Theory for Diffusion-Limited Oscillating Chemical Reactions
Bussemaker, H J
1997-01-01
A kinetic description of lattice-gas automaton models for reaction-diffusion systems is presented. It provides corrections to the mean-field rate equations in the diffusion-limited regime. When applied to the two-species Maginu model, the theory gives an excellent quantitative prediction of the effect of slow diffusion on the periodic oscillations of the average concentrations in a spatially homogeneous state.
Theory of diffusion-influenced reactions in complex geometries
Galanti, Marta; Fanelli, Duccio; Traytak, Sergey D.; Piazza, Francesco
Chemical reactions involving diffusion of reactants and subsequent chemical fixation steps are generally termed "diffusion-influenced" (DI). Virtually all biochemical processes in living media can be counted among them, together with those occurring in an ever-growing number of emerging nano-technologies. The role of the environment's geometry (obstacles, compartmentalization) and distributed reactivity (competitive reactants, traps) is key in modulating the rate constants of DI reactions, and is therefore a prime design parameter. Yet, it is a formidable challenge to build a comprehensive theory able to describe the environment's "reactive geometry". Here we show that such a theory can be built by unfolding this many-body problem through addition theorems for special functions. Our method is powerful and general and allows one to study a given DI reaction occurring in arbitrary "reactive landscapes", made of multiple spherical boundaries of given size and reactivity. Importantly, ready-to-use analytical formulas can be derived easily in most cases.
Theory of diffusion-influenced reactions in complex geometries
Galanti, Marta; Piazza, Francesco
2015-01-01
Chemical reactions involving diffusion of reactants and subsequent chemical fixation steps are generally termed "diffusion-influenced" (DI). Virtually all biochemical processes in living media can be counted among them, together with those occurring in an ever-growing number of emerging nano-technologies. The role of the environment's geometry (obstacles, compartmentalization) and distributed reactivity (competitive reactants, traps) is key in modulating the rate constants of DI reactions, and is therefore a prime design parameter. Yet, it is a formidable challenge to build a comprehensive theory able to describe the environment's "reactive geometry". Here we show that such a theory can be built by unfolding this many-body problem through addition theorems for special functions. Our method is powerful and general and allows one to study a given DI reaction occurring in arbitrary "reactive landscapes", made of multiple spherical boundaries of given size and reactivity. Importantly, ready-to-use analytical form...
Theory of diffusion-influenced reactions in complex geometries.
Galanti, Marta; Fanelli, Duccio; Traytak, Sergey D; Piazza, Francesco
2016-06-21
Chemical transformations involving the diffusion of reactants and subsequent chemical fixation steps are generally termed "diffusion-influenced reactions" (DIR). Virtually all biochemical processes in living media can be counted among them, together with those occurring in an ever-growing number of emerging nano-technologies. The role of the environment's geometry (obstacles, compartmentalization) and distributed reactivity (competitive reactants, traps) is key in modulating the rate constants of DIRs, and is therefore a prime design parameter. Yet, it is a formidable challenge to build a comprehensive theory that is able to describe the environment's "reactive geometry". Here we show that such a theory can be built by unfolding this many-body problem through addition theorems for special functions. Our method is powerful and general and allows one to study a given DIR reaction occurring in arbitrary "reactive landscapes", made of multiple spherical boundaries of given size and reactivity. Importantly, ready-to-use analytical formulas can be derived easily in most cases.
Theory and application of stability for stochastic reaction diffusion systems
LUO Qi; DENG FeiQi; MAO XueRong; BAO JunDong; ZHANG YuTian
2008-01-01
So far, the Lyapunov direct method is still the moat effective technique in the study of stability for ordinary differential equations and stochastic differential equations. Due to the shortage of the corresponding Ito formula, this useful method has not been popularized in stochastic partial differential equations. The aim of this work is to try to extend the Lyapunov direct method to the Ito stochastic reaction diffusion systems and to establish the corresponding Lyapunov stability theory, including stability in probablity, asymptotic stability in probablity, end exponential stability in mean square. As the application of the obtained theorems, this paper addresses the stability of the Hopfield neural network and points out that the main results ob-tained by Holden Helge and Liao Xiaoxin et al. can be all regarded as the corollaries of the theorems presented in this paper.
Unified path integral approach to theories of diffusion-influenced reactions
Prüstel, Thorsten; Meier-Schellersheim, Martin
2017-08-01
Building on mathematical similarities between quantum mechanics and theories of diffusion-influenced reactions, we develop a general approach for computational modeling of diffusion-influenced reactions that is capable of capturing not only the classical Smoluchowski picture but also alternative theories, as is here exemplified by a volume reactivity model. In particular, we prove the path decomposition expansion of various Green's functions describing the irreversible and reversible reaction of an isolated pair of molecules. To this end, we exploit a connection between boundary value and interaction potential problems with δ - and δ'-function perturbation. We employ a known path-integral-based summation of a perturbation series to derive a number of exact identities relating propagators and survival probabilities satisfying different boundary conditions in a unified and systematic manner. Furthermore, we show how the path decomposition expansion represents the propagator as a product of three factors in the Laplace domain that correspond to quantities figuring prominently in stochastic spatially resolved simulation algorithms. This analysis will thus be useful for the interpretation of current and the design of future algorithms. Finally, we discuss the relation between the general approach and the theory of Brownian functionals and calculate the mean residence time for the case of irreversible and reversible reactions.
Borisenko, Alexander
2016-05-01
During the processes of nucleation and growth of a precipitate cluster from a supersaturated solution, the diffusion flux between the cluster and the solution changes the solute concentration near the cluster-solution interface from its average bulk value. This feature affects the rates of attachment and detachment of solute atoms at the interface, and, therefore, the entire nucleation-growth kinetics is altered. Unless quite obvious, this effect has been ignored in classical nucleation theory. To illustrate the results of this approach, for the case of homogeneous nucleation, we calculate the total solubility and the nucleation rate as functions of two parameters of the model (the reduced interface energy and the inverse second Damköhler number), and we compare these results to the classical ones. One can conclude that discrepancies with classical nucleation theory are great in the diffusion-limited regime, when the rate of bulk diffusion is small compared to the rate of interface reactions, while in the opposite interface-limited case they vanish.
Numerical methods for one-dimensional reaction-diffusion equations arising in combustion theory
Ramos, J. I.
1987-01-01
A review of numerical methods for one-dimensional reaction-diffusion equations arising in combustion theory is presented. The methods reviewed include explicit, implicit, quasi-linearization, time linearization, operator-splitting, random walk and finite-element techniques and methods of lines. Adaptive and nonadaptive procedures are also reviewed. These techniques are applied first to solve two model problems which have exact traveling wave solutions with which the numerical results can be compared. This comparison is performed in terms of both the wave profile and computed wave speed. It is shown that the computed wave speed is not a good indicator of the accuracy of a particular method. A fourth-order time-linearized, Hermitian compact operator technique is found to be the most accurate method for a variety of time and space sizes.
Brownian motion in a field of force and the diffusion theory of chemical reactions. II
Brinkman, H.C.
1956-01-01
H. A. Kramers has studied the rate of chemical reactions in view of the Brownian forces caused by a surrounding medium in temperature equilibrium. In a previous paper 3) the author gave a solution of Kramers' diffusion equation in phase space by systematic development. In this paper the general prob
Reaction-diffusion theory in the presence of an attractive harmonic potential
Spendier, K.; Sugaya, S.; Kenkre, V. M.
2013-12-01
Problems involving the capture of a moving entity by a trap occur in a variety of physical situations, the moving entity being an electron, an excitation, an atom, a molecule, a biological object such as a receptor cluster, a cell, or even an animal such as a mouse carrying an epidemic. Theoretical considerations have almost always assumed that the particle motion is translationally invariant. We study here the case when that assumption is relaxed, in that the particle is additionally subjected to a harmonic potential. This tethering to a center modifies the reaction-diffusion phenomenon. Using a Smoluchowski equation to describe the system, we carry out a study which is explicit in one dimension but can be easily extended for arbitrary dimensions. Interesting features emerge depending on the relative location of the trap, the attractive center, and the initial placement of the diffusing particle.
Velikanov, M V; Velikanov, Mikhail V.; Kapral, Raymond
1998-01-01
Spatially-distributed, nonequilibrium chemical systems described by a Markov chain model are considered. The evolution of such systems arises from a combination of local birth-death reactive events and random walks executed by the particles on a lattice. The parameter \\gamma, the ratio of characteristic time scales of reaction and diffusion, is used to gauge the relative contributions of these two processes to the overall dynamics. For the case of relatively fast diffusion, i.e. \\gamma 0 these memory terms vanish and the mass-action law is recovered; b) the memory kernel is found to assume a simple exponential form. A comparison with numerical results from lattice gas automaton simulations is also carried out.
Wavefronts in time-delayed reaction-diffusion systems. Theory and comparison to experiment
Fort, Joaquim [Departament de Fisica, Universitat de Girona, Girona (Spain)]. E-mail: joaquim.fort@udg.es; Mendez, Vicenc [Facultat de Ciencies de la Salut, Universitat Internacional de Catalunya, Ssant Cugat del Valles (Spain)]. E-mail: vmendez@csc.unica.edu
2002-06-01
We review the recent theoretical progress in the formulation and solution of the front speed problem for time-delayed reaction-diffusion systems. Most of the review is focused on hyperbolic equations. They have been widely used in recent years, because they allow for analytical solutions and yield a realistic description of some relevant phenomena. The theoretical methods are applied to a range of applications, including population dynamics, forest fire models, bistable systems and combustion wavefronts. We also present a detailed account of successful predictions of the models, as assessed by comparison to experimental data for some biophysical systems, without making use of any free parameters. Areas where the work reviewed may contribute to future progress are discussed. (author)
Diffusion coefficient in photon diffusion theory
Graaff, R; Ten Bosch, JJ
2000-01-01
The choice of the diffusion coefficient to be used in photon diffusion theory has been a subject of discussion in recent publications on tissue optics. We compared several diffusion coefficients with the apparent diffusion coefficient from the more fundamental transport theory, D-app. Application to
Diffusion coefficient in photon diffusion theory
Graaff, R; Ten Bosch, JJ
2000-01-01
The choice of the diffusion coefficient to be used in photon diffusion theory has been a subject of discussion in recent publications on tissue optics. We compared several diffusion coefficients with the apparent diffusion coefficient from the more fundamental transport theory, D-app. Application to
Shustorovich, E. (ed.)
1991-01-01
The title is esoteric. The subtitle is specialized. This is an edited book containing five chapters written by eight authors. It is not a book to read from beginning to end, but kept perusing this handsomely printed and well-edited volume, learned so much that he wishes to convey his message to a small but very successful group of chemists and chemical engineers in heterogeneous catalysis: there is a lot to learn in this book, not so much in theory but in the facts that the theorists who wrote the book are trying to explain today with the faint hope that tomorrow they will actually predict new chemistry in as yet unknown catalytic cycles.
Langevin Equations for Reaction-Diffusion Processes
Benitez, Federico; Duclut, Charlie; Chaté, Hugues; Delamotte, Bertrand; Dornic, Ivan; Muñoz, Miguel A.
2016-09-01
For reaction-diffusion processes with at most bimolecular reactants, we derive well-behaved, numerically tractable, exact Langevin equations that govern a stochastic variable related to the response field in field theory. Using duality relations, we show how the particle number and other quantities of interest can be computed. Our work clarifies long-standing conceptual issues encountered in field-theoretical approaches and paves the way for systematic numerical and theoretical analyses of reaction-diffusion problems.
Connectionist and diffusion models of reaction time.
Ratcliff, R; Van Zandt, T; McKoon, G
1999-04-01
Two connectionist frameworks, GRAIN (J. L. McClelland, 1993) and brain-state-in-a-box (J. A. Anderson, 1991), and R. Ratcliff's (1978) diffusion model were evaluated using data from a signal detection task. Dependent variables included response probabilities, reaction times for correct and error responses, and shapes of reaction-time distributions. The diffusion model accounted for all aspects of the data, including error reaction times that had previously been a problem for all response-time models. The connectionist models accounted for many aspects of the data adequately, but each failed to a greater or lesser degree in important ways except for one model that was similar to the diffusion model. The findings advance the development of the diffusion model and show that the long tradition of reaction-time research and theory is a fertile domain for development and testing of connectionist assumptions about how decisions are generated over time.
Resonance Reaction in Diffusion-Influenced Bimolecular Reactions
Kolb, Jakob J; Dzubiella, Joachim
2016-01-01
We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new resonant reaction behavior with rate enhancement if an appropriately defined fluctuation decay length is of the order of the system size. Importantly, we find that in the proximity of resonance the standard reciprocal additivity law for diffusion and surface reaction rates is violated due to the dynamical coupling of multiple kinetic processes. Together, these findings may have important repercussions on the correct interpretation of various kinetic reaction problems in complex systems, as, e.g., in biomolecular association or catalysis.
Victor Kardashov
2002-01-01
Full Text Available This paper has considered a novel approach to structural recognition and control of nonlinear reaction-diffusion systems (systems with density dependent diffusion. The main consistence of the approach is interactive variation of the nonlinear diffusion and sources structural parameters that allows to implement a qualitative control and recognition of transitional system conditions (transients. The method of inverse solutions construction allows formulating the new analytic conditions of compactness and periodicity of the transients that is also available for nonintegrated systems. On the other hand, using of energy conservations laws, allows transfer to nonlinear dynamics models that gives the possiblity to apply the modern deterministic chaos theory (particularly the Feigenboum's universal constants and scenario of chaotic transitions.
Reaction diffusion equations with boundary degeneracy
Huashui Zhan
2016-03-01
Full Text Available In this article, we consider the reaction diffusion equation $$ \\frac{\\partial u}{\\partial t} = \\Delta A(u,\\quad (x,t\\in \\Omega \\times (0,T, $$ with the homogeneous boundary condition. Inspired by the Fichera-Oleinik theory, if the equation is not only strongly degenerate in the interior of $\\Omega$, but also degenerate on the boundary, we show that the solution of the equation is free from any limitation of the boundary condition.
Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion
Del Razo, Mauricio J; Qian, Hong; Lin, Guang
2014-01-01
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. We first discuss this nonlinear effect for reaction systems without diffusion. For nonlinear stochastic reaction-diffusion systems here 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. Our results show that current linear FCS theory could be adequate ...
NONLINEAR SINGULARLY PERTURBED PREDATOR-PREY REACTION DIFFUSION SYSTEMS
MoJiaqi; TangRongrong
2004-01-01
A class of nonlinear predator-prey reaction diffusion systems for singularly perturbedproblems are considered. Under suitable conditions, by using theory of differential inequalitiesthe existence and asymptotic behavior of solution for initial boundary value problems arestudied.
Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion
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.
Diffusion-limited reactions in crowded environments.
Dorsaz, N; De Michele, C; Piazza, F; De Los Rios, P; Foffi, G
2010-09-17
Diffusion-limited reactions are usually described within the Smoluchowski theory, which neglects interparticle interactions. We propose a simple way to incorporate excluded-volume effects building on simulations of hard sphere in the presence of a sink. For large values of the sink-to-particle size ratio R(s), the measured encounter rate is in good agreement with a simple generalization of the Smoluchowski equation at high densities. Reducing R(s), the encounter rate is substantially depressed and becomes even nonmonotonic for R(s)saturation of the rate, stationary density waves set in close to the sink. A mean-field analysis helps to shed light on the subtle link between such ordering and the slowing down of the encounter dynamics. Finally, we show how an infinitesimal amount of nonreacting impurities can equally slow down dramatically the reaction.
Physarum machines: encapsulating reaction-diffusion to compute spanning tree
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.
Some Aspects of Diffusion Theory
Pignedoli, A
2011-01-01
This title includes: V.C.A. Ferraro: Diffusion of ions in a plasma with applications to the ionosphere; P.C. Kendall: On the diffusion in the atmosphere and ionosphere; F. Henin: Kinetic equations and Brownian motion; T. Kahan: Theorie des reacteurs nucleaires: methodes de resolution perturbationnelles, interactives et variationnelles; C. Cattaneo: Sulla conduzione del calore; C. Agostinelli: Formule di Green per la diffusione del campo magnetico in un fluido elettricamente conduttore; A. Pignedoli: Transformational methods applied to some one-dimensional problems concerning the equations of t
Turing instability in reaction-diffusion systems with nonlinear diffusion
Zemskov, E. P., E-mail: zemskov@ccas.ru [Russian Academy of Sciences, Dorodnicyn Computing Center (Russian Federation)
2013-10-15
The Turing instability is studied in two-component reaction-diffusion systems with nonlinear diffusion terms, and the regions in parametric space where Turing patterns can form are determined. The boundaries between super- and subcritical bifurcations are found. Calculations are performed for one-dimensional brusselator and oregonator models.
Modeling of Reaction Processes Controlled by Diffusion
Revelli, J
2003-01-01
Stochastic modeling is quite powerful in science and technology.The technics derived from this process have been used with great success in laser theory, biological systems and chemical reactions.Besides, they provide a theoretical framework for the analysis of experimental results on the field of particle's diffusion in ordered and disordered materials.In this work we analyze transport processes in one-dimensional fluctuating media, which are media that change their state in time.This fact induces changes in the movements of the particles giving rise to different phenomena and dynamics that will be described and analyzed in this work.We present some random walk models to describe these fluctuating media.These models include state transitions governed by different dynamical processes.We also analyze the trapping problem in a lattice by means of a simple model which predicts a resonance-like phenomenon.Also we study effective diffusion processes over surfaces due to random walks in the bulk.We consider differe...
Diffusion theory of slow responses
李景德; 陈敏; 郑凤; 周镇宏
1997-01-01
When an action is applied to a macroscopic substance, there is a particular sort of slow response he sides the well-known fast response. Using diffusion theory, the characteristics of slow response in dielectric, elastic, piezoelectric, and pyroelectric relaxation may he explained A time domain spectroscopy method suitable for slow and fast responses in linear and nonlinear effects is given. Every relaxation mechanism contributes a peak in differential spectroscopy, and its position, height, and line shape show the dynamical properties of the mechanism The method of frequency domain spectroscopy is suitable only for linear fast response. Time domain spectroscopy is another nonequiv-alent powerful method. The theory is confirmed by a lot of experimental data
Diffusion and reaction in crowded environments
EcheverIa, Carlos [Laboratorio de Fisica Aplicada y Computacional, Departamento de Matematica y Fisica, Universidad Nacional Experimental del Tachira, San Cristobal 5001 (Venezuela); Tucci, Kay [Centro de Fisica Fundamental, Universidad de Los Andes, Merida 5101 (Venezuela); Kapral, Raymond [Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, ON, M5S 3H6 (Canada)
2007-02-14
The effects of molecular crowding on small molecule diffusion and chemical reaction rate coefficients are investigated. The systems considered comprise a random distribution of stationary spherical obstacles occupying a volume fraction {phi} of the system and a large number of small molecules whose dynamics are followed. Chemical reactions are studied in such crowded systems where, in addition to the obstacles, a large reactive sphere C is present that catalyses the reaction A+C {yields} B+C. Using a mesoscopic description of the dynamics employing multiparticle collisions among the small molecules, the {phi} dependence of the diffusion and reaction rate coefficients is computed. Both the diffusion and reaction rate coefficients decrease with increase of the obstacle volume fraction as expected but variations of these quantities with {phi} are not predicted by simple models of the dynamics.
Reaction rates for reaction-diffusion kinetics on unstructured meshes
Hellander, Stefan; Petzold, Linda
2017-02-01
The reaction-diffusion master equation is a stochastic model often utilized in the study of biochemical reaction networks in living cells. It is applied when the spatial distribution of molecules is important to the dynamics of the system. A viable approach to resolve the complex geometry of cells accurately is to discretize space with an unstructured mesh. Diffusion is modeled as discrete jumps between nodes on the mesh, and the diffusion jump rates can be obtained through a discretization of the diffusion equation on the mesh. Reactions can occur when molecules occupy the same voxel. In this paper, we develop a method for computing accurate reaction rates between molecules occupying the same voxel in an unstructured mesh. For large voxels, these rates are known to be well approximated by the reaction rates derived by Collins and Kimball, but as the mesh is refined, no analytical expression for the rates exists. We reduce the problem of computing accurate reaction rates to a pure preprocessing step, depending only on the mesh and not on the model parameters, and we devise an efficient numerical scheme to estimate them to high accuracy. We show in several numerical examples that as we refine the mesh, the results obtained with the reaction-diffusion master equation approach those of a more fine-grained Smoluchowski particle-tracking model.
Energy diffusion controlled reaction rate in dissipative Hamiltonian systems
Deng Mao-Lin; Zhu Wei-Qiu
2007-01-01
In this paper the energy diffusion controlled reaction rate in dissipative Hamiltonian systems is investigated by using the stochastic averaging method for quasi Hamiltonian systems. The boundary value problem of mean first-passage time (MFPT) of averaged system is formulated and the energy diffusion controlled reaction rate is obtained as the inverse of MFPT. The energy diffusion controlled reaction rate in the classical Kramers bistable potential and in a two-dimensional bistable potential with a heat bath are obtained by using the proposed approach respectively. The obtained results are then compared with those from Monte Carlo simulation of original systems and from the classical Kramers theory. It is shown that the reaction rate obtained by using the proposed approach agrees well with that from Monte Carlo simulation and is more accurate than the classical Kramers rate.
Theories on diffusion of technology
Munch, Birgitte
Tracing the body of the diffusion proces by analysing the diffusion process from historical, sociological, economic and technical approaches. Discussing central characteristics of the proces of diffusion og CAD/CAM in Denmark.......Tracing the body of the diffusion proces by analysing the diffusion process from historical, sociological, economic and technical approaches. Discussing central characteristics of the proces of diffusion og CAD/CAM in Denmark....
Layer-adapted meshes for reaction-convection-diffusion problems
Linß, Torsten
2010-01-01
This book on numerical methods for singular perturbation problems - in particular, stationary reaction-convection-diffusion problems exhibiting layer behaviour is devoted to the construction and analysis of layer-adapted meshes underlying these numerical methods. A classification and a survey of layer-adapted meshes for reaction-convection-diffusion problems are included. This structured and comprehensive account of current ideas in the numerical analysis for various methods on layer-adapted meshes is addressed to researchers in finite element theory and perturbation problems. Finite differences, finite elements and finite volumes are all covered.
Reaction-Diffusion Automata Phenomenology, Localisations, Computation
Adamatzky, Andrew
2013-01-01
Reaction-diffusion and excitable media are amongst most intriguing substrates. Despite apparent simplicity of the physical processes involved the media exhibit a wide range of amazing patterns: from target and spiral waves to travelling localisations and stationary breathing patterns. These media are at the heart of most natural processes, including morphogenesis of living beings, geological formations, nervous and muscular activity, and socio-economic developments. This book explores a minimalist paradigm of studying reaction-diffusion and excitable media using locally-connected networks of finite-state machines: cellular automata and automata on proximity graphs. Cellular automata are marvellous objects per se because they show us how to generate and manage complexity using very simple rules of dynamical transitions. When combined with the reaction-diffusion paradigm the cellular automata become an essential user-friendly tool for modelling natural systems and designing future and emergent computing arch...
Fluctuation in nonextensive reaction-diffusion systems
Wu Junlin; Chen Huaijun [Department of Physics, Shaanxi Normal University, Xian 710062 (China)
2007-05-15
The density fluctuation in a nonextensive reaction-diffusion system is investigated, where the nonequilibrium stationary-state distribution is described by the generalized Maxwell-Boltzmann distribution in the framework of Tsallis statistics (or nonextensive statistics). By using the density operator technique, the nonextensive pressure effect is introduced into the master equation and thus the generalized master equation is derived for the system. As an example, we take the{sup 3}He reaction-diffusion model inside stars to analyse the nonextensive effect on the density fluctuation and we find that the nonextensive parameter q different from one plays a very important role in determining the characteristics of the fluctuation waves.
Yahiro, Masanobu; Minomo, Kosho
2011-01-01
We present an accurate method of treating the one-neutron removal reaction at intermediate incident energies induced by both nuclear and Coulomb interactions. In the method, the nuclear and Coulomb breakup processes are consistently treated by the method of continuum discretized coupled channels without making the adiabatic approximation to the Coulomb interaction, so that the removal cross section calculated never diverges. This method is applied to recently measured one-neutron removal cross section for $^{31}$Ne+$^{12}$C scattering at 230 MeV/nucleon and $^{31}$Ne+$^{208}$Pb scattering at 234 MeV/nucleon. The spectroscopic factor and the asymptotic normalization coefficient of the last neutron in $^{31}$Ne are evaluated.
Diffusion and Surface Reaction in Heterogeneous Catalysis
Baiker, A.; Richarz, W.
1978-01-01
Ethylene hydrogenation on a platinum catalyst, electrolytically applied to a tube wall, is a good system for the study of the interactions between diffusion and surface reaction in heterogeneous catalysis. Theoretical background, apparatus, procedure, and student performance of this experiment are discussed. (BB)
Approximating parameters in nonlinear reaction diffusion equations
Robert R. Ferdinand
2001-07-01
Full Text Available We present a model describing population dynamics in an environment. The model is a nonlinear, nonlocal, reaction diffusion equation with Neumann boundary conditions. An inverse method, involving minimization of a least-squares cost functional, is developed to identify unknown model parameters. Finally, numerical results are presented which display estimates of these parameters using computationally generated data.
String theory as a diffusing system
Calcagni, Gianluca
2009-01-01
Recent results on the effective non-local dynamics of the tachyon mode of open string field theory (OSFT) show that approximate solutions can be constructed which obey the diffusion equation. We argue that this structure is inherited from the full theory, where it admits a background-independent formulation. In fact, all known exact OSFT solutions are superpositions of diffusing surface states. In particular, the diffusion equation is a spacetime manifestation of OSFT gauge symmetries.
Reaction-Diffusion in the NEURON Simulator
Robert A. McDougal
2013-11-01
Full Text Available 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 has developed a Reaction-Diffusion (rxd module in Python which 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.
Reaction-diffusion in the NEURON simulator.
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.
Reaction rates for a generalized reaction-diffusion master equation.
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.
Reaction rates for a generalized reaction-diffusion master equation
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.
Reaction-diffusion basis of retroviral infectivity
Sadiq, S. Kashif
2016-11-01
Retrovirus particle (virion) infectivity requires diffusion and clustering of multiple transmembrane envelope proteins (Env3) on the virion exterior, yet is triggered by protease-dependent degradation of a partially occluding, membrane-bound Gag polyprotein lattice on the virion interior. The physical mechanism underlying such coupling is unclear and only indirectly accessible via experiment. Modelling stands to provide insight but the required spatio-temporal range far exceeds current accessibility by all-atom or even coarse-grained molecular dynamics simulations. Nor do such approaches account for chemical reactions, while conversely, reaction kinetics approaches handle neither diffusion nor clustering. Here, a recently developed multiscale approach is considered that applies an ultra-coarse-graining scheme to treat entire proteins at near-single particle resolution, but which also couples chemical reactions with diffusion and interactions. A model is developed of Env3 molecules embedded in a truncated Gag lattice composed of membrane-bound matrix proteins linked to capsid subunits, with freely diffusing protease molecules. Simulations suggest that in the presence of Gag but in the absence of lateral lattice-forming interactions, Env3 diffuses comparably to Gag-absent Env3. Initial immobility of Env3 is conferred through lateral caging by matrix trimers vertically coupled to the underlying hexameric capsid layer. Gag cleavage by protease vertically decouples the matrix and capsid layers, induces both matrix and Env3 diffusion, and permits Env3 clustering. Spreading across the entire membrane surface reduces crowding, in turn, enhancing the effect and promoting infectivity. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.
Statistical theory of breakup reactions
Bertulani, Carlos A., E-mail: carlos.bertulani@tamuc.edu [Department of Physics and Astronomy, Texas A and M University-Commerce, Commerce, TX (United States); Descouvemont, Pierre, E-mail: pdesc@ulb.ac.be [Physique Nucleaire Theorique et Physique Mathematique, Universite Libre de Bruxelles (ULB), Brussels (Belgium); Hussein, Mahir S., E-mail: hussein@if.usp.br [Universidade de Sao Paulo (USP), Sao Paulo, SP (Brazil). Instituto de Estudos Avancados
2014-07-01
We propose an alternative for Coupled-Channels calculations with loosely bound exotic nuclei (CDCC), based on the the Random Matrix Model of the statistical theory of nuclear reactions. The coupled channels equations are divided into two sets. The first set, described by the CDCC, and the other set treated with RMT. The resulting theory is a Statistical CDCC (CDCC{sub s}), able in principle to take into account many pseudo channels. (author)
Statistical Theory of Breakup Reactions
Bertulani Carlos A.
2014-04-01
Full Text Available We propose an alternative for Coupled-Channels calculations with looselybound exotic nuclei(CDCC, based on the the Random Matrix Model of the statistical theory of nuclear reactions. The coupled channels equations are divided into two sets. The first set, described by the CDCC, and the other set treated with RMT. The resulting theory is a Statistical CDCC (CDCCs, able in principle to take into account many pseudo channels.
Statistical Theory of Breakup Reactions
Bertulani, Carlos A; Hussein, Mahir S
2014-01-01
We propose alternatives to coupled-channels calculations with loosely-bound exotic nuclei (CDCC), based on the the random matrix (RMT) and the optical background (OPM) models for the statistical theory of nuclear reactions. The coupled channels equations are divided into two sets. The first set, described by the CDCC, and the other set treated with RMT. The resulting theory is a Statistical CDCC (CDCC$_S$), able in principle to take into account many pseudo channels.
Statistical Theory of Breakup Reactions
Bertulani, Carlos A.; Descouvemont, Pierre; Hussein, Mahir S.
2014-04-01
We propose an alternative for Coupled-Channels calculations with looselybound exotic nuclei(CDCC), based on the the Random Matrix Model of the statistical theory of nuclear reactions. The coupled channels equations are divided into two sets. The first set, described by the CDCC, and the other set treated with RMT. The resulting theory is a Statistical CDCC (CDCCs), able in principle to take into account many pseudo channels.
ALTERNATING DIRECTION FINITE ELEMENT METHOD FOR SOME REACTION DIFFUSION MODELS
江成顺; 刘蕴贤; 沈永明
2004-01-01
This paper is concerned with some nonlinear reaction - diffusion models. To solve this kind of models, the modified Laplace finite element scheme and the alternating direction finite element scheme are established for the system of patrical differential equations. Besides, the finite difference method is utilized for the ordinary differential equation in the models. Moreover, by the theory and technique of prior estimates for the differential equations, the convergence analyses and the optimal L2- norm error estimates are demonstrated.
Reaction-diffusion pulses: a combustion model
Campos, Daniel [Grup de FIsica EstadIstica, Dept. de FIsica, Universitat Autonoma de Barcelona, E-08193 Bellaterrra (Spain); Llebot, Josep Enric [Grup de FIsica EstadIstica, Dept. de FIsica, Universitat Autonoma de Barcelona, E-08193 Bellaterrra (Spain); Fort, Joaquim [Dept. de FIsica, Univ. de Girona, Campus de Montilivi, 17071 Girona, Catalonia (Spain)
2004-07-02
We focus on a reaction-diffusion approach proposed recently for experiments on combustion processes, where the heat released by combustion follows first-order reaction kinetics. This case allows us to perform an exhaustive analytical study. Specifically, we obtain the exact expressions for the speed of the thermal pulses, their maximum temperature and the condition of self-sustenance. Finally, we propose two generalizations of the model, namely, the case of several reactants burning together, and that of time-delayed heat conduction. We find an excellent agreement between our analytical results and simulations.
Reaction diffusion equation with spatio-temporal delay
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.
Turing patterns in a reaction-diffusion model with the Degn-Harrison reaction scheme
Li, Shanbing; Wu, Jianhua; Dong, Yaying
2015-09-01
In this paper, we consider a reaction-diffusion model with Degn-Harrison reaction scheme. Some fundamental analytic properties of nonconstant positive solutions are first investigated. We next study the stability of constant steady-state solution to both ODE and PDE models. Our result also indicates that if either the size of the reactor or the effective diffusion rate is large enough, then the system does not admit nonconstant positive solutions. Finally, we establish the global structure of steady-state bifurcations from simple eigenvalues by bifurcation theory and the local structure of the steady-state bifurcations from double eigenvalues by the techniques of space decomposition and implicit function theorem.
Reaction rates for mesoscopic reaction-diffusion kinetics.
Hellander, Stefan; Hellander, Andreas; Petzold, Linda
2015-02-01
The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In this paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. We show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results.
