate a computer model of the WESP. In Phase II, measurements were made at two utility scrubber installations to determine the loadings of acid mist, fly ash, and scrubber carryover. These measurements were used as input to the model to project the performance of a retrofitted WESP.

  18. Boundary of Phase Co-existence in Docosahexaenoic Acid System

    NASA Astrophysics Data System (ADS)

    Lor, Chai; Hirst, Linda S.

    2011-11-01

    Docosahexaenoic acid (DHA) is a highly polyunsaturated fatty acid (PUFA) that exhibits six double bonds in the hydrocarbon tail. It induces phase separation of the membrane into liquid order and liquid disorder in mixtures containing other lipids with more saturation and cholesterol. With the utilization of atomic force microscopy, phase co-existence is observed in lipid mixtures containing DHA on a single supported lipid bilayer. The boundary of phase co-existence with decreasing DHA concentration is explored. The elastic force, thickness, and roughness of the different phases are investigated.

  19. Neutrophil migration inhibitory properties of polyunsaturated fatty acids. The role of fatty acid structure, metabolism, and possible second messenger systems.

    PubMed Central

    Ferrante, A; Goh, D; Harvey, D P; Robinson, B S; Hii, C S; Bates, E J; Hardy, S J; Johnson, D W; Poulos, A

    1994-01-01

    The n-3 polyunsaturated fatty acids (PUFA) appear to have antiinflammatory properties that can be partly explained by their biological activity on leukocytes. Since leukocyte emigration is an essential component of the inflammatory response, we have examined the effects of the n-3 PUFA (eicosapentaenoic and docosahexaenoic acids) on neutrophil random and chemotactic movement. Preexposure of neutrophils for 15-30 min to 1-10 micrograms/ml PUFA reduced the random and chemotactic migration to both FMLP- and fungi-activated complement. The inhibitory effect diminished with increasing saturation and carbon chain length, and methylation abolished this activity. Arachidonic and docosahexaenoic acids were the most active fatty acids. The PUFA concentration required to inhibit migration was dependent on cell number, suggesting that the fatty acid effects on leukocyte migration in vivo may be governed by the stage of the inflammatory response. It was concluded that the PUFA rather than their metabolites were responsible for the inhibition since: (a) antioxidants did not prevent the PUFA-induced migration inhibition and the hydroxylated intermediates were less active, and (b) inhibitors of the cyclooxygenase and lipoxygenase pathways were without effect. Inhibitors of protein kinases and calmodulin-dependent enzyme system did not prevent the PUFA-induced migration inhibition, which was also independent of phospholipase D-catalyzed hydrolysis of phospholipids. It is also shown that PUFA decrease the FMLP-induced Ca2+ mobilization. Images PMID:8132744

  20. IUPAC-NIST Solubility Data Series. 90. Hydroxybenzoic Acid Derivatives in Binary, Ternary, and Multicomponent Systems. Part I. Hydroxybenzoic Acids, Hydroxybenzoates, and Hydroxybenzoic Acid Salts in Water and Aqueous Systems

    NASA Astrophysics Data System (ADS)

    Goto, Rensuke; Fukuda, Hiroshi; Königsberger, Erich; Königsberger, Lan-Chi

    2011-03-01

    The solubility data for well-defined binary, ternary, and multicomponent systems of solid-liquid type are reviewed. One component, which is 2-, 3-, and 4-hydroxybenzoic acids, 4-hydroxybenzoate alkyl esters (parabens), or hydroxybenzoic acid salts, is in the solid state at room temperature and another component is liquid water, meaning that all of the systems are aqueous solutions. The ternary or multicomponent systems include organic substances of various classes (hydrocarbons of several structural types, halogenated hydrocarbons, alcohols, acids, ethers, esters, amides, and surfactants) or inorganic substances. Systems reported in the primary literature from 1898 through 2000 are compiled. For seven systems, sufficient binary data for hydroxybenzoic acids or parabens in water are available to allow critical evaluation. Almost all data are expressed as mass and mole fractions as well as the originally reported units, while some data are expressed as molar concentration.

  1. Co-oxidation of the sulfur-containing amino acids in an autoxidizing lipid system

    USGS Publications Warehouse

    Wedemeyer, G.A.; Dollar, A.M.

    1963-01-01

    Oxidation of the sulfur amino acids by autoxidizing lipids was studied in a model system consisting of an amino acid dispersed in cold-pressed, molecularly distilled menhaden oil (20–80% w/w). Under all conditions investigated, cysteine was oxidized completely to cystine. Preliminary results suggest that at 110°C the oxidation follows first-order kinetics for at least the first 8 hr. A specific reaction rate constant of 0.25 per hour was calculated. When fatty acids were added to the system, cystine was oxidized to its thiosulfinate ester. When the fatty acid-cystine ratio was 1:2, oxidation of cystine was a maximum. No oxidation of cystine occurred unless either a fatty acid, volatile organic acid, or ethanol was added. Under the conditions investigated, methionine was not oxidized to either its sulfoxide or its sulfone.

  2. System for NO reduction using sublimation of cyanuric acid

    DOEpatents

    Perry, R.A.

    1989-01-24

    An arrangement for reducing the NO content of a gas stream comprises contacting the gas stream with HNCO at a temperature effective for heat induced decomposition of HNCO and for resultant lowering of the NO content of the gas stream. Preferably, the HNCO is generated by sublimation of cyanuric acid. 1 fig.

  3. DEVELOPMENT OF SRB TREATMENT SYSTEMS FOR ACID MINE DRAINAGE

    EPA Science Inventory

    Over the past decade, significant advances have been made in the development of sulfate- reducing bacteria (SRB) technology to treat acid mine drainage (AMD), Bench-scale testing, field demonstrations, and engineered applications of SRBs for the treatment of AMD will be presented...

  4. System for NO reduction using sublimation of cyanuric acid

    DOEpatents

    Perry, Robert A.

    1989-01-01

    An arrangement for reducing the NO content of a gas stream comprises contacting the gas stream with HNCO at a temperature effective for heat induced decomposition of HNCO and for resultant lowering of the NO content of the gas stream. Preferably, the HNCO is generated by sublimation of cyanuric acid.

  5. Disinfection of water in recirculating aquaculture systems with peracetic acid

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Peracetic acid (PAA) has become a favoured alternative to chlorination in the disinfection of municipal waste water in recent years. It is also commonly used in the food industry as a disinfectant. Based on PAA concentration, the disulfide linkage in enzymes and proteins of microorganisms can be bro...

  6. Solvent extraction study of the thorium nitrate, nitric acid, and tributyl phosphate-dodecane system: density and acidity relationships

    SciTech Connect

    Weinberger, A.J.; Marley, J.L.; Costanzo, D.A.

    1980-05-01

    A solvent extraction study to determine equilibrium conditions of thorium nitrate-nitric acid with 30% tributyl phosphate in normal dodecane has been completed. Experimental conditions studied were 30 to 60{sup 0}C, 0.05 to 1.5 M Th(NO{sub 3}){sub 4}, and 0.0 to 3.0 M HNO{sub 3}. The extractant concentration was constant at 30% tributyl phosphate. The equilibrium experiments have produced data which demonstrate that thorium nitrate concentration, free acid, and density are related in equilibrium behavior between the aqueous and organic phases from 30 to 60{sup 0}C in the 30% tributyl phosphate-dodecane solvent extraction system. The concentration interactions apply to both the two- and three-phase regions. A linear correlation was observed for the density (D) of the aqueous or organic phase and the concentration of thorium and free acid. The general form of the equation is D = a(C/sub Th/ + bC/sub H/) + c, where a is the slope, b is the constant, c is the intercept, and C/sub Th/ and C/sub H/ are the molar concentrations of thorium and free acid respectively. The relationship of temperature, thorium nitrate, and free acid makes possible the definitions of the boundaries between the two- and three-phase regions. This dependence, in turn, permits operational control or simulation studies of the system within the two-phase region. The data demonstrate the interactions of the components of the Thorex system and can be used to improve the mathematical description of equilibrium in the SEPHIS-Thorex computer program.

  7. Development of anti-scale poly(aspartic acid-citric acid) dual polymer systems for water treatment.

    PubMed

    Nayunigari, Mithil Kumar; Gupta, Sanjay Kumar; Kokkarachedu, Varaprasad; Kanny, K; Bux, F

    2014-01-01

    The formation of calcium sulphate and calcium carbonate scale poses major problems in heat exchangers and water cooling systems, thereby affecting the performance of these types of equipment. In order to inhibit these scale formations, new types of biodegradable water soluble single polymer and dual poly(aspartic acid-citric acid) polymers were developed and tested. The effectiveness of single polymer and four different compositions of poly aspartic acid and citric acid dual polymer systems as scale inhibitors were evaluated. Details of the synthesis, thermal stability, scale inhibition and the morphological characterization of single and dual polymers are presented in this scientific paper. It was found that the calcium sulphate scale inhibition rate was in the range 76.06-91.45%, while the calcium carbonate scale inhibition rate observed was in the range 23.37-30.0% at 65-70 °C. The finding suggests that the water soluble dual polymers are very effective in sulphate scale inhibition in comparison of calcium carbonate scale inhibition. PMID:25189837

  8. Dynamical dimer structure and liquid structure of fatty acids in their binary liquid mixture: decanoic/octadecanoic acid and decanoic/dodecanoic acid systems.

    PubMed

    Iwahashi, Makio; Takebayashi, Shintaro; Taguchi, Masakazu; Kasahara, Yasutoshi; Minami, Hideyuki; Matsuzawa, Hideyo

    2005-02-01

    Dimer structure and liquid structure of fatty acids in their binary mixtures such as decanoic acid (DA)/octadecanoic acid (SA) and DA/dodecanoic acid (LA) were studied through the measurements of self-diffusion coefficient (D), differential scanning calorimetry (DSC), density and viscosity. The obtained phase diagrams showed that DA and SA form a eutectic in the solid state but partly a solid solution in the SA-rich region; DA and LA form an incongruent-melting compound which forms a eutectic with DA. In the liquid mixture of DA and SA, the D of DA is larger than that of SA over the entire range of compositions and tends to approach the D of SA with increasing SA-mole fraction; the D of DA in the DA/LA system is also larger than that of LA especially in the LA-poor region and steeply approaches that of LA with increasing LA-mole fraction. These D values and phase diagrams were compared with those for the binary mixtures of n-alkanes (C14/C20, C19/C20 and C20/C24); it is concluded that the two kinds of fatty acids always form their individual homodimers in their liquid mixtures regardless of their compositions and temperatures. PMID:15642581

  9. Spatially dependent parameter estimation and nonlinear data assimilation by autosynchronization of a system of partial differential equations

    NASA Astrophysics Data System (ADS)

    Kramer, Sean; Bollt, Erik M.

    2013-09-01

    Given multiple images that describe chaotic reaction-diffusion dynamics, parameters of a partial differential equation (PDE) model are estimated using autosynchronization, where parameters are controlled by synchronization of the model to the observed data. A two-component system of predator-prey reaction-diffusion PDEs is used with spatially dependent parameters to benchmark the methods described. Applications to modeling the ecological habitat of marine plankton blooms by nonlinear data assimilation through remote sensing are discussed.

  10. The sensory interactions of organic acids and various flavors in ramen soup systems.

    PubMed

    Kang, M-W; Chung, S-J; Lee, H-S; Kim, Y; Kim, K-O

    2007-11-01

    This study was conducted to investigate the sensory interactions between various organic acids and flavorants in 3 types of ramen soup ('beef,' seafood, and 'kimchi') when types and levels of organic acids (citric, malic, and lactic) varied. For 'beef' and seafood ramen soup, weak suprathreshold levels of acids (0.0039% to 0.0071%) were applied to the system and medium suprathreshold of acids (0.0128% to 0.0299%) were applied to the kimchi ramen soup. The amount of acid applied to each system was chosen based on the equiweight level. Descriptive analyses were performed separately for each ramen soup system using 8 trained panelists. A total of 11, 13, and 12 flavor descriptors were generated for 'beef,' seafood, and 'kimchi' soup, respectively. Analysis of variance was conducted to evaluate the effect of organic acid on the sensory characteristics of ramen soup. Principal component analysis was conducted to summarize the relationship between the soup samples and attributes. The effect of organic acids on the flavor attributes of ramen soup was dependent on the soup system as well as adding levels of acid. Addition of lactic acid power (at 0.0066%) in 'beef'ramen soup showed enhancement effect on the sour, salty, beefy, 'mushroom' flavor, and fermented soybean paste soup flavor, whereas lactic acid powder (at 0.0071%) showed enhancement effect only on the sour and fermented soybean paste soup flavor in seafood ramen soup due to the strong 'hot' flavor characteristics of the soup. In kimchi ramen soup, flavor attributes congruent to sourness were enhanced by the addition of organic acids to the system. PMID:18034748

  11. Acid and alkali doped PBI electrolyte in electrochemical system

    NASA Astrophysics Data System (ADS)

    Xing, Baozhong

    In this work the conductivity of blank PBI membrane, acid doped PBI and alkaline doped PBI was systematically studied. A new methodology for sorption kinetics study in electrolyte solution has been established by monitoring the conductivity change during the sorption process. The model of the doping process and mechanism of conductivity are proposed. The performance of PBI (doped under optimum conditions) in fuel cell as PEM was evaluated. The experimental results show that the blank PBI in acid solution is an ionic insulator. It clarified the long time confusion in this area. The acid doped PBI membrane is an ionic conductor. The conductivity increases with the concentration of the acid solution. In high concentration acid solution, the conductivity increases with the type of acid in the order: H2SO 4 > H3PO4 > HClO4 > HNO3 > HCl. The kinetics of the doping process was studied, by a continuous method. The ionic conductivity mechanism was established. The PBI membranes doped with H2SO4 and H3PO4 exhibit better performance than NafionRTM. The doped FBI has more resistance to CO poison. 3% CO in H2 has little effect on the H3PO 4 doped PBI membrane at 185°C. The conductivity of the alkali doped PBI membrane changes with the concentration of the alkaline solution and the type of the alkalis. The conductivity has a maximum in KOH and NaOH solution. The maximum conductivity in KOH is higher than in NaOH and LiOH. It is about 5 times of that of NafionRTM in alkaline solution. The two-step sorption process in alkaline solution was observed. The first step is the permeation process of the alkalis in the PBI membrane. The permeation is the results of diffusion and interaction. It is concluded that the permeation process is controlled by the rate of interaction between the alkali and PBI molecule. The second step is the relaxation process in the membrane. This step contributes more to the conductivity for the membrane than the first step. The ionic conductivity mechanism

  12. Reprocessing system with nuclide separation based on chromatography in hydrochloric acid solution

    SciTech Connect

    Suzuki, Tatsuya; Tachibana, Yu; Koyama, Shi-ichi

    2013-07-01

    We have proposed the reprocessing system with nuclide separation processes based on the chromatographic technique in the hydrochloric acid solution system. Our proposed system consists of the dissolution process, the reprocessing process, the minor actinide separation process, and nuclide separation processes. In the reprocessing and separation processes, the pyridine resin is used as a main separation media. It was confirmed that the dissolution in the hydrochloric acid solution is easily achieved by the plasma voloxidation and by the addition of oxygen peroxide into the hydrochloric acid solution.

  13. Removal of an acid fume system contaminated with perchlorates located within hot cell

    SciTech Connect

    Rosenberg, K.E.; Henslee, S.P.; Vroman, W.R.; Krsul, J.R.; Michelbacher, J.A.; Knighton, G.C.

    1992-09-01

    An add scrubbing system located within the confines of a highly radioactive hot cell at Argonne National Laboratory-West (ANL-W) was remotely removed. The acid scrubbing system was routinely used for the dissolution of irradiated reactor fuel samples and structural materials. Perchloric acid was one of the acids used in the dissolution process and remained in the system with its inherent risks. Personnel could not enter the hot cell to perform the dismantling of the acid scabbing system due to the high radiation field and the explosion potential associated with the perchlorates. A robot was designed and built at ANL-W and used to dismantle the system without the need for personnel entry into the hot cell. The robot was also used for size reduction of removed components and loading of the removed components into waste containers.

  14. Disinfection of water in recirculating aquaculture systems with peracetic acid (PAA)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The disinfection behaviour of peracetic acid (PAA) in recirculating aquaculture systems (RAS) was investigated. Peracetic acid is a strong oxidizing agent found in various concentrations in different products. Three Wofasteril PAA products (E400 (c), Lspecical; AC 150) were tested in vitro for the...

  15. Utilization of a bipolar lead acid battery for the advanced launch system

    NASA Technical Reports Server (NTRS)

    Gentry, William O.; Vidas, Robin; Miles, Ronald; Eckles, Steven

    1991-01-01

    The development of a battery comprised of bipolar lead acid modules is discussed. The battery is designed to satisfy the requirements of the Advanced Launch System (ALS). The battery will have the following design features: (1) conventional lead acid chemistry; (2) thin electrode/active materials; (3) a thin separator; (4) sealed construction (gas recombinant); and (5) welded plastic frames for the external seal.

  16. STATE ACID RAIN RESEARCH AND SCREENING SYSTEM - VERSION 1.0 USER'S MANUAL

    EPA Science Inventory

    The report is a user's manual that describes Version 1.0 of EPA's STate Acid Rain Research and Screening System (STARRSS), developed to assist utility regulatory commissions in reviewing utility acid rain compliance plans. It is a screening tool that is based on scenario analysis...

  17. ANALYSIS SYSTEM FOR TOTAL SULFURIC ACID IN AMBIENT AIR. DEVELOPMENT AND PRELIMINARY EVALUATION

    EPA Science Inventory

    A total sulfuric acid analysis (TSAA) system was developed and shown to provide quantitative determinations of sulfuric acid in air at concentrations as low as 0.26 micrograms/cu m. Quantitation at lower concentrations appears to be possible. The general approach in the design an...

  18. ADIPIC ACID DEGRADATION MECHANISM IN AQUEOUS FGD (FLUE GAS DESULFURIZATION) SYSTEMS

    EPA Science Inventory

    The report gives results of a field and laboratory study of the adipic acid degradation mechanism in aqueous flue gas desulfurization (FGD) systems. (Adding adipic acid to limestone-based, SO2 wet scrubbers increases SO2 removal and limestone utilization. However, as much as 80% ...

  19. PERFORMANCE AND MODELING OF A HOT POTASSIUM CARBONATE ACID GAS REMOVAL SYSTEM IN TREATING COAL GAS

    EPA Science Inventory

    The report discusses the performance and modeling of a hot potassium carbonate (K2CO3) acid gas removal system (AGRS) in treating coal gas. Aqueous solutions of K2CO3, with and without amine additive, were used as the acid gas removal solvent in the Coal Gasification/Gas Cleaning...

  20. Citric Acid-Modified Fenton's Reaction for the Oxidation of Chlorinated Ethylenes in Soil Solution Systems

    SciTech Connect

    Seol, Yongkoo; Javandel, Iraj

    2008-03-15

    Fenton's reagent, a solution of hydrogen peroxide and ferrous iron catalyst, is used for an in-situ chemical oxidation of organic contaminants. Sulfuric acid is commonly used to create an acidic condition needed for catalytic oxidation. Fenton's reaction often involves pressure buildup and precipitation of reaction products, which can cause safety hazards and diminish efficiency. We selected citric acid, a food-grade substance, as an acidifying agent to evaluate its efficiencies for organic contaminant removal in Fenton's reaction, and examined the impacts of using citric acid on the unwanted reaction products. A series of batch and column experiments were performed with varying H{sub 2}O{sub 2} concentrations to decompose selected chlorinated ethylenes. Either dissolved iron from soil or iron sulfate salt was added to provide the iron catalyst in the batch tests. Batch experiments revealed that both citric and sulfuric acid systems achieved over 90% contaminant removal rates, and the presence of iron catalyst was essential for effective decontamination. Batch tests with citric acid showed no signs of pressure accumulation and solid precipitations, however the results suggested that an excessive usage of H{sub 2}O{sub 2} relative to iron catalysts (Fe{sup 2+}/H{sub 2}O{sub 2} < 1/330) would result in lowering the efficiency of contaminant removal by iron chelations in the citric acid system. Column tests confirmed that citric acid could provide suitable acidic conditions to achieve higher than 55% contaminant removal rates.