Reaction rates for mesoscopic reaction-diffusion kinetics
Hellander, Stefan; Hellander, Andreas; Petzold, Linda
2015-02-01
The mesoscopic reaction-diffusion master equation (RDME) is a popular modeling framework frequently applied to stochastic reaction-diffusion kinetics in systems biology. The RDME is derived from assumptions about the underlying physical properties of the system, and it may produce unphysical results for models where those assumptions fail. In that case, other more comprehensive models are better suited, such as hard-sphere Brownian dynamics (BD). Although the RDME is a model in its own right, and not inferred from any specific microscale model, it proves useful to attempt to approximate a microscale model by a specific choice of mesoscopic reaction rates. In this paper we derive mesoscopic scale-dependent reaction rates by matching certain statistics of the RDME solution to statistics of the solution of a widely used microscopic BD model: the Smoluchowski model with a Robin boundary condition at the reaction radius of two molecules. We also establish fundamental limits on the range of mesh resolutions for which this approach yields accurate results and show both theoretically and in numerical examples that as we approach the lower fundamental limit, the mesoscopic dynamics approach the microscopic dynamics. We show that for mesh sizes below the fundamental lower limit, results are less accurate. Thus, the lower limit determines the mesh size for which we obtain the most accurate results.
Diffusion in the special theory of relativity.
Herrmann, Joachim
2009-11-01
The Markovian diffusion theory is generalized within the framework of the special theory of relativity. Since the velocity space in relativity is a hyperboloid, the mathematical stochastic calculus on Riemanian manifolds can be applied but adopted here to the velocity space. A generalized Langevin equation in the fiber space of position, velocity, and orthonormal velocity frames is defined from which the generalized relativistic Kramers equation in the phase space in external force fields is derived. The obtained diffusion equation is invariant under Lorentz transformations and its stationary solution is given by the Jüttner distribution. Besides, a nonstationary analytical solution is derived for the example of force-free relativistic diffusion.
Chastang, C. [CEA Centre d`Etudes de Saclay, 91 - Gif-sur-Yvette (France). Dept. des Procedes d`Enrichissement]|[Ecole Polytechnique Feminine France (France)
1997-12-31
Different theories concerning the calculation of diffusion coefficients in liquid metals, as well for auto as for hetero-diffusion are presented and some experimental procedures using tracer techniques in shear cells and capillary tubes are described. Diffusion curves are calculated with the TRIO-EF code. Calculated and measured values of diffusion coefficients are compared and discussed with regard to various diffusion mechanisms. Copper gadolinium mixtures have been investigated in more detail. (C.B.). 35 refs.
Distribution in flowing reaction-diffusion systems
Kamimura, Atsushi
2009-12-28
A power-law distribution is found in the density profile of reacting systems A+B→C+D and 2A→2C under a flow in two and three dimensions. Different densities of reactants A and B are fixed at both ends. For the reaction A+B, the concentration of reactants asymptotically decay in space as x-1/2 and x-3/4 in two dimensions and three dimensions, respectively. For 2A, it decays as log (x) /x in two dimensions. The decay of A+B is explained considering the effect of segregation of reactants in the isotropic case. The decay for 2A is explained by the marginal behavior of two-dimensional diffusion. A logarithmic divergence of the diffusion constant with system size is found in two dimensions. © 2009 The American Physical Society.
Untangling knots via reaction-diffusion dynamics of vortex strings
Maucher, Fabian
2016-01-01
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.
Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings
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.
Inverse Diffusion Theory of Photoacoustics
Bal, Guillaume
2009-01-01
This paper analyzes the reconstruction of diffusion and absorption parameters in an elliptic equation from knowledge of internal data. In the application of photo-acoustics, the internal data are the amount of thermal energy deposited by high frequency radiation propagating inside a domain of interest. These data are obtained by solving an inverse wave equation, which is well-studied in the literature. We show that knowledge of two internal data based on well-chosen boundary conditions uniquely determines two constitutive parameters in diffusion and Schroedinger equations. Stability of the reconstruction is guaranteed under additional geometric constraints of strict convexity. No geometric constraints are necessary when $2n$ internal data for well-chosen boundary conditions are available, where $n$ is spatial dimension. The set of well-chosen boundary conditions is characterized in terms of appropriate complex geometrical optics (CGO) solutions.
Nonlinear predator-prey singularly perturbed Robin Problems for reaction diffusion systems
莫嘉琪; 韩祥临
2003-01-01
The nonlinear predator-prey reaction diffusion systems for singularly perturbed Robin Problems are considered. Under suitable conditions, the theory of differential inequalities can be used to study the asymptotic behavior of the solution for initial boundary value problems.
莫嘉琪
2003-01-01
The nonlinear predator-prey singularly perturbed Robin initial boundary value problems for reaction diffusion systems were considered. Under suitable conditions, using theory of differential inequalities the existence and asymptotic behavior of solution for initial boundary value problems were studied.
THE CORNER LAYER SOLUTION TO ROBIN PROBLEM FOR REACTION DIFFUSION EQUATION
无
2012-01-01
A class of Robin boundary value problem for reaction diffusion equation is considered. Under suitable conditions, using the theory of differential inequalities the existence and asymptotic behavior of the corner layer solution to the initial boundary value problem are studied.
Hamiltonian perspective on compartmental reaction-diffusion networks
Seslija, Marko; van der Schaft, Arjan; Scherpen, Jacquelien M. A.
2014-01-01
Inspired by the recent developments in modeling and analysis of reaction networks, we provide a geometric formulation of the reversible reaction networks under the influence of diffusion. Using the graph knowledge of the underlying reaction network, the obtained reaction diffusion system is a distri
Chemical computing with reaction-diffusion processes.
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.
A Note on the Kinetics of Diffusion-mediated Reactions
Naqvi, K Razi
2014-01-01
The prevalent scheme of a diffusion-mediated bimolecular reaction $A+B\\rightarrow P$ is an adaptation of that proposed by Briggs and Haldane for enzyme action [{\\em Biochem J.\\/}, 19:338--339, 1925]. The purpose of this Note is to explain, {\\em by using an argument involving no mathematics\\/}, why the breakup of the encounter complex cannot be described, except in special circumstances, in terms of a first-order process $\\{AB\\}\\rightarrow A+B$. Briefly, such a description neglects the occurrence of re-encounters, which lie at the heart of Noyes's theory of diffusion-mediated reactions. The relation $k=\\alpha k_{\\mbox{\\scriptsize e}}$ becomes valid only when $\\alpha$ (the reaction probability per encounter) is very much smaller than unity (activation-controlled reactions), or when $\\beta$ (the re-encounter probability) is negligible (as happens in a gas-phase reaction). References to some works (by the author and his collaborators) which propound the correct approach for finding $k$ are also supplied.
Evolution of diffusion and dissemination theory.
Dearing, James W
2008-01-01
The article provides a review and considers how the diffusion of innovations Research paradigm has changed, and offers suggestions for the further development of this theory of social change. Main emphases of diffusion Research studies are compared over time, with special attention to applications of diffusion theory-based concepts as types of dissemination science. A considerable degree of paradigmatic evolution is observed. The classical diffusion model focused on adopter innovativeness, individuals as the locus of decision, communication channels, and adoption as the primary outcome measures in post hoc observational study designs. The diffusion systems in question were centralized, with fidelity of implementation often assumed. Current dissemination Research and practice is better characterized by tests of interventions that operationalize one or more diffusion theory-based concepts and concepts from other change approaches, involve complex organizations as the units of adoption, and focus on implementation issues. Foment characterizes dissemination and implementation Research, Reflecting both its interdisciplinary Roots and the imperative of spreading evidence-based innovations as a basis for a new paradigm of translational studies of dissemination science.
Galactic disks as reaction-diffusion systems
Smolin, L
1996-01-01
A model of a galactic disk is presented which extends the homogeneous one zone models by incorporating propagation of material and energy in the disk. For reasonable values of the parameters the homogeneous steady state is unstable to the development of inhomogeneities, leading to the development of spatial and temporal structure. At the linearized level a prediction for the length and time scales of the patterns is found. These instabilities arise for the same reason that pattern formation is seen in non-equilibrium chemical and biological systems, which is that the positive and negative feedback effects which govern the rates of the critical processes act over different distance scales, as in Turing's reaction-diffusion models. This shows that patterns would form in the disk even in the absence of gravitational effects, density waves, rotation, shear and external perturbations. These nonlinear effects may thus explain the spiral structure seen in the star forming regions of isolated flocculent galaxies.
Laser Spot Detection Based on Reaction Diffusion
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
Laser Spot Detection Based on Reaction Diffusion
Alejandro Vázquez-Otero
2016-03-01
Full Text Available 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.
Reaction and diffusion in turbulent combustion
Pope, S.B. [Mechanical and Aerospace Engineering, Ithaca, NY (United States)
1993-12-01
The motivation for this project is the need to obtain a better quantitative understanding of the technologically-important phenomenon of turbulent combustion. In nearly all applications in which fuel is burned-for example, fossil-fuel power plants, furnaces, gas-turbines and internal-combustion engines-the combustion takes place in a turbulent flow. Designers continually demand more quantitative information about this phenomenon-in the form of turbulent combustion models-so that they can design equipment with increased efficiency and decreased environmental impact. For some time the PI has been developing a class of turbulent combustion models known as PDF methods. These methods have the important virtue that both convection and reaction can be treated without turbulence-modelling assumptions. However, a mixing model is required to account for the effects of molecular diffusion. Currently, the available mixing models are known to have some significant defects. The major motivation of the project is to seek a better understanding of molecular diffusion in turbulent reactive flows, and hence to develop a better mixing model.
INNOVATION DIFFUSION THEORY MAIN DEVELOPMENT STAGES
S. V. Lisafiev
2011-01-01
Full Text Available Abstract: Main innovation diffusion development theory stages are: Rogers model of moving new products to the market including characteristics of its segments; mathematic substantiation of this model by Bass; Moor model taking into account gaps between adjacent market segments; Goldenberg model making it possible to predict sales drops at new product life cycle initial stages. It is reasonable to use this theory while moving innovative products to the market.
Defects and diffusion, theory and simulation an annual retrospective I
Fisher, David J
2009-01-01
This first volume, in a new series covering entirely general results in the fields of defects and diffusion, includes abstracts of papers which appeared between the beginning of 2008 and the end of October 2009 (journal availability permitting).This new series replaces the 'general' section which was previously part of each issue of the Metals, Ceramics and Semiconductor retrospective series. As well as 356 abstracts, the volume includes original papers on all of the usual material groups: ""Predicting Diffusion Coefficients from First Principles via Eyring's Reaction Rate Theory"" (Mantina, C
Generalized theory of diffusion based on kinetic theory
Schäfer, T.
2016-10-01
We propose to use spin hydrodynamics, a two-fluid model of spin propagation, as a generalization of the diffusion equation. We show that in the dense limit spin hydrodynamics reduces to Fick's law and the diffusion equation. In the opposite limit spin hydrodynamics is equivalent to a collisionless Boltzmann treatment of spin propagation. Spin hydrodynamics avoids unphysical effects that arise when the diffusion equation is used to describe to a strongly interacting gas with a dilute corona. We apply spin hydrodynamics to the problem of spin diffusion in a trapped atomic gas. We find that the observed spin relaxation rate in the high-temperature limit [Sommer et al., Nature (London) 472, 201 (2011), 10.1038/nature09989] is consistent with the diffusion constant predicted by kinetic theory.
A generalized Theory of Diffusion based on Kinetic Theory
Schaefer, Thomas
2016-01-01
We propose to use spin hydrodynamics, a two-fluid model of spin propagation, as a generalization of the diffusion equation. We show that in the dense limit spin hydrodynamics reduces to Fick's law and the diffusion equation. In the opposite limit spin hydrodynamics is equivalent to a collisionless Boltzmann treatment of spin propagation. Spin hydrodynamics avoids unphysical effects that arise when the diffusion equation is used to describe to a strongly interacting gas with a dilute corona. We apply spin hydrodynamics to the problem of spin diffusion in a trapped atomic gas. We find that the observed spin relaxation rate in the high temperature limit [Sommer et al., Nature 472, 201 (2011)] is consistent with the diffusion constant predicted by kinetic theory.
Fedotov, Sergei
1998-10-01
An asymptotic method is presented for the analysis of the traveling waves in the one-dimensional reaction-diffusion system with the diffusion with a finite velocity and Kolmogorov-Petrovskii-Piskunov kinetics. The analysis makes use of the path-integral approach, scaling procedure, and the singular perturbation techniques involving the large deviations theory for the Poisson random walk. The exact formula for the position and speed of reaction front is derived. It is found that the reaction front dynamics is formally associated with the relativistic Hamiltonian/Lagrangian mechanics.
Diffusion Controlled Reactions, Fluctuation Dominated Kinetics, and Living Cell Biochemistry
Konkoli, Zoran
2009-01-01
In recent years considerable portion of the computer science community has focused its attention on understanding living cell biochemistry and efforts to understand such complication reaction environment have spread over wide front, ranging from systems biology approaches, through network analysis (motif identification) towards developing language and simulators for low level biochemical processes. Apart from simulation work, much of the efforts are directed to using mean field equations (equivalent to the equations of classical chemical kinetics) to address various problems (stability, robustness, sensitivity analysis, etc.). Rarely is the use of mean field equations questioned. This review will provide a brief overview of the situations when mean field equations fail and should not be used. These equations can be derived from the theory of diffusion controlled reactions, and emerge when assumption of perfect mixing is used.
Defects and diffusion, theory & simulation II
Fisher, David J
2010-01-01
This second volume in a new series covering entirely general results in the fields of defects and diffusion includes 356 abstracts of papers which appeared between the end of 2009 and the end of 2010. As well as the abstracts, the volume includes original papers on theory/simulation, semiconductors and metals: ""Predicting Diffusion Coefficients from First Principles ..."" (Mantina, Chen & Liu), ""Gouge Assessment for Pipes ..."" (Meliani, Pluvinage & Capelle), ""Simulation of the Impact Behaviour of ... Hollow Sphere Structures"" (Ferrano, Speich, Rimkus, Merkel & Öchsner), ""Elastic-Plastic
Applicability of diffusion of innovation theory in organic agriculture
Tomaš-Simin Mirela
2014-01-01
Full Text Available The authors discuss the possibility of applying the theory of diffusion of innovations in the concept of organic farming. Agricultural and food sector has been exposed to significant changes over the past two centuries. That was very significant for the theory of diffusion of innovations that sought to better understand the process of knowledge transfer and adoption of innovations. Organic farming has developed as a response to the environmental and other problems of conventional agriculture. Also, it is a reaction to some issues regarding rural development. By introducing the theory of diffusion of innovation, the aim of the paper is to take into the consideration the possibility of its application to the organic system analysis. By that, we wish to take into account all the specifics which enable to observe the system of organic farming as an innovation itself. The authors conclude that the theory of diffusion of innovations can be used in the research of organic farming systems, with the respect of all characteristics and particularities of organic farming.
Voter Model Perturbations and Reaction Diffusion Equations
Cox, J Theodore; Perkins, Edwin
2011-01-01
We consider particle systems that are perturbations of the voter model and show that when space and time are rescaled the system converges to a solution of a reaction diffusion equation in dimensions $d \\ge 3$. Combining this result with properties of the PDE, some methods arising from a low density super-Brownian limit theorem, and a block construction, we give general, and often asymptotically sharp, conditions for the existence of non-trivial stationary distributions, and for extinction of one type. As applications, we describe the phase diagrams of three systems when the parameters are close to the voter model: (i) a stochastic spatial Lotka-Volterra model of Neuhauser and Pacala, (ii) a model of the evolution of cooperation of Ohtsuki, Hauert, Lieberman, and Nowak, and (iii) a continuous time version of the non-linear voter model of Molofsky, Durrett, Dushoff, Griffeath, and Levin. The first application confirms a conjecture of Cox and Perkins and the second confirms a conjecture of Ohtsuki et al in the ...
Travelling waves in nonlinear diffusion-convection-reaction
Gilding, B.H.; Kersner, R.
2001-01-01
The study of travelling waves or fronts has become an essential part of the mathematical analysis of nonlinear diffusion-convection-reaction processes. Whether or not a nonlinear second-order scalar reaction-convection-diffusion equation admits a travelling-wave solution can be determined by the stu
Speed ot travelling waves in reaction-diffusion equations
Benguria, R D; Méndez, V
2002-01-01
Reaction diffusion equations arise in several problems of population dynamics, flame propagation and others. In one dimensional cases the systems may evolve into travelling fronts. Here we concentrate on a reaction diffusion equation which arises as a simple model for chemotaxis and present results for the speed of the travelling fronts. (Author)
Speed ot travelling waves in reaction-diffusion equations
Benguria, R.D.; Depassier, M.C. [Facultad de Fisica, Pontificia Universidad Catolica de Chile, Avda. Vicuna Mackenna 4860, Santiago (Chile); Mendez, V. [Facultat de Ciencies de la Salut, Universidad Internacional de Catalunya, Gomera s/n 08190 Sant Cugat del Valles, Barcelona (Spain)
2002-07-01
Reaction diffusion equations arise in several problems of population dynamics, flame propagation and others. In one dimensional cases the systems may evolve into travelling fronts. Here we concentrate on a reaction diffusion equation which arises as a simple model for chemotaxis and present results for the speed of the travelling fronts. (Author)
QUENCHING PROBLEMS OF DEGENERATE FUNCTIONAL REACTION-DIFFUSION EQUATION
无
2006-01-01
This paper is concerned with the quenching problem of a degenerate functional reaction-diffusion equation. The quenching problem and global existence of solution for the reaction-diffusion equation are derived and, some results of the positive steady state solutions for functional elliptic boundary value are also presented.
Diffusion-reaction compromise the polymorphs of precipitated calcium carbonate
Han Wang; Wenlai Huang; Yongsheng Han
2013-01-01
Diffusion is seldom considered by chemists and materialists in the preparation of materials while it plays an important role in the field of chemical engineering.If we look at crystallization at the atomic level,crystal growth in a solution starts from the diffusion of ions to the growing surface followed by the incorporation of ions into its lattice.Diffusion can be a rate determining step for the growth of crystals.In this paper,we take the crystallization of calcium carbonate as an example to illustrate the microscopic processes of diffusion and reaction and their compromising influence on the morphology of the crystals produced.The diffusion effect is studied in a specially designed three-cell reactor.Experiments show that a decrease of diffusion leads to retardation of supersaturation and the formation of a continuous concentration gradient in the reaction cell,thus promoting the formation of cubic calcite particles.The reaction rate is regulated by temperature.Increase of reaction rate favors the formation of needle-like aragonite particles.When diffusion and reaction play joint roles in the reaction system,their compromise dominates the formation of products,leading to a mixture of cubic and needle-like particles with a controllable ratio.Since diffusion and reaction are universal factors in the preparation of materials,the finding of this paper could be helpful in the controlled synthesis of other materials.
Adaptive mesh refinement for stochastic reaction-diffusion processes
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.
Diffusion Reaction of Carbon Monoxide in the Human Lung
Kang, M.-Y.; Guénard, H.; Sapoval, B.
2017-08-01
The capture of CO, a standard lung function test, results from diffusion-reaction processes of CO with hemoglobin inside red blood cells (RBCs). In its current understanding, suggested by Roughton and Forster in 1957, the capture is represented by two independent resistances in series, one for diffusion from the gas to the RBC periphery, the second for internal diffusion reaction. Numerical studies in 3D model structures described here contradict the independence hypothesis. This results from two different theoretical reasons: (i) The RBC peripheries are not equi-concentrations; (ii) diffusion times in series are not additive.
Kinetic theory of diffusion-limited nucleation
Philippe, T.; Bonvalet, M.; Blavette, D.
2016-05-01
We examine binary nucleation in the size and composition space {R,c} using the formalism of the multivariable theory [N. V. Alekseechkin, J. Chem. Phys. 124, 124512 (2006)]. We show that the variable c drops out of consideration for very large curvature of the new phase Gibbs energy with composition. Consequently nuclei around the critical size have the critical composition, which is derived from the condition of criticality for the canonical variables and is found not to depend on surface tension. In this case, nucleation kinetics can be investigated in the size space only. Using macroscopic kinetics, we determine the general expression for the condensation rate when growth is limited by bulk diffusion, which accounts for both diffusion and capillarity and exhibits a different dependence with the critical size, as compared with the interface-limited regime. This new expression of the condensation rate for bulk diffusion-limited nucleation is the counterpart of the classical interface-limited result. We then extend our analysis to multicomponent solutions.
Reciprocity theory of homogeneous reactions
Agbormbai, Adolf A.
1990-03-01
The reciprocity formalism is applied to the homogeneous gaseous reactions in which the structure of the participating molecules changes upon collision with one another, resulting in a change in the composition of the gas. The approach is applied to various classes of dissociation, recombination, rearrangement, ionizing, and photochemical reactions. It is shown that for the principle of reciprocity to be satisfied it is necessary that all chemical reactions exist in complementary pairs which consist of the forward and backward reactions. The backward reaction may be described by either the reverse or inverse process. The forward and backward processes must satisfy the same reciprocity equation. Because the number of dynamical variables is usually unbalanced on both sides of a chemical equation, it is necessary that this balance be established by including as many of the dynamical variables as needed before the reciprocity equation can be formulated. Statistical transformation models of the reactions are formulated. The models are classified under the titles free exchange, restricted exchange and simplified restricted exchange. The special equations for the forward and backward processes are obtained. The models are consistent with the H theorem and Le Chatelier's principle. The models are also formulated in the context of the direct simulation Monte Carlo method.
LAGRANGE STABILITY IN MEAN SQUARE OF STOCHASTIC REACTION DIFFUSION EQUATIONS
无
2006-01-01
This work is devoted to the discussion of stochastic reaction diffusion equations and some new theorems on Lagrange stability in mean square of the solution are established via Lyapunov method which is nothing to be done in the past.
Multiresolution stochastic simulations of reaction-diffusion processes.
Bayati, B; Chatelain, P.; Koumoutsakos, P.
2008-01-01
Stochastic simulations of reaction-diffusion processes are used extensively for the modeling of complex systems in areas ranging from biology and social sciences to ecosystems and materials processing. These processes often exhibit disparate scales that render their simulation prohibitive even for massive computational resources. The problem is resolved by introducing a novel stochastic multiresolution method that enables the efficient simulation of reaction-diffusion processes as modeled by ...
A Reaction-Diffusion Model of Cholinergic Retinal Waves
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
Microscopic effective reaction theory for deuteron-induced reactions
Neoh, Yuen Sim; Minomo, Kosho; Ogata, Kazuyuki
2016-01-01
The microscopic effective reaction theory is applied to deuteron-induced reactions. A reaction model-space characterized by a $p+n+{\\rm A}$ three-body model is adopted, where A is the target nucleus, and the nucleon-target potential is described by a microscopic folding model based on an effective nucleon-nucleon interaction in nuclear medium and a one-body nuclear density of A. The three-body scattering wave function in the model space is obtained with the continuum-discretized coupled-channels method (CDCC), and the eikonal reaction theory (ERT), an extension of CDCC, is applied to the calculation of neutron removal cross sections. Elastic scattering cross sections of deuteron on $^{58}$Ni and $^{208}$Pb target nuclei at several energies are compared with experimental data. The total reaction cross sections and the neutron removal cross sections at 56 MeV on 14 target nuclei are calculated and compared with experimental values.
Microscopic effective reaction theory for deuteron-induced reactions
Neoh, Yuen Sim; Yoshida, Kazuki; Minomo, Kosho; Ogata, Kazuyuki
2016-10-01
The microscopic effective reaction theory is applied to deuteron-induced reactions. A reaction model space characterized by a p +n +A three-body model is adopted, where A is the target nucleus, and the nucleon-target potential is described by a microscopic folding model based on an effective nucleon-nucleon interaction in nuclear medium and a one-body nuclear density of A . The three-body scattering wave function in the model space is obtained with the continuum-discretized coupled-channels (CDCC) method, and the eikonal reaction theory (ERT), an extension of CDCC, is applied to the calculation of neutron removal cross sections. Elastic scattering cross sections of deuteron on 58Ni and 208Pb target nuclei at several energies are compared with experimental data. The total reaction cross sections and the neutron removal cross sections at 56 MeV on 14 target nuclei are calculated and compared with experimental values.
Target Patterns in Reaction-Diffusion Systems,
1981-01-01
new variable xd, the diffusion matrix in (1.1) is just DM and the velocities Vph and v,, in (4.20) and (4.21) are multiplied by C-I/2, Finally except...the (ksr)-’ / factors in (4.4), (4.19), (5.1), and (5.2) are absent in one dimension. However, the analysis for three dimensions hinges on whether (4.2
Distributed order reaction-diffusion systems associated with Caputo derivatives
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
Simple computation of reaction-diffusion processes on point clouds.
Macdonald, Colin B; Merriman, Barry; Ruuth, Steven J
2013-06-04
The study of reaction-diffusion processes is much more complicated on general curved surfaces than on standard Cartesian coordinate spaces. Here we show how to formulate and solve systems of reaction-diffusion equations on surfaces in an extremely simple way, using only the standard Cartesian form of differential operators, and a discrete unorganized point set to represent the surface. Our method decouples surface geometry from the underlying differential operators. As a consequence, it becomes possible to formulate and solve rather general reaction-diffusion equations on general surfaces without having to consider the complexities of differential geometry or sophisticated numerical analysis. To illustrate the generality of the method, computations for surface diffusion, pattern formation, excitable media, and bulk-surface coupling are provided for a variety of complex point cloud surfaces.
A Unified Theory of Chemical Reactions
Aubry, S
2014-01-01
We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent. Our theory reveals the existence of an intermediate situation between ionic and covalent which may be almost barrierless and isoenegetic and which should be of high interest for understanding biochemistry.
Dynamic Simulation of Backward Diffusion Based on Random Walk Theory
Dung, Vu Ba; Nguyen, Bui Huu
2016-06-01
Results of diffusion study in silicon showed that diffusion of the selfinterstitial and vacancy could be backward diffusion and their diffusivity could be negative [1]. The backward diffusion process and negative diffusivity is contrary to the fundamental laws of diffusion such as the law of Fick law, namely the diffusive flux of backward diffusion goes from regions of low concentration to regions of high concentration. The backward diffusion process have been explained [2]. In this paper, the backward diffusion process is simulated. Results is corresponding to theory and show that when thermal velocity of the low concentration area is greater than thermal velocity of the high concentration area, the backward diffusion can be occurred.
Exact solutions for logistic reaction-diffusion equations in biology
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.
Bifurcation Analysis of Gene Propagation Model Governed by Reaction-Diffusion Equations
Guichen Lu
2016-01-01
Full Text Available We present a theoretical analysis of the attractor bifurcation for gene propagation model governed by reaction-diffusion equations. We investigate the dynamical transition problems of the model under the homogeneous boundary conditions. By using the dynamical transition theory, we give a complete characterization of the bifurcated objects in terms of the biological parameters of the problem.
Byron, F. W.; Joachain, C. J.
1989-08-01
A comprehensive survey is given of the theory of (e, 2e) reactions. We begin by discussing the kinematics of these reactions, with special attention devoted to the coplanar asymmetric (Ehrhardt-type) geometry and the fully symmetric geometry in which most of the recent (e, 2e) coincidence measurements have been performed. We then review the foundations of the theory of the ionization of atoms by electron impact, first for one-electron atoms and then for target atoms with N electrons. Next, we discussed the Wannier theory of threshold ionization and its excitations. We then turn to the analysis of (e, 2e) reactions at intermediate and high energies. The theory of fast coplanar asymmetric (e, 2e) reactions is analyzed and it is shown that the eikonal-Born series method successfully accounts for all the dynamical features of these reactions. In particular, it is shown that second order effects are essential in explaining all the features exhibited by the measured by the measured triple differential cross sections at intermediate energies. Finally, we review the theory of fast symmetric (e, 2e) reactions. We consider first the (e, 2e) spectroscopy regime in which the momentum transfer Δ is large, but the recoil momentum Q of the ion is small or moderate. We then turn to the regime of large Δ and large Q, for which second order effects are of paramount importance, so that the coplanar symmetric triple differential cross section exhibits a striking behaviour in the large angle region.
Eikonal reaction theory for two-neutron removal reactions
Minomo, K; Egashira, K; Ogata, K; Yahiro, M
2014-01-01
The eikonal reaction theory (ERT) proposed lately is a method of calculating one-neutron removal reactions at intermediate incident energies in which Coulomb breakup is treated accurately with the continuum discretized coupled-channels method. ERT is extended to two-neutron removal reactions. ERT reproduces measured one- and two-neutron removal cross sections for 6He scattering on 12C and 208Pb targets at 240 MeV/nucleon and also on a 28Si target at 52 MeV/nucleon. For the heavier target in which Coulomb breakup is important, ERT yields much better agreement with the measured cross sections than the Glauber model.
Restrictive liquid-phase diffusion and reaction in bidispersed catalysts
Lee, S.Y.; Seader, J.D. (Utah Univ., Salt Lake City, UT (United States). Dept. of Chemical Engineering); Tsai, C.H.; Massoth, F.E. (Utah Univ., Salt Lake City, UT (United States). Dept. of Fuels Engineering)
1991-08-01
In this paper, the effect of bidispersed pore-size distribution on liquid-phase diffusion and reaction in NiMo/Al{sub 2}O{sub 3} catalysts is investigated by applying two bidispersed-pore-structure models, the random-pore model and a globular-structure model, to extensive experimental data, which were obtained from sorptive diffusion measurements at ambient conditions and catalytic reaction rate measurements on nitrogen-containing compounds. Transport of the molecules in the catalysts was found to be controlled by micropore diffusion, in accordance with the random-pore model, rather than macropore diffusion as predicted by the globular-structure model. A qualitative criterion for micropore-diffusion control is proposed: relatively small macroporosity and high catalyst pellet density. Since most hydrotreating catalysts have high density, diffusion in these types of catalysts may be controlled by micropore diffusion. Accordingly, it is believed in this case that increasing the size of micropores may be more effective to reduce intraparticle diffusion resistance than incorporating macropores alone.
ASYMPTOTIC SOLUTION OF ACTIVATOR INHIBITOR SYSTEMS FOR NONLINEAR REACTION DIFFUSION EQUATIONS
Jiaqi MO; Wantao LIN
2008-01-01
A nonlinear reaction diffusion equations for activator inhibitor systems is considered. Under suitable conditions, firstly, the outer solution of the original problem is obtained, secondly, using the variables of multiple scales and the expanding theory of power series the formal asymptotic expansions of the solution are constructed, and finally, using the theory of differential inequalities the uniform validity and asymptotic behavior of the solution are studied.
Reaction-diffusion models of decontamination
Hjorth, Poul G.
A contaminant, which also contains a polymer is in the form of droplets on a solid surface. It is to be removed by the action of a decontaminant, which is applied in aqueous solution. The contaminant is only sparingly soluble in water, so the reaction mechanism is that it slowly dissolves...... in the aqueous solution and then is oxidized by the decontaminant. The polymer is insoluble in water, and so builds up near the interface, where its presence can impede the transport of contaminant. In these circumstances, Dstl wish to have mathematical models that give an understanding of the process, and can...
Microscopic effective reaction theory for direct nuclear reactions
Ogata Kazuyuki
2016-01-01
Full Text Available Some recent activities with the microscopic effective reaction theory (MERT on elastic, inelastic, breakup, transfer, and knockout processes are reviewed briefly. As a possible alternative to MERT, a description of elastic and inelastic scattering with the continuum particle-vibration coupling (cPVC method is also discussed.
Exact solutions for a diffusion-reaction process in one dimension
Spouge, John L.
1988-03-01
This paper presents a new method for the solution of diffusion-reaction problems in one dimension. The method is used to derive some new exact results for the polymerization (cl-cl aggregation) and annihilation processes on openR and openZ. Through well-known dualities, these results have implications for the T=0 limit of the kinetic Ising model and for two interacting particle processes, the invasion and voter models. Prospectively, the method may be useful in providing one-dimensional verification for speculations in the theory of diffusion reaction.
Reaction-diffusion problems in the physics of hot plasmas
Wilhelmsson, H
2000-01-01
The physics of hot plasmas is of great importance for describing many phenomena in the universe and is fundamental for the prospect of future fusion energy production on Earth. Nontrivial results of nonlinear electromagnetic effects in plasmas include the self-organization and self-formation in the plasma of structures compact in time and space. These are the consequences of competing processes of nonlinear interactions and can be best described using reaction-diffusion equations. Reaction-Diffusion Problems in the Physics of Hot Plasmas is focused on paradigmatic problems of a reaction-diffusion type met in many branches of science, concerning in particular the nonlinear interaction of electromagnetic fields with plasmas.
Theory and experiments on surface diffusion
Silvestri, W.L.
1998-11-01
The following topics were dealt with: adatom formation and self-diffusion on the Ni(100) surface, helium atom scattering measurements, surface-diffusion parameter measurements, embedded atom method calculations.
Distributed order reaction-diffusion systems associated with Caputo derivatives
Saxena, R K; Haubold, H J
2011-01-01
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. [23,24], for the fundamental solution of the space-time fractional equation, including Haubold et al. [13] and Saxena et al. [38] 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...