  1. Possible involvement of lipoic acid in binding protein-dependent transport systems in Escherichia coli.

    PubMed

    Richarme, G

    1985-04-01

    We describe the properties of the binding protein dependent-transport of ribose, galactose, and maltose and of the lactose permease, and the phosphoenolpyruvate-glucose phosphotransferase transport systems in a strain of Escherichia coli which is deficient in the synthesis of lipoic acid, a cofactor involved in alpha-keto acid dehydrogenation. Such a strain can grow in the absence of lipoic acid in minimal medium supplemented with acetate and succinate. Although the lactose permease and the phosphoenolypyruvate-glucose phosphotransferase are not affected by lipoic acid deprivation, the binding protein-dependent transports are reduced by 70% in conditions of lipoic acid deprivation when compared with their activity in conditions of lipoic acid supply. The remaining transport is not affected by arsenate but is inhibited by the uncoupler carbonylcyanide-m-chlorophenylhydrazone; however the lipoic acid-dependent transport is completely inhibited by arsenate and only weakly inhibited by carbonylcyanide-m-chlorophenylhydrazone. The known inhibitor of alpha-keto acid dehydrogenases, 5-methoxyindole-2-carboxylic acid, completely inhibits all binding protein-dependent transports whether in conditions of lipoic supply or deprivation; the results suggest a possible relation between binding protein-dependent transport and alpha-keto acid dehydrogenases and shed light on the inhibition of these transports by arsenicals and uncouplers. PMID:3920206

  2. Micro-Detection System for Determination of the Biotic or Abiotic Origin of Amino Acids

    NASA Technical Reports Server (NTRS)

    Bada, Jeffrey L.; Betts, Bruce (Technical Monitor)

    2002-01-01

    The research involved the development of a breadboard version of a spacecraft based system for the detection of amino acid chirality (handedness) on solar system bodies. The design concept has three distinct components: a sublimation chamber for the release of amino acids from an acquired sample; a microchip based capillary electrophoresis (CE) chip for the separation of amino acids and their enantiomers; and a fluorescent based detection system. In addition, we have investigated the use of a microfluidics system for the extraction of amino acids in samples in which sublimation has proven to be problematic. This is a joint project carried out at the Scripps Institution of Oceanography (SIO), University of California at San Diego; the Jet Propulsion Laboratory (JPL), Pasadena; and the Department of Chemistry, University of California, Berkeley.

  3. Salicylic acid and jasmonic acid are essential for systemic resistance against tobacco mosaic virus in Nicotiana benthamiana.

    PubMed

    Zhu, Feng; Xi, De-Hui; Yuan, Shu; Xu, Fei; Zhang, Da-Wei; Lin, Hong-Hui

    2014-06-01

    Systemic resistance is induced by pathogens and confers protection against a broad range of pathogens. Recent studies have indicated that salicylic acid (SA) derivative methyl salicylate (MeSA) serves as a long-distance phloem-mobile systemic resistance signal in tobacco, Arabidopsis, and potato. However, other experiments indicate that jasmonic acid (JA) is a critical mobile signal. Here, we present evidence suggesting both MeSA and methyl jasmonate (MeJA) are essential for systemic resistance against Tobacco mosaic virus (TMV), possibly acting as the initiating signals for systemic resistance. Foliar application of JA followed by SA triggered the strongest systemic resistance against TMV. Furthermore, we use a virus-induced gene-silencing-based genetics approach to investigate the function of JA and SA biosynthesis or signaling genes in systemic response against TMV infection. Silencing of SA or JA biosynthetic and signaling genes in Nicotiana benthamiana plants increased susceptibility to TMV. Genetic experiments also proved the irreplaceable roles of MeSA and MeJA in systemic resistance response. Systemic resistance was compromised when SA methyl transferase or JA carboxyl methyltransferase, which are required for MeSA and MeJA formation, respectively, were silenced. Moreover, high-performance liquid chromatography-mass spectrometry analysis indicated that JA and MeJA accumulated in phloem exudates of leaves at early stages and SA and MeSA accumulated at later stages, after TMV infection. Our data also indicated that JA and MeJA could regulate MeSA and SA production. Taken together, our results demonstrate that (Me)JA and (Me)SA are required for systemic resistance response against TMV. PMID:24450774

  4. Nanofiltration, bipolar electrodialysis and reactive extraction hybrid system for separation of fumaric acid from fermentation broth.

    PubMed

    Prochaska, Krystyna; Staszak, Katarzyna; Woźniak-Budych, Marta Joanna; Regel-Rosocka, Magdalena; Adamczak, Michalina; Wiśniewski, Maciej; Staniewski, Jacek

    2014-09-01

    A novel approach based on a hybrid system allowing nanofiltration, bipolar electrodialysis and reactive extraction, was proposed to remove fumaric acid from fermentation broth left after bioconversion of glycerol. The fumaric salts can be concentrated in the nanofiltration process to a high yield (80-95% depending on pressure), fumaric acid can be selectively separated from other fermentation components, as well as sodium fumarate can be conversed into the acid form in bipolar electrodialysis process (stack consists of bipolar and anion-exchange membranes). Reactive extraction with quaternary ammonium chloride (Aliquat 336) or alkylphosphine oxides (Cyanex 923) solutions (yield between 60% and 98%) was applied as the final step for fumaric acid recovery from aqueous streams after the membrane techniques. The hybrid system permitting nanofiltration, bipolar electrodialysis and reactive extraction was found effective for recovery of fumaric acid from the fermentation broth. PMID:24983693

  5. Synaptic inhibition and γ-aminobutyric acid in the mammalian central nervous system

    PubMed Central

    OBATA, Kunihiko

    2013-01-01

    Signal transmission through synapses connecting two neurons is mediated by release of neurotransmitter from the presynaptic axon terminals and activation of its receptor at the postsynaptic neurons. γ-Aminobutyric acid (GABA), non-protein amino acid formed by decarboxylation of glutamic acid, is a principal neurotransmitter at inhibitory synapses of vertebrate and invertebrate nervous system. On one hand glutamic acid serves as a principal excitatory neurotransmitter. This article reviews GABA researches on; (1) synaptic inhibition by membrane hyperpolarization, (2) exclusive localization in inhibitory neurons, (3) release from inhibitory neurons, (4) excitatory action at developmental stage, (5) phenotype of GABA-deficient mouse produced by gene-targeting, (6) developmental adjustment of neural network and (7) neurological/psychiatric disorder. In the end, GABA functions in simple nervous system and plants, and non-amino acid neurotransmitters were supplemented. PMID:23574805

  6. 21 CFR 862.1055 - Newborn screening test system for amino acids, free carnitine, and acylcarnitines using tandem...

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Newborn screening test system for amino acids... screening test system for amino acids, free carnitine, and acylcarnitines using tandem mass spectrometry. (a) Identification. A newborn screening test system for amino acids, free carnitine, and acylcarnitines using...

  7. 21 CFR 862.1055 - Newborn screening test system for amino acids, free carnitine, and acylcarnitines using tandem...

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Newborn screening test system for amino acids... screening test system for amino acids, free carnitine, and acylcarnitines using tandem mass spectrometry. (a) Identification. A newborn screening test system for amino acids, free carnitine, and acylcarnitines using...

  8. 21 CFR 862.1055 - Newborn screening test system for amino acids, free carnitine, and acylcarnitines using tandem...

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Newborn screening test system for amino acids... screening test system for amino acids, free carnitine, and acylcarnitines using tandem mass spectrometry. (a) Identification. A newborn screening test system for amino acids, free carnitine, and acylcarnitines using...

  9. 21 CFR 862.1055 - Newborn screening test system for amino acids, free carnitine, and acylcarnitines using tandem...

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Newborn screening test system for amino acids... screening test system for amino acids, free carnitine, and acylcarnitines using tandem mass spectrometry. (a) Identification. A newborn screening test system for amino acids, free carnitine, and acylcarnitines using...

  10. A novel system combining biocatalytic dephosphorylation of L-ascorbic acid 2-phosphate and electrochemical oxidation of resulting ascorbic acid.

    PubMed

    Kuwahara, Takashi; Homma, Toshimasa; Kondo, Mizuki; Shimomura, Masato

    2011-03-15

    An enzyme electrode was prepared with acid phosphatase (ACP) for development of a new electric power generation system using ascorbic acid 2-phosphate (AA2P) as a fuel. The properties of the electrode were investigated with respect to biocatalytic dephosphorylation of AA2P and electrochemical oxidation of resulting ascorbic acid (AA). The enzyme electrode was fabricated by immobilization of ACP through amide linkage onto a self-assembled monolayer of 3-mercaptopropionic acid on a gold electrode. AA2P was not oxidized on a bare gold electrode in the potential sweep range from -0.1 to +0.5 V vs. Ag/AgCl. However, the enzyme electrode gave an oxidation current in citric buffer solution of pH 5 containing 10 mM of AA2P. The oxidation current began to increase at +0.2V, and reached to 5.0 μA cm(-2) at +0.5 V. The potential +0.2 V corresponded to the onset of oxidation of ascorbic acid (AA). These results suggest that the oxidation current observed with the enzyme electrode is due to AA resulting from dephosphorylation of AA2P. The oxidation current increased with increasing concentration of AA2P and almost leveled off at around the concentration of 5mM. Thus the enzyme electrode brought about biocatalytic conversion of AA2P to AA, followed by electrochemical oxidation of the AA. The oxidation current is likely to be controlled by the biocatalytic reaction. PMID:21247749

  11. Fatty Acids in Energy Metabolism of the Central Nervous System

    PubMed Central

    Orynbayeva, Zulfiya; Vavilin, Valentin; Lyakhovich, Vyacheslav

    2014-01-01

    In this review, we analyze the current hypotheses regarding energy metabolism in the neurons and astroglia. Recently, it was shown that up to 20% of the total brain's energy is provided by mitochondrial oxidation of fatty acids. However, the existing hypotheses consider glucose, or its derivative lactate, as the only main energy substrate for the brain. Astroglia metabolically supports the neurons by providing lactate as a substrate for neuronal mitochondria. In addition, a significant amount of neuromediators, glutamate and GABA, is transported into neurons and also serves as substrates for mitochondria. Thus, neuronal mitochondria may simultaneously oxidize several substrates. Astrocytes have to replenish the pool of neuromediators by synthesis de novo, which requires large amounts of energy. In this review, we made an attempt to reconcile β-oxidation of fatty acids by astrocytic mitochondria with the existing hypothesis on regulation of aerobic glycolysis. We suggest that, under condition of neuronal excitation, both metabolic pathways may exist simultaneously. We provide experimental evidence that isolated neuronal mitochondria may oxidize palmitoyl carnitine in the presence of other mitochondrial substrates. We also suggest that variations in the brain mitochondrial metabolic phenotype may be associated with different mtDNA haplogroups. PMID:24883315

  12. The reduction process of phytic acid silver ion system: A pulse radiolysis study

    NASA Astrophysics Data System (ADS)

    Joshi, Ravi; Mukherjee, Tulsi

    2007-05-01

    Reduction of silver ion in a silver-phytic acid (1:1 ratio) system has been studied using pulse radiolysis technique. Time-resolved transformation of the intermediates, Ag +→Ag 0→Ag 2+→Ag 32+, has been clearly observed in the reduction of silver-phytic acid (1:1) system. The effect of phytic acid on the formation and decay of initial silver clusters has been also studied. The surface plasmon absorption band of stable silver nanoparticle (410 nm) and dynamic light scattering technique has been used to characterize the nanoparticles and measure the average size ( Rav=100 nm).

  13. System and process for capture of acid gasses at elevated pressure from gaseous process streams

    DOEpatents

    Heldebrant, David J.; Koech, Phillip K.; Linehan, John C.; Rainbolt, James E.; Bearden, Mark D.; Zheng, Feng

    2016-09-06

    A system, method, and material that enables the pressure-activated reversible chemical capture of acid gasses such as CO.sub.2 from gas volumes such as streams, flows or any other volume. Once the acid gas is chemically captured, the resulting product typically a zwitterionic salt, can be subjected to a reduced pressure whereupon the resulting product will release the captures acid gas and the capture material will be regenerated. The invention includes this process as well as the materials and systems for carrying out and enabling this process.

  14. Kinetics of color development of melanoidins formed from fructose/amino acid model systems.

    PubMed

    Echavarría, A P; Pagán, J; Ibarz, A

    2014-03-01

    The formation of soluble melanoidins from a single combination of sugar (fructose) and amino acid model systems were evaluated kinetically. The selected amino acids, commonly found in apple juice and highly reactive in the Maillard reaction, were asparagine, aspartic acid, and glutamic acid. The effect of these reagents and the treatment at different temperatures (50 , 85 , and 100 ) during 96 h on the color intensity of the melanoidin formed was measured by absorbance at different wavelengths (280, 325, 405, and 420 nm). The absorbance of the melanoidin formed from all model systems was located on the wavelength of 405 nm, that is, the area of the visible spectrum close to the UV region. The color of the melanoidins was directly measured using the CIELAB color space system. A first-order kinetic model was applied to the evolution of the ΔE * (color difference) and L * (lightness) of the color. The fructose/aspartic acid model system values of a * (redness) and b * (yellowness) were found in the brown-red zone. Therefore, the color development of the melanoidins was influenced by the type of amino acid and temperature. Especially, it is thought that the a * and b * values can be used to explain the differences among the amino acids in the color development of melanoidins. PMID:23744115

  15. Micro-Detection System for Determination of the Biotic or Abiotic Origin of Amino Acids

    NASA Technical Reports Server (NTRS)

    Bada, Jeffrey L.

    2003-01-01

    The research carried out under this PIDDP involves the development of a breadboard version of a spacecraft-based system for the detection of amino acid chirality (molecular handedness) on solar system bodies. Chirality provides an unambiguous way of distinguishing between abiotic and biotic origins since only one mirror-image form is used in the functional molecules of life. Recent advances in a variety of nano-fabrication technologies have resulted in concepts for enabling miniaturized chemical and biological analytical systems. These are complete application-specific systems that integrate fluid micro handling systems for extracting and reacting target molecules, micro-separation technologies for enhanced sensitivity and resolution, and advanced detection technologies. This effort makes use of a relatively new technology that shows demonstrated promise for spacecraft-based amino acid analysis: microchip-based capillary electrophoresis (muCE). The muCE system is capable of analyzing the type of amino acids present as well as the relative amounts of their mirror image forms. The system we developed will be able to chirally resolve all of the major amino acids found in extraterrestrial material (Gly, Ala, Val, Pro, Asp, Glu, a-aminoisobutyric acid, and isovaline) at sub-part-per-billion levels. The _CE analysis requires that the amino acids be extracted from the sample and derivatized for either optical or electrochemical detection. In our implementation, the amino acids are released from the sample by sublimation and prepared for muCE analysis using a microfluidic circuit. In addition, we have investigated the use of a microfluidic circuit for the release of amino acids from samples in which sublimation has proven to be problematic.

  16. Organic Acids as Hetrotrophic Energy Sources in Hydrothermal Systems

    NASA Astrophysics Data System (ADS)

    Windman, T. O.; Zolotova, N.; Shock, E.

    2004-12-01

    Many thermophilic microbes are heterotrophs, but little is known about the organic compounds present in hydrothermal ecosystems. More is known about what these organisms will metabolize in lab experiments than what they do metabolize in nature. In an effort to bridge this gap, we have begun to incorporate organic analyses into ongoing research on Yellowstone hydrothermal ecosystems. After filtering at least a liter of hot spring water to minimize contamination, samples were collected into sixty-milliliter serum vials containing ultra-pure phosphoric acid, sodium hydroxide, or benzalkonium chloride. Approximately 80 sites were sampled spanning temperatures from 60 to 90°C and pH values from 2 to 9. Analytical data for organic acid anions (including formate, acetate, lactate, and succinate) were obtained by ion chromatography. Preliminary results indicate that concentrations of organic acids anions range from 5 to 300 ppb. These results can be used with other field and lab data (sulfate, sulfide, nitrate, ammonia, bicarbonate, pH, hydrogen) in thermodynamic calculations to evaluate the amounts of energy available in heterotrophic reactions. Preliminary results of such calculations show that sulfate reduction to sulfide coupled to succinate oxidation to bicarbonate yields about 6 kcal per mole of electrons transferred. When formate oxidation to bicarbonate or hydrogen oxidation to water is coupled to sulfate reduction there is less energy available by approximately a factor of two. A comparison with nitrate reduction to ammonia involving succinate and/or formate oxidation reveals several similarities. Using formate to reduce nitrate can yield about as much energy as nitrate reduction with hydrogen (typically 12 to 14 kcal per mole of electrons transferred), but using succinate can yield more than twice as much energy. In fact, reduction of nitrate with succinate can provide more energy than any of the inorganic nitrate reduction reactions involving sulfur, iron

  17. Acidity field of soils as ion-exchange systems and the diagnostics of genetic soil horizons

    NASA Astrophysics Data System (ADS)

    Kokotov, Yu. A.; Sukhacheva, E. Yu.; Aparin, B. F.

    2014-12-01

    For the comprehensive description of the acidity of a two-phase ion-exchange system, we should analyze two curves of the ionite titration by a strong base in water and salt solutions and find the quantitative relationships between the corresponding pH characteristics. An idea of the three-dimensional field of acidity of ion-exchange systems (the phase space of the soil acidity characteristics) and its three two-dimensional projections is suggested. For soils, three interrelated characteristics—the pH values of the salt and water extracts and the degree of base saturation—can serve as spatial coordinates for the acidity field. Representation of factual data in this field makes it possible to compare and analyze the acidity characteristics of different soils and soil horizons and to determine their specific features. Differentiation of the field into separate volumes allows one to present the data in a discrete form. We have studied the distribution patterns of the groups of soil horizons from Leningrad oblast and other regions of northwestern Russia in the acidity field. The studied samples are grouped in different partially overlapping areas of the projections of the acidity field. The results of this grouping attest to the correctness of the modern classification of Russian soils. A notion of the characteristic soil area in the acidity field is suggested; it can be applied to all the soils with a leaching soil water regime.

  18. Adsorption/desorption in a system consisting of humic acid, heavy metals, and clay minerals

    SciTech Connect

    Liu, A.; Gonzalez, R.D.

    1999-10-01

    Metal adsorption/desorption in a system consisting of humic acid, metal ions, and clay minerals is described. Montmorillonite and purified humic acid were selected as prototype materials for this study. At a constant ionic strength, the amount of humic acid adsorbed on montmorillonite decreases when pH is increased. A slight increase in humic acid adsorption on montmorillonite is observed when there are bivalent metals present in the system. The metal adsorption on montmorillonite does not correlate to the amount of humic acid adsorbed on montmorillonite. Montmorillonite with preadsorbed humic acid does not show a significant change in the capacity of adsorbed metal ions. An increase in the ionic strength at a pH of 6.5 results in an increase in the adsorption of lead on montmorillonite in the presence of humic acid, while at a lower pH, the increase in ionic strength results in a decrease in metal adsorption. The bridging of bivalent metal ions between montmorillonite and humic acid is proposed as the dominant adsorption mechanism.

  19. Bilayers and wormlike micelles at high pH in fatty acid soap systems.

    PubMed

    Xu, Wenlong; Liu, Huizhong; Song, Aixin; Hao, Jingcheng

    2016-03-01

    Bilayers at high pH in the fatty acid systems of palmitic acid/KOH/H2O, palmitic acid/CsOH/H2O, stearic acid/KOH/H2O and stearic acid/CsOH/H2O can form spontaneously (Xu et al., 2014, 2015). In this work, the bilayers can still be observed at 25°C with an increase of the concentration of fatty acids. We found that wormlike micelles can also be prepared in the fatty acid soap systems at high pH, even though the temperature was increased to be 50°C. The viscoelasticity, apparent viscosity, yield stress of the bilayers were determined by the rheological measurements. Wormlike micelles were identified by cryogenic transmission electron microscopy (cryo-TEM) and emphasized by the rheological characterizations, which are in accordance with the Maxwell fluids with good fit of Cole-Cole plots. The phase transition temperature was determined by differential scanning calorimetry (DSC) and the transition process was recorded. The regulating role of counterions of fatty acids were discussed by (CH3)4N(+), (C2H5)4N(+), (C3H7)4N(+), and (C4H9)4N(+) as comparison, concluding that counterions with appropriate hydrated radius were the vital factor in the formation wormlike micelles. PMID:26688122

  20. An automatic system for acidity determination based on sequential injection titration and the monosegmented flow approach.

    PubMed

    Kozak, Joanna; Wójtowicz, Marzena; Gawenda, Nadzieja; Kościelniak, Paweł

    2011-06-15

    An automatic sequential injection system, combining monosegmented flow analysis, sequential injection analysis and sequential injection titration is proposed for acidity determination. The system enables controllable sample dilution and generation of standards of required concentration in a monosegmented sequential injection manner, sequential injection titration of the prepared solutions, data collecting, and handling. It has been tested on spectrophotometric determination of acetic, citric and phosphoric acids with sodium hydroxide used as a titrant and phenolphthalein or thymolphthalein (in the case of phosphoric acid determination) as indicators. Accuracy better than |4.4|% (RE) and repeatability better than 2.9% (RSD) have been obtained. It has been applied to the determination of total acidity in vinegars and various soft drinks. The system provides low sample (less than 0.3 mL) consumption. On average, analysis of a sample takes several minutes. PMID:21641455

  1. Prediction of liquid-liquid equilibrium for systems of vegetable oils, fatty acids, and ethanol

    SciTech Connect

    Batista, E.; Monnerat, S.; Stragevitch, L.; Pina, C.G.; Goncalves, C.B.; Meirelles, A.J.A.