Stability analysis of non-autonomous reaction-diffusion systems: the effects of growing domains
Madzvamuse, Anotida
2009-08-29
By using asymptotic theory, we generalise the Turing diffusively-driven instability conditions for reaction-diffusion systems with slow, isotropic domain growth. There are two fundamental biological differences between the Turing conditions on fixed and growing domains, namely: (i) we need not enforce cross nor pure kinetic conditions and (ii) the restriction to activator-inhibitor kinetics to induce pattern formation on a growing biological system is no longer a requirement. Our theoretical findings are confirmed and reinforced by numerical simulations for the special cases of isotropic linear, exponential and logistic growth profiles. In particular we illustrate an example of a reaction-diffusion system which cannot exhibit a diffusively-driven instability on a fixed domain but is unstable in the presence of slow growth. © Springer-Verlag 2009.
Reaction-diffusion-branching models of stock price fluctuations
Tang, Lei-Han; Tian, Guang-Shan
Several models of stock trading (Bak et al., Physica A 246 (1997) 430.) are analyzed in analogy with one-dimensional, two-species reaction-diffusion-branching processes. Using heuristic and scaling arguments, we show that the short-time market price variation is subdiffusive with a Hurst exponent H=1/4. Biased diffusion towards the market price and blind-eyed copying lead to crossovers to the empirically observed random-walk behavior ( H=1/2) at long times. The calculated crossover forms and diffusion constants are shown to agree well with simulation data.
Practical improvements on photon diffusion theory : application to isotropic scattering
Graaff, R; Rinzema, K
2001-01-01
Based on the analysis of an isotropic point source in an infinite, isotropically scattering turbid medium, we suggest several modifications to the well-known diffusion theory. Compared with standard diffusion theory these modifications, which require very little extra mathematics, lead to a substant
Chaotic advection, diffusion, and reactions in open flows
Tel, Tamas [Institute for Theoretical Physics, Eoetvoes University, P.O. Box 32, H-1518 Budapest, (Hungary); Karolyi, Gyoergy [Department of Civil Engineering Mechanics, Technical University of Budapest, Mueegyetem rpk. 3, H-1521 Budapest, (Hungary); Pentek, Aron [Marine Physical Laboratory, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0238 (United States); Scheuring, Istvan [Department of Plant Taxonomy and Ecology, Research Group of Ecology and Theoretical Biology, Eoetvoes University, Ludovika ter 2, H-1083 Budapest, (Hungary); Toroczkai, Zoltan [Department of Physics, University of Maryland, College Park, Maryland 20742-4111 (United States); Department of Physics, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0435 (United States); Grebogi, Celso [Institute for Plasma Research, University of Maryland, College Park, Maryland 20742 (United States); Kadtke, James [Marine Physical Laboratory, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, California 92093-0238 (United States)
2000-03-01
We review and generalize recent results on advection of particles in open time-periodic hydrodynamical flows. First, the problem of passive advection is considered, and its fractal and chaotic nature is pointed out. Next, we study the effect of weak molecular diffusion or randomness of the flow. Finally, we investigate the influence of passive advection on chemical or biological activity superimposed on open flows. The nondiffusive approach is shown to carry some features of a weak diffusion, due to the finiteness of the reaction range or reaction velocity. (c) 2000 American Institute of Physics.
Liquid Film Diffusion on Reaction Rate in Submerged Biofilters
Christiansen, Pia; Hollesen, Line; Harremoës, Poul
1995-01-01
Experiments were carried out in order to investigate the influence of liquid film diffusion on reaction rate in a submerged biofilter with denitrification and in order to compare with a theoretical study of the mass transfer coefficient. The experiments were carried out with varied flow, identified...... by the empty bed velocity of inflow and recirculation, respectively 1.3, 2.8, 5.6 and 10.9 m/h. The filter material consisted of 3 mm biostyren spheres. The results indicate that the influence of liquid film diffusion on reaction rate can be ignored....
Diffuse Optical Tomography for Brain Imaging: Theory
Yuan, Zhen; Jiang, Huabei
Diffuse optical tomography (DOT) is a noninvasive, nonionizing, and inexpensive imaging technique that uses near-infrared light to probe tissue optical properties. Regional variations in oxy- and deoxy-hemoglobin concentrations as well as blood flow and oxygen consumption can be imaged by monitoring spatiotemporal variations in the absorption spectra. For brain imaging, this provides DOT unique abilities to directly measure the hemodynamic, metabolic, and neuronal responses to cells (neurons), and tissue and organ activations with high temporal resolution and good tissue penetration. DOT can be used as a stand-alone modality or can be integrated with other imaging modalities such as fMRI/MRI, PET/CT, and EEG/MEG in studying neurophysiology and pathology. This book chapter serves as an introduction to the basic theory and principles of DOT for neuroimaging. It covers the major aspects of advances in neural optical imaging including mathematics, physics, chemistry, reconstruction algorithm, instrumentation, image-guided spectroscopy, neurovascular and neurometabolic coupling, and clinical applications.
Dynamical Behavior of Core 3 He Nuclear Reaction-Diffusion Systems and Sun's Gravitational Field
DU Jiulin; SHEN Hong
2005-01-01
The coupling of the sun's gravitational field with processes of diffusion and convection exerts a significant influence on the dynamical behavior of the core 3He nuclear reaction-diffusion system. Stability analyses of the system are made in this paper by using the theory of nonequilibrium dynamics. It is showed that, in the nuclear reaction regions extending from the center to about 0.38 times of the radius of the sun, the gravitational field enables the core 3He nuclear reaction-diffusion system to become unstable and, after the instability, new states to appear in the system have characteristic of time oscillation. This may change the production rates of both 7Be and 8B neutrinos.
The speed of reaction-diffusion wavefronts in nonsteady media
Mendez, Vicenc [Departament de Medicina, Facultat de Ciencies de la Salut, Universitat Internacional de Catalunya. c/Gomera s/n, 08190-Sant Cugat del Valles (Barcelona) (Spain); Fort, Joaquim [Departament de Fisica, Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia (Spain); Pujol, Toni [Departament de Fisica, Universitat de Girona, Campus Montilivi, 17071 Girona, Catalonia (Spain)
2003-04-11
The evolution of the speed of wavefronts for reaction-diffusion equations with time-varying parameters is analysed. We make use of singular perturbative analysis to study the temporal evolution of the speed for pushed fronts. The analogy with Hamilton-Jacobi dynamics allows us to consider the problem for pulled fronts, which is described by Kolmogorov-Petrovskii-Piskunov (KPP) reaction kinetics. Both analytical studies are in good agreement with the results of numerical solutions.
The speed of reaction-diffusion wavefronts in nonsteady media
Méndez, V; Pujol, T
2003-01-01
The evolution of the speed of wavefronts for reaction-diffusion equations with time-varying parameters is analysed. We make use of singular perturbative analysis to study the temporal evolution of the speed for pushed fronts. The analogy with Hamilton-Jacobi dynamics allows us to consider the problem for pulled fronts, which is described by Kolmogorov-Petrovskii-Piskunov (KPP) reaction kinetics. Both analytical studies are in good agreement with the results of numerical solutions.
Universal Charge Diffusion and the Butterfly Effect in Holographic Theories
Blake, Mike
2016-08-01
We study charge diffusion in holographic scaling theories with a particle-hole symmetry. We show that these theories have a universal regime in which the diffusion constant is given by Dc=C vB2/(2 π T ), where vB is the velocity of the butterfly effect. The constant of proportionality C depends only on the scaling exponents of the infrared theory. Our results suggest an unexpected connection between transport at strong coupling and quantum chaos.
Reaction Diffusion and Chemotaxis for Decentralized Gathering on FPGAs
Bernard Girau
2009-01-01
and rapid simulations of the complex dynamics of this reaction-diffusion model. Then we describe the FPGA implementation of the environment together with the agents, to study the major challenges that must be solved when designing a fast embedded implementation of the decentralized gathering model. We analyze the results according to the different goals of these hardware implementations.
Internal Stabilization of a Mutualistic Reaction Diffusion System
Wang Yuan DONG
2007-01-01
We study the internal stabilization of steady-state solutions to a 2-species mutualistic reaction diffusion system via finite-dimensional feedback controllers. Our main idea is to use differ- ent internal controllers to stabilize different steady-state solutions. The controllers are provided by considering LQ problems associated with the lineaxized systems at steady-state solutions.
A Note on a Nonlocal Nonlinear Reaction-Diffusion Model
Walker, Christoph
2011-01-01
We give an application of the Crandall-Rabinowitz theorem on local bifurcation to a system of nonlinear parabolic equations with nonlocal reaction and cross-diffusion terms as well as nonlocal initial conditions. The system arises as steady-state equations of two interacting age-structured populations.
Cohabitation reaction-diffusion model for virus focal infections
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.
Mixed, Nonsplit, Extended Stability, Stiff Integration of Reaction Diffusion Equations
Alzahrani, Hasnaa H.
2016-07-26
A tailored integration scheme is developed to treat stiff reaction-diffusion prob- lems. The construction adapts a stiff solver, namely VODE, to treat reaction im- plicitly together with explicit treatment of diffusion. The second-order Runge-Kutta- Chebyshev (RKC) scheme is adjusted to integrate diffusion. Spatial operator is de- scretised by second-order finite differences on a uniform grid. The overall solution is advanced over S fractional stiff integrations, where S corresponds to the number of RKC stages. The behavior of the scheme is analyzed by applying it to three simple problems. The results show that it achieves second-order accuracy, thus, preserving the formal accuracy of the original RKC. The presented development sets the stage for future extensions, particularly, to multidimensional reacting flows with detailed chemistry.
Theory of diffusive light scattering cancellation cloaking
Farhat, Mohamed; Guenneau, Sebastien; Bagci, Hakan; Salama, Khaled Nabil; Alu, Andrea
2016-01-01
We report on a new concept of cloaking objects in diffusive light regime using the paradigm of the scattering cancellation and mantle cloaking techniques. We show numerically that an object can be made completely invisible to diffusive photon density waves, by tailoring the diffusivity constant of the spherical shell enclosing the object. This means that photons' flow outside the object and the cloak made of these spherical shells behaves as if the object were not present. Diffusive light invisibility may open new vistas in hiding hot spots in infrared thermography or tissue imaging.
De Oliveira Santos, F. [Grand Accelerateur National d' Ions Lourds, UMR 6415, 14 - Caen (France)
2007-07-01
Nuclear reactions can occur at low kinetic energy. Low-energy reactions are characterized by a strong dependence on the structure of the compound nucleus. It turns out that it is possible to study the nuclear structure by measuring these reactions. In this course, three types of reactions are treated: Resonant Elastic Scattering (such as N{sup 14}(p,p)N{sup 14}), Inelastic Scattering (such as N{sup 14}(p,p')N{sup 14*}) and Astrophysical reactions (such as N{sup 14}(p,{gamma})O{sup 15}). (author)
Reaction-diffusion pattern in shoot apical meristem of plants.
Hironori Fujita
Full Text Available A fundamental question in developmental biology is how spatial patterns are self-organized from homogeneous structures. In 1952, Turing proposed the reaction-diffusion model in order to explain this issue. Experimental evidence of reaction-diffusion patterns in living organisms was first provided by the pigmentation pattern on the skin of fishes in 1995. However, whether or not this mechanism plays an essential role in developmental events of living organisms remains elusive. Here we show that a reaction-diffusion model can successfully explain the shoot apical meristem (SAM development of plants. SAM of plants resides in the top of each shoot and consists of a central zone (CZ and a surrounding peripheral zone (PZ. SAM contains stem cells and continuously produces new organs throughout the lifespan. Molecular genetic studies using Arabidopsis thaliana revealed that the formation and maintenance of the SAM are essentially regulated by the feedback interaction between WUSHCEL (WUS and CLAVATA (CLV. We developed a mathematical model of the SAM based on a reaction-diffusion dynamics of the WUS-CLV interaction, incorporating cell division and the spatial restriction of the dynamics. Our model explains the various SAM patterns observed in plants, for example, homeostatic control of SAM size in the wild type, enlarged or fasciated SAM in clv mutants, and initiation of ectopic secondary meristems from an initial flattened SAM in wus mutant. In addition, the model is supported by comparing its prediction with the expression pattern of WUS in the wus mutant. Furthermore, the model can account for many experimental results including reorganization processes caused by the CZ ablation and by incision through the meristem center. We thus conclude that the reaction-diffusion dynamics is probably indispensable for the SAM development of plants.
Maximum Principles for Discrete and Semidiscrete Reaction-Diffusion Equation
Petr Stehlík
2015-01-01
Full Text Available We study reaction-diffusion equations with a general reaction function f on one-dimensional lattices with continuous or discrete time ux′ (or Δtux=k(ux-1-2ux+ux+1+f(ux, x∈Z. We prove weak and strong maximum and minimum principles for corresponding initial-boundary value problems. Whereas the maximum principles in the semidiscrete case (continuous time exhibit similar features to those of fully continuous reaction-diffusion model, in the discrete case the weak maximum principle holds for a smaller class of functions and the strong maximum principle is valid in a weaker sense. We describe in detail how the validity of maximum principles depends on the nonlinearity and the time step. We illustrate our results on the Nagumo equation with the bistable nonlinearity.
Parametric spatiotemporal oscillation in reaction-diffusion systems.
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.
Reaction-diffusion master equation in the microscopic limit
Hellander, Stefan; Hellander, Andreas; Petzold, Linda
2012-04-01
Stochastic modeling of reaction-diffusion kinetics has emerged as a powerful theoretical tool in the study of biochemical reaction networks. Two frequently employed models are the particle-tracking Smoluchowski framework and the on-lattice reaction-diffusion master equation (RDME) framework. As the mesh size goes from coarse to fine, the RDME initially becomes more accurate. However, recent developments have shown that it will become increasingly inaccurate compared to the Smoluchowski model as the lattice spacing becomes very fine. Here we give a general and simple argument for why the RDME breaks down. Our analysis reveals a hard limit on the voxel size for which no local RDME can agree with the Smoluchowski model and lets us quantify this limit in two and three dimensions. In this light we review and discuss recent work in which the RDME has been modified in different ways in order to better agree with the microscale model for very small voxel sizes.
On the Reaction Diffusion Master Equation in the Microscopic Limit
Hellander, Stefan; Petzold, Linda
2011-01-01
Stochastic modeling of reaction-diffusion kinetics has emerged as a powerful theoretical tool in the study of biochemical reaction networks. Two frequently employed models are the particle-tracking Smoluchowski framework and the on-lattice Reaction-Diffusion Master Equation (RDME) framework. As the mesh size goes from coarse to fine, the RDME initially becomes more accurate. However, recent developments have shown that it will become increasingly inaccurate compared to the Smoluchowski model as the lattice spacing becomes very fine. In this paper we give a new, general and simple argument for why the RDME breaks down. Our analysis reveals a hard limit on the voxel size for which no local RDME can agree with the Smoluchowski model.
Oscillatory pulses and wave trains in a bistable reaction-diffusion system with cross diffusion.
Zemskov, Evgeny P; Tsyganov, Mikhail A; Horsthemke, Werner
2017-01-01
We study waves with exponentially decaying oscillatory tails in a reaction-diffusion system with linear cross diffusion. To be specific, we consider a piecewise linear approximation of the FitzHugh-Nagumo model, also known as the Bonhoeffer-van der Pol model. We focus on two types of traveling waves, namely solitary pulses that correspond to a homoclinic solution, and sequences of pulses or wave trains, i.e., a periodic solution. The effect of cross diffusion on wave profiles and speed of propagation is analyzed. We find the intriguing result that both pulses and wave trains occur in the bistable cross-diffusive FitzHugh-Nagumo system, whereas only fronts exist in the standard bistable system without cross diffusion.
Wang, Chi-Jen [Iowa State Univ., Ames, IA (United States)
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.
Diffusion, quantum theory, and radically elementary mathematics (MN-47)
Faris, William G
2014-01-01
Diffusive motion--displacement due to the cumulative effect of irregular fluctuations--has been a fundamental concept in mathematics and physics since Einstein''s work on Brownian motion. It is also relevant to understanding various aspects of quantum theory. This book explains diffusive motion and its relation to both nonrelativistic quantum theory and quantum field theory. It shows how diffusive motion concepts lead to a radical reexamination of the structure of mathematical analysis. The book''s inspiration is Princeton University mathematics professor Edward Nelson''s influential work in
A Weak Comparison Principle for Reaction-Diffusion Systems
José Valero
2012-01-01
Full Text Available We prove a weak comparison principle for a reaction-diffusion system without uniqueness of solutions. We apply the abstract results to the Lotka-Volterra system with diffusion, a generalized logistic equation, and to a model of fractional-order chemical autocatalysis with decay. Moreover, in the case of the Lotka-Volterra system a weak maximum principle is given, and a suitable estimate in the space of essentially bounded functions L∞ is proved for at least one solution of the problem.
Exact solutions of certain nonlinear chemotaxis diffusion reaction equations
MISHRA AJAY; KAUSHAL R S; PRASAD AWADHESH
2016-05-01
Using the auxiliary equation method, we obtain exact solutions of certain nonlinear chemotaxis diffusion reaction equations in the presence of a stimulant. In particular, we account for the nonlinearities arising not only from the density-dependent source terms contributed by the particles and the stimulant but also from the coupling term of the stimulant. In addition to this, the diffusion of the stimulant and the effect of long-range interactions are also accounted for in theconstructed coupled differential equations. The results obtained here could be useful in the studies of several biological systems and processes, e.g., in bacterial infection, chemotherapy, etc.
A weak comparison principle for reaction-diffusion systems
Valero, José
2012-01-01
In this paper we prove a weak comparison principle for a reaction-diffusion system without uniqueness of solutions. We apply the abstract results to the Lotka-Volterra system with diffusion, a generalized logistic equation and to a model of fractional-order chemical autocatalysis with decay. Morever, in the case of the Lotka-Volterra system a weak maximum principle is given, and a suitable estimate in the space of essentially bounded functions $L^{\\infty}$ is proved for at least one solution of the problem.
Oxygen Diffusion and Reaction Kinetics in Continuous Fiber Ceramic Matrix Composites
Halbig, Michael C.; Eckel, Andrew J.; Cawley, James D.
1999-01-01
Previous stressed oxidation tests of C/SiC composites at elevated temperatures (350 C to 1500 C) and sustained stresses (69 MPa and 172 MPa) have led to the development of a finite difference cracked matrix model. The times to failure in the samples suggest oxidation occurred in two kinetic regimes defined by the rate controlling mechanisms (i.e. diffusion controlled and reaction controlled kinetics). Microstructural analysis revealed preferential oxidation along as-fabricated, matrix microcracks and also suggested two regimes of oxidation kinetics dependent on the oxidation temperature. Based on experimental results, observation, and theory, a finite difference model was developed. The model simulates the diffusion of oxygen into a matrix crack bridged by carbon fibers. The model facilitates the study of the relative importance of temperature, the reaction rate constant, and the diffusion coefficient on the overall oxidation kinetics.
Stochastic reaction-diffusion kinetics in the microscopic limit
Fange, David; Berg, Otto G.; Sjöberg, Paul; Elf, Johan
2010-01-01
Quantitative analysis of biochemical networks often requires consideration of both spatial and stochastic aspects of chemical processes. Despite significant progress in the field, it is still computationally prohibitive to simulate systems involving many reactants or complex geometries using a microscopic framework that includes the finest length and time scales of diffusion-limited molecular interactions. For this reason, spatially or temporally discretized simulations schemes are commonly used when modeling intracellular reaction networks. The challenge in defining such coarse-grained models is to calculate the correct probabilities of reaction given the microscopic parameters and the uncertainty in the molecular positions introduced by the spatial or temporal discretization. In this paper we have solved this problem for the spatially discretized Reaction-Diffusion Master Equation; this enables a seamless and physically consistent transition from the microscopic to the macroscopic frameworks of reaction-diffusion kinetics. We exemplify the use of the methods by showing that a phosphorylation-dephosphorylation motif, commonly observed in eukaryotic signaling pathways, is predicted to display fluctuations that depend on the geometry of the system. PMID:21041672
A reaction-diffusion model of human brain development.
Julien Lefèvre
2010-04-01
Full Text Available Cortical folding exhibits both reproducibility and variability in the geometry and topology of its patterns. These two properties are obviously the result of the brain development that goes through local cellular and molecular interactions which have important consequences on the global shape of the cortex. Hypotheses to explain the convoluted aspect of the brain are still intensively debated and do not focus necessarily on the variability of folds. Here we propose a phenomenological model based on reaction-diffusion mechanisms involving Turing morphogens that are responsible for the differential growth of two types of areas, sulci (bottom of folds and gyri (top of folds. We use a finite element approach of our model that is able to compute the evolution of morphogens on any kind of surface and to deform it through an iterative process. Our model mimics the progressive folding of the cortical surface along foetal development. Moreover it reveals patterns of reproducibility when we look at several realizations of the model from a noisy initial condition. However this reproducibility must be tempered by the fact that a same fold engendered by the model can have different topological properties, in one or several parts. These two results on the reproducibility and variability of the model echo the sulcal roots theory that postulates the existence of anatomical entities around which the folding organizes itself. These sulcal roots would correspond to initial conditions in our model. Last but not least, the parameters of our model are able to produce different kinds of patterns that can be linked to developmental pathologies such as polymicrogyria and lissencephaly. The main significance of our model is that it proposes a first approach to the issue of reproducibility and variability of the cortical folding.
Turbulent thermal diffusion in strongly stratified turbulence: theory and experiments
Amir, G; Eidelman, A; Elperin, T; Kleeorin, N; Rogachevskii, I
2016-01-01
Turbulent thermal diffusion is a combined effect of the temperature stratified turbulence and inertia of small particles. It causes the appearance of a non-diffusive turbulent flux of particles in the direction of the turbulent heat flux. This non-diffusive turbulent flux of particles is proportional to the product of the mean particle number density and the effective velocity of inertial particles. The theory of this effect has been previously developed only for small temperature gradients and small Stokes numbers (Phys. Rev. Lett. {\\bf 76}, 224, 1996). In this study a generalized theory of turbulent thermal diffusion for arbitrary temperature gradients and Stokes numbers has been developed. The laboratory experiments in the oscillating grid turbulence and in the multi-fan produced turbulence have been performed to validate the theory of turbulent thermal diffusion in strongly stratified turbulent flows. It has been shown that the ratio of the effective velocity of inertial particles to the characteristic ve...
A reaction-diffusion SIS epidemic model in an almost periodic environment
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.
A Lattice Boltzmann Model for Oscillating Reaction-Diffusion
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.
Does reaction-diffusion support the duality of fragmentation effect?
Roques, Lionel
2009-01-01
There is a gap between single-species model predictions, and empirical studies, regarding the effect of habitat fragmentation per se, i.e., a process involving the breaking apart of habitat without loss of habitat. Empirical works indicate that fragmentation can have positive as well as negative effects, whereas, traditionally, single-species models predict a negative effect of fragmentation. Within the class of reaction-diffusion models, studies almost unanimously predict such a detrimental effect. In this paper, considering a single-species reaction-diffusion model with a removal -- or similarly harvesting -- term, in two dimensions, we find both positive and negative effects of fragmentation of the reserves, i.e. the protected regions where no removal occurs. Fragmented reserves lead to higher population sizes for time-constant removal terms. On the other hand, when the removal term is proportional to the population density, higher population sizes are obtained on aggregated reserves, but maximum yields ar...
Multiresolution stochastic simulations of reaction-diffusion processes.
Bayati, Basil; Chatelain, Philippe; Koumoutsakos, Petros
2008-10-21
Stochastic simulations of reaction-diffusion processes are used extensively for the modeling of complex systems in areas ranging from biology and social sciences to ecosystems and materials processing. These processes often exhibit disparate scales that render their simulation prohibitive even for massive computational resources. The problem is resolved by introducing a novel stochastic multiresolution method that enables the efficient simulation of reaction-diffusion processes as modeled by many-particle systems. The proposed method quantifies and efficiently handles the associated stiffness in simulating the system dynamics and its computational efficiency and accuracy are demonstrated in simulations of a model problem described by the Fisher-Kolmogorov equation. The method is general and can be applied to other many-particle models of physical processes.
Controllability of Degenerating Reaction-Diffusion System in Electrocardiology
Bendahmane, Mostafa
2011-01-01
This paper is devoted to analyze the null controllability of a nonlinear reaction-diffusion system approximating a parabolic-elliptic system modeling electrical activity in the heart. The uniform, with respect to the degenerating parameter, null controllability of the approximating system by a single control force acting on a subdomain is shown. The proof needs a precisely estimate with respect to the degenerating parameter and it is done combining Carleman estimates and energy inequalities.
An Application of Equivalence Transformations to Reaction Diffusion Equations
Mariano Torrisi
2015-10-01
Full Text Available In this paper, we consider a quite general class of advection reaction diffusion systems. By using an equivalence generator, derived in a previous paper, the authors apply a projection theorem to determine some special forms of the constitutive functions that allow the extension by one of the two-dimensional principal Lie algebra. As an example, a special case is discussed at the end of the paper.
Resonant Phase Patterns in a Reaction-Diffusion System
Lin, Anna L.; Bertram, Matthias; Martinez, Karl; Swinney, Harry L.; Ardelea, Alexandre; Carey, Graham F.
2000-05-01
Resonance regions similar to the Arnol'd tongues found in single oscillator frequency locking are observed in experiments using a spatially extended periodically forced Belousov-Zhabotinsky system. We identify six distinct 2:1 subharmonic resonant patterns and describe them in terms of the position-dependent phase and magnitude of the oscillations. Some experimentally observed features are also found in numerical studies of a forced Brusselator reaction-diffusion model. (c) 2000 The American Physical Society.
O'Hara, Kieran
2007-08-01
In the southern Appalachians, the Blue Ridge-Piedmont crystalline thrust sheet was emplaced onto low-grade Late Precambrian and Paleozoic sedimentary rocks in the footwall along a basal detachment consisting of phyllosilicate-rich mylonites (phyllonites). The phyllonites developed first by mechanical breakdown of feldspar followed by chemical breakdown to white mica in the presence of a pore fluid. Diffusion of solute in the pore fluid is the rate limiting step in controlling reaction rate and also the strain rate. Assuming solute diffusion follows the Stokes-Einstein equation, the shear strain rate is given by ⅆγ/ⅆt=2ωkT/5ηrx for shear stress ≥20 MPa, where n is a constant, ω is a geometric factor, k is Boltzmann's constant, T is absolute temperature, η is water viscosity, r is the atomic radius of the diffusing species, and x is the diffusion distance. A bulk diffusion coefficient in the range of ˜10 -10 to 10 -12 m 2/s over distances of 10-100 m results in strain rates of 10 -14 to 10 -13 s -1 in the temperature range 200-400 °C. It is concluded that greenschist grade crystalline thrust sheets develop on pre-existing basement faults that become weak during reaction softening and localize into high strain phyllonite zones in which pore fluid diffusion controls reaction rate and strain rate.
Exact Markov chains versus diffusion theory for haploid random mating.
Tyvand, Peder A; Thorvaldsen, Steinar
2010-05-01
Exact discrete Markov chains are applied to the Wright-Fisher model and the Moran model of haploid random mating. Selection and mutations are neglected. At each discrete value of time t there is a given number n of diploid monoecious organisms. The evolution of the population distribution is given in diffusion variables, to compare the two models of random mating with their common diffusion limit. Only the Moran model converges uniformly to the diffusion limit near the boundary. The Wright-Fisher model allows the population size to change with the generations. Diffusion theory tends to under-predict the loss of genetic information when a population enters a bottleneck.
A coupled theory for chemically active and deformable solids with mass diffusion and heat conduction
Zhang, Xiaolong; Zhong, Zheng
2017-10-01
To analyse the frequently encountered thermo-chemo-mechanical problems in chemically active material applications, we develop a thermodynamically-consistent continuum theory of coupled deformation, mass diffusion, heat conduction and chemical reaction. Basic balance equations of force, mass and energy are presented at first, and then fully coupled constitutive laws interpreting multi-field interactions and evolving equations governing irreversible fluxes are constructed according to the energy dissipation inequality and the chemical kinetics. To consider the essential distinction between mass diffusion and chemical reactions in affecting free energy and dissipations of a highly coupled system, we regard both the concentrations of diffusive species and the extent of reaction as independent state variables. This new formulation then distinguishes between the energy contribution from the diffusive species entering the solid and that from the subsequent chemical reactions occurring among these species and the host solid, which not only interact with stresses or strains in different manners and on different time scales, but also induce different variations of solid microstructures and material properties. Taking advantage of this new description, we further establish a specialized isothermal model to predict precisely the transient chemo-mechanical response of a swelling solid with a proposed volumetric constraint that accounts for material incompressibility. Coupled kinetics is incorporated to capture the volumetric swelling of the solid caused by imbibition of external species and the simultaneous dilation arised from chemical reactions between the diffusing species and the solid. The model is then exemplified with two numerical examples of transient swelling accompanied by chemical reaction. Various ratios of characteristic times of diffusion and chemical reaction are taken into account to shed light on the dependency on kinetic time scales of evolution patterns for
Applying Diffusion of Innovation Theory to Intervention Development.
Dearing, James W
2009-09-01
Few social science theories have a history of conceptual and empirical study as long as does the diffusion of innovations. The robustness of this theory derives from the many disciplines and fields of study in which diffusion has been studied, from the international richness of these studies, and from the variety of new ideas, practices, programs, and technologies that have been the objects of diffusion research. Early theorizing from the beginning of the 20th century was gradually displaced by post hoc empirical research that described and explained diffusion processes. By the 1950s, diffusion researchers had begun to apply the collective knowledge learned about naturalistic diffusion in tests of process interventions to affect the spread of innovations. Now, this purposive objective has given form to a science of dissemination in which evidence-based practices are designed a priori not just to result in internal validity but to increase the likelihood that external validity and diffusion both are more likely to result. Here, I review diffusion theory and focus on seven concepts-intervention attributes, intervention clusters, demonstration projects, societal sectors, reinforcing contextual conditions, opinion leadership, and intervention adaptation-with potential for accelerating the spread of evidence-based practices, programs, and policies in the field of social work.
Hydrodynamic theory of diffusion in two-temperature multicomponent plasmas
Ramshaw, J.D.; Chang, C.H. [Idaho National Engineering Lab., Idaho Falls, ID (United States)
1995-12-31
Detailed numerical simulations of multicomponent plasmas require tractable expressions for species diffusion fluxes, which must be consistent with the given plasma current density J{sub q} to preserve local charge neutrality. The common situation in which J{sub q} = 0 is referred to as ambipolar diffusion. The use of formal kinetic theory in this context leads to results of formidable complexity. We derive simple tractable approximations for the diffusion fluxes in two-temperature multicomponent plasmas by means of a generalization of the hydrodynamical approach used by Maxwell, Stefan, Furry, and Williams. The resulting diffusion fluxes obey generalized Stefan-Maxwell equations that contain driving forces corresponding to ordinary, forced, pressure, and thermal diffusion. The ordinary diffusion fluxes are driven by gradients in pressure fractions rather than mole fractions. Simplifications due to the small electron mass are systematically exploited and lead to a general expression for the ambipolar electric field in the limit of infinite electrical conductivity. We present a self-consistent effective binary diffusion approximation for the diffusion fluxes. This approximation is well suited to numerical implementation and is currently in use in our LAVA computer code for simulating multicomponent thermal plasmas. Applications to date include a successful simulation of demixing effects in an argon-helium plasma jet, for which selected computational results are presented. Generalizations of the diffusion theory to finite electrical conductivity and nonzero magnetic field are currently in progress.
Jingsun Yao; Jiaqi Mo
2005-01-01
The nonlinear nonlocal singularly perturbed initial boundary value problems for reaction diffusion equations with a boundary perturbation is considered. Under suitable conditions, the outer solution of the original problem is obtained. Using the stretched variable, the composing expansion method and the expanding theory of power series the initial layer is constructed. And then using the theory of differential inequalities the asymptotic behavior of solution for the initial boundary value problems is studied. Finally the existence and uniqueness of solution for the original problem and the uniformly valid asymptotic estimation are discussed.
New methods in nuclear reaction theory
Redish, E. F.
1979-01-01
Standard nuclear reaction methods are limited to treating problems that generalize two-body scattering. These are problems with only one continuous (vector) degree of freedom (CDOF). The difficulty in extending these methods to cases with two or more CDOFs is not just the additional numerical complexity: the mathematical problem is usually not well-posed. It is hard to guarantee that the proper boundary conditions (BCs) are satisfied. Since this is not generally known, the discussion is begun by considering the physics of this problem in the context of coupled-channel calculations. In practice, the difficulties are usually swept under the rug by the use of a highly developed phenomenology (or worse, by the failure to test a calculation for convergence). This approach limits the kind of reactions that can be handled to ones occurring on the surface of where a second CDOF can be treated perturbatively. In the past twenty years, the work of Faddeev, the quantum three-body problem has been solved. Many techniques (and codes) are now available for solving problems with two CDOFs. A method for using these techniques in the nuclear N-body problem is presented. A set of well-posed (connected kernal) equations for physical scattering operators is taken. Then it is shown how approximation schemes can be developed for a wide range of reaction mechanisms. The resulting general framework for a reaction theory can be applied to a number of nuclear problems. One result is a rigorous treatment of multistep transfer reactions with the possibility of systematically generating corrections. The application of the method to resonance reactions and knock-out is discussed. 12 figures.
Radiation reaction in quantum field theory
Higuchi, Atsushi
2002-11-01
We investigate radiation-reaction effects for a charged scalar particle accelerated by an external potential realized as a space-dependent mass term in quantum electrodynamics. In particular, we calculate the position shift of the final-state wave packet of the charged particle due to radiation at lowest order in the fine structure constant α and in the small ħ approximation. We show that it disagrees with the result obtained using the Lorentz-Dirac formula for the radiation-reaction force, and that it agrees with the classical theory if one assumes that the particle loses its energy to radiation at each moment of time according to the Larmor formula in the static frame of the potential. However, the discrepancy is much smaller than the Compton wavelength of the particle. We also point out that the electromagnetic correction to the potential has no classical limit.
Intracellular transport mechanisms: a critique of diffusion theory.
Agutter, P S; Malone, P C; Wheatley, D N
1995-09-21
It is argued that Brownian motion makes a less significant contribution to the movements of molecules and particles inside cells than is commonly believed, and that the numbers of similar molecules and particles within any near-homogeneous subcompartment of the cell internum are insufficient to justify the statistical assumptions implicit in the derivation of the diffusion equation. For these reasons, it is contended that, contrary to accepted opinion, diffusion theory cannot provide an explanation for intracellular transport at the molecular level. Although attempts have been made to adapt diffusion theory to complex media, the conclusion is that none satisfactorily overcomes the problem of applying the theory to cell biology. However, the heuristic influence of the theory on cellular biophysics and physiology is noted, and possible alternative frameworks for interpreting the valuable experimental data obtained from such studies are outlined.
Quantum theory of chemical reaction rates
Miller, W.H. [Univ. of California, Berkeley, CA (United States). Dept. of Chemistry]|[Lawrence Berkeley Lab., CA (United States). Chemical Sciences Div.
1994-10-01
If one wishes to describe a chemical reaction at the most detailed level possible, i.e., its state-to-state differential scattering cross section, then it is necessary to solve the Schroedinger equation to obtain the S-matrix as a function of total energy E and total angular momentum J, in terms of which the cross sections can be calculated as given by equation (1) in the paper. All other physically observable attributes of the reaction can be derived from the cross sections. Often, in fact, one is primarily interested in the least detailed quantity which characterizes the reaction, namely its thermal rate constant, which is obtained by integrating Eq. (1) over all scattering angles, summing over all product quantum states, and Boltzmann-averaging over all initial quantum states of reactants. With the proper weighting factors, all of these averages are conveniently contained in the cumulative reaction probability (CRP), which is defined by equation (2) and in terms of which the thermal rate constant is given by equation (3). Thus, having carried out a full state-to-state scattering calculation to obtain the S-matrix, one can obtain the CRP from Eq. (2), and then rate constant from Eq. (3), but this seems like ``overkill``; i.e., if one only wants the rate constant, it would clearly be desirable to have a theory that allows one to calculate it, or the CRP, more directly than via Eq. (2), yet also correctly, i.e., without inherent approximations. Such a theory is the subject of this paper.
Self-similar fast-reaction limits for reaction-diffusion systems on unbounded domains
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.
Cumulative signal transmission in nonlinear reaction-diffusion networks.
Diego A Oyarzún
Full Text Available Quantifying signal transmission in biochemical systems is key to uncover the mechanisms that cells use to control their responses to environmental stimuli. In this work we use the time-integral of chemical species as a measure of a network's ability to cumulatively transmit signals encoded in spatiotemporal concentrations. We identify a class of nonlinear reaction-diffusion networks in which the time-integrals of some species can be computed analytically. The derived time-integrals do not require knowledge of the solution of the reaction-diffusion equation, and we provide a simple graphical test to check if a given network belongs to the proposed class. The formulae for the time-integrals reveal how the kinetic parameters shape signal transmission in a network under spatiotemporal stimuli. We use these to show that a canonical complex-formation mechanism behaves as a spatial low-pass filter, the bandwidth of which is inversely proportional to the diffusion length of the ligand.
Variational methods applied to problems of diffusion and reaction
Strieder, William
1973-01-01
This monograph is an account of some problems involving diffusion or diffusion with simultaneous reaction that can be illuminated by the use of variational principles. It was written during a period that included sabbatical leaves of one of us (W. S. ) at the University of Minnesota and the other (R. A. ) at the University of Cambridge and we are grateful to the Petroleum Research Fund for helping to support the former and the Guggenheim Foundation for making possible the latter. We would also like to thank Stephen Prager for getting us together in the first place and for showing how interesting and useful these methods can be. We have also benefitted from correspondence with Dr. A. M. Arthurs of the University of York and from the counsel of Dr. B. D. Coleman the general editor of this series. Table of Contents Chapter 1. Introduction and Preliminaries . 1. 1. General Survey 1 1. 2. Phenomenological Descriptions of Diffusion and Reaction 2 1. 3. Correlation Functions for Random Suspensions 4 1. 4. Mean Free ...
Mechanical reaction-diffusion model for bacterial population dynamics
Ngamsaad, Waipot
2015-01-01
The effect of mechanical interaction between cells on the spreading of bacterial population was investigated in one-dimensional space. A nonlinear reaction-diffusion equation has been formulated as a model for this dynamics. In this model, the bacterial cells are treated as the rod-like particles that interact, when contacting each other, through the hard-core repulsion. The repulsion introduces the exclusion process that causes the fast diffusion in bacterial population at high density. The propagation of the bacterial density as the traveling wave front in long time behavior has been analyzed. The analytical result reveals that the front speed is enhanced by the exclusion process---and its value depends on the packing fraction of cell. The numerical solutions of the model have been solved to confirm this prediction.
Turing instability in reaction-diffusion models on complex networks
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.
Traveling wavefront solutions to nonlinear reaction-diffusion-convection equations
Indekeu, Joseph O.; Smets, Ruben
2017-08-01
Physically motivated modified Fisher equations are studied in which nonlinear convection and nonlinear diffusion is allowed for besides the usual growth and spread of a population. It is pointed out that in a large variety of cases separable functions in the form of exponentially decaying sharp wavefronts solve the differential equation exactly provided a co-moving point source or sink is active at the wavefront. The velocity dispersion and front steepness may differ from those of some previously studied exact smooth traveling wave solutions. For an extension of the reaction-diffusion-convection equation, featuring a memory effect in the form of a maturity delay for growth and spread, also smooth exact wavefront solutions are obtained. The stability of the solutions is verified analytically and numerically.
Control of DNA replication by anomalous reaction-diffusion kinetics
Bechhoefer, John; Gauthier, Michel
2010-03-01
DNA replication requires two distinct processes: the initiation of pre-licensed replication origins and the propagation of replication forks away from the fired origins. Experiments indicate that these origins are triggered over the whole genome at a rate I(t) (the number of initiations per unreplicated length per time) that increases throughout most of the synthesis (S) phase, before rapidly decreasing to zero at the end of the replication process. We propose a simple model for the control of DNA replication in which the rate of initiation of replication origins is controlled by protein-DNA interactions. Analyzing recent data from Xenopus frog embryos, we find that the initiation rate is reaction limited until nearly the end of replication, when it becomes diffusion limited. Initiation of origins is suppressed when the diffusion-limited search time dominates. To fit the experimental data, we find that the interaction between DNA and the rate-limiting protein must be subdiffusive.
Entropy methods for reaction-diffusion equations: slowly growing a-priori bounds
Desvillettes, Laurent
2008-01-01
In the continuation of [Desvillettes, L., Fellner, K.: Exponential Decay toward Equilibrium via Entropy Methods for Reaction-Diffusion Equations. J. Math. Anal. Appl. 319 (2006), no. 1, 157-176], we study reversible reaction-diffusion equations via entropy methods (based on the free energy functional) for a 1D system of four species. We improve the existing theory by getting 1) almost exponential convergence in L1 to the steady state via a precise entropy-entropy dissipation estimate, 2) an explicit global L∞ bound via interpolation of a polynomially growing H1 bound with the almost exponential L1 convergence, and 3), finally, explicit exponential convergence to the steady state in all Sobolev norms.
Front propagation in cellular flows for fast reaction and small diffusivity
Tzella, Alexandra; Vanneste, Jacques
2014-07-01
We investigate the influence of fluid flows on the propagation of chemical fronts arising in Fisher-Kolmogorov-Petrovsky-Piskunov (FKPP) type models. We develop an asymptotic theory for the front speed in a cellular flow in the limit of small molecular diffusivity and fast reaction, i.e., large Péclet (Pe) and Damköhler (Da) numbers. The front speed is expressed in terms of a periodic path—an instanton—that minimizes a certain functional. This leads to an efficient procedure to calculate the front speed, and to closed-form expressions for (logPe)-1≪Da≪Pe and for Da≫Pe. Our theoretical predictions are compared with (i) numerical solutions of an eigenvalue problem and (ii) simulations of the advection-diffusion-reaction equation.
Reaction diffusion and solid state chemical kinetics handbook
Dybkov, V I
2010-01-01
This monograph deals with a physico-chemical approach to the problem of the solid-state growth of chemical compound layers and reaction-diffusion in binary heterogeneous systems formed by two solids; as well as a solid with a liquid or a gas. It is explained why the number of compound layers growing at the interface between the original phases is usually much lower than the number of chemical compounds in the phase diagram of a given binary system. For example, of the eight intermetallic compounds which exist in the aluminium-zirconium binary system, only ZrAl3 was found to grow as a separate
Enhanced Diffusion of Enzymes that Catalyze Exothermic Reactions
Golestanian, Ramin
2015-09-01
Enzymes have been recently found to exhibit enhanced diffusion due to their catalytic activities. A recent experiment [C. Riedel et al., Nature (London) 517, 227 (2015)] has found evidence that suggests this phenomenon might be controlled by the degree of exothermicity of the catalytic reaction involved. Four mechanisms that can lead to this effect, namely, self-thermophoresis, boost in kinetic energy, stochastic swimming, and collective heating are critically discussed, and it is shown that only the last two can be strong enough to account for the observations. The resulting quantitative description is used to examine the biological significance of the effect.
Global dynamics of a reaction-diffusion system
Yuncheng You
2011-02-01
Full Text Available In this work the existence of a global attractor for the semiflow of weak solutions of a two-cell Brusselator system is proved. The method of grouping estimation is exploited to deal with the challenge in proving the absorbing property and the asymptotic compactness of this type of coupled reaction-diffusion systems with cubic autocatalytic nonlinearity and linear coupling. It is proved that the Hausdorff dimension and the fractal dimension of the global attractor are finite. Moreover, the existence of an exponential attractor for this solution semiflow is shown.
On the solutions of fractional reaction-diffusion equations
Jagdev Singh
2013-05-01
Full Text Available In this paper, we obtain the solution of a fractional reaction-diffusion equation associated with the generalized Riemann-Liouville fractional derivative as the time derivative and Riesz-Feller fractional derivative as the space-derivative. The results are derived by the application of the Laplace and Fourier transforms in compact and elegant form in terms of Mittag-Leffler function and H-function. The results obtained here are of general nature and include the results investigated earlier by many authors.
ENERGY ESTIMATES FOR DELAY DIFFUSION-REACTION EQUATIONS
J.A.Ferreira; P.M.da Silva
2008-01-01
In this paper we consider nonlinear delay diffusion-reaction equations with initial and Dirichlet boundary conditions.The behaviour and the stability of the solution of such initial boundary value problems(IBVPs)are studied using the energy method.Simple numerical methods are considered for the computation of numerical approximations to the solution of the nonlinear IBVPs.Using the discrete energy method we study the stability and convergence of the numerical approximations.Numerical experiments are carried out to illustrate our theoretical results.
Parametric pattern selection in a reaction-diffusion model.
Michael Stich
Full Text Available We compare spot patterns generated by Turing mechanisms with those generated by replication cascades, in a model one-dimensional reaction-diffusion system. We determine the stability region of spot solutions in parameter space as a function of a natural control parameter (feed-rate where degenerate patterns with different numbers of spots coexist for a fixed feed-rate. While it is possible to generate identical patterns via both mechanisms, we show that replication cascades lead to a wider choice of pattern profiles that can be selected through a tuning of the feed-rate, exploiting hysteresis and directionality effects of the different pattern pathways.
Parabolic equations in biology growth, reaction, movement and diffusion
Perthame, Benoît
2015-01-01
This book presents several fundamental questions in mathematical biology such as Turing instability, pattern formation, reaction-diffusion systems, invasion waves and Fokker-Planck equations. These are classical modeling tools for mathematical biology with applications to ecology and population dynamics, the neurosciences, enzymatic reactions, chemotaxis, invasion waves etc. The book presents these aspects from a mathematical perspective, with the aim of identifying those qualitative properties of the models that are relevant for biological applications. To do so, it uncovers the mechanisms at work behind Turing instability, pattern formation and invasion waves. This involves several mathematical tools, such as stability and instability analysis, blow-up in finite time, asymptotic methods and relative entropy properties. Given the content presented, the book is well suited as a textbook for master-level coursework.
Miyazaki, Tetsuo; Aratono, Yasuyuki; Ichikawa, Tsuneki; Shiotani, Masaru [eds.
1998-10-01
Present report is the proceedings of the 4th Meeting on Tunneling Reaction and Low Temperature Chemistry held in August 3 and 4, 1998. The main subject of the meeting is `Tunneling Reaction and Its Theory`. In the present meeting the theoretical aspects of tunneling phenomena in the chemical reaction were discussed intensively as the main topics. Ten reports were presented on the quantum diffusion of muon and proton in the metal and H{sub 2}{sup -} anion in the solid para-hydrogen, the theory of tunnel effect in the nuclear reaction and the tunneling reaction in the organic compounds. One special lecture was presented by Prof. J. Kondo on `Proton Tunneling in Solids`. The 11 of the presented papers are indexed individually. (J.P.N.)
Salem Abdelmalek
2014-11-01
Full Text Available In this article we construct the invariant regions for m-component reaction-diffusion systems with a tridiagonal symmetric Toeplitz matrix of diffusion coefficients and with nonhomogeneous boundary conditions. We establish the existence of global solutions, and use Lyapunov functional methods. The nonlinear reaction term is assumed to be of polynomial growth.
Diffusion theory in biology: a relic of mechanistic materialism.
Agutter, P S; Malone, P C; Wheatley, D N
2000-01-01
Diffusion theory explains in physical terms how materials move through a medium, e.g. water or a biological fluid. There are strong and widely acknowledged grounds for doubting the applicability of this theory in biology, although it continues to be accepted almost uncritically and taught as a basis of both biology and medicine. Our principal aim is to explore how this situation arose and has been allowed to continue seemingly unchallenged for more than 150 years. The main shortcomings of diffusion theory will be briefly reviewed to show that the entrenchment of this theory in the corpus of biological knowledge needs to be explained, especially as there are equally valid historical grounds for presuming that bulk fluid movement powered by the energy of cell metabolism plays a prominent note in the transport of molecules in the living body. First, the theory's evolution, notably from its origins in connection with the mechanistic materialist philosophy of mid nineteenth century physiology, is discussed. Following this, the entrenchment of the theory in twentieth century biology is analyzed in relation to three situations: the mechanism of oxygen transport between air and mammalian tissues; the structure and function of cell membranes; and the nature of the intermediary metalbolism, with its implicit presumptions about the intracellular organization and the movement of molecules within it. In our final section, we consider several historically based alternatives to diffusion theory, all of which have their precursors in nineteenth and twentieth century philosophy of science.
A discrete model to study reaction-diffusion-mechanics systems.
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.
A discrete model to study reaction-diffusion-mechanics systems.
Louis D Weise
Full Text Available 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.
Cross-diffusional effect in a telegraph reaction diffusion Lotka-Volterra two competitive system
Abdusalam, H.A E-mail: hosny@operamail.com; Fahmy, E.S
2003-10-01
It is known now that, telegraph equation is more suitable than ordinary diffusion equation in modelling reaction diffusion in several branches of sciences. Telegraph reaction diffusion Lotka-Volterra two competitive system is considered. We observed that this system can give rise to diffusive instability only in the presence of cross-diffusion. Local and global stability analysis in the cross-diffusional effect are studied by considering suitable Lyapunov functional.
Revisiting blob theory for DNA diffusivity in slitlike confinement
Dai, Liang; Tree, Douglas R.; van der Maarel, Johan R. C.; Dorfman, Kevin D.; Doyle, Patrick S.
2013-01-01
Blob theory has been widely applied to describe polymer conformations and dynamics in nanoconfinement. In slit confinement, blob theory predicts a scaling exponent of 2/3 for polymer diffusivity as a function of slit height, yet a large body of experimental studies using DNA produce a scaling exponent significantly less than 2/3. In this work, we develop a theory that predicts that this discrepancy occurs because the segment correlation function for a semiflexible chain such as DNA does not follow the Flory exponent for length scales smaller than the persistence length. We show that these short length scale effects contribute significantly to the scaling for the DNA diffusivity, but do not appreciably affect the scalings for static properties. Our theory is fully supported by Monte Carlo simulations, quantitative agreement with DNA experiments, and the results reconcile this outstanding problem for confined polymers. PMID:23679643
反应扩散方程的奇摄动%SINGULAR PERTURBATION FOR REACTION DIFFUSION EQUATIONS
莫嘉琪; 王辉; 朱江
2003-01-01
The singularly perturbed initial boundary value problems for reaction diffusion equations are considered. Under suitable conditions and by using the theory of differential inequality, the asymptotic behavior of solution for initial boundary value problems are studied, where the reduced problems possess two intersecting solutions.
A non-scale-invariant form for coarse-grained diffusion-reaction equations
Ostvar, Sassan; Wood, Brian D.
2016-09-01
The process of mixing and reaction is a challenging problem to understand mathematically. Although there have been successes in describing the effective properties of mixing and reaction under a number of regimes, process descriptions for early times have been challenging for cases where the structure of the initial conditions is highly segregated. In this paper, we use the method of volume averaging to develop a rigorous theory for diffusive mixing with reactions from initial to asymptotic times under highly segregated initial conditions in a bounded domain. One key feature that arises in this development is that the functional form of the averaged differential mass balance equations is not, in general, scale invariant. Upon upscaling, an additional source term arises that helps to account for the initial configuration of the reacting chemical species. In this development, we derive the macroscopic parameters (a macroscale source term and an effectiveness factor modifying the reaction rate) defined in the macroscale diffusion-reaction equation and provide example applications for several initial configurations.
Shalchi, A.
2015-09-01
A fundamental problem in plasma physics, space science, and astrophysics is the transport of energetic particles interacting with stochastic magnetic fields. In particular the motion of particles across a large scale magnetic field is difficult to describe analytically. However, progress has been achieved in the recent years due to the development of the unified non-linear transport theory which can be used to describe magnetic field line diffusion as well as perpendicular diffusion of energetic particles. The latter theory agrees very well with different independently performed test-particle simulations. However, the theory is still based on different approximations and assumptions. In the current article we extend the theory by taking into account the finite gyroradius of the particle motion and calculate corrections in different asymptotic limits. We consider different turbulence models as examples such as the slab model, noisy slab turbulence, and the two-dimensional model. Whereas there are no finite gyroradius corrections for slab turbulence, the perpendicular diffusion coefficient is reduced in the other two cases. The matter investigated in this article is also related to the parameter "a2 " occurring in non-linear diffusion theories.
Judd, S L; Judd, Stephen L.; Silber, Mary
1998-01-01
This paper investigates the competition between both simple (e.g. stripes, hexagons) and ``superlattice'' (super squares, super hexagons) Turing patterns in two-component reaction-diffusion systems. ``Superlattice'' patterns are formed from eight or twelve Fourier modes, and feature structure at two different length scales. Using perturbation theory, we derive simple analytical expressions for the bifurcation equation coefficients on both rhombic and hexagonal lattices. These expressions show that, no matter how complicated the reaction kinectics, the nonlinear reaction terms reduce to just four effective terms within the bifurcation equation coefficients. Moreover, at the hexagonal degeneracy -- when the quadratic term in the hexagonal bifurcation equation disappears -- the number of effective system parameters drops to two, allowing a complete characterization of the possible bifurcation results at this degeneracy. The general results are then applied to specific model equations, to investigate the stabilit...
Extending Molecular Theory to Steady-State Diffusing Systems
FRINK,LAURA J. D.; SALINGER,ANDREW G.; THOMPSON,AIDAN P.
1999-10-22
Predicting the properties of nonequilibrium systems from molecular simulations is a growing area of interest. One important class of problems involves steady state diffusion. To study these cases, a grand canonical molecular dynamics approach has been developed by Heffelfinger and van Swol [J. Chem. Phys., 101, 5274 (1994)]. With this method, the flux of particles, the chemical potential gradients, and density gradients can all be measured in the simulation. In this paper, we present a complementary approach that couples a nonlocal density functional theory (DFT) with a transport equation describing steady-state flux of the particles. We compare transport-DFT predictions to GCMD results for a variety of ideal (color diffusion), and nonideal (uphill diffusion and convective transport) systems. In all cases excellent agreement between transport-DFT and GCMD calculations is obtained with diffusion coefficients that are invariant with respect to density and external fields.
Explicit studies of the quantum theory of light interstitial diffusion
Emin, D.; Baskes, M.I.; Wilson, W.D.
1978-01-01
The formalism associated with small-polaron diffusion in the high temperature semiclassical regime is generalized so as to transcend simplifications employed in developing the nonadiabatic theory. The diffusion constant is then calculated for simple models in which the metal atoms interact with each other and with the interstitial atom with two-body forces. Studies of these models not only confirm the necessity of generalizing the formalism but also yield diffusion constants whose magnitudes and temperature dependenes ar consistent with the general features of the existing data for the diffusion of hydrogen and its isotopes in bcc metals. The motion of a positive muon between interstitial positions of a metal is also investigated. (GHT)
Shalchi, Andreas
2015-01-01
A fundamental problem in plasma physics, space science, and astrophysics is the transport of energetic particles interacting with stochastic magnetic fields. In particular the motion of particles across a large scale magnetic field is difficult to describe analytically. However, progress has been achieved in the recent years due to the development of the unified non-linear transport theory which can be used to describe magnetic field line diffusion as well as perpendicular diffusion of energetic particles. The latter theory agrees very well with different independently performed test-particle simulations. However, the theory is still based on different approximations and assumptions. In the current article we extend the theory by taking into account the finite gyroradius of the particle motion and calculate corrections in different asymptotic limits. We consider different turbulence models as examples such as the slab model, noisy slab turbulence, and the two-dimensional model. Whereas there are no finite gyr...
Asymptotic solution for a class of weakly nonlinear singularly perturbed reaction diffusion problem
TANG Rong-rong
2009-01-01
Under appropriate conditions, with the perturbation method and the theory of differential inequalities, a class of weakly nonlinear singularly perturbed reaction diffusion problem is considered. The existence of solution of the original problem is proved by constructing the auxiliary functions. The uniformly valid asymptotic expansions of the solution for arbitrary mth order approximation are obtained through constructing the formal solutions of the original problem, expanding the nonlinear terms to the power in small parameter e and comparing the coefficient for the same powers of ε. Finally, an example is provided, resulting in the error of O(ε2).
Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics
Franz, Benjamin
2013-06-19
Two algorithms that combine Brownian dynami cs (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface, which partitions the domain, and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that the overlap region is required to accurately compute variances using PBD simulations. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented. © 2013 Society for Industrial and Applied Mathematics.
Multiscale reaction-diffusion algorithms: PDE-assisted Brownian dynamics
Franz, Benjamin; Chapman, S Jonathan; Erban, Radek
2012-01-01
Two algorithms that combine Brownian dynamics (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface which partitions the domain and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that to accurately compute variances using the PBD simulation requires the overlap region. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented.
Guiding brine shrimp through mazes by solving reaction diffusion equations
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.
SDDEs limits solutions to sublinear reaction-diffusion SPDEs
Hassan Allouba
2003-11-01
Full Text Available We start by introducing a new definition of solutions to heat-based SPDEs driven by space-time white noise: SDDEs (stochastic differential-difference equations limits solutions. In contrast to the standard direct definition of SPDEs solutions; this new notion, which builds on and refines our SDDEs approach to SPDEs from earlier work, is entirely based on the approximating SDDEs. It is applicable to, and gives a multiscale view of, a variety of SPDEs. We extend this approach in related work to other heat-based SPDEs (Burgers, Allen-Cahn, and others and to the difficult case of SPDEs with multi-dimensional spacial variable. We focus here on one-spacial-dimensional reaction-diffusion SPDEs; and we prove the existence of a SDDEs limit solution to these equations under less-than-Lipschitz conditions on the drift and the diffusion coefficients, thus extending our earlier SDDEs work to the nonzero drift case. The regularity of this solution is obtained as a by-product of the existence estimates. The uniqueness in law of our SPDEs follows, for a large class of such drifts/diffusions, as a simple extension of our recent Allen-Cahn uniqueness result. We also examine briefly, through order parameters $epsilon_1$ and $epsilon_2$ multiplied by the Laplacian and the noise, the effect of letting $epsilon_1,epsilon_2o 0$ at different speeds. More precisely, it is shown that the ratio $epsilon_2/epsilon_1^{1/4}$ determines the behavior as $epsilon_1,epsilon_2o 0$.
Characterization of Cocycle Attractors for Nonautonomous Reaction-Diffusion Equations
Cardoso, C. A.; Langa, J. A.; Obaya, R.
In this paper, we describe in detail the global and cocycle attractors related to nonautonomous scalar differential equations with diffusion. In particular, we investigate reaction-diffusion equations with almost-periodic coefficients. The associated semiflows are strongly monotone which allow us to give a full characterization of the cocycle attractor. We prove that, when the upper Lyapunov exponent associated to the linear part of the equations is positive, the flow is persistent in the positive cone, and we study the stability and the set of continuity points of the section of each minimal set in the global attractor for the skew product semiflow. We illustrate our result with some nontrivial examples showing the richness of the dynamics on this attractor, which in some situations shows internal chaotic dynamics in the Li-Yorke sense. We also include the sublinear and concave cases in order to go further in the characterization of the attractors, including, for instance, a nonautonomous version of the Chafee-Infante equation. In this last case we can show exponentially forward attraction to the cocycle (pullback) attractors in the positive cone of solutions.
Yan, David; Bazant, Martin Z.; Biesheuvel, P. M.; Pugh, Mary C.; Dawson, Francis P.
2017-03-01
Linear sweep and cyclic voltammetry techniques are important tools for electrochemists and have a variety of applications in engineering. Voltammetry has classically been treated with the Randles-Sevcik equation, which assumes an electroneutral supported electrolyte. In this paper, we provide a comprehensive mathematical theory of voltammetry in electrochemical cells with unsupported electrolytes and for other situations where diffuse charge effects play a role, and present analytical and simulated solutions of the time-dependent Poisson-Nernst-Planck equations with generalized Frumkin-Butler-Volmer boundary conditions for a 1:1 electrolyte and a simple reaction. Using these solutions, we construct theoretical and simulated current-voltage curves for liquid and solid thin films, membranes with fixed background charge, and cells with blocking electrodes. The full range of dimensionless parameters is considered, including the dimensionless Debye screening length (scaled to the electrode separation), Damkohler number (ratio of characteristic diffusion and reaction times), and dimensionless sweep rate (scaled to the thermal voltage per diffusion time). The analysis focuses on the coupling of Faradaic reactions and diffuse charge dynamics, although capacitive charging of the electrical double layers is also studied, for early time transients at reactive electrodes and for nonreactive blocking electrodes. Our work highlights cases where diffuse charge effects are important in the context of voltammetry, and illustrates which regimes can be approximated using simple analytical expressions and which require more careful consideration.
Interior Controllability of a 2×2 Reaction-Diffusion System with Cross-Diffusion Matrix
Hugo Leiva
2009-01-01
Full Text Available We prove the interior approximate controllability for the following 2×2 reaction-diffusion system with cross-diffusion matrix ut=aΔu−β(−Δ1/2u+bΔv+1ωf1(t,x in (0,τ×Ω, vt=cΔu−dΔv−β(−Δ1/2v+1ωf2(t,x in (0,τ×Ω, u=v=0, on (0,T×∂Ω, u(0,x=u0(x, v(0,x=v0(x, x∈Ω, where Ω is a bounded domain in ℝN (N≥1, u0,v0∈L2(Ω, the 2×2 diffusion matrix D=[abcd] has semisimple and positive eigenvalues 0<ρ1≤ρ2, β is an arbitrary constant, ω is an open nonempty subset of Ω, 1ω denotes the characteristic function of the set ω, and the distributed controls f1,f2∈L2([0,τ];L2(Ω. Specifically, we prove the following statement: if λ11/2ρ1+β>0 (where λ1 is the first eigenvalue of −Δ, then for all τ>0 and all open nonempty subset ω of Ω the system is approximately controllable on [0,τ].
Effective Potential Theory for Diffusion in Binary Ionic Mixtures
Shaffer, Nathaniel R; Daligault, Jérôme
2016-01-01
Self-diffusion and interdiffusion coefficients of binary ionic mixtures are evaluated using the Effective Potential Theory (EPT), and the predictions are compared with the results of molecular dynamics simulations. We find that EPT agrees with molecular dynamics from weak coupling well into the strong coupling regime, which is a similar range of coupling strengths as previously observed in comparisons with the one-component plasma. Within this range, typical relative errors of approximately 20% and worst-case relative errors of approximately 40% are observed. We also examine the Darken model, which approximates the interdiffusion coefficients based on the self-diffusion coefficients.
Theory for Spin Diffusion in Disordered Organic Semiconductors
Bobbert, P. A.; Wagemans, W.; van Oost, F. W. A.; Koopmans, B.; Wohlgenannt, M.
2009-04-01
We present a theory for spin diffusion in disordered organic semiconductors, based on incoherent hopping of a charge carrier and coherent precession of its spin in an effective magnetic field, composed of the random hyperfine field of hydrogen nuclei and an applied magnetic field. From Monte Carlo simulations and an analysis of the waiting-time distribution of the carrier we predict a surprisingly weak temperature dependence, but a considerable magnetic-field dependence of the spin-diffusion length. We show that both predictions are in agreement with experiments on organic spin valves.
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.
Application of the evolution theory in modelling of innovation diffusion
Krstić Milan
2016-01-01
Full Text Available The theory of evolution has found numerous analogies and applications in other scientific disciplines apart from biology. In that sense, today the so-called 'memetic-evolution' has been widely accepted. Memes represent a complex adaptable system, where one 'meme' represents an evolutional cultural element, i.e. the smallest unit of information which can be identified and used in order to explain the evolution process. Among others, the field of innovations has proved itself to be a suitable area where the theory of evolution can also be successfully applied. In this work the authors have started from the assumption that it is also possible to apply the theory of evolution in the modelling of the process of innovation diffusion. Based on the conducted theoretical research, the authors conclude that the process of innovation diffusion in the interpretation of a 'meme' is actually the process of imitation of the 'meme' of innovation. Since during the process of their replication certain 'memes' show a bigger success compared to others, that eventually leads to their natural selection. For the survival of innovation 'memes', their manifestations are of key importance in the sense of their longevity, fruitfulness and faithful replicating. The results of the conducted research have categorically confirmed the assumption of the possibility of application of the evolution theory with the innovation diffusion with the help of innovation 'memes', which opens up the perspectives for some new researches on the subject.
Accelerated stochastic and hybrid methods for spatial simulations of reaction-diffusion systems
Rossinelli, D; Bayati, B; Koumoutsakos, P.
2008-01-01
Spatial distributions characterize the evolution of reaction-diffusion models of several physical, chemical, and biological systems. We present two novel algorithms for the efficient simulation of these models: Spatial т-Leaping (Sт -Leaping), employing a unified acceleration of the stochastic simulation of reaction and diffusion, and Hybrid т-Leaping (Hт-Leaping), combining a deterministic diffusion approximation with a т-Leaping acceleration of the stochastic reactions. The algorithms are v...
Ohmori, Shousuke; Yamazaki, Yoshihiro
2016-01-01
Ultradiscrete equations are derived from a set of reaction-diffusion partial differential equations, and cellular automaton rules are obtained on the basis of the ultradiscrete equations. Some rules reproduce the dynamical properties of the original reaction-diffusion equations, namely, bistability and pulse annihilation. Furthermore, other rules bring about soliton-like preservation and periodic pulse generation with a pacemaker, which are not obtained from the original reaction-diffusion equations.
A practical guide to stochastic simulations of reaction-diffusion processes
Erban, Radek; Chapman, Jonathan; Maini, Philip
2007-01-01
A practical introduction to stochastic modelling of reaction-diffusion processes is presented. No prior knowledge of stochastic simulations is assumed. The methods are explained using illustrative examples. The article starts with the classical Gillespie algorithm for the stochastic modelling of chemical reactions. Then stochastic algorithms for modelling molecular diffusion are given. Finally, basic stochastic reaction-diffusion methods are presented. The connections between stochastic simul...