    1999-12-01

    Group interaction parameters for the UNIFAC and ASOG models were specially adjusted for predicting liquid-liquid equilibrium (LLE) for systems of vegetable oils, fatty acids, and ethanol at temperatures ranging from 20 to 45 C. Experimental liquid-liquid equilibrium data for systems of triolein, oleic acid, and ethanol and of triolein, stearic acid, and ethanol were measured and utilized in the adjustment. The average percent deviation between experimental and calculated compositions was 0.79% and 0.52% for the UNIFAC and ASOG models, respectively. The prediction of liquid-liquid equilibrium for systems of vegetable oils, fatty acids, and ethanol was quite successful, with an average deviation of 1.31% and 1.32% for the UNIFAC and ASOG models, respectively.

  2. Solid/liquid phase diagram of the ammonium sulfate/succinic acid/water system.

    PubMed

    Pearson, Christian S; Beyer, Keith D

    2015-05-14

    We have studied the low-temperature phase diagram and water activities of the ammonium sulfate/succinic acid/water system using differential scanning calorimetry and infrared spectroscopy of thin films. Using the results from our experiments, we have mapped the solid/liquid ternary phase diagram, determined the water activities based on the freezing point depression, and determined the ice/succinic acid phase boundary as well as the ternary eutectic composition and temperature. We also compared our results to the predictions of the extended AIM aerosol thermodynamics model (E-AIM) and found good agreement for the ice melting points in the ice primary phase field of this system; however, differences were found with respect to succinic acid solubility temperatures. We also compared the results of this study with those of previous studies that we have published on ammonium sulfate/dicarboxylic acid/water systems. PMID:25431860

  3. Self-microemulsifying drug delivery system for improved oral bioavailability of oleanolic acid: design and evaluation

    PubMed Central

    Yang, Rui; Huang, Xin; Dou, Jinfeng; Zhai, Guangxi; Su, Lequn

    2013-01-01

    Oleanolic acid is a poorly water-soluble drug with low oral bioavailability. A self-microemulsifying drug delivery system (SMEDDS) has been developed to enhance the solubility and oral bioavailability of oleanolic acid. The formulation design was optimized by solubility assay, compatibility tests, and pseudoternary phase diagrams. The morphology, droplet size distribution, zeta potential, viscosity, electrical conductivity, and refractive index of a SMEDDS loaded with oleanolic acid were studied in detail. Compared with oleanolic acid solution, the in vitro release of oleanolic acid from SMEDDS showed that the drug could be released in a sustained manner. A highly selective and sensitive high-performance liquid chromatographymass spectrometry method was developed for determination of oleanolic acid in rat plasma. This method was used for a pharmacokinetic study of an oleanolic acid-loaded SMEDDS compared with the conventional tablet in rats. Promisingly, a 5.07-fold increase in oral bioavailability of oleanolic acid was achieved for the SMEDDS compared with the marketed product in tablet form. Our studies illustrate the potential use of a SMEDDS for delivery of oleanolic acid via the oral route. PMID:23966781

  4. Commercial phosphoric acid fuel cell system technology development

    NASA Technical Reports Server (NTRS)

    Prokopius, P. R.; Warshay, M.; Simons, S. N.; King, R. B.

    1979-01-01

    Reducing cost and increasing reliability were the technology drivers in both the electric utility and on-site integrated energy system applications. The longstanding barrier to the attainment of these goals was materials. Differences in approaches and their technological features, including electrodes, matrices, intercell cooling, bipolar/separator plates, electrolyte management, fuel selection, and system design philosophy were discussed.

  5. Evidence of Two Functionally Distinct Ornithine Decarboxylation Systems in Lactic Acid Bacteria

    PubMed Central

    Romano, Andrea; Trip, Hein; Lonvaud-Funel, Aline; Lolkema, Juke S.

    2012-01-01

    Biogenic amines are low-molecular-weight organic bases whose presence in food can result in health problems. The biosynthesis of biogenic amines in fermented foods mostly proceeds through amino acid decarboxylation carried out by lactic acid bacteria (LAB), but not all systems leading to biogenic amine production by LAB have been thoroughly characterized. Here, putative ornithine decarboxylation pathways consisting of a putative ornithine decarboxylase and an amino acid transporter were identified in LAB by strain collection screening and database searches. The decarboxylases were produced in heterologous hosts and purified and characterized in vitro, whereas transporters were heterologously expressed in Lactococcus lactis and functionally characterized in vivo. Amino acid decarboxylation by whole cells of the original hosts was determined as well. We concluded that two distinct types of ornithine decarboxylation systems exist in LAB. One is composed of an ornithine decarboxylase coupled to an ornithine/putrescine transmembrane exchanger. Their combined activities results in the extracellular release of putrescine. This typical amino acid decarboxylation system is present in only a few LAB strains and may contribute to metabolic energy production and/or pH homeostasis. The second system is widespread among LAB. It is composed of a decarboxylase active on ornithine and l-2,4-diaminobutyric acid (DABA) and a transporter that mediates unidirectional transport of ornithine into the cytoplasm. Diamines that result from this second system are retained within the cytosol. PMID:22247134

  6. Model Systems of Precursor Cellular Membranes: Long-Chain Alcohols Stabilize Spontaneously Formed Oleic Acid Vesicles

    PubMed Central

    Rendón, Adela; Carton, David Gil; Sot, Jesús; García-Pacios, Marcos; Montes, Ruth; Valle, Mikel; Arrondo, José-Luis R.; Goñi, Felix M.; Ruiz-Mirazo, Kepa

    2012-01-01

    Oleic acid vesicles have been used as model systems to study the properties of membranes that could be the evolutionary precursors of more complex, stable, and impermeable phospholipid biomembranes. Pure fatty acid vesicles in general show high sensitivity to ionic strength and pH variation, but there is growing evidence that this lack of stability can be counterbalanced through mixtures with other amphiphilic or surfactant compounds. Here, we present a systematic experimental analysis of the oleic acid system and explore the spontaneous formation of vesicles under different conditions, as well as the effects that alcohols and alkanes may have in the process. Our results support the hypothesis that alcohols (in particular 10- to 14-C-atom alcohols) contribute to the stability of oleic acid vesicles under a wider range of experimental conditions. Moreover, studies of mixed oleic-acid-alkane and oleic-acid-alcohol systems using infrared spectroscopy and Langmuir trough measurements indicate that precisely those alcohols that increased vesicle stability also decreased the mobility of oleic acid polar headgroups, as well as the area/molecule of lipid. PMID:22339864

  7. Incinerator ash dissolution model for the system: Plutonium, nitric acid and hydrofluoric acid

    SciTech Connect

    Brown, E V

    1988-06-01

    This research accomplished two goals. The first was to develop a computer program to simulate a cascade dissolver system. This program would be used to predict the bulk rate of dissolution in incinerator ash. The other goal was to verify the model in a single-stage dissolver system using Dy/sub 2/O/sub 3/. PuO/sub 2/ (and all of the species in the incinerator ash) was assumed to exist as spherical particles. A model was used to calculate the bulk rate of plutonium oxide dissolution using fluoride as a catalyst. Once the bulk rate of PuO/sub 2/ dissolution and the dissolution rate of all soluble species were calculated, mass and energy balances were written. A computer program simulating the cascade dissolver system was then developed. Tests were conducted on a single-stage dissolver. A simulated incinerator ash mixture was made and added to the dissolver. CaF/sub 2/ was added to the mixture as a catalyst. A 9M HNO/sub 3/ solution was pumped into the dissolver system. Samples of the dissolver effluent were analyzed for dissolved and F concentrations. The computer program proved satisfactory in predicting the F concentrations in the dissolver effluent. The experimental sparge air flow rate was predicted to within 5.5%. The experimental percentage of solids dissolved (51.34%) compared favorably to the percentage of incinerator ash dissolved (47%) in previous work. No general conclusions on model verification could be reached. 56 refs., 11 figs., 24 tabs.

  8. Improved one-pot multienzyme (OPME) systems for synthesizing UDP-uronic acids and glucuronides†

    PubMed Central

    Muthana, Musleh M.; Qu, Jingyao; Xue, Mengyang; Klyuchnik, Timofey; Siu, Alex; Li, Yanhong; Zhang, Lei; Yu, Hai; Li, Lei; Wang, Peng G.

    2015-01-01

    Arabidopsis thaliana glucuronokinase (AtGlcAK) was cloned and shown to be able to use various uronic acids as substrates to produce the corresponding uronic acid-1-phosphates. AtGlcAK or Bifidobacterium infantis galactokinase (BiGalK) was used with a UDP-sugar pyrophosphorylase, an inorganic pyrophosphatase, with or without a glycosyltransferase for highly efficient synthesis of UDP-uronic acids and glucuronides. These improved cost-effective one-pot multienzyme (OPME) systems avoid the use of nicotinamide adenine dinucleotide (NAD+)-cofactor in dehydrogenase-dependent UDP-glucuronic acid production processes and can be broadly applied for synthesizing various glucuronic acid-containing molecules. PMID:25686901

  9. Faecal bile acids are natural ligands of the mouse accessory olfactory system.

    PubMed

    Doyle, Wayne I; Dinser, Jordan A; Cansler, Hillary L; Zhang, Xingjian; Dinh, Daniel D; Browder, Natasha S; Riddington, Ian M; Meeks, Julian P

    2016-01-01

    The accessory olfactory system (AOS) guides behaviours that are important for survival and reproduction, but understanding of AOS function is limited by a lack of identified natural ligands. Here we report that mouse faeces are a robust source of AOS chemosignals and identify bile acids as a class of natural AOS ligands. Single-unit electrophysiological recordings from accessory olfactory bulb neurons in ex vivo preparations show that AOS neurons are strongly and selectively activated by peripheral stimulation with mouse faecal extracts. Faecal extracts contain several unconjugated bile acids that cause concentration-dependent neuronal activity in the AOS. Many AOS neurons respond selectively to bile acids that are variably excreted in male and female mouse faeces, and others respond to bile acids absent in mouse faeces. These results identify faeces as a natural source of AOS information, and suggest that bile acids may be mammalian pheromones and kairomones. PMID:27324439

  10. Faecal bile acids are natural ligands of the mouse accessory olfactory system

    PubMed Central

    Doyle, Wayne I.; Dinser, Jordan A.; Cansler, Hillary L.; Zhang, Xingjian; Dinh, Daniel D.; Browder, Natasha S.; Riddington, Ian M.; Meeks, Julian P.