A reaction diffusion model of pattern formation in clustering of adatoms on silicon surfaces
Trilochan Bagarti
2012-12-01
Full Text Available We study a reaction diffusion model which describes the formation of patterns on surfaces having defects. Through this model, the primary goal is to study the growth process of Ge on Si surface. We consider a two species reaction diffusion process where the reacting species are assumed to diffuse on the two dimensional surface with first order interconversion reaction occuring at various defect sites which we call reaction centers. Two models of defects, namely a ring defect and a point defect are considered separately. As reaction centers are assumed to be strongly localized in space, the proposed reaction-diffusion model is found to be exactly solvable. We use Green's function method to study the dynamics of reaction diffusion processes. Further we explore this model through Monte Carlo (MC simulations to study the growth processes in the presence of a large number of defects. The first passage time statistics has been studied numerically.
Sigaut, Lorena; Villarruel, Cecilia; Ponce, María Laura; Ponce Dawson, Silvina
2017-06-01
Many cell signaling pathways involve the diffusion of messengers that bind and unbind to and from intracellular components. Quantifying their net transport rate under different conditions then requires having separate estimates of their free diffusion coefficient and binding or unbinding rates. In this paper, we show how performing sets of fluorescence correlation spectroscopy (FCS) experiments under different conditions, it is possible to quantify free diffusion coefficients and on and off rates of reaction-diffusion systems. We develop the theory and present a practical implementation for the case of the universal second messenger, calcium (Ca2 +) and single-wavelength dyes that increase their fluorescence upon Ca2 + binding. We validate the approach with experiments performed in aqueous solutions containing Ca2 + and Fluo4 dextran (both in its high and low affinity versions). Performing FCS experiments with tetramethylrhodamine-dextran in Xenopus laevis oocytes, we infer the corresponding free diffusion coefficients in the cytosol of these cells. Our approach can be extended to other physiologically relevant reaction-diffusion systems to quantify biophysical parameters that determine the dynamics of various variables of interest.
Rate Theory for Correlated Processes: Double Jumps in Adatom Diffusion
Jacobsen, J.; Jacobsen, Karsten Wedel; Sethna, J.
1997-01-01
We study the rate of activated motion over multiple barriers, in particular the correlated double jump of an adatom diffusing on a missing-row reconstructed platinum (110) surface. We develop a transition path theory, showing that the activation energy is given by the minimum-energy trajectory...... which succeeds in the double jump. We explicitly calculate this trajectory within an effective-medium molecular dynamics simulation. A cusp in the acceptance region leads to a root T prefactor for the activated rate of double jumps. Theory and numerical results agree....
Global existence and asymptotic stability of equilibria to reaction-diffusion systems
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).
Minimal wave speed for a class of non-cooperative diffusion-reaction system
Zhang, Tianran; Wang, Wendi; Wang, Kaifa
2016-02-01
In this paper, we consider a class of non-cooperative diffusion-reaction systems, which include prey-predator models and disease-transmission models. The concept of weak traveling wave solutions is proposed. The necessary and sufficient conditions for the existence of such solutions are obtained by the Schauder's fixed-point theorem and persistence theory. The introduction of persistence theory is very technical and crucial. The LaSalle's invariance principle is applied to show that traveling wave solutions connect two equilibria. The nonexistence of traveling wave solutions is proved by introducing a negative one-sided Laplace transform. The results are applied to a prey-predator model and a disease-transmission model with specific interaction functions. We find that the profile of traveling wave solutions may depend on different eigenvalues according to the corresponding condition, which is a new phenomenon.
The First Integral Method to Study a Class of Reaction-Diffusion Equations
KE Yun-Quan; YU Jun
2005-01-01
In this letter, a class of reaction-diffusion equations, which arise in chemical reaction or ecology and other fields of physics, are investigated. A more general analytical solution of the equation is obtained by using the first integral method.
Bifurcation Analysis of Reaction Diffusion Systems on Arbitrary Surfaces.
Dhillon, Daljit Singh J; Milinkovitch, Michel C; Zwicker, Matthias
2017-04-01
In this paper, we present computational techniques to investigate the effect of surface geometry on biological pattern formation. In particular, we study two-component, nonlinear reaction-diffusion (RD) systems on arbitrary surfaces. We build on standard techniques for linear and nonlinear analysis of RD systems and extend them to operate on large-scale meshes for arbitrary surfaces. In particular, we use spectral techniques for a linear stability analysis to characterise and directly compose patterns emerging from homogeneities. We develop an implementation using surface finite element methods and a numerical eigenanalysis of the Laplace-Beltrami operator on surface meshes. In addition, we describe a technique to explore solutions of the nonlinear RD equations using numerical continuation. Here, we present a multiresolution approach that allows us to trace solution branches of the nonlinear equations efficiently even for large-scale meshes. Finally, we demonstrate the working of our framework for two RD systems with applications in biological pattern formation: a Brusselator model that has been used to model pattern development on growing plant tips, and a chemotactic model for the formation of skin pigmentation patterns. While these models have been used previously on simple geometries, our framework allows us to study the impact of arbitrary geometries on emerging patterns.
Stochastic flows, reaction-diffusion processes, and morphogenesis
Kozak, J.J.; Hatlee, M.D.; Musho, M.K.; Politowicz, P.A.; Walsh, C.A.
1983-02-01
Recently, an exact procedure has been introduced (C. A. Walsh and J. J. Kozak, Phys. Rev. Lett.. 47: 1500 (1981)) for calculating the expected walk length
Reaction Diffusion Voronoi Diagrams: From Sensors Data to Computing
Alejandro Vázquez-Otero
2015-05-01
Full Text Available 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.
Using Perturbation theory to reduce noise in diffusion tensor fields.
Bansal, Ravi; Staib, Lawrence H; Xu, Dongrong; Laine, Andrew F; Liu, Jun; Peterson, Bradley S
2009-08-01
We propose the use of Perturbation theory to reduce noise in Diffusion Tensor (DT) fields. Diffusion Tensor Imaging (DTI) encodes the diffusion of water molecules along different spatial directions in a positive definite, 3 x 3 symmetric tensor. Eigenvectors and eigenvalues of DTs allow the in vivo visualization and quantitative analysis of white matter fiber bundles across the brain. The validity and reliability of these analyses are limited, however, by the low spatial resolution and low Signal-to-Noise Ratio (SNR) in DTI datasets. Our procedures can be applied to improve the validity and reliability of these quantitative analyses by reducing noise in the tensor fields. We model a tensor field as a three-dimensional Markov Random Field and then compute the likelihood and the prior terms of this model using Perturbation theory. The prior term constrains the tensor field to be smooth, whereas the likelihood term constrains the smoothed tensor field to be similar to the original field. Thus, the proposed method generates a smoothed field that is close in structure to the original tensor field. We evaluate the performance of our method both visually and quantitatively using synthetic and real-world datasets. We quantitatively assess the performance of our method by computing the SNR for eigenvalues and the coherence measures for eigenvectors of DTs across tensor fields. In addition, we quantitatively compare the performance of our procedures with the performance of one method that uses a Riemannian distance to compute the similarity between two tensors, and with another method that reduces noise in tensor fields by anisotropically filtering the diffusion weighted images that are used to estimate diffusion tensors. These experiments demonstrate that our method significantly increases the coherence of the eigenvectors and the SNR of the eigenvalues, while simultaneously preserving the fine structure and boundaries between homogeneous regions, in the smoothed tensor
High energy reactions and string theory
Peschanski, R
2002-01-01
String theory has long ago been initiated by the quest for a theoretical explanation of the observed high-energy ``Reggeization'' of strong interaction amplitudes. In terms of quantum field theory, it is the so-called ``soft'' regime, where the coupling constant is expected to be large and thus perturbative calculations inadequate. However, since then, no convincing derivation of the link between gauge field theory at strong coupling and string theory has come out. This 35-years-old puzzle is thus still unsolved. We discuss how modern tools like the AdS/CFT correspondence give a new insight on the problem by applying it to two-body elastic and inelastic scattering amplitudes. We obtain a geometrical interpretation of Reggeization and its relation with confinement in gauge theory.
Estimation and prediction of convection-diffusion-reaction systems from point measurement
Vries, D.
2008-01-01
Different procedures with respect to estimation and prediction of systems characterized by convection, diffusion and reactions on the basis of point measurement data, have been studied. Two applications of these convection-diffusion-reaction (CDR) systems have been used as a case study of the propos
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.
Quantum Theory of Fast Chemical Reactions
Light, John C
2007-07-30
The aims of the research under this grant were to develop a theoretical understanding and predictive abiility for a variety of processes occurring in the gas phase. These included bimolecular chemical exchange reactions, photodissociation, predissociation resonances, unimolecular reactions and recombination reactions. In general we assumed a knowledge, from quantum chemistry, of the interactions of the atoms and molecular fragments involved. Our focus was primarily on the accurate (quantum) dynamics of small molecular systems. This has been important for many reactions related to combustion and atmospheric chemistry involving light atom transfer reactions and, for example, resonances in dissociation and recombination reactions. The rates of such reactions, as functions of temperature, internal states, and radiation (light), are fundamental for generating models of overall combustion processes. A number of new approaches to these problems were developed inclluding the use of discrete variable representations (DVR's) for evaluating rate constants with the flux-flux correlation approach, finite range approaches to exact quantum scattering calculations, energy selected basis representations, transition state wave packet approaches and improved semiclassical approaches. These (and others) were applied to a number of reactive systems and molecular systems of interest including (many years ago) the isotopic H + H2 exchange reactions, the H2 + OH (and H + H2O) systems, Ozone resonances, van der Waals molecule reactions, etc. A total of 7 graduate students, and 5 post-doctoral Research Associates were supported, at least in part, under this grant and seven papers were published with a total of 10 external collaborators. The majority of the 36 publications under this grant were supported entirely by DOE.
Efficient Diffuse Basis Sets for Density Functional Theory.
Papajak, Ewa; Truhlar, Donald G
2010-03-09
Eliminating all but the s and p diffuse functions on the non-hydrogenic atoms and all diffuse functions on the hydrogen atoms from the aug-cc-pV(x+d)Z basis sets of Dunning and co-workers, where x = D, T, Q, ..., yields the previously proposed "minimally augmented" basis sets, called maug-cc-pV(x+d)Z. Here, we present extensive and systematic tests of these basis sets for density functional calculations of chemical reaction barrier heights, hydrogen bond energies, electron affinities, ionization potentials, and atomization energies. The tests show that the maug-cc-pV(x+d)Z basis sets are as accurate as the aug-cc-pV(x+d)Z ones for density functional calculations, but the computational cost savings are a factor of about two to seven.
A molecular theory of large-solute diffusion
A.Yoshimori
2007-12-01
Full Text Available The limit of a large solute in the molecular theory of diffusion developed by Yamaguchi et al. [Yamaguchi T. et al., J. Chem. Phys., 2005, 123, 034504] is studied. By the limit, the Stokes approximation to the hydrodynamic equations is derived in the outside region of a diffusing solute. The limit of a large solute also leads to equations in the inside region of the solute. The analytical solution of the inside equation allows one to derive the boundary condition, which is needed on the surface of the solute when the hydrodynamic equations are calculated. The boundary condition includes stick and slip boundary conditions employed by the Stokes law, in the special case. Besides stick and slip conditions, other conditions can be expressed. The boundary condition depends on properties of a solvent.
无
2012-01-01
In this paper,we consider the reaction diffusion equations with strong generic delay kernel and non-local effect,which models the microbial growth in a flow reactor.The existence of traveling waves is established for this model.More precisely,using the geometric singular perturbation theory,we show that traveling wave solutions exist provided that the delay is sufficiently small with the strong generic delay kernel.
Initial Crisis Reaction and Poliheuristic Theory
DeRouen, Karl, Jr.; Sprecher, Christopher
2004-01-01
Poliheuristic (PH) theory models foreign policy decisions using a two-stage process. The first step eliminates alternatives on the basis of a simplifying heuristic. The second step involves a selection from among the remaining alternatives and can employ a more rational and compensatory means of processing information. The PH model posits that…
Barrier heights of hydrogen-transfer reactions with diffusion quantum monte carlo method.
Zhou, Xiaojun; Wang, Fan
2017-04-30
Hydrogen-transfer reactions are an important class of reactions in many chemical and biological processes. Barrier heights of H-transfer reactions are underestimated significantly by popular exchange-correlation functional with density functional theory (DFT), while coupled-cluster (CC) method is quite expensive and can be applied only to rather small systems. Quantum Monte-Carlo method can usually provide reliable results for large systems. Performance of fixed-node diffusion quantum Monte-Carlo method (FN-DMC) on barrier heights of the 19 H-transfer reactions in the HTBH38/08 database is investigated in this study with the trial wavefunctions of the single-Slater-Jastrow form and orbitals from DFT using local density approximation. Our results show that barrier heights of these reactions can be calculated rather accurately using FN-DMC and the mean absolute error is 1.0 kcal/mol in all-electron calculations. Introduction of pseudopotentials (PP) in FN-DMC calculations improves efficiency pronouncedly. According to our results, error of the employed PPs is smaller than that of the present CCSD(T) and FN-DMC calculations. FN-DMC using PPs can thus be applied to investigate H-transfer reactions involving larger molecules reliably. In addition, bond dissociation energies of the involved molecules using FN-DMC are in excellent agreement with reference values and they are even better than results of the employed CCSD(T) calculations using the aug-cc-pVQZ basis set. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Vorticity field, helicity integral and persistence of entanglement in reaction-diffusion systems
Trueba, J L; Arrayas, M [Area de Electromagnetismo, Universidad Rey Juan Carlos, Camino del Molino s/n, 28943 Fuenlabrada, Madrid (Spain)
2009-07-17
We show that a global description of the stability of entangled structures in reaction-diffusion systems can be made by means of a helicity integral. A vorticity vector field is defined for these systems, as in electromagnetism or fluid dynamics. We have found under which conditions the helicity is conserved or lost through the boundaries of the medium, so the entanglement of structures observed is preserved or disappears during time evolution. We illustrate the theory with an example of knotted entanglement in a FitzHugh-Nagumo model. For this model, we introduce new non-trivial initial conditions using the Hopf fibration and follow the time evolution of the entanglement. (fast track communication)
Scenarios of domain pattern formation in a reaction-diffusion system
Muratov, C B
1996-01-01
We performed an extensive numerical study of a two-dimensional reaction-diffusion system of the activator-inhibitor type in which domain patterns can form. We showed that both multidomain and labyrinthine patterns may form spontaneously as a result of Turing instability. In the stable homogeneous system with the fast inhibitor one can excite both localized and extended patterns by applying a localized stimulus. Depending on the parameters and the excitation level of the system stripes, spots, wriggled stripes, or labyrinthine patterns form. The labyrinthine patterns may be both connected and disconnected. In the the stable homogeneous system with the slow inhibitor one can excite self-replicating spots, breathing patterns, autowaves and turbulence. The parameter regions in which different types of patterns are realized are explained on the basis of the asymptotic theory of instabilities for patterns with sharp interfaces developed by us in Phys. Rev. E. 53, 3101 (1996). The dynamics of the patterns observed i...
Lattice Boltzmann Method for Diffusion-Reaction-Transport Processes in Heterogeneous Porous Media
XU You-Sheng; ZHONG Yi-Jun; HUANG Guo-Xiang
2004-01-01
Based on the lattice Boltzmann method and general theory of fluids flowing in porous media, a numerical model is presented for the diffusion-reaction-transport (DRT) processes in porous media. As a test, we simulate a DRT process in a two-dimensional horizontal heterogeneous porous medium. The influence of gravitation in this case can be neglected, and the DRT process can be described by a strongly heterogeneous diagnostic test strip or a thin confined piece of soil with stochastically distributing property in horizontal directions. The results obtained for the relations between reduced fluid saturation S, concentration c1, and concentration c2 are shown by using the visualization computing technique. The computational efficiency and stability of the model are satisfactory.
Theory of nanoparticle diffusion in unentangled and entangled polymer melts.
Yamamoto, Umi; Schweizer, Kenneth S
2011-12-14
We propose a statistical dynamical theory for the violation of the hydrodynamic Stokes-Einstein (SE) diffusion law for a spherical nanoparticle in entangled and unentangled polymer melts based on a combination of mode coupling, Brownian motion, and polymer physics ideas. The non-hydrodynamic friction coefficient is related to microscopic equilibrium structure and the length-scale-dependent polymer melt collective density fluctuation relaxation time. When local packing correlations are neglected, analytic scaling laws (with numerical prefactors) in various regimes are derived for the non-hydrodynamic diffusivity as a function of particle size, polymer radius-of-gyration, tube diameter, degree of entanglement, melt density, and temperature. Entanglement effects are the origin of large SE violations (orders of magnitude mobility enhancement) which smoothly increase as the ratio of particle radius to tube diameter decreases. Various crossover conditions for the recovery of the SE law are derived, which are qualitatively distinct for unentangled and entangled melts. The dynamical influence of packing correlations due to both repulsive and interfacial attractive forces is investigated. A central finding is that melt packing fraction, temperature, and interfacial attraction strength all influence the SE violation in qualitatively different directions depending on whether the polymers are entangled or not. Entangled systems exhibit seemingly anomalous trends as a function of these variables as a consequence of the non-diffusive nature of collective density fluctuation relaxation and the different response of polymer-particle structural correlations to adsorption on the mesoscopic entanglement length scale. The theory is in surprisingly good agreement with recent melt experiments, and new parametric studies are suggested. © 2011 American Institute of Physics
Progress in all-order breakup reaction theories
R Chatterjee
2010-07-01
Progress in breakup reaction theories, like the distorted wave Born approximation, the continuum discretized coupled channels method and the dynamical eikonal approximation, is brought into focus. The need to calculate exclusive reaction observables and the utility of benchmark tests as arbitrators of theoretical models are discussed.
1D to 3D diffusion-reaction kinetics of defects in crystals
Trinkaus, H.; Heinisch, H.L.; Barashev, A.V.
2002-01-01
Microstructural features evolving in crystalline solids from diffusion-reaction kinetics of mobile components depend crucially on the dimension of the underlying diffusion process which is commonly assumed to be three-dimensional (3D). In metals, irradiation-induced displacement cascades produce ...... and 3D limiting cases. The analytical result is fully confirmed by kinetic Monte Carlo simulations.......Microstructural features evolving in crystalline solids from diffusion-reaction kinetics of mobile components depend crucially on the dimension of the underlying diffusion process which is commonly assumed to be three-dimensional (3D). In metals, irradiation-induced displacement cascades produce...
Effect of macromolecular crowding on the rate of diffusion-limited enzymatic reaction
Manish Agrawal; S B Santra; Rajat Anand; Rajaram Swaminathan
2008-08-01
The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with increase in macromolecular crowding. Moreover, many cellular processes are dependent on molecular diffusion in the cell cytosol. The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecular crowding on the enzymatic reaction rates. The model qualitatively explains some of the experimental observations.
Apparent Rate Constant for Diffusion-Controlled Three molecular (catalytic) reaction
Burlatsky, S. F.; Moreau, M
1996-01-01
We present simple explicit estimates for the apparent reaction rate constant for three molecular reactions, which are important in catalysis. For small concentrations and $d> 1$, the apparent reaction rate constant depends only on the diffusion coefficients and sizes of the particles. For small concentrations and $d\\le 1$, it is also time -- dependent. For large concentrations, it gains the dependence on concentrations.
Reaction-Diffusion Systems: Front Propagation and Spatial Structures
Cencini, Massimo; Lopez, Cristobal; Vergni, Davide
After the pioneering works of Kolmogorov, Petrovskii and Piskunov [1] and Fisher [2] in 1937 on the nonlinear diffusion equation and its traveling wave solutions, scientists from many different disciplines have been captivated by questions about structure, formation and dynamics of patterns in reactive media. Combustion, spreading of epidemics, diffusive transport of chemicals in cells and population dynamics are just a few examples bearing witness of the influence of those works in different areas of modern science.
Theory of exciton transfer and diffusion in conjugated polymers
Barford, William, E-mail: william.barford@chem.ox.ac.uk [Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ (United Kingdom); Tozer, Oliver Robert [Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ (United Kingdom); University College, University of Oxford, Oxford OX1 4BH (United Kingdom)
2014-10-28
We describe a theory of Förster-type exciton transfer between conjugated polymers. The theory is built on three assumptions. First, we assume that the low-lying excited states of conjugated polymers are Frenkel excitons coupled to local normal modes, and described by the Frenkel-Holstein model. Second, we assume that the relevant parameter regime is ℏω < J, i.e., the adiabatic regime, and thus the Born-Oppenheimer factorization of the electronic and nuclear degrees of freedom is generally applicable. Finally, we assume that the Condon approximation is valid, i.e., the exciton-polaron wavefunction is essentially independent of the normal modes. The resulting expression for the exciton transfer rate has a familiar form, being a function of the exciton transfer integral and the effective Franck-Condon factors. The effective Franck-Condon factors are functions of the effective Huang-Rhys parameters, which are inversely proportional to the chromophore size. The Born-Oppenheimer expressions were checked against DMRG calculations, and are found to be within 10% of the exact value for a tiny fraction of the computational cost. This theory of exciton transfer is then applied to model exciton migration in conformationally disordered poly(p-phenylene vinylene). Key to this modeling is the assumption that the donor and acceptor chromophores are defined by local exciton ground states (LEGSs). Since LEGSs are readily determined by the exciton center-of-mass wavefunction, this theory provides a quantitative link between polymer conformation and exciton migration. Our Monte Carlo simulations indicate that the exciton diffusion length depends weakly on the conformation of the polymer, with the diffusion length increasing slightly as the chromophores became straighter and longer. This is largely a geometrical effect: longer and straighter chromophores extend over larger distances. The calculated diffusion lengths of ∼10 nm are in good agreement with experiment. The spectral
Johannesson, Björn
2009-01-01
Results from a systematic continuum mixture theory will be used to establish the governing equations for ionic diffusion and chemical reactions in the pore solution of a porous material subjected to moisture transport. The theory in use is the hybrid mixture theory (HMT), which in its general form...... general description of chemical reactions among constituents is described. The Petrov – Galerkin approach are used in favour of the standard Galerkin weighting in order to improve the solution when the convective part of the problem is dominant. A modified type of Newton – Raphson scheme is derived...... for the non-linear global matrix formulation. The developed model and its numerical solution procedure are checked by running test examples which results demonstrates robustness of the proposed approach....
Simulation of reaction-diffusion processes in three dimensions using CUDA
Molnar, Ferenc; Meszaros, Robert; Lagzi, Istvan
2010-01-01
Numerical solution of reaction-diffusion equations in three dimensions is one of the most challenging applied mathematical problems. Since these simulations are very time consuming, any ideas and strategies aiming at the reduction of CPU time are important topics of research. A general and robust idea is the parallelization of source codes/programs. Recently, the technological development of graphics hardware created a possibility to use desktop video cards to solve numerically intensive problems. We present a powerful parallel computing framework to solve reaction-diffusion equations numerically using the Graphics Processing Units (GPUs) with CUDA. Four different reaction-diffusion problems, (i) diffusion of chemically inert compound, (ii) Turing pattern formation, (iii) phase separation in the wake of a moving diffusion front and (iv) air pollution dispersion were solved, and additionally both the Shared method and the Moving Tiles method were tested. Our results show that parallel implementation achieves t...
Reaction diffusion in Ni–Al diffusion couples in steady magnetic fields
Li, Chuanjun, E-mail: cjli21@shu.edu.cn [School of Materials Science and Engineering, Shanghai University, Shanghai 200072 (China); Yuan, Zhaojing; Guo, Rui; Xuan, Weidong; Ren, Zhongming; Zhong, Yunbo; Li, Xi [School of Materials Science and Engineering, Shanghai University, Shanghai 200072 (China); Wang, Hui; Wang, Qiuliang [Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190 (China)
2015-08-25
Highlights: • The Ni–Al diffusion couples were prepared by the electrodeposition technique. • The magnetic field reduced the growth rates of product layers in diffusion couples. • The effect of the magnetic field on diffusion depends on its intensity and direction. • The spiral motion of an atom in the magnetic field reduces diffusivity. - Abstract: The effect of a steady magnetic field on reactive diffusion in Ni–Al diffusion couples was investigated. The diffusion couples prepared by the electrodeposition technique were annealed in the temperature range of 530–590 °C with and without the magnetic field of 6 T. Regardless of the magnetic field, two intermetallic compounds, i.e., Ni{sub 2}Al{sub 3} and NiAl{sub 3}, were present in the product layers of diffusion couples. NiAl{sub 3} phase shows island-like structures at relatively lower temperatures while the Ni{sub 2}Al{sub 3} phase forms a typical layered structure. The growth of Ni{sub 2}Al{sub 3} layer was found to be parabolic. When the diffusion direction was perpendicular to the direction of the magnetic field, the external magnetic field reduced the growth rate of the Ni{sub 2}Al{sub 3} phase. Whereas the magnetic field had no obvious effect on the growth rate of Ni{sub 2}Al{sub 3} layers in the diffusion configuration of mutually parallel directions. The magnetic field intensity and direction dependence of growth rate of Ni{sub 2}Al{sub 3} intermetallic layers can be attributed to the change in number of collision of an atom with neighbors during diffusion due to spiral motion under the action of the Lorentz force, which leads to change the frequency factor, not activation energy, for layer growth.
A semiclassical non-adiabatic theory for elementary chemical reactions
Aubry, Serge
2014-01-01
Electron Transfer (ET) reactions are modeled by the dynamics of a quantum two-level system (representing the electronic state) coupled to a thermalized bath of classical harmonic oscillators (representing the nuclei degrees of freedom). Unlike for the standard Marcus theory, the complex amplitudes of the electronic state are chosen as reaction coordinates. Then, the dynamical equations at non vanishing temperature become those of an effective Hamiltonian submitted to damping terms and their associated Langevin random forces. The advantage of this new formalism is to extend the original theory by taking into account both ionic and covalent interactions. The standard theory is recovered only when covalent interactions are neglected. Increasing these covalent interactions from zero, the energy barrier predicted by the standard theory first depresses, next vanish (or almost vanish) and for stronger covalent interactions, covalent bond formation takes place of ET. In biochemistry, the standard Marcus theory often ...
A theory of post-Newtonian radiation and reaction
Birnholtz, Ofek; Kol, Barak
2013-01-01
We address issues with extant formulations of dissipative effects in the effective field theory (EFT) which describes the post-Newtonian (PN) inspiral of two gravitating bodies by (re)formulating several parts of the theory. Novel ingredients include gauge invariant spherical fields in the radiation zone; a system zone which preserves time reversal such that its violation arises not from local odd propagation but rather from interaction with the radiation sector in a way which resembles the balayage method; 2-way multipoles to perform zone matching within the EFT action; and a double-field radiation-reaction action which is the non-quantum version of the Closed Time Path formalism and generalizes to any theory with directed propagators including theories which are defined by equations of motion rather than an action. This formulation unifies the treatment of outgoing radiation and its reaction force. We demonstrate the theory in the scalar, electromagnetic and gravitational cases by economizing the following:...
Accelerated stochastic and hybrid methods for spatial simulations of reaction diffusion systems
Rossinelli, Diego; Bayati, Basil; Koumoutsakos, Petros
2008-01-01
Spatial distributions characterize the evolution of reaction-diffusion models of several physical, chemical, and biological systems. We present two novel algorithms for the efficient simulation of these models: Spatial τ-Leaping ( Sτ-Leaping), employing a unified acceleration of the stochastic simulation of reaction and diffusion, and Hybrid τ-Leaping ( Hτ-Leaping), combining a deterministic diffusion approximation with a τ-Leaping acceleration of the stochastic reactions. The algorithms are validated by solving Fisher's equation and used to explore the role of the number of particles in pattern formation. The results indicate that the present algorithms have a nearly constant time complexity with respect to the number of events (reaction and diffusion), unlike the exact stochastic simulation algorithm which scales linearly.
A Lagrangian particle method for reaction-diffusion systems on deforming surfaces.
Bergdorf, Michael; Sbalzarini, Ivo F; Koumoutsakos, Petros
2010-11-01
Reaction-diffusion processes on complex deforming surfaces are fundamental to a number of biological processes ranging from embryonic development to cancer tumor growth and angiogenesis. The simulation of these processes using continuum reaction-diffusion models requires computational methods capable of accurately tracking the geometric deformations and discretizing on them the governing equations. We employ a Lagrangian level-set formulation to capture the deformation of the geometry and use an embedding formulation and an adaptive particle method to discretize both the level-set equations and the corresponding reaction-diffusion. We validate the proposed method and discuss its advantages and drawbacks through simulations of reaction-diffusion equations on complex and deforming geometries.
A CLASS OF REACTION-DIFFUSION EQUATIONS WITH HYSTERESIS DIFFERENTIAL OPERATOR
XuLongfeng
2002-01-01
In this paper, the classical and weak derivatives with respect to spatial variable of a class of hysteresis functional are discussed. Some conclusions about solutions of a class of reaction-diffusion equations with hysteresis differential operator are given.
Jia-qi Mo; Wan-tao Lin
2006-01-01
In this paper the singularly perturbed initial boundary value problems for the nonlocal reaction diffusion system are considered. Using the iteration method and the comparison theorem, the existence and its asymptotic behavior of the solution for the problem are studied.
An optimal adaptive time-stepping scheme for solving reaction-diffusion-chemotaxis systems.
Chiu, Chichia; Yu, Jui-Ling
2007-04-01
Reaction-diffusion-chemotaxis systems have proven to be fairly accurate mathematical models for many pattern formation problems in chemistry and biology. These systems are important for computer simulations of patterns, parameter estimations as well as analysis of the biological systems. To solve reaction-diffusion-chemotaxis systems, efficient and reliable numerical algorithms are essential for pattern generations. In this paper, a general reaction-diffusion-chemotaxis system is considered for specific numerical issues of pattern simulations. We propose a fully explicit discretization combined with a variable optimal time step strategy for solving the reaction-diffusion-chemotaxis system. Theorems about stability and convergence of the algorithm are given to show that the algorithm is highly stable and efficient. Numerical experiment results on a model problem are given for comparison with other numerical methods. Simulations on two real biological experiments will also be shown.
A CLASS OF SINGULARLY PERTURBED INITIAL BOUNDARY PROBLEM FOR REACTION DIFFUSION EQUATION
Xie Feng
2003-01-01
The singularly perturbed initial boundary value problem for a class of reaction diffusion equation isconsidered. Under appropriate conditions, the existence-uniqueness and the asymptotic behavior of the solu-tion are showed by using the fixed-point theorem.
Simulating Some Complex Phenomena in Hydrothermal Ore-Forming Processes by Reaction-Diffusion CNN
Xu Deyi; Yu Chongwen; Bao Zhengyu
2003-01-01
Complexity phenomena like dynamic and static patterns, order from disorder, chaos and catastrophe were simulated by the application of 2-D reaction-diffusion CNN of two state variables and two diffusion coefficients transformed from Zhabotinksii model. They revealed somehow the mechanism of hydrothermal ore-forming processes, and answered several questions about the onset of ore forming.
熊岳山; 韦永康
2001-01-01
The sediment reaction and diffusion equation with generalized initial and boundary condition is studied. By using Laplace transform and Jordan lemma , an analytical solution is got, which is an extension of analytical solution provided by Cheng Kwokming James ( only diffusion was considered in analytical solution of Cheng ). Some problems arisen in the computation of analytical solution formula are also analysed.
Spreading speeds and traveling waves for non-cooperative reaction-diffusion systems
Wang, Haiyan
2010-01-01
Much has been studied on the spreading speed and traveling wave solutions for cooperative reaction-diffusion systems. In this paper, we shall establish the spreading speed for a large class of non-cooperative reaction-diffusion systems and characterize the spreading speed as the slowest speed of a family of non-constant traveling wave solutions. As an application, our results are applied to a partially cooperative system describing interactions between ungulates and grass.
Abstracts of International Conference on Diffusion and Reactions: From Basis to Applications
NONE
1994-12-31
The conference has been devoted to diffusion of corrosion agents and chemical reactions (sulfidation and oxidation) in metals, alloys and composite materials from the view point of their corrosion mechanism and material resistance in different conditions.The three main topics have been broadly represented at the conference sessions: heterogeneous reactions; high temperature diffusion and corrosion mechanism and current problems and trends in development and characterization of materials.
AUTO-DARBOUX TRANSFORMATION AND EXACT SOLUTIONS OF THE BRUSSELATOR REACTION DIFFUSION MODEL
闫振亚; 张鸿庆
2001-01-01
Firstly, using the improved homogeneous balance method, an auto-Darboux transformation (ADT) for the Brusselator reaction diffusion model is found. Based on the ADT, several exact solutions are obtained which contain some authors' results known.Secondly, by using a series of transformations, the model is reduced into a nonlinear reaction diffusion equation and then through using sine- cosine method, more exact solutions are found which contain soliton solutions.
Musho, M.K.; Kozak, J.J.
1984-10-01
A method is presented for calculating exactly the relative width (sigma/sup 2/)/sup 1/2//
Solutions of fractional reaction-diffusion equations in terms of the H-function
Haubold, H. J.; Mathai, A. M.; Saxena, R. K.
2007-12-01
This paper deals with the investigation of the solution of an unified fractional reaction-diffusion equation associated with the Caputo derivative as the time-derivative and Riesz-Feller fractional derivative as the space-derivative. The solution is derived by the application of the Laplace and Fourier transforms in closed form in terms of the H-function. The results derived are of general nature and include the results investigated earlier by many authors, notably by Mainardi et al. (2001, 2005) for the fundamental solution of the space-time fractional diffusion equation, and Saxena et al. (2006a, b) for fractional reaction-diffusion equations. The advantage of using 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 neutral fractional diffusion, space-fractional diffusion, and time-fractional diffusion. These specialized types of diffusion can be interpreted as spatial probability density functions evolving in time and are expressible in terms of the H-functions in compact form.
Cherniha, Roman
2017-01-01
This book presents several fundamental results in solving nonlinear reaction-diffusion equations and systems using symmetry-based methods. Reaction-diffusion systems are fundamental modeling tools for mathematical biology with applications to ecology, population dynamics, pattern formation, morphogenesis, enzymatic reactions and chemotaxis. The book discusses the properties of nonlinear reaction-diffusion systems, which are relevant for biological applications, from the symmetry point of view, providing rigorous definitions and constructive algorithms to search for conditional symmetry (a nontrivial generalization of the well-known Lie symmetry) of nonlinear reaction-diffusion systems. In order to present applications to population dynamics, it focuses mainly on two- and three-component diffusive Lotka-Volterra systems. While it is primarily a valuable guide for researchers working with reaction-diffusion systems and those developing the theoretical aspects of conditional symmetry conception,...
On the perturbation solution of interface-reaction controlled diffusion in solids
Zhi-Wei Cui; Feng Gao; Jian-Min Qu
2012-01-01
Insertion of species A into species B forms a product P through two kinetic processes,namely,(1) the chemical reaction between A and B that occurs at the B-P interface,and (2) the diffusion of species A in product P.These two processes are symbiotic in that the chemical reaction provides the driving force for the diffusion,while the diffusion sustains the chemical reaction by providing sufficient reactant to the reactive interface.In this paper,a mathematical framework is developed for the coupled reactiondiffusion processes.The resulting system of boundary and initial value problem is solved analytically for the case of interface-reaction controlled diffusion,i.e.,the rate of diffusion is much faster than the rate of chemical reaction at the interface so that the final kinetics are limited by the interface chemical reaction.Asymptotic expressions are given for the velocity of the reactive interface and the concentration of diffusing species under two different boundary conditions.
Defect reactions in gallium antimonide studied by zinc and self-diffusion
Sunder, Kirsten; Bracht, Hartmut
2007-12-01
Extrinsic diffusion of zinc (Zn) in gallium antimonide (GaSb) under Ga-rich conditions was analyzed on the basis of the kick-out and the dissociative diffusion mechanism. It is concluded that the changeover of interstitial Zn to substitutional gallium (Ga) sites is mainly mediated by Ga interstitials ( IGa). Fitting of the Zn profiles provides the relative contributions of IGa to Ga diffusion. This contribution is lower than the directly measured Ga diffusion coefficient indicating that Ga diffusion in GaSb is rather mediated by Ga vacancies than by Ga interstitials even under Ga-rich conditions. This finding supports transformation reactions between native point defects that are confirmed by first-principles total-energy calculations. In addition Ga and Sb diffusion experiments under H22 atmosphere were performed to reconcile the controversial data on self-diffusion in GaSb published by Weiler et al. and Bracht et al.
Wang, Jing [Iowa State Univ., Ames, IA (United States)
2013-01-11
We analyze the spatiotemporal behavior of species concentrations in a diffusion-mediated conversion reaction which occurs at catalytic sites within linear pores of nanometer diameter. A strict single-file (no passing) constraint occurs in the diffusion within such narrow pores. Both transient and steady-state behavior is precisely characterized by kinetic Monte Carlo simulations of a spatially discrete lattice–gas model for this reaction–diffusion process considering various distributions of catalytic sites. Exact hierarchical master equations can also be developed for this model. Their analysis, after application of mean-field type truncation approximations, produces discrete reaction–diffusion type equations (mf-RDE). For slowly varying concentrations, we further develop coarse-grained continuum hydrodynamic reaction–diffusion equations (h-RDE) incorporating a precise treatment of single-file diffusion (SFD) in this multispecies system. Noting the shortcomings of mf-RDE and h-RDE, we then develop a generalized hydrodynamic (GH) formulation of appropriate gh-RDE which incorporates an unconventional description of chemical diffusion in mixed-component quasi-single-file systems based on a refined picture of tracer diffusion for finite-length pores. The gh-RDE elucidate the non-exponential decay of the steady-state reactant concentration into the pore and the non-mean-field scaling of the reactant penetration depth. Then an extended model of a catalytic conversion reaction within a functionalized nanoporous material is developed to assess the effect of varying the reaction product – pore interior interaction from attractive to repulsive. The analysis is performed utilizing the generalized hydrodynamic formulation of the reaction-diffusion equations which can reliably capture the complex interplay between reaction and restricted transport for both irreversible and reversible reactions.
张连顺; 张春平; 王新宇; 祁胜文; 许棠; 田建国; 张光寅
2002-01-01
The applicability of diffusion theory for the determination of tissue optical properties from steady-state diffuse reflectance is investigated. Analytical expressions from diffusion theory using the two most commonly assumed boundary conditions at the air-tissue interface and the two definitions of the diffusion coefficient are compared with Monte Carlo simulations. The effects of the choice of the boundary conditions and diffusion coefficients on the accuracy of the findings for the optical parameters are quantified, and criteria for accurate curve-fitting algorithms are developed. It is shown that the error in deriving the optical coefficients is considerably smaller for the solution which uses the extrapolated boundary condition and the diffusion coefficient independence of absorption coefficient, compared to the other three solutions.
Describing diffusion, reaction and convection on porous medium
D'Ajello, P C T; Nunes, G L
2013-01-01
In this paper we present a mathematical model for the electrochemical deposition aimed at the production of inverse opals. The real system consists of an arrangement of sub micrometer spheres, through which the species in an electrolytic medium diffuses until they react to the electrode surface and become part thereof. Our model consists in formulating convenient boundary conditions for the transport equation, that somewhat resembles the real system but is nevertheless simple enough to be solved, and then solve it. Similar approach was taken by Nicholson [1, 2], except that, to avoid the difficulties regarding the boundary conditions, he considered none whatsoever, and proposed a modified diffusion coefficient for the porous medium instead. Apropos, our model, with moving boundary condition pertain to the class of problems know as The Stefan problem [3].
von Kameke, A.; Huhn, F.; Muñuzuri, A. P.; Pérez-Muñuzuri, V.
2013-02-01
In the absence of advection, reaction-diffusion systems are able to organize into spatiotemporal patterns, in particular spiral and target waves. Whenever advection is present that can be parametrized in terms of effective or turbulent diffusion D*, these patterns should be attainable on a much greater, boosted length scale. However, so far, experimental evidence of these boosted patterns in a turbulent flow was lacking. Here, we report the first experimental observation of boosted target and spiral patterns in an excitable chemical reaction in a quasi-two-dimensional turbulent flow. The wave patterns observed are ˜50 times larger than in the case of molecular diffusion only. We vary the turbulent diffusion coefficient D* of the flow and find that the fundamental Fisher-Kolmogorov-Petrovsky-Piskunov equation, vf∝D*, for the asymptotic speed of a reactive wave remains valid. However, not all measures of the boosted wave scale with D* as expected from molecular diffusion, since the wave fronts turn out to be highly filamentous.
Spiral and Antispiral Waves in Reaction-Diffusion Systems
LIUYu-Fang; WUYan-Ning; XUHou-Ju; SUNJin-Feng
2004-01-01
Spiral waves are ubiquitous phenomena in nonlinear chemical, physical, and biological systems. But antispiral waves are infrequent to date. The transition between spiral and antispiral waves has been rarely explored. We have analyzed the extended Brusselator model and the extended Oregonator model by linear stability analysis. We have demonstrated that it is possible and plausible to realize the transition between them by control of diffusion coefficient of inactivator from theoretical analysis and numerical simulations.
Fu, Jin; Wu, Sheng; Li, Hong; Petzold, Linda R.
2014-10-01
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.
Minimal coupling schemes in N-body reaction theory
Picklesimer, A.; Tandy, P. C.; Thaler, R. M.
1982-08-01
A new derivation of the N-body equations of Bencze, Redish, and Sloan is obtained through the use of Watson-type multiple scattering techniques. The derivation establishes an intimate connection between these partition-labeled N-body equations and the particle-labeled Rosenberg equations. This result yields new insight into the implicit role of channel coupling in, and the minimal dimensionality of, the partition-labeled equations. NUCLEAR REACTIONS Scattering theory, multiple scattering, connected kernel reaction theory, minimal coupling, coupling schemes.
Lueptow, Richard M.; Schlick, Conor P.; Umbanhowar, Paul B.; Ottino, Julio M.
2013-11-01
We investigate chaotic advection and diffusion in competitive autocatalytic reactions. To study this subject, we use a computationally efficient method for solving advection-reaction-diffusion equations for periodic flows using a mapping method with operator splitting. In competitive autocatalytic reactions, there are two species, B and C, which both react autocatalytically with species A (A +B -->2B and A +C -->2C). If there is initially a small amount of spatially localized B and C and a large amount of A, all three species will be advected by the velocity field, diffuse, and react until A is completely consumed and only B and C remain. We find that the small scale interactions associated with the chaotic velocity field, specifically the local finite-time Lyapunov exponents (FTLEs), can accurately predict the final average concentrations of B and C after the reaction is complete. The species, B or C, that starts in the region with the larger FTLE has, with high probability, the larger average concentration at the end of the reaction. If species B and C start in regions having similar FTLEs, their average concentrations at the end of the reaction will also be similar. Funded by NSF Grant CMMI-1000469.
Cubic autocatalysis in a reaction-diffusion annulus: semi-analytical solutions
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.
Drift and breakup of spiral waves in reaction-diffusion-mechanics systems.
Panfilov, A V; Keldermann, R H; Nash, M P
2007-05-08
Rotating spiral waves organize excitation in various biological, physical, and chemical systems. They underpin a variety of important phenomena, such as cardiac arrhythmias, morphogenesis processes, and spatial patterns in chemical reactions. Important insights into spiral wave dynamics have been obtained from theoretical studies of the reaction-diffusion (RD) partial differential equations. However, most of these studies have ignored the fact that spiral wave rotation is often accompanied by substantial deformations of the medium. Here, we show that joint consideration of the RD equations with the equations of continuum mechanics for tissue deformations (RD-mechanics systems), yield important effects on spiral wave dynamics. We show that deformation can induce the breakup of spiral waves into complex spatiotemporal patterns. We also show that mechanics leads to spiral wave drift throughout the medium approaching dynamical attractors, which are determined by the parameters of the model and the size of the medium. We study mechanisms of these effects and discuss their applicability to the theory of cardiac arrhythmias. Overall, we demonstrate the importance of RD-mechanics systems for mathematics applied to life sciences.
Luisa Malaguti
2011-01-01
Full Text Available The paper deals with a degenerate reaction-diffusion equation, including aggregative movements and convective terms. The model also incorporates a real parameter causing the change from a purely diffusive to a diffusive-aggregative and to a purely aggregative regime. Existence and qualitative properties of traveling wave solutions are investigated, and estimates of their threshold speeds are furnished. Further, the continuous dependence of the threshold wave speed and of the wave profiles on a real parameter is studied, both when the process maintains its diffusion-aggregation nature and when it switches from it to another regime.
Realistic boundary conditions for stochastic simulations of reaction-diffusion processes
Erban, R; Erban, Radek
2006-01-01
Many cellular and subcellular biological processes can be described in terms of diffusing and chemically reacting species (e.g. enzymes). Such reaction-diffusion processes can be mathematically modelled using either deterministic partial-differential equations or stochastic simulation algorithms. The latter provide a more detailed and precise picture, and several stochastic simulation algorithms have been proposed in recent years. Such models typically give the same description of the reaction-diffusion processes far from the boundary of the simulated domain, but the behaviour close to a reactive boundary (e.g. a membrane with receptors) is unfortunately model-dependent. In this paper, we study four different approaches to stochastic modelling of reaction-diffusion problems and show the correct choice of the boundary condition for each model. The reactive boundary is treated as partially reflective, which means that some molecules hitting the boundary are adsorbed (e.g. bound to the receptor) and some molecul...
Spreading Speed for a Periodic Reaction-diffusion Model with Nonmonotone Birth Function
HUANG Ye-hui; WENG Pei-xuan
2012-01-01
A reaction-diffusion model for a single spccies with age structure and nonlocal reaction for periodic time t is derived.Some results about the model with monotone birth function are firstly introduced,and then by constructing two auxiliary equations and squeezing method,the spreading speed for the system with nonmonotone birth function is obtained.
Concentration fluctuations in non-isothermal reaction-diffusion systems. II. The nonlinear case
Bedeaux, D.; Ortiz de Zárate, J.M.; Pagonabarraga, I.; Sengers, J.V.; Kjelstrup, S.
2011-01-01
In this paper, we consider a simple reaction-diffusion system, namely, a binary fluid mixture with an association-dissociation reaction between two species. We study fluctuations at hydrodynamic spatiotemporal scales when this mixture is driven out of equilibrium by the presence of a temperature gra
Existence of global solutions to reaction-diffusion systems via a Lyapunov functional
Said Kouachi
2001-10-01
Full Text Available The purpose of this paper is to construct polynomial functionals (according to solutions of the coupled reaction-diffusion equations which give $L^{p}$-bounds for solutions. When the reaction terms are sufficiently regular, using the well known regularizing effect, we deduce the existence of global solutions. These functionals are obtained independently of work done by Malham and Xin [11].
Gokoglu, Suleyman A.
1988-01-01
This paper investigates the role played by vapor-phase chemical reactions on CVD rates by comparing the results of two extreme theories developed to predict CVD mass transport rates in the absence of interfacial kinetic barrier: one based on chemically frozen boundary layer and the other based on local thermochemical equilibrium. Both theories consider laminar convective-diffusion boundary layers at high Reynolds numbers and include thermal (Soret) diffusion and variable property effects. As an example, Na2SO4 deposition was studied. It was found that gas phase reactions have no important role on Na2SO4 deposition rates and on the predictions of the theories. The implications of the predictions of the two theories to other CVD systems are discussed.
Thermally activated reaction–diffusion-controlled chemical bulk reactions of gases and solids
S. Möller
2015-01-01
Full Text Available The chemical kinetics of the reaction of thin films with reactive gases is investigated. The removal of thin films using thermally activated solid–gas to gas reactions is a method to in-situ control deposition inventory in vacuum and plasma vessels. Significant scatter of experimental deposit removal rates at apparently similar conditions was observed in the past, highlighting the need for understanding the underlying processes. A model based on the presence of reactive gas in the films bulk and chemical kinetics is presented. The model describes the diffusion of reactive gas into the film and its chemical interaction with film constituents in the bulk using a stationary reaction–diffusion equation. This yields the reactive gas concentration and reaction rates. Diffusion and reaction rate limitations are depicted in parameter studies. Comparison with literature data on tokamak co-deposit removal results in good agreement of removal rates as a function of pressure, film thickness and temperature.
Cross-Diffusion-Driven Instability in a Reaction-Diffusion Harrison Predator-Prey Model
Xiaoqin Wang
2013-01-01
Full Text Available We present a theoretical analysis of processes of pattern formation that involves organisms distribution and their interaction of spatially distributed population with cross-diffusion in a Harrison-type predator-prey model. We analyze the global behaviour of the model by establishing a Lyapunov function. We carry out the analytical study in detail and find out the certain conditions for Turing’s instability induced by cross-diffusion. And the numerical results reveal that, on increasing the value of the half capturing saturation constant, the sequences “spots → spot-stripe mixtures → stripes → hole-stripe mixtures → holes” are observed. The results show that the model dynamics exhibits complex pattern replication controlled by the cross-diffusion.
Voituriez, R.; Moreau, M.; Oshanin, G.
2004-01-01
The validity of two fundamental concepts of classical chemical kinetics - the notion of "Chemical Equilibrium" and the "Law of Mass Action" - are re-examined for reversible \\textit{diffusion-limited} reactions (DLR), as exemplified here by association/dissociation $A+A \\rightleftharpoons B$ reactions. We consider a general model of long-ranged reactions, such that any pair of $A$ particles, separated by distance $\\mu$, may react with probability $\\omega_+(\\mu)$, and any $B$ may dissociate wit...
Xin-yu Lai; Nan-rong Zhao
2013-01-01
Time-dependent diffusion coefficient and conventional diffusion constant are calculated and analyzed to study diffusion of nanoparticles in polymer melts.A generalized Langevin equation is adopted to describe the diffusion dynamics.Mode-coupling theory is employed to calculate the memory kernel of friction.For simplicity,only microscopic terms arising from binary collision and coupling to the solvent density fluctuation are included in the formalism.The equilibrium structural information functions of the polymer nanocomposites required by mode-coupling theory are calculated on the basis of polymer reference interaction site model with Percus-Yevick closure.The effect of nanoparticle size and that of the polymer size are clarified explicitly.The structural functions,the friction kernel,as well as the diffusion coefficient show a rich variety with varying nanoparticle radius and polymer chain length.We find that for small nanoparticles or short chain polymers,the characteristic short time non-Markov diffusion dynamics becomes more prominent,and the diffusion coefficient takes longer time to approach asymptotically the conventional diffusion constant.This constant due to the microscopic contributions will decrease with the increase of nanoparticle size,while increase with polymer size.Furthermore,our result of diffusion constant from modecoupling theory is compared with the value predicted from the Stokes-Einstein relation.It shows that the microscopic contributions to the diffusion constant are dominant for small nanoparticles or long chain polymers.Inversely,when nanonparticle is big,or polymer chain is short,the hydrodynamic contribution might play a significant role.
Flow-Injection Responses of Diffusion Processes and Chemical Reactions
Andersen, Jens Enevold Thaulov
2000-01-01
The technique of Flow-injection Analysis (FIA), now aged 25 years, offers unique analytical methods that are fast, reliable and consuming an absolute minimum of chemicals. These advantages together with its inherent feasibility for automation warrant the future applications of FIA as an attractive...... be used in the resolution of FIA profiles to obtain information about the content of interference’s, in the study of chemical reaction kinetics and to measure absolute concentrations within the FIA-detector cell....
Contribution to an effective design method for stationary reaction-diffusion patterns
Szalai, István; Horváth, Judit [Laboratory of Nonlinear Chemical Dynamics, Institute of Chemistry, Eötvös Loránd University, P.O. Box 32, H-1518 Budapest 112 (Hungary); De Kepper, Patrick [Centre de Recherche Paul Pascal, CNRS, University of Bordeaux, 115, Avenue Schweitzer, F-33600 Pessac (France)
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.
Contribution to an effective design method for stationary reaction-diffusion patterns
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.
Contribution to an effective design method for stationary reaction-diffusion patterns.
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.
Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach
Kim, Changho; Nonaka, Andy; Bell, John B.; Garcia, Alejandro L.; Donev, Aleksandar
2017-03-01
We develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules, to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two
Traveling wave solutions for reaction-diffusion systems
Pedersen, Michael; Lin, Zhigui; Tian, Canrong
2010-01-01
This paper is concerned with traveling waves of reaction–diffusion systems. The definition of coupled quasi-upper and quasi-lower solutions is introduced for systems with mixed quasimonotone functions, and the definition of ordered quasi-upper and quasi-lower solutions is also given for systems...... with quasimonotone nondecreasing functions. By the monotone iteration method, it is shown that if the system has a pair of coupled quasi-upper and quasi-lower solutions, then there exists at least a traveling wave solution. Moreover, if the system has a pair of ordered quasi-upper and quasi-lower solutions......, then there exists at least a traveling wavefront. As an application we consider the delayed system of a mutualistic model....
Kinetic pathways of diffusion and solid-state reactions in nanostructured thin films
Beke, D. L.; Langer, G. A.; Molnár, G.; Erdélyi, G.; Katona, G. L.; Lakatos, A.; Vad, K.
2013-06-01
Mass transport and solid-state reactions in nanocrystalline thin films are reviewed. It is illustrated that diffusion along different grain boundaries (GBs) can have important effects on the overall intermixing process between two pure films. These processes can be well characterized by a bimodal GB network, with different (fast and slow) diffusivities. First the atoms migrate along fast GBs and accumulate at the film surface. These accumulated atoms form a secondary diffusion source for back diffusion along slow boundaries. Thus the different GBs of the thin films can be gradually filled up with the diffusing atoms and composition depth profiles reflect the result of these processes. Similar processes can be observed in binary systems with intermetallic layers: instead of nucleation and growth of the reaction layer at the initial interface, the reaction takes place in the GBs and the amount of the product phase grows by the motion of its interfaces perpendicular to the GBs. Thus, the entire layer of the pure parent films can be consumed by this GB diffusion-induced solid-state reaction (GBDIREAC), and a fully homogeneous product layer can be obtained.
Qiankun Song
2007-06-01
Full Text Available Impulsive bidirectional associative memory neural network model with time-varying delays and reaction-diffusion terms is considered. Several sufficient conditions ensuring the existence, uniqueness, and global exponential stability of equilibrium point for the addressed neural network are derived by M-matrix theory, analytic methods, and inequality techniques. Moreover, the exponential convergence rate index is estimated, which depends on the system parameters. The obtained results in this paper are less restrictive than previously known criteria. Two examples are given to show the effectiveness of the obtained results.
Cao Jinde
2007-01-01
Full Text Available Impulsive bidirectional associative memory neural network model with time-varying delays and reaction-diffusion terms is considered. Several sufficient conditions ensuring the existence, uniqueness, and global exponential stability of equilibrium point for the addressed neural network are derived by M-matrix theory, analytic methods, and inequality techniques. Moreover, the exponential convergence rate index is estimated, which depends on the system parameters. The obtained results in this paper are less restrictive than previously known criteria. Two examples are given to show the effectiveness of the obtained results.
Gan, Qintao
2017-01-01
In this paper, the exponential synchronization problem of generalized reaction-diffusion neural networks with mixed time-varying delays is investigated concerning Dirichlet boundary conditions in terms of p-norm. Under the framework of the Lyapunov stability method, stochastic theory, and mathematical analysis, some novel synchronization criteria are derived, and an aperiodically intermittent control strategy is proposed simultaneously. Moreover, the effects of diffusion coefficients, diffusion space, and stochastic perturbations on the synchronization process are explicitly expressed under the obtained conditions. Finally, some numerical simulations are performed to illustrate the feasibility of the proposed control strategy and show different synchronization dynamics under a periodically/aperiodically intermittent control.
Reaction theories for N* excitations in {pi}N and {gamma}N reactions
Lee, T.S.H.
1996-12-31
The importance of developing reaction theories for investigating N* physics is illustrated in an analysis of pion photoproduction on the nucleon. It is shown that the {gamma}N {leftrightarrow} {Delta} transition amplitudes predicted by the constituent quark model are in agreement with the values extracted from the {gamma}N {r_arrow} {pi}N data only when the contributions from the reaction mechanisms calculated using a dynamical approach are taken into account in the analysis.
2002-01-01
The Feshbach-Kerman_Koonin multistep compound theory (MSC) of the pre - equilibrium reaction isfurther improved and perfected. The nucleon is treated as a spin-half particle, target nucleus is allowed toa non-zero spin, the angular momentum coupling is treated rigorously. The expressions of the
Politowicz, P.A.; Kozak, J.J.
1987-12-01
The authors study surface-mediated, diffusion-controlled reactive processes on particles whose overall geometry is homeomorphic to a sphere. Rather than assuming that a coreactant can diffuse freely over the surface of the particle to a target site (reaction center), they consider the case where the coreactant can migrate only among N-1 satellite sites that are networked to the reaction site by means of a number of pathways or reaction channels. Five distinct lattice topologies are considered and they study the reaction efficiency both for the case where the satellite sites are passive and for the case where reaction may occur with finite probability at these sites. The results obtained for this class of surface problems are compared with those obtained by assuming that the reaction-diffusion process takes place on a planar, two-dimensional surface (lattice). The applicability of their results to surface-mediated processes on organizates (cells, vesicles, micelles) and on colloidally dispersed catalyst particles is brought out in the Introduction, and the correspondence between the lattice-based, Markovian approach developed here and Fickian models of surface diffusion, particularly with regard to the exponentiality of the decay, is discussed in the concluding section.
Modelling the impact of an invasive insect via reaction-diffusion.
Roques, Lionel; Auger-Rozenberg, Marie-Anne; Roques, Alain
2008-11-01
An exotic, specialist seed chalcid, Megastigmus schimitscheki, has been introduced along with its cedar host seeds from Turkey to southeastern France during the early 1990s. It is now expanding in plantations of Atlas Cedar (Cedrus atlantica). We propose a model to predict the expansion and impact of this insect. This model couples a time-discrete equation for the ovo-larval stage with a two-dimensional reaction-diffusion equation for the adult stage, through a formula linking the solution of the reaction-diffusion equation to a seed attack rate. Two main diffusion operators, of Fokker-Planck and Fickian types, are tested. We show that taking account of the dependence of the insect mobility with respect to spatial heterogeneity, and choosing the appropriate diffusion operator, are critical factors for obtaining good predictions.
Scaling of morphogenetic patterns in reaction-diffusion systems.
Rasolonjanahary, Manan'Iarivo; Vasiev, Bakhtier
2016-09-07
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.
Qualitative Analysis on a Reaction-Diffusion Prey Predator Model and the Corresponding Steady-States
Qunyi BIE; Rui PENG
2009-01-01
The authors study a diffusive prey-predator model subject to the homogeneous Neumann boundary condition and give some qualitative descriptions of solutions to this reaction-diffusion system and its corresponding steady-state problem.The local and global stability of the positive constant steady-state are discussed,and then some results for nonexistence of positive non-constant steady-states are derived.
Cox process representation and inference for stochastic reaction-diffusion processes
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.
A Domain Decomposition Method for Time Fractional Reaction-Diffusion Equation
Chunye Gong
2014-01-01
Full Text Available The computational complexity of one-dimensional time fractional reaction-diffusion equation is O(N2M compared with O(NM for classical integer reaction-diffusion equation. Parallel computing is used to overcome this challenge. Domain decomposition method (DDM embodies large potential for parallelization of the numerical solution for fractional equations and serves as a basis for distributed, parallel computations. A domain decomposition algorithm for time fractional reaction-diffusion equation with implicit finite difference method is proposed. The domain decomposition algorithm keeps the same parallelism but needs much fewer iterations, compared with Jacobi iteration in each time step. Numerical experiments are used to verify the efficiency of the obtained algorithm.
A Series Solution of the Cauchy Problem for Turing Reaction-diffusion Model
L. Päivärinta
2011-12-01
Full Text Available In this paper, the series pattern solution of the Cauchy problem for Turing reaction-diffusion model is obtained by using the homotopy analysis method (HAM. Turing reaction-diffusion model is nonlinear reaction-diffusion system which usually has power-law nonlinearities or may be rewritten in the form of power-law nonlinearities. Using the HAM, it is possible to find the exact solution or an approximate solution of the problem. This technique provides a series of functions which converges rapidly to the exact solution of the problem. The efficiency of the approach will be shown by applying the procedure on two problems. Furthermore, the so-called homotopy-Pade technique (HPT is applied to enlarge the convergence region and rate of solution series given by the HAM.
Sample Duplication Method for Monte Carlo Simulation of Large Reaction-Diffusion System
张红东; 陆建明; 杨玉良
1994-01-01
The sample duplication method for the Monte Carlo simulation of large reaction-diffusion system is proposed in this paper. It is proved that the sample duplication method will effectively raise the efficiency and statistical precision of the simulation without changing the kinetic behaviour of the reaction-diffusion system and the critical condition for the bifurcation of the steady-states. The method has been applied to the simulation of spatial and time dissipative structure of Brusselator under the Dirichlet boundary condition. The results presented in this paper definitely show that the sample duplication method provides a very efficient way to sol-’e the master equation of large reaction-diffusion system. For the case of two-dimensional system, it is found that the computation time is reduced at least by a factor of two orders of magnitude compared to the algorithm reported in literature.
Finite volume element method for analysis of unsteady reaction-diffusion problems
Sutthisak Phongthanapanich; Pramote Dechaumphai
2009-01-01
A finite volume element method is developed for analyzing unsteady scalar reaction--diffusion problems in two dimensions. The method combines the concepts that are employed in the finite volume and the finite element method together. The finite volume method is used to discretize the unsteady reaction--diffusion equation, while the finite element method is applied to estimate the gradient quantities at cell faces. Robustness and efficiency of the combined method have been evaluated on uniform rectangular grids by using available numerical solutions of the two-dimensional reaction-diffusion problems. The numerical solutions demonstrate that the combined method is stable and can provide accurate solution without spurious oscillation along the highgradient boundary layers.
Chen, Weiliang
2016-01-01
Stochastic, spatial reaction-diffusion simulations have been widely used in systems biology and computational neuroscience. However, the increasing scale and complexity of simulated models and morphologies have exceeded the capacity of any serial implementation. This led to development of parallel solutions that benefit from the boost in performance of modern large-scale supercomputers. In this paper, we describe an MPI-based, parallel Operator-Splitting implementation for stochastic spatial reaction-diffusion simulations with irregular tetrahedral meshes. The performance of our implementation is first examined and analyzed with simulations of a simple model. We then demonstrate its usage in real-world research by simulating the reaction-diffusion components of a published calcium burst model in both Purkinje neuron sub-branch and full dendrite morphologies. Simulation results indicate that our implementation is capable of achieving super-linear speedup for balanced loading simulations with reasonable molecul...
Turing bifurcation in a reaction-diffusion system with density-dependent dispersal
Kumar, Niraj; Horsthemke, Werner
2010-05-01
Motivated by the recent finding [N. Kumar, G.M. Viswanathan, V.M. Kenkre, Physica A 388 (2009) 3687] that the dynamics of particles undergoing density-dependent nonlinear diffusion shows sub-diffusive behaviour, we study the Turing bifurcation in a two-variable system with this kind of dispersal. We perform a linear stability analysis of the uniform steady state to find the conditions for the Turing bifurcation and compare it with the standard Turing condition in a reaction-diffusion system, where dispersal is described by simple Fickian diffusion. While activator-inhibitor kinetics are a necessary condition for the Turing instability as in standard two-variable systems, the instability can occur even if the diffusion constant of the inhibitor is equal to or smaller than that of the activator. We apply these results to two model systems, the Brusselator and the Gierer-Meinhardt model.
The entropy dissipation method for spatially inhomogeneous reaction-diffusion-type systems
Di Francesco, M.
2008-12-08
We study the long-time asymptotics of reaction-diffusion-type systems that feature a monotone decaying entropy (Lyapunov, free energy) functional. We consider both bounded domains and confining potentials on the whole space for arbitrary space dimensions. Our aim is to derive quantitative expressions for (or estimates of) the rates of convergence towards an (entropy minimizing) equilibrium state in terms of the constants of diffusion and reaction and with respect to conserved quantities. Our method, the so-called entropy approach, seeks to quantify convergence to equilibrium by using functional inequalities, which relate quantitatively the entropy and its dissipation in time. The entropy approach is well suited to nonlinear problems and known to be quite robust with respect to model variations. It has already been widely applied to scalar diffusion-convection equations, and the main goal of this paper is to study its generalization to systems of partial differential equations that contain diffusion and reaction terms and admit fewer conservation laws than the size of the system. In particular, we successfully apply the entropy approach to general linear systems and to a nonlinear example of a reaction-diffusion-convection system arising in solid-state physics as a paradigm for general nonlinear systems. © 2008 The Royal Society.
Marangoni flows induced by A + B -> C reaction fronts with arbitrary diffusion coefficients
Tiani, Reda; Rongy, Laurence
2016-11-01
We consider horizontal aqueous solutions in contact with air where three reacting species A, B, and C can affect the surface tension of the solution, thereby driving Marangoni flows. When the two reactants A and B, that are initially separated, are brought into contact, a reaction front producing species C is formed and evolves in time due to diffusion, convection and reaction processes. The resulting dynamics is studied by numerically integrating the incompressible Navier-Stokes equations coupled to reaction-diffusion-convection equations for the three chemical species. For equal initial concentrations of reactants and equal diffusion coefficients, we have explained how chemically-driven Marangoni flows can lead to complex dynamics of the front propagation. Here we extend such results for arbitrary values of the diffusion coefficients and initial concentrations of reactants. We give the general classification of the surface tension profiles as a function of the Marangoni numbers quantifying the effect of each species on the surface tension, the ratio of initial concentrations of reactants and the ratios of diffusion coefficients. Such a classification allows us then to study the resulting structure of the convective rolls as well as the nonlinear dynamics of the reaction front. F.R.S.- FNRS, ARC.