    2016-01-01

    The accessory olfactory system (AOS) guides behaviours that are important for survival and reproduction, but understanding of AOS function is limited by a lack of identified natural ligands. Here we report that mouse faeces are a robust source of AOS chemosignals and identify bile acids as a class of natural AOS ligands. Single-unit electrophysiological recordings from accessory olfactory bulb neurons in ex vivo preparations show that AOS neurons are strongly and selectively activated by peripheral stimulation with mouse faecal extracts. Faecal extracts contain several unconjugated bile acids that cause concentration-dependent neuronal activity in the AOS. Many AOS neurons respond selectively to bile acids that are variably excreted in male and female mouse faeces, and others respond to bile acids absent in mouse faeces. These results identify faeces as a natural source of AOS information, and suggest that bile acids may be mammalian pheromones and kairomones. PMID:27324439

  11. Centrifugal Microfluidic System for Nucleic Acid Amplification and Detection

    PubMed Central

    Miao, Baogang; Peng, Niancai; Li, Lei; Li, Zheng; Hu, Fei; Zhang, Zengming; Wang, Chaohui

    2015-01-01

    We report here the development of a rapid PCR microfluidic system comprising a double-shaft turntable and centrifugal-based disc that rapidly drives the PCR mixture between chambers set at different temperatures, and the bidirectional flow improved the space utilization of the disc. Three heating resistors and thermistors maintained uniform, specific temperatures for the denaturation, annealing, and extension steps of the PCR. Infrared imaging showed that there was little thermal interference between reaction chambers; the system enabled the cycle number and reaction time of each step to be independently adjusted. To validate the function and efficiency of the centrifugal microfluidic system, a 350-base pair target gene from the hepatitis B virus was amplified and quantitated by fluorescence detection. By optimizing the cycling parameters, the reaction time was reduced to 32 min as compared to 120 min for a commercial PCR machine. DNA samples with concentrations ranging from 10 to 106 copies/mL could be quantitatively analyzed using this system. This centrifugal-based microfluidic platform is a useful system and possesses industrialization potential that can be used for portable diagnostics. PMID:26556354

  12. Physiological and regulatory properties of the general amino acid transport system of Neurospora crassa.

    PubMed Central

    DeBusk, R M; DeBusk, A G

    1980-01-01

    The fundamental properties of the general amino acid transport system of Neurospora crassa were investigated in the conidial stage of the life cycle. The transport activity was found to be under genetic control, and an isogenic set of mutants deficient for the neutral, basic, or general amino acid transport systems and combinations thereof was constructed and used for analyzing the properties specific to the general permease. Amino acid transport by this system was found to be a carrier-mediated active process with broad specificity for the neutral and basic amino acids. Kinetic analysis revealed that a common binding site functioned to transport both neutral and basic amino acids and that the permease had a high affinity for its substrates. The kinetic parameters Km, Vmax, and Ki were defined for several substrates. Two modes of regulation were detected: substrate inhibition and ammonium repression. Activity of the general system was enhanced by the removal of ammonium ions from the incubation medium with a concomitant decline in either neutral or basic permease activity, suggesting that a common component exists between the neutral and the general systems and between the basic and the general systems. PMID:6447141

  13. Solvent systems combining neutral and acidic extractants for separating trivalent lanthanides from the transuranic elements.

    SciTech Connect

    Lumetta, G. J.; Gelis, A. V.; Vandegrift, G. F.; Chemical Sciences and Engineering Division; PNL

    2010-01-01

    This paper is a review of recent publications that have focused on combined extractant systems for separating trivalent actinides from the lanthanides. These mixed solvent systems combine an acidic extractant with a neutral extractant to achieve the actinide/lanthanide separation. Depending on the neutral extractant used, three categorizations of systems can be considered, including combinations of acidic extractants with 1 diamides, 2 carbamoylmethylphosphine oxides, and 3 polydentate nitrogen-donor ligands. This review of relevant publications indicates that, although there is significant potential for practical exploitation of mixed neutral/acidic extractant systems to achieve a single-step separation of trivalent actinides from acidic high-level waste solutions, the fundamental chemistry underlying these combined systems is not yet well understood. For example, although there is strong evidence suggesting that adducts form between the neutral and acidic extractants, the nature of these adducts generally is not known. Likewise, the structures of the mixed complexes formed between the metal ions and the two different extractants are not fully understood. Research into these basic phenomena likely will provide clues about how to design practical mixed-extractant systems that can be used to efficiently separate the transuranic elements from the lanthanides and other components of irradiated fuel.

  14. Solvent Systems Combining Neutral and Acidic Extractants for Separating Trivalent Lanthanides from the Transuranic Elements

    SciTech Connect

    Lumetta, Gregg J.; Gelis, Artem V.; Vandegrift, George F.

    2010-04-23

    This paper is a review of recent publications that have focused on combined extractant systems for separating trivalent actinides from the lanthanides. These mixed solvent systems combine an acidic extractant with a neutral extractant to achieve the actinide/lanthanide separation. Depending on the neutral extractant used, three categorizations of systems can be considered, including combinations of acidic extractants with 1) diamides, 2) carbamoylmethylphosphine oxides, and 3) polydentate nitrogen-donor ligands. This review of relevant publications indicates that, although there is significant potential for practical exploitation of mixed neutral/acidic extractant systems to achieve a single-step separation of trivalent actinides from acidic high-level waste solutions, the fundamental chemistry underlying these combined systems is not yet well understood. For example, although there is strong evidence suggesting that adducts form between the neutral and acidic extractants, the nature of these adducts generally is not known. Likewise, the structures of the mixed complexes formed between the metal ions and the two different extactants are not fully understood. Research into these basic phenomena likely will provide clues about how to design practical mixed-extractant systems that can be used to efficiently separate the transuranic elements from the lanthanides and other components of irradiated fuel.

  15. Status of commercial phosphoric acid fuel cell system development

    NASA Technical Reports Server (NTRS)

    Warshay, M.; Prokopius, P. R.; Simons, S. N.; King, R. B.

    1981-01-01

    In both the electric utility and onsite integrated energy system applications, reducing cost and increasing reliability are the main technology drivers. The longstanding barrier to the attainment of these goals, which manifests itself in a number of ways, was materials. The differences in approach among the three major participants (United Technologies Corporation, Westinghouse Electric Corporation/Energy Research Corporation, and Engelhard Industries) and their unique technological features, including electrodes, matrices, intercell cooling, bipolar/separator plates, electrolyte management, fuel selection and system design philosophy are discussed.

  16. Influence of phenolic acids on indole acetic acid production and on the type III secretion system gene transcription in food-associated Pseudomonas fluorescens KM05.

    PubMed

    Myszka, Kamila; Schmidt, Marcin T; Olejnik-Schmidt, Agnieszka K; Leja, Katarzyna; Czaczyk, Katarzyna

    2014-12-01

    The purpose of these investigations was to evaluate the reduction capability of phenolic acids (ferulic, chlorogenic, gallic, and p-coumaric acids) on indole acetic acid synthesis by food-associated Pseudomonas fluorescens KM05. Specific genetic primer for the type III secretion system (TTSS) in P. fluorescens KM05 was designed and the influence of phenolic acids on its expression was investigated. In the work the ferulic and chlorogenic acids at the concentration of 0.02 and 0.04 μg/ml affected on bacterial growth pattern and the signal molecules production. The phenolic acids, that were appreciable effective against P. fluorescens KM05 indole acetic acid production, significantly suppressed TTSS gene. PMID:24994472

  17. Amino Acid Chemistry as a Link Between Small Solar System Bodies and Carbonaceous Chondrites

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Ehrenfreund, Pascale; Botta, Oliver; Cooper, George; Bada, Jeffrey L.

    2000-01-01

    Establishing chemical links between meteorites and small solar system bodies, such as comets and asteroids, provides a tool for investigating the processes that occurred during the formation of the solar system. Carbonaceous meteorites are of particular interest, since they may have seeded the early Earth with a variety of prebiotic organic compounds including amino acids, purines and pyrimidines, which are thought to be necessary for the origin of life. Here we report the results of high-performance liquid chromatography (HPLC) based amino acid analyses of the acid-hydrolyzed hot water extracts from pristine interior pieces of the CI carbonaceous chondrites Orgueil and Ivuna and the CM meteorites Murchison and Murray. We found that the CI meteorites Orgueil and Ivuna contained high abundances of beta-alanine and glycine, while only traces of other amino acids like alanine, alpha-amino-n-butryic acid (ABA) and alpha-aminoisobutyric acid (AIB) were detected in these meteorites. Carbon isotopic measurements of beta-alanine and glycine in Orgueil by gas chromatography combustion-isotope ratio mass spectrometry clearly indicate an extraterrestrial origin of these amino acids. The amino acid composition of Orgueil and Ivuna was strikingly different from the CM chondrites Murchison and Murray. The most notable difference was the high relative abundance of B-alanine in Orgueil and Ivuna compared to Murchison and Murray. Furthermore, AIB, which is one of the most abundant amino acids found in Murchison and Murray, was present in only trace amounts in Orgueil and Ivuna. Our amino acid data strongly suggest that the CI meteorites Orgueil and Ivuna came from a different type of parent body than the CM meteorites Murchison and Murray, possibly from an extinct comet. It is generally thought that carbonaceous meteorites are fragments of larger asteroidal bodies delivered via near Earth objects (NEO). Orbital and dynamic studies suggest that both fragments of main belt asteroids

  18. Optimization of conjugated linoleic acid triglycerides via enzymatic esterification in no-solvent system

    NASA Astrophysics Data System (ADS)

    Yi, Dan; Sun, Xiuqin; Li, Guangyou; Liu, Fayi; Lin, Xuezheng; Shen, Jihong

    2009-09-01

    We compared four esterifiable enzymes. The lipase Novozym 435 possessed the highest activity for the conjugated linoleic acid esterification during the synthesis of triglycerides. The triglycerides were synthesized by esterification of glycerol and conjugated linoleic acid (CLA) in a no-solvent system using lipase catalysis. We investigated the effects of temperature, enzyme concentration, water content, and time on esterification. Enzyme and water concentrations of up to 1% of the total reaction volume and a system temperature of 60°C proved optimal for esterification. Similarly, when the esterification was carried out for 24 h, the reaction ratio improved to 94.11%. The esterification rate of the rotating screen basket remained high (87.28%) when the enzyme was re-used for the 5th time. We evaluated the substrate selectivity of lipase (NOVO 435) and determined that this lipase prefers the 10,12-octadacadienoic acid to the 9,11-octadecadienoic acid.