Unified connected theory of few-body reaction mechanisms in N-body scattering theory
Polyzou, W. N.; Redish, E. F.
1978-01-01
A unified treatment of different reaction mechanisms in nonrelativistic N-body scattering is presented. The theory is based on connected kernel integral equations that are expected to become compact for reasonable constraints on the potentials. The operators T/sub +-//sup ab/(A) are approximate transition operators that describe the scattering proceeding through an arbitrary reaction mechanism A. These operators are uniquely determined by a connected kernel equation and satisfy an optical theorem consistent with the choice of reaction mechanism. Connected kernel equations relating T/sub +-//sup ab/(A) to the full T/sub +-//sup ab/ allow correction of the approximate solutions for any ignored process to any order. This theory gives a unified treatment of all few-body reaction mechanisms with the same dynamic simplicity of a model calculation, but can include complicated reaction mechanisms involving overlapping configurations where it is difficult to formulate models.
Extension of Newman's method to electrochemical reaction-diffusion in a fuel cell catalyst layer
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.
MAXIMAL ATTRACTORS OF CLASSICAL SOLUTIONS FOR REACTION DIFFUSION EQUATIONS WITH DISPERSION
Li Yanling; Ma Yicheng
2005-01-01
The paper first deals with the existence of the maximal attractor of classical solution for reaction diffusion equation with dispersion, and gives the sup-norm estimate for the attractor. This estimate is optimal for the attractor under Neumann boundary condition. Next, the same problem is discussed for reaction diffusion system with uniformly contracting rectangle, and it reveals that the maximal attractor of classical solution for such system in the whole space is only necessary to be established in some invariant region.Finally, a few examples of application are given.
Instability and pattern formation in reaction-diffusion systems: a higher order analysis.
Riaz, Syed Shahed; Sharma, Rahul; Bhattacharyya, S P; Ray, D S
2007-08-14
We analyze the condition for instability and pattern formation in reaction-diffusion systems beyond the usual linear regime. The approach is based on taking into account perturbations of higher orders. Our analysis reveals that nonlinearity present in the system can be instrumental in determining the stability of a system, even to the extent of destabilizing one in a linearly stable parameter regime. The analysis is also successful to account for the observed effect of additive noise in modifying the instability threshold of a system. The analytical study is corroborated by numerical simulation in a standard reaction-diffusion system.
Modeling cardiac mechano-electrical feedback using reaction-diffusion-mechanics systems
Keldermann, R. H.; Nash, M. P.; Panfilov, A. V.
2009-06-01
In many practically important cases, wave propagation described by the reaction-diffusion equation initiates deformation of the medium. Mathematically, such processes are described by coupled reaction-diffusion-mechanics (RDM) systems. RDM systems were recently used to study the effects of deformation on wave propagation in cardiac tissue, so called mechano-electrical feedback (MEF). In this article, we review the results of some of these studies, in particular those relating to the effects of deformation on pacemaker activity and spiral wave dynamics in the heart. We also provide brief descriptions of the numerical methods used, and the underlying cardiac physiology.
Time capsule: an autonomous sensor and recorder based on diffusion-reaction.
Gerber, Lukas C; Rosenfeld, Liat; Chen, Yunhan; Tang, Sindy K Y
2014-11-21
We describe the use of chemical diffusion and reaction to record temporally varying chemical information as spatial patterns without the need for external power. Diffusion of chemicals acts as a clock, while reactions forming immobile products possessing defined optical properties perform sensing and recording functions simultaneously. The spatial location of the products reflects the history of exposure to the detected substances of interest. We refer to our device as a time capsule and show an initial proof of principle in the autonomous detection of lead ions in water.
Stability Analysis of a Reaction-Diffusion System Modeling Atherogenesis
Ibragimov, Akif
2010-01-01
This paper presents a linear, asymptotic stability analysis for a reaction-diffusionconvection system modeling atherogenesis, the initiation of atherosclerosis, as an inflammatory instability. Motivated by the disease paradigm articulated by Ross, atherogenesis is viewed as an inflammatory spiral with a positive feedback loop involving key cellular and chemical species interacting and reacting within the intimal layer of muscular arteries. The inflammatory spiral is initiated as an instability from a healthy state which is defined to be an equilibrium state devoid of certain key inflammatory markers. Disease initiation is studied through a linear, asymptotic stability analysis of a healthy equilibrium state. Various theorems are proved, giving conditions on system parameters guaranteeing stability of the health state, and a general framework is developed for constructing perturbations from a healthy state that exhibit blow-up, which are interpreted as corresponding to disease initiation. The analysis reveals key features that arterial geometry, antioxidant levels, and the source of inflammatory components (through coupled third-kind boundary conditions or through body sources) play in disease initiation. © 2010 Society for Industrial and Applied Mathematics.
Liechty, Derek S.; Lewis, Mark J.
2010-01-01
Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties (i.e., no macroscopic reaction rate information) are extended to include reactions involving charged particles and electronic energy levels. The proposed extensions include ionization reactions, exothermic associative ionization reactions, endothermic and exothermic charge exchange reactions, and other exchange reactions involving ionized species. The extensions are shown to agree favorably with the measured Arrhenius rates for near-equilibrium conditions.
Singh, Jagdev; Rashidi, M. M.; Kumar, Devendra; Swroop, Ram
2016-12-01
In this paper, we study a dynamical Brusselator reaction-diffusion system arising in triple collision and enzymatic reactions with time fractional Caputo derivative. The present article involves a more generalized effective approach, proposed for the Brusselator system say q-homotopy analysis transform method (q-HATM), providing the family of series solutions with nonlocal generalized effects. The convergence of the q-HATM series solution is adjusted and controlled by auxiliary parameter ℏ and asymptotic parameter n. The numerical results are demonstrated graphically. The outcomes of the study show that the q-HATM is computationally very effective and accurate to analyze nonlinear fractional differential equations.
Multiconfigurational self-consistent reaction field theory for nonequilibrium solvation
Mikkelsen, Kurt V.; Cesar, Amary; Ågren, Hans
1995-01-01
We present multiconfigurational self-consistent reaction field theory and implementation for solvent effects on a solute molecular system that is not in equilibrium with the outer solvent. The approach incorporates two different polarization vectors for studying the influence of the solvent...... states influenced by the two types of polarization vectors. The general treatment of the correlation problem through the use of complete and restricted active space methodologies makes the present multiconfigurational self-consistent reaction field approach general in that it can handle any type of state......, open-shell, excited, and transition states. We demonstrate the theory by computing solvatochromatic shifts in optical/UV spectra of some small molecules and electron ionization and electron detachment energies of the benzene molecule. It is shown that the dependency of the solvent induced affinity...
Open Effective Field Theories from Deeply Inelastic Reactions
Braaten, Eric; Hammer, Hans-Werner; Lepage, G. Peter
2017-01-01
Effective field theories have often been applied to systems with inelastic reactions that produce particles with large momenta outside the domain of validity of the effective theory. The effects of the deeply inelastic reactions have been taken into account in previous work by adding local anti-Hermitian terms to the effective Hamiltonian density. We show that an additional modification is required in equations governing the density matrix when multi-particle states are considered. We define an effective density matrix by tracing out states containing high-momentum particles, and show that it satisfies a Lindblad equation, with Lindblad operators determined by the anti-Hermitian terms in the effective Hamiltonian density. This research was supported in part by the Department of Energy, the National Science Foundation, and the Simons Foundation.
Open Effective Field Theories from Deeply Inelastic Reactions
Braaten, Eric; Lepage, G Peter
2016-01-01
Effective field theories have often been applied to systems with deeply inelastic reactions that produce particles with large momenta outside the domain of validity of the effective theory. The effects of the deeply inelastic reactions have been taken into account in previous work by adding local anti-Hermitian terms to the effective Hamiltonian. Here we show that when multi-particle systems are considered, an additional modification is required in equations governing the density matrix. We define an effective density matrix by tracing over the states containing high-momentum particles, and show that it satisfies a Lindblad equation, with local Lindblad operators determined by the anti-Hermitian terms in the effective Hamiltonian density.
Understanding Diffusion Theory and Fick's Law through Food and Cooking
Zhou, Larissa; Nyberg, Kendra; Rowat, Amy C.
2015-01-01
Diffusion is critical to physiological processes ranging from gas exchange across alveoli to transport within individual cells. In the classroom, however, it can be challenging to convey the concept of diffusion on the microscopic scale. In this article, we present a series of three exercises that use food and cooking to illustrate diffusion…
Uniform asymptotic approximation of diffusion to a small target: Generalized reaction models
Isaacson, Samuel A.; Mauro, Ava J.; Newby, Jay
2016-10-01
The diffusion of a reactant to a binding target plays a key role in many biological processes. The reaction radius at which the reactant and target may interact is often a small parameter relative to the diameter of the domain in which the reactant diffuses. We develop uniform in time asymptotic expansions in the reaction radius of the full solution to the corresponding diffusion equations for two separate reactant-target interaction mechanisms: the Doi or volume reactivity model and the Smoluchowski-Collins-Kimball partial-absorption surface reactivity model. In the former, the reactant and target react with a fixed probability per unit time when within a specified separation. In the latter, upon reaching a fixed separation, they probabilistically react or the reactant reflects away from the target. Expansions of the solution to each model are constructed by projecting out the contribution of the first eigenvalue and eigenfunction to the solution of the diffusion equation and then developing matched asymptotic expansions in Laplace-transform space. Our approach offers an equivalent, but alternative, method to the pseudopotential approach we previously employed [Isaacson and Newby, Phys. Rev. E 88, 012820 (2013), 10.1103/PhysRevE.88.012820] for the simpler Smoluchowski pure-absorption reaction mechanism. We find that the resulting asymptotic expansions of the diffusion equation solutions are identical with the exception of one parameter: the diffusion-limited reaction rates of the Doi and partial-absorption models. This demonstrates that for biological systems in which the reaction radius is a small parameter, properly calibrated Doi and partial-absorption models may be functionally equivalent.
An analytic algorithm for the space-time fractional reaction-diffusion equation
M. G. Brikaa
2015-11-01
Full Text Available In this paper, we solve the space-time fractional reaction-diffusion equation by the fractional homotopy analysis method. Solutions of different examples of the reaction term will be computed and investigated. The approximation solutions of the studied models will be put in the form of convergent series to be easily computed and simulated. Comparison with the approximation solution of the classical case of the studied modeled with their approximation errors will also be studied.
Blowup Analysis for a Nonlocal Diffusion Equation with Reaction and Absorption
Yulan Wang
2012-01-01
Full Text Available We investigate a nonlocal reaction diffusion equation with absorption under Neumann boundary. We obtain optimal conditions on the exponents of the reaction and absorption terms for the existence of solutions blowing up in finite time, or for the global existence and boundedness of all solutions. For the blowup solutions, we also study the blowup rate estimates and the localization of blowup set. Moreover, we show some numerical experiments which illustrate our results.
Chemical reaction network approaches to Biochemical Systems Theory.
Arceo, Carlene Perpetua P; Jose, Editha C; Marin-Sanguino, Alberto; Mendoza, Eduardo R
2015-11-01
This paper provides a framework to represent a Biochemical Systems Theory (BST) model (in either GMA or S-system form) as a chemical reaction network with power law kinetics. Using this representation, some basic properties and the application of recent results of Chemical Reaction Network Theory regarding steady states of such systems are shown. In particular, Injectivity Theory, including network concordance [36] and the Jacobian Determinant Criterion [43], a "Lifting Theorem" for steady states [26] and the comprehensive results of Müller and Regensburger [31] on complex balanced equilibria are discussed. A partial extension of a recent Emulation Theorem of Cardelli for mass action systems [3] is derived for a subclass of power law kinetic systems. However, it is also shown that the GMA and S-system models of human purine metabolism [10] do not display the reactant-determined kinetics assumed by Müller and Regensburger and hence only a subset of BST models can be handled with their approach. Moreover, since the reaction networks underlying many BST models are not weakly reversible, results for non-complex balanced equilibria are also needed.
Statistical theory for the kinetics and dynamics of roaming reactions.
Klippenstein, Stephen J; Georgievskii, Yuri; Harding, Lawrence B
2011-12-22
We present a statistical theory for the effect of roaming pathways on product branching fractions in both unimolecular and bimolecular reactions. The analysis employs a separation into three distinct steps: (i) the formation of weakly interacting fragments in the long-range/van der Waals region of the potential via either partial decomposition (for unimolecular reactants) or partial association (for bimolecular reactants), (ii) the roaming step, which involves the reorientation of the fragments from one region of the long-range potential to another, and (iii) the abstraction, addition, and/or decomposition from the long-range region to yield final products. The branching between the roaming induced channel(s) and other channels is obtained from a steady-state kinetic analysis for the two (or more) intermediates in the long-range region of the potential. This statistical theory for the roaming-induced product branching is illustrated through explicit comparisons with reduced dimension trajectory simulations for the decompositions of H(2)CO, CH(3)CHO, CH(3)OOH, and CH(3)CCH. These calculations employ high-accuracy analytic potentials obtained from fits to wide-ranging CASPT2 ab initio electronic structure calculations. The transition-state fluxes for the statistical theory calculations are obtained from generalizations of the variable reaction coordinate transition state theory approach. In each instance, at low energy the statistical analysis accurately reproduces the branching obtained from the trajectory simulations. At higher energies, e.g., above 1 kcal/mol, increasingly large discrepancies arise, apparently due to a dynamical biasing toward continued decomposition of the incipient molecular fragments (for unimolecular reactions). Overall, the statistical theory based kinetic analysis is found to provide a useful framework for interpreting the factors that determine the significance of roaming pathways in varying chemical environments.
Density Function Theory Studies on Reaction of HCS with OH
PEI Ke-Mei; LI Yi-Min; LI Hai-Yang
2003-01-01
The exothermic reaction of HCS with OH on the single-state potential energy surface was explored by means of Density Function Theory(DFT). The equilibrium structural parameters, the harmonic vibrational frequencies, the total energies and the zero point energies(ZPE) of all the species in the reaction were computed. Six intermediates and seven transition states were located, three exothermic channels were found. The frequency analysis and the Intrinsic Reaction Coordinate(IRC) calculation confirm that the transitions are truthful. The results indicate that there are three exothermic channels and their corresponding products are: P1(H2O+CS), P2(H2S+CO), P3(OCS+H2), and P1 has a larger branch ratio.
Salles, N.; Richard, N.; Mousseau, N.; Hemeryck, A.
2017-08-01
The reaction of oxygen molecules on an oxidized silicon model-substrate is investigated using an efficient potential energy hypersurface exploration that provides a rich picture of the associated energy landscape, energy barriers, and insertion mechanisms. Oxygen molecules are brought in, one by one, onto an oxidized silicon substrate, and accurate pathways for sublayer oxidation are identified through the coupling of density functional theory to the activation relaxation technique nouveau, an open-ended unbiased reaction pathway searching method, allowing full exploration of potential energy surface. We show that strain energy increases with O coverage, driving the kinetics of diffusion at the Si/SiO2 interface in the interfacial layer and deeper into the bulk: at low coverage, interface reconstruction dominates while at high coverage, oxygen diffusion at the interface or even deeper into the bottom layers is favored. A changing trend in energetics is observed that favors atomic diffusions to occur at high coverage while they appear to be unlikely at low coverage. Upon increasing coverage, strain is accumulated at the interface, allowing the oxygen atom to diffuse as the strain becomes large enough. The observed atomic diffusion at the interface releases the accumulated strain, which is consistent with a layer-by-layer oxidation growth.
Feminist psychoanalytic theory: American and French reactions to Freud.
Rosen, H; Zickler, E
1996-01-01
Ever since Freud's observations on women and their psychology were published, there have been revisions, expansions, and reactions to his ideas. Most recently, feminist psychoanalytic theorists from the United States and France have been fertile in producing revisions to traditional psychoanalytic theory about women. Reviewing the disjointed psychoanalytic traditions of the two countries provides a context for understanding the different approaches to feminist thinking that each country has produced. American feminist psychoanalytic theorists tend to stage reversals of traditional Freudian theory, while the French feminist psychoanalytic theorists have had to position themselves intellectually and politically with reference to the teachings of Lacan. This paper examines selected contemporary theorists from these two countries--Jean Baker Miller, Nancy Chodorow, and Carol Gilligan from the United States and Julia Kristeva, Luce Irigaray, and Helene Cixous from France--and discusses the difficulties of constructing a theory of sexual difference that avoids the pitfalls of either biological essentialism or its reverse, social constructionism.
Wang, Jin-Liang; Wu, Huai-Ning; Huang, Tingwen; Ren, Shun-Yan
2016-04-01
Two types of coupled neural networks with reaction-diffusion terms are considered in this paper. In the first one, the nodes are coupled through their states. In the second one, the nodes are coupled through the spatial diffusion terms. For the former, utilizing Lyapunov functional method and pinning control technique, we obtain some sufficient conditions to guarantee that network can realize synchronization. In addition, considering that the theoretical coupling strength required for synchronization may be much larger than the needed value, we propose an adaptive strategy to adjust the coupling strength for achieving a suitable value. For the latter, we establish a criterion for synchronization using the designed pinning controllers. It is found that the coupled reaction-diffusion neural networks with state coupling under the given linear feedback pinning controllers can realize synchronization when the coupling strength is very large, which is contrary to the coupled reaction-diffusion neural networks with spatial diffusion coupling. Moreover, a general criterion for ensuring network synchronization is derived by pinning a small fraction of nodes with adaptive feedback controllers. Finally, two examples with numerical simulations are provided to demonstrate the effectiveness of the theoretical results.
Fluid Registration of Diffusion Tensor Images Using Information Theory
Chiang, Ming-Chang; Leow, Alex D.; Klunder, Andrea D.; Dutton, Rebecca A.; Barysheva, Marina; Rose, Stephen E.; McMahon, Katie L.; de Zubicaray, Greig I.; Toga, Arthur W.; Thompson, Paul M.
2008-01-01
We apply an information-theoretic cost metric, the symmetrized Kullback-Leibler (sKL) divergence, or J-divergence, to fluid registration of diffusion tensor images. The difference between diffusion tensors is quantified based on the sKL-divergence of their associated probability density functions (PDFs). Three-dimensional DTI data from 34 subjects were fluidly registered to an optimized target image. To allow large image deformations but preserve image topology, we regularized the flow with a large-deformation diffeomorphic mapping based on the kinematics of a Navier-Stokes fluid. A driving force was developed to minimize the J-divergence between the deforming source and target diffusion functions, while reorienting the flowing tensors to preserve fiber topography. In initial experiments, we showed that the sKL-divergence based on full diffusion PDFs is adaptable to higher-order diffusion models, such as high angular resolution diffusion imaging (HARDI). The sKL-divergence was sensitive to subtle differences between two diffusivity profiles, showing promise for nonlinear registration applications and multisubject statistical analysis of HARDI data. PMID:18390342
Affine diffusions and related processes simulation, theory and applications
Alfonsi, Aurélien
2015-01-01
This book gives an overview of affine diffusions, from Ornstein-Uhlenbeck processes to Wishart processes and it considers some related diffusions such as Wright-Fisher processes. It focuses on different simulation schemes for these processes, especially second-order schemes for the weak error. It also presents some models, mostly in the field of finance, where these methods are relevant and provides some numerical experiments. The book explains the mathematical background to understand affine diffusions and analyze the accuracy of the schemes.
R S Kaushal; Ranjit Kumar; Awadhesh Prasad
2006-08-01
Attempts have been made to look for the soliton content in the solutions of the recently studied nonlinear diffusion-reaction equations [R S Kaushal, J. Phys. 38, 3897 (2005)] involving quadratic or cubic nonlinearities in addition to the convective flux term which renders the system nonconservative and the corresponding Hamiltonian non-Hermitian.
The Induced Dimension Reduction method applied to convection-diffusion-reaction problems
Astudillo, R.; Van Gijzen, M.B.
2016-01-01
Discretization of (linearized) convection-diffusion-reaction problems yields a large and sparse non symmetric linear system of equations, Ax = b. (1) In this work, we compare the computational behavior of the Induced Dimension Reduction method (IDR(s)) [10], with other short-recurrences Krylov met
Convective wave front locking for a reaction-diffusion system in a conical flow reactor
Kuptsov, P.V.; Kuznetsov, S.P.; Knudsen, Carsten
2002-01-01
We consider reaction-diffusion instabilities in a flow reactor whose cross-section slowly expands with increasing longitudinal coordinate (cone shaped reactor). Due to deceleration of the flow in this reactor, the instability is convective near the inlet to the reactor and absolute at the downstr...
The constructive technique and its application in solving a nonlinear reaction diffusion equation
Lai Shao-Yong; Guo Yun-Xi; Qing Yin; Wu Yong-Hong
2009-01-01
A mathematical technique based on the consideration of a nonlinear partial differential equation together with an additional condition in the form of an ordinary differential equation is employed to study a nonlinear reaction diffusion equation which describes a real process in physics and in chemistry. Several exact solutions for the equation are acquired under certain circumstances.
Allergic Contact Dermatitis with Diffuse Erythematous Reaction from Diisopropanolamine in a Compress
Tomoko Rind
2010-04-01
Full Text Available Compresses containing a nonsteroidal antiinflammatory drug (NSAID are commonly used in Japan. However, this treatment may induce both allergic and photoallergic contact dermatitis from the NSAIDs and their ingredients. Here, we describe a case of allergic contact dermatitis with diffuse erythematous reaction due to diisopropanolamine in the applied compress. The absorption of diisopropanolamine might have been enhanced by the occlusive condition.
Allergic Contact Dermatitis with Diffuse Erythematous Reaction from Diisopropanolamine in a Compress
Tomoko Rind; Naoki Oiso; Ayaka Hirao; Akira Kawada
2010-01-01
Compresses containing a nonsteroidal antiinflammatory drug (NSAID) are commonly used in Japan. However, this treatment may induce both allergic and photoallergic contact dermatitis from the NSAIDs and their ingredients. Here, we describe a case of allergic contact dermatitis with diffuse erythematous reaction due to diisopropanolamine in the applied compress. The absorption of diisopropanolamine might have been enhanced by the occlusive condition.
Weakly nonlinear dynamics in reaction-diffusion systems with Levy flights
Nec, Y; Nepomnyashchy, A A [Department of Mathematics, Technion-Israel Institute of Technology, Haifa 32000 (Israel); Golovin, A A [Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208 (United States)], E-mail: flyby@techunix.technion.ac.il
2008-12-15
Reaction-diffusion equations with a fractional Laplacian are reduced near a long wave Hopf bifurcation. The obtained amplitude equation is shown to be the complex Ginzburg-Landau equation with a fractional Laplacian. Some of the properties of the normal complex Ginzburg-Landau equation are generalized for the fractional analogue. In particular, an analogue of the Kuramoto-Sivashinsky equation is derived.
Asymptotic Speed of Wave Propagation for A Discrete Reaction-Diffusion Equation
Xiu-xiang Liu; Pei-xuan Weng
2006-01-01
We deal with asymptotic speed of wave propagation for a discrete reaction-diffusion equation. We find the minimal wave speed c* from the characteristic equation and show that c* is just the asymptotic speed of wave propagation. The isotropic property and the existence of solution of the initial value problem for the given equation are also discussed.
Travelling Wave Solutions in Delayed Reaction Diffusion Systems with Partial Monotonicity
Jian-hua Huang; Xing-fu Zou
2006-01-01
This paper deals with the existence of travelling wave fronts of delayed reaction diffusion systems with partial quasi-monotonicity. We propose a concept of "desirable pair of upper-lower solutions", through which a subset can be constructed. We then apply the Schauder's fixed point theorem to some appropriate operator in this subset to obtain the existence of the travelling wave fronts.
Ranjit Kumar
2012-09-01
Travelling and solitary wave solutions of certain coupled nonlinear diffusion-reaction equations have been constructed using the auxiliary equation method. These equations arise in a variety of contexts not only in biological, chemical and physical sciences but also in ecological and social sciences.
Ranjit Kumar; R S Kaushal; Awadhesh Prasad
2010-10-01
An auto-Bäcklund transformation derived in the homogeneous balance method is employed to obtain several new exact solutions of certain kinds of nonlinear diffusion-reaction (D-R) equations. These equations arise in a variety of problems in physical, chemical, biological, social and ecological sciences.
LONG-TIME BEHAVIOR OF A CLASS OF REACTION DIFFUSION EQUATIONS WITH TIME DELAYS
无
2006-01-01
The present paper devotes to the long-time behavior of a class of reaction diffusion equations with delays under Dirichlet boundary conditions. The stability and global attractability for the zero solution are provided, and the existence, stability and attractability for the positive stationary solution are also obtained.
An Efficient Implicit FEM Scheme for Fractional-in-Space Reaction-Diffusion Equations
Burrage, Kevin
2012-01-01
Fractional differential equations are becoming increasingly used as a modelling tool for processes associated with anomalous diffusion or spatial heterogeneity. However, the presence of a fractional differential operator causes memory (time fractional) or nonlocality (space fractional) issues that impose a number of computational constraints. In this paper we develop efficient, scalable techniques for solving fractional-in-space reaction diffusion equations using the finite element method on both structured and unstructured grids via robust techniques for computing the fractional power of a matrix times a vector. Our approach is show-cased by solving the fractional Fisher and fractional Allen-Cahn reaction-diffusion equations in two and three spatial dimensions, and analyzing the speed of the traveling wave and size of the interface in terms of the fractional power of the underlying Laplacian operator. © 2012 Society for Industrial and Applied Mathematics.
Mix and Inject: Reaction Initiation by Diffusion for Time-Resolved Macromolecular Crystallography
Marius Schmidt
2013-01-01
Full Text Available Time-resolved macromolecular crystallography unifies structure determination with chemical kinetics, since the structures of transient states and chemical and kinetic mechanisms can be determined simultaneously from the same data. To start a reaction in an enzyme, typically, an initially inactive substrate present in the crystal is activated. This has particular disadvantages that are circumvented when active substrate is directly provided by diffusion. However, then it is prohibitive to use macroscopic crystals because diffusion times become too long. With small micro- and nanocrystals diffusion times are adequately short for most enzymes and the reaction can be swiftly initiated. We demonstrate here that a time-resolved crystallographic experiment becomes feasible by mixing substrate with enzyme nanocrystals which are subsequently injected into the X-ray beam of a pulsed X-ray source.
Park, Soohyung; Agmon, Noam
2008-05-15
We develop a uniform theory for the many-particle diffusion-control effects on the Michaelis-Menten scheme in solution, based on the Gopich-Szabo relaxation-time approximation (Gopich, I. V.; Szabo, A. J. Chem. Phys. 2002, 117, 507). We extend the many-particle simulation algorithm to the Michaelis-Menten case by utilizing the Green function previously derived for excited-state reversible geminate recombination with different lifetimes (Gopich, I. V.; Agmon, N. J. Chem. Phys. 2000, 110, 10433). Running the simulation for representative parameter sets in the time domain and under steady-state conditions, we find poor agreement with classical kinetics but excellent agreement with some of the modern theories for bimolecular diffusion-influenced reactions. Our simulation algorithm can be readily extended to the biologically interesting case of dense patches of membrane-bound enzymes.
Entropy Solution Theory for Fractional Degenerate Convection-Diffusion Equations
Jakobsen, Simone Cifani And Espen R
2010-01-01
We study a class of degenerate convection diffusion equations with a fractional nonlinear diffusion term. These equations are natural generalizations of anomalous diffusion equations, fractional conservations laws, local convection diffusion equations, and some fractional Porous medium equations. In this paper we define weak entropy solutions for this class of equations and prove well-posedness under weak regularity assumptions on the solutions, e.g. uniqueness is obtained in the class of bounded integrable functions. Then we introduce a monotone conservative numerical scheme and prove convergence toward an Entropy solution in the class of bounded integrable functions of bounded variation. We then extend the well-posedness results to non-local terms based on general L\\'evy type operators, and establish some connections to fully non-linear HJB equations. Finally, we present some numerical experiments to give the reader an idea about the qualitative behavior of solutions of these equations.
Evaluation of diffusion coefficients in multicomponent mixtures by means of the fluctuation theory
Shapiro, Alexander
2003-01-01
We derive general expressions for diffusion coefficients in multicomponent non-ideal gas or liquid mixtures. The derivation is based on the general statistical theory of fluctuations around an equilibrium state. The matrix of diffusion coefficients is expressed in terms of the equilibrium thermod...... characteristics. We demonstrate on several examples that the developed theory is in agreement with the established experimental facts and dependencies for the diffusion coefficients. (C) 2002 Elsevier Science B.V. All rights reserved.......We derive general expressions for diffusion coefficients in multicomponent non-ideal gas or liquid mixtures. The derivation is based on the general statistical theory of fluctuations around an equilibrium state. The matrix of diffusion coefficients is expressed in terms of the equilibrium...
Relation between the complex Ginzburg-Landau equation and reaction-diffusion System
Shao Xin; Ren Yi; Ouyang Qi
2006-01-01
The complex Ginzburg-Landau equation(CGLE)has been used to describe the travelling wave behaviour in reaction-diffusion (RD) systems. We argue that this description is valid only when the RD system is close to the Hopf bifurcation,and is not valid when a RD system is away from the onset.To test this,we study spirals and anti-spirals in the chlorite-iodide-malonic acid (CIMA) reaction and the corresponding CGLE.Numerical simulations confirm that the CGLE can only be applied to the CIMA reaction when it is very near the Hopf onset.
Phenomenological theory of bulk diffusion in metal oxides
Chuvil'deev, V. N.; Smirnova, E. S.
2016-07-01
Phenomenological description of bulk diffusion in oxide ceramics has been proposed. Variants of vacancy and vacancy-free diffusion models have been considered. In the vacancy models, ion migration is described as a fluctuation with the formation of a "liquid corridor," along which the diffusion ion transport in a "melt" is performed, or, as a fluctuation with the formation of an "empty corridor," in which the ion motion proceeds without activation. The vacancy-free model considers a fluctuation with the formation of a spherical liquid region whose sizes correspond to the first coordination sphere. It has been shown that both the vacancy models work in cubic metal oxides and the vacancy-free model is effective for describing diffusion in oxides having a noncubic structure. Detailed comparison of the models developed has been performed. It has been shown that the values of the activation energies for diffusion of metal and oxygen ions agree with the published data on bulk diffusion in stoichiometric oxide ceramics.
Sayed Ameenuddin Irfan
2017-03-01
Full Text Available A mathematical model for the reaction-diffusion equation is developed to describe the nutrient release profiles and degradation of poly(lactic acid (PLA-coated controlled-release fertilizer. A multi-diffusion model that consists of coupled partial differential equations is used to study the diffusion and chemical reaction (autocatalytic degradation simultaneously. The model is solved using an analytical-numerical method. Firstly, the model equation is transformed using the Laplace transformation as the Laplace transform cannot be inverted analytically. Numerical inversion of the Laplace transform is used by employing the Zakian method. The solution is useful in predicting the nutrient release profiles at various diffusivity, concentration of extraction medium, and reaction rates. It also helps in explaining the transformation of autocatalytic concentration in the coating material for various reaction rates, times of reaction, and reaction-multi diffusion. The solution is also applicable to the other biodegradable polymer-coated controlled-release fertilizers.
Konukoglu, Ender; Clatz, Olivier; Menze, Bjoern H; Stieltjes, Bram; Weber, Marc-André; Mandonnet, Emmanuel; Delingette, Hervé; Ayache, Nicholas
2010-01-01
Reaction-diffusion based tumor growth models have been widely used in the literature for modeling the growth of brain gliomas. Lately, recent models have started integrating medical images in their formulation. Including different tissue types, geometry of the brain and the directions of white matter fiber tracts improved the spatial accuracy of reaction-diffusion models. The adaptation of the general model to the specific patient cases on the other hand has not been studied thoroughly yet. In this paper, we address this adaptation. We propose a parameter estimation method for reaction-diffusion tumor growth models using time series of medical images. This method estimates the patient specific parameters of the model using the images of the patient taken at successive time instances. The proposed method formulates the evolution of the tumor delineation visible in the images based on the reaction-diffusion dynamics; therefore, it remains consistent with the information available. We perform thorough analysis of the method using synthetic tumors and show important couplings between parameters of the reaction-diffusion model. We show that several parameters can be uniquely identified in the case of fixing one parameter, namely the proliferation rate of tumor cells. Moreover, regardless of the value the proliferation rate is fixed to, the speed of growth of the tumor can be estimated in terms of the model parameters with accuracy. We also show that using the model-based speed, we can simulate the evolution of the tumor for the specific patient case. Finally, we apply our method to two real cases and show promising preliminary results.
Application of diffusion-reaction equations to model carious lesion progress
Lewandowska, Katarzyna D.; Kosztołowicz, Tadeusz
2012-04-01
Nonlinear equations that describe the diffusion-reaction process with one static and one mobile substance are used to model a carious lesion process. The system under consideration consists of two initially separated substances A (an acid causing caries) and C (a static enamel mineral) which react chemically according to the formula A+C→0̸(inert). The so-called surface layer, which is formed in this process and in which chemical reactions can be neglected, is also included in this model. Changes in the substance concentrations are calculated approximately using the perturbation method. We show that the experimental data on the enamel mineral concentrations are well described by the analytical solutions of the diffusion-reaction equations.