  19. Carbon isotope composition of dissolved humic and fulvic acids in the Tokachi River system.

    PubMed

    Nagao, Seiya; Kodama, Hiroki; Aramaki, Takafumi; Fujitake, Nobuhide; Uchida, Masao; Shibata, Yasuyuki

    2011-07-01

    This study reports carbon isotopic ratios (Δ(14)C and δ(13)C) of dissolved humic and fulvic acids in the Tokachi River system, northern Japan. These acids have a refractory feature and they represent the largest fraction of dissolved organic matter in aquatic environments. The acids were isolated using the XAD extraction method from river water samples collected at three sites (on the upper and lower Tokachi River, and from one of its tributaries) in June 2004 and 2005. δ(13)C values were -27.8 to -26.9 ‰ for humic and fulvic acids. On the other hand, the Δ(14)C values ranged from -247 to +26 ‰ and the average values were -170 ± 79 ‰ for humic acid and -44 ± 73 ‰ for fulvic acid. The difference was attributed to the residence time of fulvic acid in the watershed being shorter than that of humic acid. The large variation suggested that humic substances have a different pathway in each watershed environment. PMID:21515623

  20. Wireless Biosensor System for Real-Time l-Lactic Acid Monitoring in Fish

    PubMed Central

    Hibi, Kyoko; Hatanaka, Kengo; Takase, Mai; Ren, Huifeng; Endo, Hideaki

    2012-01-01

    We have developed a wireless biosensor system to continuously monitor l-lactic acid concentrations in fish. The blood l-lactic acid level of fish is a barometer of stress. The biosensor comprised Pt-Ir wire (φ0.178 mm) as the working electrode and Ag/AgCl paste as the reference electrode. Lactate oxidase was immobilized on the working electrode using glutaraldehyde. The sensor calibration was linear and good correlated with l-lactic acid levels (R = 0.9959) in the range of 0.04 to 6.0 mg·dL−1. We used the eyeball interstitial sclera fluid (EISF) as the site of sensor implantation. The blood l-lactic acid levels correlated closely with the EISF l-lactic acid levels in the range of 3 to 13 mg·dL−1 (R = 0.8173, n = 26). Wireless monitoring of l-lactic acid was performed using the sensor system in free-swimming fish in an aquarium. The sensor response was stable for over 60 h. Thus, our biosensor provided a rapid and convenient method for real-time monitoring of l-lactic acid levels in fish. PMID:22778641

  1. Chlorination of Betacyanins in Several Hypochlorous Acid Systems.

    PubMed

    Wybraniec, Sławomir; Starzak, Karolina; Pietrzkowski, Zbigniew

    2016-04-13

    This study presents a comparative evaluation of chlorination of betanin, betanidin, and neobetanin exposed to sodium hypochlorite and myeloperoxidase (MPO)/H2O2/Cl(-) systems. For betanin/betanidin, the chlorination takes place at the aglycone unit, but for neobetanin, no chlorinated products in the reaction mixtures can be detected. In the RP-HPLC system, monochloro-betanin/-betanidin were eluted earlier than their corresponding nonchlorinated substrates. An influence of Cl(-) concentration on betanin/betanidin chlorination efficiency in sodium hypochlorite and MPO systems was investigated. At pH 3-5, the yields of formed monochloro-betanin/-betanidin decrease dramatically at higher Cl(-) concentrations, indicating that generated Cl2 is not the chlorinating agent in the presence of sodium hypochlorite. The intriguing low activity of Cl2 in betanin/betanidin chlorination compared to HOCl and/or Cl2O can be explained by a special position of the attack by molecules of HOCl and/or Cl2O. In the MPO/H2O2/Cl(-) system, the highest efficiency of monochloro-betanin/-betanidin generation is observed at pH 5. PMID:26947920

  2. The Formation and Stability of Carbonic Acid on Outer Solar System Bodies

    NASA Technical Reports Server (NTRS)

    Peeters, Z.; Hudson, R. L.; Moore, M. H.; Lewis, Ariel

    2009-01-01

    The radiation chemistry, thermal stability, and vapor pressure of solid-phase carbonic acid (H2CO3) have been studied with mid-infrared spectroscopy. A new procedure for measuring this molecule's radiation stability has been used to obtain intrinsic IR band strengths and half-lives for radiolytic destruction. Results are compared to literature values. We report, for the first time, measurements of carbonic acid's vapor pressure and its heat of sublimation. We also report the first observation of a chemical reaction involving solid-phase carbonic acid. Possible applications of these findings are discussed, with an emphasis on the outer Solar System.

  3. Single-Plasmid-Based System for Efficient Noncanonical Amino Acid Mutagenesis in Cultured Mammalian Cells.

    PubMed

    Cohen, Sarit; Arbely, Eyal

    2016-06-01

    We describe a new expression system for efficient non-canonical amino acid mutagenesis in cultured mammalian cells by using the pyrrolysine tRNA synthetase/tRNACUA (Pyl) pair. A significant improvement in the incorporation of non-canonical amino acids into proteins was obtained by combining all the required genetic components into a single and compact vector that can be efficiently delivered to different mammalian cell lines by conventional transfection reagents. PMID:27120490

  4. Acid Gas Removal by Customized Sorbents for Integrated Gasification Fuel Cell Systems

    SciTech Connect

    Kapfenberger, J.; Sohnemann, J.; Schleitzer, D.; Loewen, A.

    2002-09-20

    In order to reduce exergy losses, gas cleaning at high temperatures is favored in IGFC systems. As shown by thermodynamic data, separation efficiencies of common sorbents decrease with increasing temperature. Therefore, acid gas removal systems have to be developed for IGFC applications considering sorbent capacity, operation temperature, gasification feedstock composition and fuel cell threshold values.

  5. Effect of Finishing System on Subcutaneous Fat Melting Point and Fatty Acid Composition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Angus-cross steers (n = 69) were used to determine the effect of finishing system on subcutaneous fat melting point and fatty acid composition. Three finishing systems were evaluated: 1) mixed pasture for 134 d [MP], 2) mixed pasture for 93 d and alfalfa for 41 d [AL], or 3) concentrate finishing f...

  6. 21 CFR 862.1390 - 5-Hydroxyindole acetic acid/serotonin test system.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 8 2013-04-01 2013-04-01 false 5-Hydroxyindole acetic acid/serotonin test system. 862.1390 Section 862.1390 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES CLINICAL CHEMISTRY AND CLINICAL TOXICOLOGY DEVICES Clinical Chemistry Test Systems § 862.1390...

  7. A Novel Technique of Supra Superficial Musculoaponeurotic System Hyaluronic Acid Injection for Lower Face Lifting

    PubMed Central

    Sahawatwong, Sinijchaya; Sirithanabadeekul, Punyaphat; Patanajareet, Vasiyapha; Wattanakrai, Penpun

    2016-01-01

    Background: Various methods attempting to correct sagging of the lower face focus mainly on manipulation of the superficial musculoaponeurotic System. Each technique has its own limitation. The authors propose a relatively simple, conservative method utilizing hyaluronic acid injection just above the superficial musculoaponeurotic System. Objective: To address a novel hyaluronic injection technique to lift the lower face. Methods: Details of the injection techniques are described. The Position of the hyaluronic acid injected and the effect of hyaluronic acid on the superficial musculoaponeurotic System were confirmed by ultrasonography in one of the cases. Results: Sonogram images demonstrated the location of the injected hyaluronic acid and pressure effect of hyaluronic acid on the superficial musculoaponeurotic System, confirming the ability to manipulate the superficial musculoaponeurotic System by this injection technique. The lifting result of this Single injection technique was immediately visible and maintained for at least 26 weeks. Conclusion: This is a less invasive, reproducible method that provides a sustained face lifting result. The authors propose the term “supraSMAS lift” for this novel injection technique. PMID:27047633

  8. Reaction-Diffusion Patterns in Structured Media

    NASA Astrophysics Data System (ADS)

    Epstein, Irving

    I will look at pattern formation in the Belousov-Zhabotinsky (BZ) oscillating chemical reaction in media that are structured at length scales ranging from ten nanometers to a few centimeters. A reverse microemulsion consisting of nanometer diameter droplets of water containing the reactants dispersed in oil allows the physical structure (size, spacing) of the droplets and their chemical composition to be controlled independently, enabling one to generate a remarkable variety of stationary and moving patterns, including Turing structures, ordinary and antispirals, packet waves and spatiotemporal chaos. One- and two-dimensional arrays of aqueous droplets in oil generated by microfluidic techniques have diameters of the order of 100 micrometers and produce a different array of patterns that can be precisely controlled with light. In particular, circular arrays of droplets provide a testing ground for some of Turing's ideas about morphogenesis. By attaching the BZ catalyst to a polymer that shrinks and swells in response to changes in the redox state of the catalyst, one can construct gel materials that transduce chemical changes to mechanical motion, a phenomenon modeled with considerable success by the Balazs group. If time permits, I will also discuss the BZ reaction in coupled macroscopic flow reactors that mimic small neural networks.

  9. The active transport of 5-hydroxyindol-3-ylacetic acid and 3-methoxy-4-hydroxyphenylacetic acid from a recirculatory perfusion system of the cerebral ventricles of the unanaesthetized dog

    PubMed Central

    Ashcroft, G. W.; Dow, R. C.; Moir, A. T. B.

    1968-01-01

    1. An operation on dogs for the implantation of guide tubes to the lateral ventricle and cisterna magna and a method whereby the ventricular space can be repeatedly perfused in conscious and unrestrained animals are described. 2. The characteristics of a recirculatory perfusion system were examined and the bulk formation and absorption of cerebrospinal fluid and the volume of the ventricular space perfused were derived from the concentrations achieved during the infusion of inulin into the system. 3. 5-hydroxyindol-3-ylacetic acid (5-HIAA), the acid metabolite of 5-hydroxytryptamine, and 3-methoxy-4-hydroxyphenylacetic acid (HVA), the main acid metabolite of dopamine, were demonstrated to be mainly removed from cerebrospinal fluid (c.s.f.) by an active transport system localized in the region of the fourth ventricle. 4. It was possible to inhibit the active transport of these acids from cerebrospinal fluid by pre-treating the dogs with probenecid. ImagesPlate 1Plate 2 PMID:5723518

  10. Aspartic acid

    MedlinePlus

    ... also called asparaginic acid. Aspartic acid helps every cell in the body work. It plays a role in: Hormone production and release Normal nervous system function Plant sources of aspartic acid include: Legumes such as ...

  11. Continuous ion-exclusion chromatography system for acid/sugar separation

    SciTech Connect

    Springfield, R.M.; Hester, R.D.

    1999-04-01

    A simulated moving bed ion exclusion chromatography system was constructed for the continuous separation of the components in an aqueous feed solution of sucrose and sulfuric acid. A system of 18 columns was arrayed about a central manifold system. Each column was packed with approximately 820 mL of porous cationic exchange resin. The system was designed for the flexibility to use fluid recycle loops and unrestricted placement of all inlet and outlet streams. Monitoring and control functions were performed using a Camile 2000 process controller integrated with a custom-built control computer. The aqueous feed solution, usually containing 10 wt.% sucrose and 10 wt.% sulfuric acid, was generally introduced into the system at a rate of roughly 2 L/hr. Approximately 4 L/hr of water was used to elute materials through the separation system. After optimization, the separation system allowed greater than 95% recovery of the feed sucrose in an exit stream containing 8.8 wt.% sucrose and 98% recovery of the feed acid in a second exit stream containing 5 wt.% acid.

  12. Characterization of methylaminoisobutyric acid transport by system A in rat mammary gland.

    PubMed

    Tovar, A R; Avila, E; DeSantiago, S; Torres, N

    2000-07-01

    During lactation, the mammary gland has a large demand for amino acids for the synthesis of milk proteins and fatty acids. Arteriovenous differences in amino acids across the mammary gland show an elevated uptake of small neutral amino acids that are mainly transported via system A. The purpose of this study was to characterize the transport of methylaminoisobutyric acid (MeAIB), an amino acid analog used to model transport by system A in lactating rat mammary gland explants. MeAIB accumulation in mammary gland cells increased steadily, and after 3 hours of incubation, the intracellular concentration of the analog was 8-fold higher than the concentration in the medium. MeAIB transport into mammary gland explants showed a Km of 3.3 +/- 0.4 mmol/L and a maximal velocity (Vmax) of 555 +/- 23 pmol/microL intracellular fluid (ICF) x min, indicating a system with high capacity but low affinity for its substrate. MeAIB transport into mammary tissue depended highly on Na+, and the uptake was inhibited by addition of natural and analog small neutral amino acids. Cationic, anionic, and large neutral amino acids did not reduce MeAIB transport into mammary gland explants. Preincubation of mammary gland explants in an amino acid-free medium stimulated MeAIB transport, suggesting an adaptive regulation. The addition of an equimolar mixture of alanine, glycine, and serine to the preincubation medium inhibited stimulation of MeAIB transport. Furthermore, stimulation of MeAIB uptake by amino acid starvation was also prevented by the addition of actinomycin D, cycloheximide, tunicamycin, and colchicine. Dibutyryl cyclic adenosine monophosphate (cAMP) increased MeAIB uptake, whereas phorbol 12-myristate 13-acetate (PMA) did not stimulate MeAIB transport. During the first postweaning days, kinetic analyses showed a decrease of 27% in the Vmax. Injection of rat lactating mammary gland mRNA into Xenopus laevis oocytes induced expression of the MeAIB transport system; however, the

  13. Escherichia coli O157:H7 Glutamate- and Arginine-dependent Acid Resistance Systems Protect Against Oxidative Stress During Extreme Acid Challenge

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To investigate the protection that several known Escherichia coli O157:H7 acid resistance systems provide against oxidative stress, the addition of diamide or hydrogen peroxide were used concomitant with acid challenge at pH 2.5 to determine bacterial survival. Diamide and hydrogen peroxide both de...

  14. Escherichia coli O157:H7 Glutamate- and Arginine-dependent Acid Resistance Systems Protect Against Oxidative Stress During Extreme Acid Challenge

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microorganisms may simultaneously encounter multiple stresses in their environment. To investigate the protection that several known Escherichia coli O157:H7 acid resistance systems might provide against both oxidative and acid stress, the addition of diamide, a membrane-permeable thiol-specific ox...

  15. [Polyunsaturated omega-3 fatty acids and systemic lupus erythematosus: what do we know?].

    PubMed

    Borges, Mariane Curado; Santos, Fabiana de Miranda Moura; Telles, Rosa Weiss; Correia, Maria Isabel Toulson Davisson; Lanna, Cristina Costa Duarte

    2014-01-01

    Various studies have demonstrated the impact of omega-3 fatty acids on the concentration of C reactive protein (CRP), pro-inflammatory eicosanoids, cytokines, chemokines and other inflammatory mediators. Therefore, the supplementation of these types of lipids may represent additional option treatment for chronic systemic diseases, such as Systemic Lupus Erythematous and other rheumatic diseases. The role of these lipids has not been well established, yet. However, it seems there is a direct relationship between its intake and the decrease of the disease clinical manifestations as well as of the inflammatory status of the patients. Thus, the aim of this manuscript is to present a thorough review on the effects of omega-3 fatty acids in patients with SLE. Bibliographic data set as the Medical Literature Analysis and Retrieval System Online (MEDLINE) and Literatura Latino-Americana e do Caribe em Ciências da Saúde (LILACS) were searched using as key words: systemic lupus erythematous (SLE), polyunsaturated fatty acids omega-3, eicosapentanoic acid (EPA), docosahexanoic acid (DHA), antioxidants and diet. Manuscripts published up to September 2013 were included. There were 43 articles related to the topic, however only 15 pertained human studies, with three review articles and 12 clinical studies. PMID:25445629

  16. Neuroprotective Activity of Thioctic Acid in Central Nervous System Lesions Consequent to Peripheral Nerve Injury

    PubMed Central

    Ghelardini, Carla; Nwankwo, Innocent E.; Pacini, Alessandra

    2013-01-01

    Peripheral neuropathies are heterogeneous disorders presenting often with hyperalgesia and allodynia. This study has assessed if chronic constriction injury (CCI) of sciatic nerve is accompanied by increased oxidative stress and central nervous system (CNS) changes and if these changes are sensitive to treatment with thioctic acid. Thioctic acid is a naturally occurring antioxidant existing in two optical isomers (+)- and (−)-thioctic acid and in the racemic form. It has been proposed for treating disorders associated with increased oxidative stress. Sciatic nerve CCI was made in spontaneously hypertensive rats (SHRs) and in normotensive reference cohorts. Rats were untreated or treated intraperitoneally for 14 days with (+/−)-, (+)-, or (−)-thioctic acid. Oxidative stress, astrogliosis, myelin sheets status, and neuronal injury in motor and sensory cerebrocortical areas were assessed. Increase of oxidative stress markers, astrogliosis, and neuronal damage accompanied by a decreased expression of neurofilament were observed in SHR. This phenomenon was more pronounced after CCI. Thioctic acid countered astrogliosis and neuronal damage, (+)-thioctic acid being more active than (+/−)- or (−)-enantiomers. These findings suggest a neuroprotective activity of thioctic acid on CNS lesions consequent to CCI and that the compound may represent a therapeutic option for entrapment neuropathies. PMID:24527432

  17. Genetic evidence of a high-affinity cyanuric acid transport system in Pseudomonas sp. ADP.

    PubMed

    Platero, Ana I; Santero, Eduardo; Govantes, Fernando

    2014-03-01

    The Pseudomonas sp. ADP plasmid pADP-1 encodes the activities involved in the hydrolytic degradation of the s-triazine herbicide atrazine. Here, we explore the presence of a specific transport system for the central intermediate of the atrazine utilization pathway, cyanuric acid, in Pseudomonas sp. ADP. Growth in fed-batch cultures containing limiting cyanuric acid concentrations is consistent with high-affinity transport of this substrate. Acquisition of the ability to grow at low cyanuric acid concentrations upon conjugal transfer of pADP1 to the nondegrading host Pseudomonas putida KT2442 suggests that all activities required for this phenotype are encoded in this plasmid. Co-expression of the pADP1-borne atzDEF and atzTUVW genes, encoding the cyanuric acid utilization pathway and the subunits of an ABC-type solute transport system, in P. putida KT2442 was sufficient to promote growth at cyanuric acid concentrations as low as 50 μM in batch culture. Taken together, our results strongly suggest that the atzTUVW gene products are involved in high-affinity transport of cyanuric acid. PMID:24484197

  18. Lead-acid battery use in the development of renewable energy systems in China

    NASA Astrophysics Data System (ADS)

    Chang, Yu; Mao, Xianxian; Zhao, Yanfang; Feng, Shaoli; Chen, Hongyu; Finlow, David

    Policies and laws encouraging the development of renewable energy systems in China have led to rapid progress in the past 2 years, particularly in the solar cell (photovoltaic) industry. The development of the photovoltaic (PV) and wind power markets in China is outlined in this paper, with emphasis on the utilization of lead-acid batteries. The storage battery is a key component of PV/wind power systems, yet many deficiencies remain to be resolved. Some experimental results are presented, along with examples of potential applications of valve regulated lead-acid (VRLA) batteries, both the absorbed glass mat (AGM) and gelled types.

  19. Nucleic Acid-based Detection of Bacterial Pathogens Using Integrated Microfluidic Platform Systems

    PubMed Central

    Lui, Clarissa; Cady, Nathaniel C.; Batt, Carl A.

    2009-01-01

    The advent of nucleic acid-based pathogen detection methods offers increased sensitivity and specificity over traditional microbiological techniques, driving the development of portable, integrated biosensors. The miniaturization and automation of integrated detection systems presents a significant advantage for rapid, portable field-based testing. In this review, we highlight current developments and directions in nucleic acid-based micro total analysis systems for the detection of bacterial pathogens. Recent progress in the miniaturization of microfluidic processing steps for cell capture, DNA extraction and purification, polymerase chain reaction, and product detection are detailed. Discussions include strategies and challenges for implementation of an integrated portable platform. PMID:22412335

  20. Integrative food grade expression system for lactic acid bacteria.

    PubMed

    Douglas, Grace L; Goh, Yong Jun; Klaenhammer, Todd R

    2011-01-01

    Lactobacillus acidophilus NCFM is a probiotic microbe with the ability to survive passage to the -gastrointestinal tract, interact intimately with the host and induce immune responses. The genome of NCFM has been determined and the bacterium is genetically accessible. Therefore, L. acidophilus has excellent potential for use as a vaccine delivery vehicle to express antigens at mucosal surfaces. Plasmids, commonly used to carry antigen encoding genes, are inherently unstable and require constant selection by antibiotics, which can be problematic for in vivo studies and clinical trials. Chromosomal expression of gene cassettes encoding antigens offers enhanced genetic stability by eliminating requirements for marker selection. This work illustrates the integration and inducible expression of the reporter gene gusA3, -encoding a β-glucuronidase (GusA3), in the L. acidophilus chromosome. A previously described upp-counterselectable gene replacement system was used to direct insertion of the gusA3 gene into an intergenic chromosomal location downstream of lacZ (LBA1462), encoding a β-galactosidase. The transcriptional activity of integrated gusA3 was evaluated by GUS activity assays using 4-methyl-umbelliferyl-β-D: -glucuronide (MUG) and was determined to be one to two orders of magnitude higher than the GusA3-negative parent, NCK1909. The successful chromosomal integration and expression of GusA3 demonstrate the potential of this method for higher levels of inducible gene expression in L. acidophilus. PMID:21815104