Synthesis and materialization of a reaction-diffusion French flag pattern
Zadorin, Anton S.; Rondelez, Yannick; Gines, Guillaume; Dilhas, Vadim; Urtel, Georg; Zambrano, Adrian; Galas, Jean-Christophe; Estevez-Torres, André
2017-10-01
During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process within non-living matter and demonstrate the autonomous structuration of a synthetic material. First, we use DNA-based reaction networks to synthesize a French flag, an archetypal pattern composed of three chemically distinct zones with sharp borders whose synthetic analogue has remained elusive. A bistable network within a shallow concentration gradient creates an immobile, sharp and long-lasting concentration front through a reaction-diffusion mechanism. The combination of two bistable circuits generates a French flag pattern whose 'phenotype' can be reprogrammed by network mutation. Second, these concentration patterns control the macroscopic organization of DNA-decorated particles, inducing a French flag pattern of colloidal aggregation. This experimental framework could be used to test reaction-diffusion models and fabricate soft materials following an autonomous developmental programme.
AlHarbi, Nawaf N. S.; Treagust, David F.; Chandrasegaran, A. L.; Won, Mihye
2015-01-01
This study investigated the understanding of diffusion, osmosis and particle theory of matter concepts among 192 pre-service science teachers in Saudi Arabia using a 17-item two-tier multiple-choice diagnostic test. The data analysis showed that the pre-service teachers' understanding of osmosis and diffusion concepts was mildly correlated with…
Application of semiclassical methods to reaction rate theory
Hernandez, R.
1993-11-01
This work is concerned with the development of approximate methods to describe relatively large chemical systems. This effort has been divided into two primary directions: First, we have extended and applied a semiclassical transition state theory (SCTST) originally proposed by Miller to obtain microcanonical and canonical (thermal) rates for chemical reactions described by a nonseparable Hamiltonian, i.e. most reactions. Second, we have developed a method to describe the fluctuations of decay rates of individual energy states from the average RRKM rate in systems where the direct calculation of individual rates would be impossible. Combined with the semiclassical theory this latter effort has provided a direct comparison to the experimental results of Moore and coworkers. In SCTST, the Hamiltonian is expanded about the barrier and the ``good`` action-angle variables are obtained perturbatively; a WKB analysis of the effectively one-dimensional reactive direction then provides the transmission probabilities. The advantages of this local approximate treatment are that it includes tunneling effects and anharmonicity, and it systematically provides a multi-dimensional dividing surface in phase space. The SCTST thermal rate expression has been reformulated providing increased numerical efficiency (as compared to a naive Boltzmann average), an appealing link to conventional transition state theory (involving a ``prereactive`` partition function depending on the action of the reactive mode), and the ability to go beyond the perturbative approximation.
Chemical reactions modulated by mechanical stress: extended Bell theory.
Konda, Sai Sriharsha M; Brantley, Johnathan N; Bielawski, Christopher W; Makarov, Dmitrii E
2011-10-28
A number of recent studies have shown that mechanical stress can significantly lower or raise the activation barrier of a chemical reaction. Within a common approximation due to Bell [Science 200, 618 (1978)], this barrier is linearly dependent on the applied force. A simple extension of Bell's theory that includes higher order corrections in the force predicts that the force-induced change in the activation energy will be given by -FΔR - ΔχF(2)∕2. Here, ΔR is the change of the distance between the atoms, at which the force F is applied, from the reactant to the transition state, and Δχ is the corresponding change in the mechanical compliance of the molecule. Application of this formula to the electrocyclic ring-opening of cis and trans 1,2-dimethylbenzocyclobutene shows that this extension of Bell's theory essentially recovers the force dependence of the barrier, while the original Bell formula exhibits significant errors. Because the extended Bell theory avoids explicit inclusion of the mechanical stress or strain in electronic structure calculations, it allows a computationally efficient characterization of the effect of mechanical forces on chemical processes. That is, the mechanical susceptibility of any reaction pathway is described in terms of two parameters, ΔR and Δχ, both readily computable at zero force.
Bifurcation and pattern formation in a coupled higher autocatalator reaction diffusion system
无
2007-01-01
Spatiotemporal structures arising in two identical cells, which are governed by higher autocatalator kinetics and coupled via diffusive interchange of autocatalyst,are discussed.The stability of the unique homogeneous steady state is obtained by the linearized theory.A necessary condition for bifurcations in spatially non-uniform solutions in uncoupled and coupled systems is given.Further information about Turing pattern solutions near bifurcation points is obtained by weakly nonlinear theory.Finally, the stability of equilibrium points of the amplitude equation is discussed by weakly nonlinear theory, with the bifurcation branches of the weakly coupled system.
Selection Theory of Dendritic Growth with Anisotropic Diffusion
Martin von Kurnatowski
2015-01-01
Full Text Available Dendritic patterns frequently arise when a crystal grows into its own undercooled melt. Latent heat released at the two-phase boundary is removed by some transport mechanism, and often the problem can be described by a simple diffusion model. Its analytic solution is based on a perturbation expansion about the case without capillary effects. The length scale of the pattern is determined by anisotropic surface tension, which provides the mechanism for stabilizing the dendrite. In the case of liquid crystals, diffusion can be anisotropic too. Growth is faster in the direction of less efficient heat transport (inverted growth. Any physical solution should include this feature. A simple spatial rescaling is used to reduce the bulk equation in 2D to the case of isotropic diffusion. Subsequently, an eigenvalue problem for the growth mode results from the interface conditions. The eigenvalue is calculated numerically and the selection problem of dendritic growth with anisotropic diffusion is solved. The length scale is predicted and a quantitative description of the inverted growth phenomenon is given. It is found that anisotropic diffusion cannot take the stabilizing role of anisotropic surface tension.
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.
Jacquemet, Vincent
2010-09-01
Microscale electrical propagation in the heart can be modeled by a reaction-diffusion system, describing cell and tissue electrophysiology. Macroscale features of wavefront propagation can be reproduced by an eikonal model, a reduced formulation involving only wavefront shape. In this paper, these two approaches are combined to incorporate global information about reentrant pathways into a reaction-diffusion model. The eikonal-diffusion formulation is generalized to handle reentrant activation patterns and wavefront collisions. Boundary conditions are used to specify pathways of reentry. Finite-element-based numerical methods are presented to solve this nonlinear equation on a coarse triangular mesh. The macroscale eikonal model serves to construct an initial condition for the microscale reaction-diffusion model. Electrical propagation simulated from this initial condition is then compared to the isochrones predicted by the eikonal model. Results in 2-D and thin 3-D test-case geometries demonstrate the ability of this technique to initiate anatomical and functional reentries along prescribed pathways, thus facilitating the development of dedicated models aimed at better understanding clinical case reports.
Denoising of diffusion MRI using random matrix theory.
Veraart, Jelle; Novikov, Dmitry S; Christiaens, Daan; Ades-Aron, Benjamin; Sijbers, Jan; Fieremans, Els
2016-11-15
We introduce and evaluate a post-processing technique for fast denoising of diffusion-weighted MR images. By exploiting the intrinsic redundancy in diffusion MRI using universal properties of the eigenspectrum of random covariance matrices, we remove noise-only principal components, thereby enabling signal-to-noise ratio enhancements. This yields parameter maps of improved quality for visual, quantitative, and statistical interpretation. By studying statistics of residuals, we demonstrate that the technique suppresses local signal fluctuations that solely originate from thermal noise rather than from other sources such as anatomical detail. Furthermore, we achieve improved precision in the estimation of diffusion parameters and fiber orientations in the human brain without compromising the accuracy and spatial resolution.
Reliability theory for diffusion processes on interconnected networks
Khorramzadeh, Yasamin; Youssef, Mina; Eubank, Stephen
2014-03-01
We present the concept of network reliability as a framework to study diffusion dynamics in interdependent networks. We illustrate how different outcomes of diffusion processes, such as cascading failure, can be studied by estimating the reliability polynomial under different reliability rules. As an example, we investigate the effect of structural properties on diffusion dynamics for a few different topologies of two coupled networks. We evaluate the effect of varying the probability of failure propagating along the edges, both within a single network as well as between the networks. We exhibit the sensitivity of interdependent network reliability and connectivity to edge failures in each topology. Network Dynamics and Simulation Science Laboratory, Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia 24061, USA.
Quantum Transition State Theory for proton transfer reactions in enzymes
Bothma, Jacques P; McKenzie, Ross H
2009-01-01
We consider the role of quantum effects in the transfer of hyrogen-like species in enzyme-catalysed reactions. This study is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects imply that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We use a path integral approach which provides a general framework to understand tunneling in a quantum system which interacts with an environment at non-zero temperature. Here the quantum system is the active site of the enzyme and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature $T_0$ which is determined by the curvature of potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. For physically reasonable parameters quantum transition state theory gives a quantitative descr...
Theory of vortices in hybridized ballistic/diffusive-band superconductors
Tanaka, K.; Eschrig, M.; Agterberg, D. F.
2007-06-01
We study the electronic structure in the vicinity of a vortex in a two-band superconductor in which the quasiparticle motion is ballistic in one band and diffusive in the other. This study is based on a model appropriate for such a case, that we have introduced recently [Tanaka , Phys. Rev. B 73, 220501(R) (2006)]. We argue that in the two-band superconductor MgB2 , such a case is realized. Motivated by the experimental findings on MgB2 , we assume that superconductivity in the diffusive band is “weak,” i.e., mostly induced. We examine intriguing features of the order parameter, the current density, and the vortex core spectrum in the “strong” ballistic band under the influence of hybridization with the “weak” diffusive band. Although the order parameter in the diffusive band is induced, the characteristic length scales in the two bands differ due to Coulomb interactions. The current density in the vortex core is dominated by the contribution from the ballistic band, while outside the core the contribution from the diffusive band can be substantial, or even dominating. The current density in the diffusive band has strong temperature dependence, exhibiting the Kramer-Pesch effect when hybridization is strong. A particularly interesting feature of our model is the possibility of additional bound states near the gap edge in the ballistic band, that are prominent in the vortex center spectra. This contrasts with the single band case, where there is no gap-edge bound state in the vortex center. We find the above-mentioned unique features for parameter values relevant for MgB2 .
Diffusion theory of decision making in continuous report.
Smith, Philip L
2016-07-01
I present a diffusion model for decision making in continuous report tasks, in which a continuous, circularly distributed, stimulus attribute in working memory is matched to a representation of the attribute in the stimulus display. Memory retrieval is modeled as a 2-dimensional diffusion process with vector-valued drift on a disk, whose bounding circle represents the decision criterion. The direction and magnitude of the drift vector describe the identity of the stimulus and the quality of its representation in memory, respectively. The point at which the diffusion exits the disk determines the reported value of the attribute and the time to exit the disk determines the decision time. Expressions for the joint distribution of decision times and report outcomes are obtained by means of the Girsanov change-of-measure theorem, which allows the properties of the nonzero-drift diffusion process to be characterized as a function of a Euclidian-distance Bessel process. Predicted report precision is equal to the product of the decision criterion and the drift magnitude and follows a von Mises distribution, in agreement with the treatment of precision in the working memory literature. Trial-to-trial variability in criterion and drift rate leads, respectively, to direct and inverse relationships between report accuracy and decision times, in agreement with, and generalizing, the standard diffusion model of 2-choice decisions. The 2-dimensional model provides a process account of working memory precision and its relationship with the diffusion model, and a new way to investigate the properties of working memory, via the distributions of decision times. (PsycINFO Database Record (c) 2016 APA, all rights reserved).
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).
Dierckx, Hans; Bernus, Olivier; Verschelde, Henri
2011-09-02
The dependency of wave velocity in reaction-diffusion (RD) systems on the local front curvature determines not only the stability of wave propagation, but also the fundamental properties of other spatial configurations such as vortices. This Letter gives the first derivation of a covariant eikonal-curvature relation applicable to general RD systems with spatially varying anisotropic diffusion properties, such as cardiac tissue. The theoretical prediction that waves which seem planar can nevertheless possess a nonvanishing geometrical curvature induced by local anisotropy is confirmed by numerical simulations, which reveal deviations up to 20% from the nominal plane wave speed.
Le Novère Nicolas
2010-03-01
Full Text Available Abstract Background Most cellular signal transduction mechanisms depend on a few molecular partners whose roles depend on their position and movement in relation to the input signal. This movement can follow various rules and take place in different compartments. Additionally, the molecules can form transient complexes. Complexation and signal transduction depend on the specific states partners and complexes adopt. Several spatial simulator have been developed to date, but none are able to model reaction-diffusion of realistic multi-state transient complexes. Results Meredys allows for the simulation of multi-component, multi-feature state molecular species in two and three dimensions. Several compartments can be defined with different diffusion and boundary properties. The software employs a Brownian dynamics engine to simulate reaction-diffusion systems at the reactive particle level, based on compartment properties, complex structure, and hydro-dynamic radii. Zeroth-, first-, and second order reactions are supported. The molecular complexes have realistic geometries. Reactive species can contain user-defined feature states which can modify reaction rates and outcome. Models are defined in a versatile NeuroML input file. The simulation volume can be split in subvolumes to speed up run-time. Conclusions Meredys provides a powerful and versatile way to run accurate simulations of molecular and sub-cellular systems, that complement existing multi-agent simulation systems. Meredys is a Free Software and the source code is available at http://meredys.sourceforge.net/.
An Interface Stretching-Diffusion Model for Mixing-Limited Reactions During Convective Mixing
Hidalgo, J. J.; Dentz, M.; Cabeza, Y.; Carrera, J.
2014-12-01
We study the behavior of mixing-limited dissolution reactions under the unstable flow conditions caused by a Rayleigh-Bénard convective instability in a two fluids system. The reactions produce a dissolution pattern that follows the ascending fluids's interface where the largest concentration gradients and maximum mixing are found. Contrary to other chemical systems, the mixing history engraved by the dissolution does not map out the fingering geometry of the unstable flow. The temporal scaling of the mixing Χ and the reaction rate r are explained by a stretching-diffusion model of the interface between the fluids. The model accurately reproduces the three observed regimes: a diffusive regime at which Χ, r ~ t-1/2; a convective regime of at which the interface contracts to the Batchelor scale resulting in a constant Χf and r independent of the Rayleigh number; and an attenuated convection regime in which Χ and r decay faster than diffusion as t-3/2 and t-1, respectevely, because of the decompression of the interface and weakened reactions caused by the accumulation of dissolved fluid below the interface.
On the Emergence and Diffusion of Technological Capabilities and the Theory of the MNC
Blomkvist, Katarina; Kappen, Philip; Zander, Ivo
2015-01-01
This paper intersects extant theories of the MNC with empirically observed patterns in the intra-company emergence and diffusion of technological capabilities. It draws upon a database containing the complete patenting history of 24 Swedish multinationals over the 1890-2008 period, which allows...... as distinctive and differentiated diffusion patterns across headquarters, greenfield subsidiaries, and acquired units in the MNC group. We conclude that a theory of the MNC should recognize the shift towards more equal conditions for the generation of new technology within the multinational organization......, but that within this overall development some conspicuous inequalities in intra-company capability dif-fusion remain to be accounted for....
Ruzi, Mahmut; Anderson, David T
2015-12-17
Our group has been working to develop parahydrogen (pH2) matrix isolation spectroscopy as a method to study low-temperature condensed-phase reactions of atomic hydrogen with various reaction partners. Guided by the well-defined studies of cold atom chemistry in rare-gas solids, the special properties of quantum hosts such as solid pH2 afford new opportunities to study the analogous chemical reactions under quantum diffusion conditions in hopes of discovering new types of chemical reaction mechanisms. In this study, we present Fourier transform infrared spectroscopic studies of the 193 nm photoinduced chemistry of nitric oxide (NO) isolated in solid pH2 over the 1.8 to 4.3 K temperature range. Upon short-term in situ irradiation the NO readily undergoes photolysis to yield HNO, NOH, NH, NH3, H2O, and H atoms. We map the postphotolysis reactions of mobile H atoms with NO and document first-order growth in HNO and NOH reaction products for up to 5 h after photolysis. We perform three experiments at 4.3 K and one at 1.8 K to permit the temperature dependence of the reaction kinetics to be quantified. We observe Arrhenius-type behavior with a pre-exponential factor of A = 0.036(2) min(-1) and Ea = 2.39(1) cm(-1). This is in sharp contrast to previous H atom reactions we have studied in solid pH2 that display definitively non-Arrhenius behavior. The contrasting temperature dependence measured for the H + NO reaction is likely related to the details of H atom quantum diffusion in solid pH2 and deserves further study.
Dense fluid self-diffusion coefficient calculations using perturbation theory and molecular dynamics
COELHO L. A. F.
1999-01-01
Full Text Available A procedure to correlate self-diffusion coefficients in dense fluids by using the perturbation theory (WCA coupled with the smooth-hard-sphere theory is presented and tested against molecular simulations and experimental data. This simple algebraic expression correlates well the self-diffusion coefficients of carbon dioxide, ethane, propane, ethylene, and sulfur hexafluoride. We have also performed canonical ensemble molecular dynamics simulations by using the Hoover-Nosé thermostat and the mean-square displacement formula to compute self-diffusion coefficients for the reference WCA intermolecular potential. The good agreement obtained from both methods, when compared with experimental data, suggests that the smooth-effective-sphere theory is a useful procedure to correlate diffusivity of pure substances.
On microscopic theory of radiative nuclear reaction characteristics
Kamerdzhiev, Sergei; Avdeenkov, Alexander; Goriely, Stephane
2015-01-01
A survey of some results in the modern microscopic theory of properties of nuclear reactions with gamma-rays is given. First of all, we discuss the impact of phonon coupling (PC) on the photon strength function (PSF) because it represents the most natural physical source of additional strength found for Sn isotopes in recent experiments that could not be explained within the stan- dard HFB+QRPA approach. The self-consistent version of the Extended Theory of Finite Fermi Systems in the Quasiparticle Time Blocking Approximation, or simply QTBA, is applied. It uses the HFB mean field and includes both the QRPA and PC effects on the basis of the SLy4 Skyrme force. With our microscopic E1 PSFs, the following properties have been calculated for many stable and unstable even-even semi-magic Sn and Ni isotopes as well as for double-magic 132Sn and 208Pb using the reaction codes EMPIRE and TALYS with several nuclear level density (NLD) models: 1) the neutron capture cross sections, 2) the corresponding neutron capture...
Karniadakis, George Em [Brown University
2014-03-11
The main objective of this project is to develop new computational tools for uncertainty quantifica- tion (UQ) of systems governed by stochastic partial differential equations (SPDEs) with applications to advection-diffusion-reaction systems. We pursue two complementary approaches: (1) generalized polynomial chaos and its extensions and (2) a new theory on deriving PDF equations for systems subject to color noise. The focus of the current work is on high-dimensional systems involving tens or hundreds of uncertain parameters.
Manzini, Gianmarco [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Cangiani, Andrea [University of Leicester, Leicester (United Kingdom); Sutton, Oliver [University of Leicester, Leicester (United Kingdom)
2014-10-02
This document describes the conforming formulations for virtual element approximation of the convection-reaction-diffusion equation with variable coefficients. Emphasis is given to construction of the projection operators onto polynomial spaces of appropriate order. These projections make it possible the virtual formulation to achieve any order of accuracy. We present the construction of the internal and the external formulation. The difference between the two is in the way the projection operators act on the derivatives (laplacian, gradient) of the partial differential equation. For the diffusive regime we prove the well-posedness of the external formulation and we derive an estimate of the approximation error in the H^{1}-norm. For the convection-dominated case, the streamline diffusion stabilization (aka SUPG) is also discussed.
A reaction-diffusion model of ROS-induced ROS release in a mitochondrial network.
Lufang Zhou
2010-01-01
Full Text Available Loss of mitochondrial function is a fundamental determinant of cell injury and death. In heart cells under metabolic stress, we have previously described how the abrupt collapse or oscillation of the mitochondrial energy state is synchronized across the mitochondrial network by local interactions dependent upon reactive oxygen species (ROS. Here, we develop a mathematical model of ROS-induced ROS release (RIRR based on reaction-diffusion (RD-RIRR in one- and two-dimensional mitochondrial networks. The nodes of the RD-RIRR network are comprised of models of individual mitochondria that include a mechanism of ROS-dependent oscillation based on the interplay between ROS production, transport, and scavenging; and incorporating the tricarboxylic acid (TCA cycle, oxidative phosphorylation, and Ca(2+ handling. Local mitochondrial interaction is mediated by superoxide (O2.- diffusion and the O2.(--dependent activation of an inner membrane anion channel (IMAC. In a 2D network composed of 500 mitochondria, model simulations reveal DeltaPsi(m depolarization waves similar to those observed when isolated guinea pig cardiomyocytes are subjected to a localized laser-flash or antioxidant depletion. The sensitivity of the propagation rate of the depolarization wave to O(2.- diffusion, production, and scavenging in the reaction-diffusion model is similar to that observed experimentally. In addition, we present novel experimental evidence, obtained in permeabilized cardiomyocytes, confirming that DeltaPsi(m depolarization is mediated specifically by O2.-. The present work demonstrates that the observed emergent macroscopic properties of the mitochondrial network can be reproduced in a reaction-diffusion model of RIRR. Moreover, the findings have uncovered a novel aspect of the synchronization mechanism, which is that clusters of mitochondria that are oscillating can entrain mitochondria that would otherwise display stable dynamics. The work identifies the
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.
Partitioned coupling of advection-diffusion-reaction systems and Brinkman flows
Lenarda, Pietro; Paggi, Marco; Ruiz Baier, Ricardo
2017-09-01
We present a partitioned algorithm aimed at extending the capabilities of existing solvers for the simulation of coupled advection-diffusion-reaction systems and incompressible, viscous flow. The space discretisation of the governing equations is based on mixed finite element methods defined on unstructured meshes, whereas the time integration hinges on an operator splitting strategy that exploits the differences in scales between the reaction, advection, and diffusion processes, considering the global system as a number of sequentially linked sets of partial differential, and algebraic equations. The flow solver presents the advantage that all unknowns in the system (here vorticity, velocity, and pressure) can be fully decoupled and thus turn the overall scheme very attractive from the computational perspective. The robustness of the proposed method is illustrated with a series of numerical tests in 2D and 3D, relevant in the modelling of bacterial bioconvection and Boussinesq systems.
Dichotomous-noise-induced pattern formation in a reaction-diffusion system
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.
An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems
Padgett, Jill M. A.; Ilie, Silvana, E-mail: silvana@ryerson.ca [Department of Mathematics, Ryerson University, Toronto, ON, M5B 2K3 (Canada)
2016-03-15
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.
Front propagation in cellular flows for fast reaction and small diffusivity
Tzella, Alexandra
2014-01-01
We investigate the influence of fluid flows on the propagation of chemical fronts arising in FKPP type models. For the cellular flows we consider, the front propagation speed can be determined numerically by solving an eigenvalue problem; this is however difficult for small molecular diffusivity and fast reaction, i.e., when the P\\'eclet (Pe) and Damk\\"ohler (Da) numbers are large. Here, we employ a WKB approach to obtain the front speed for a broad range of Pe,Da$\\gg 1$ in terms of a periodic path -- an instanton -- that minimizes a certain functional, and to derive closed-form results for Da$\\ll$Pe and for Da$\\gg$Pe. Our theoretical predictions are compared with (i) numerical solutions of the eigenvalue problem and (ii) simulations of the advection--diffusion--reaction equation.
Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics
Strehl, Robert; Ilie, Silvana, E-mail: silvana@ryerson.ca [Department of Mathematics, Ryerson University, Toronto, Ontario M5B 2K3 (Canada)
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.
Reaction-diffusion equation for quark-hadron transition in heavy-ion collisions
Bagchi, Partha; Sengupta, Srikumar; Srivastava, Ajit M
2015-01-01
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 chiral order parameter for chiral symmetry breaking transition in heavy-ion collisions, with dissipative dynamics, is governed by one such equation, specifically, the Newell-Whitehead equation. Further, 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. Same thing also happens when we consider the initial confinement-deconfinement transition with 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 genet...
STOCHASTIC CRACKING AND HEALING BEHAVIORS OF THIN FILMS DURING REACTION-DIFFUSION GROWTH
S.L. Zhu; S.L. Yang; Y.M. Xiong; M.S. Li; S.J. Geng; C.S. Hu; Fuhui Wang; W. T. Wu
2001-01-01
The stochastic cracking and healing behaviors of reaction-diffusion growth of thin filmswere studied by means of Markov processes analysis. We chose the thermal growth ofoxide scales on metals as an example of reaction-diffusion growth. The thermal growthof oxide films follows power law when no cracking occurs. Our results showed that thegrowth kinetics under stochastic cracking and healing conditions was different fromthat without cracking. It might be altered to either pseudo-linear or pseudo-power lawsdependent upon the intensity and frequency of the cracking of the films. When thehoping items dominated, the growth followed pseudo-linear law; when the diffusionalitems dominated, it followed pseudo-power law with the exponentials lower than theintrinsical values. The numerical results were in good agreement with the meassuredkinetics of isothermal and cyclic oxidation of NiAl-0.1 Y (at. %) alloys in air at 1273K.
Phase transition and crossover in diffusion-limited aggregation with reaction times
Nagatani, Takashi; Stanley, H. Eugene
1990-09-01
A generalized diffusion-limited aggregation (DLA) with reaction times that has been proposed by Bunde and Miyazima [Phys. Rev. A 38, 2099 (1988)] is considered. Crossover from the DLA to the diffusion-limited self-avoiding walk (DLSAW) is investigated by using the two-parameter position-space renormalization-group method. The crossover exponent and the crossover radius are calculated. The geometrical phase transition between DLA and DLSAW found by Bunde and Miyajima is analyzed by making use of the three-parameter position-space renormalization-group method. A global flow diagram in the three-parameter space is obtained. Above the percolation threshold all the renormalization flows are merged into the DLA point. Below the threshold all the renormalization flows are merged into the DLSAW point. When the reaction time is large, the double-crossover phenomenon occurs below the threshold.
Tuan, Nguyen Huy; Van Au, Vo; Khoa, Vo Anh; Lesnic, Daniel
2017-05-01
The identification of the population density of a logistic equation backwards in time associated with nonlocal diffusion and nonlinear reaction, motivated by biology and ecology fields, is investigated. The diffusion depends on an integral average of the population density whilst the reaction term is a global or local Lipschitz function of the population density. After discussing the ill-posedness of the problem, we apply the quasi-reversibility method to construct stable approximation problems. It is shown that the regularized solutions stemming from such method not only depend continuously on the final data, but also strongly converge to the exact solution in L 2-norm. New error estimates together with stability results are obtained. Furthermore, numerical examples are provided to illustrate the theoretical results.
Turing Bifurcation and Pattern Formation of Stochastic Reaction-Diffusion System
Qianiqian Zheng
2017-01-01
Full Text Available Noise is ubiquitous in a system and can induce some spontaneous pattern formations on a spatially homogeneous domain. In comparison to the Reaction-Diffusion System (RDS, Stochastic Reaction-Diffusion System (SRDS is more complex and it is very difficult to deal with the noise function. In this paper, we have presented a method to solve it and obtained the conditions of how the Turing bifurcation and Hopf bifurcation arise through linear stability analysis of local equilibrium. In addition, we have developed the amplitude equation with a pair of wave vector by using Taylor series expansion, multiscaling, and further expansion in powers of small parameter. Our analysis facilitates finding regions of bifurcations and understanding the pattern formation mechanism of SRDS. Finally, the simulation shows that the analytical results agree with numerical simulation.
Effect of mixing on reaction-diffusion kinetics for protein hydrogel-based microchips.
Zubtsov, D A; Ivanov, S M; Rubina, A Yu; Dementieva, E I; Chechetkin, V R; Zasedatelev, A S
2006-03-09
Protein hydrogel-based microchips are being developed for high-throughput evaluation of the concentrations and activities of various proteins. To shorten the time of analysis, the reaction-diffusion kinetics on gel microchips should be accelerated. Here we present the results of the experimental and theoretical analysis of the reaction-diffusion kinetics enforced by mixing with peristaltic pump. The experiments were carried out on gel-based protein microchips with immobilized antibodies under the conditions utilized for on-chip immunoassay. The dependence of fluorescence signals at saturation and corresponding saturation times on the concentrations of immobilized antibodies and antigen in solution proved to be in good agreement with theoretical predictions. It is shown that the enhancement of transport with peristaltic pump results in more than five-fold acceleration of binding kinetics. Our results suggest useful criteria for the optimal conditions for assays on gel microchips to balance high sensitivity and rapid fluorescence saturation kinetics.
An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems
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.
Wave reflection in a reaction-diffusion system: breathing patterns and attenuation of the echo.
Tsyganov, M A; Ivanitsky, G R; Zemskov, E P
2014-05-01
Formation and interaction of the one-dimensional excitation waves in a reaction-diffusion system with the piecewise linear reaction functions of the Tonnelier-Gerstner type are studied. We show that there exists a parameter region where the established regime of wave propagation depends on initial conditions. Wave phenomena with a complex behavior are found: (i) the reflection of waves at a growing distance (the remote reflection) upon their collision with each other or with no-flux boundaries and (ii) the periodic transformation of waves with the jumping from one regime of wave propagation to another (the periodic trigger wave).
Plante, Ianik; Cucinotta, Francis A.
2011-01-01
Radiolytic species are formed approximately 1 ps after the passage of ionizing radiation through matter. After their formation, they diffuse and chemically react with other radiolytic species and neighboring biological molecules, leading to various oxidative damage. Therefore, the simulation of radiation chemistry is of considerable importance to understand how radiolytic species damage biological molecules [1]. The step-by-step simulation of chemical reactions is difficult, because the radiolytic species are distributed non-homogeneously in the medium. Consequently, computational approaches based on Green functions for diffusion-influenced reactions should be used [2]. Recently, Green functions for more complex type of reactions have been published [3-4]. We have developed exact random variate generators of these Green functions [5], which will allow us to use them in radiation chemistry codes. Moreover, simulating chemistry using the Green functions is which is computationally very demanding, because the probabilities of reactions between each pair of particles should be evaluated at each timestep [2]. This kind of problem is well adapted for General Purpose Graphic Processing Units (GPGPU), which can handle a large number of similar calculations simultaneously. These new developments will allow us to include more complex reactions in chemistry codes, and to improve the calculation time. This code should be of importance to link radiation track structure simulations and DNA damage models.
Ducrot, Arnaud; Giletti, Thomas
2014-09-01
In this work we study the asymptotic behaviour of the Kermack-McKendrick reaction-diffusion system in a periodic environment with non-diffusive susceptible population. This problem was proposed by Kallen et al. as a model for the spatial spread for epidemics, where it can be reasonable to assume that the susceptible population is motionless. For arbitrary dimensional space we prove that large classes of solutions of such a system have an asymptotic spreading speed in large time, and that the infected population has some pulse-like asymptotic shape. The analysis of the one-dimensional problem is more developed, as we are able to uncover a much more accurate description of the profile of solutions. Indeed, we will see that, for some initially compactly supported infected population, the profile of the solution converges to some pulsating travelling wave with minimal speed, that is to some entire solution moving at a constant positive speed and whose profile's shape is periodic in time.
Size-controlled synthesis of Cu2O nanoparticles via reaction-diffusion
Badr, Layla; Epstein, Irving R.
2017-02-01
Copper (I) oxide nanoparticles are synthesized by a simple reaction-diffusion process involving Cu+ ions and sodium hydroxide in gelatin. The mean diameter and the size dispersion of the nanoparticles can be controlled by two experimental parameters, the percent of gelatin in the medium and the hydroxide ion concentration. UV-visible spectroscopy, transmission electron microscopy and X-ray diffraction are used to analyze the size, morphology, and chemical composition of the nanoparticles generated.
Limiting behavior of non-autonomous stochastic reaction-diffusion equations on thin domains
Li, Dingshi; Wang, Bixiang; Wang, Xiaohu
2017-02-01
This paper deals with the limiting behavior of stochastic reaction-diffusion equations driven by multiplicative noise and deterministic non-autonomous terms defined on thin domains. We first prove the existence, uniqueness and periodicity of pullback tempered random attractors for the equations in an (n + 1)-dimensional narrow domain, and then establish the upper semicontinuity of these attractors when a family of (n + 1)-dimensional thin domains collapses onto an n-dimensional domain.
Henisch, H K
1991-01-01
Containing illustrations, worked examples, graphs and tables, this book deals with periodic precipitation (also known as Liesegang Ring formation) in terms of mathematical models and their logical consequences, and is entirely concerned with microcomputer analysis and software development. Three distinctive periodic precipitation mechanisms are included: binary diffusion-reaction; solubility modulation, and competitive particle growth. The book provides didactic illustrations of a valuable investigational procedure, in the form of hypothetical experimentation by microcomputer. The development
Solid state diffusion and reaction in ZnO/SiO{sub 2} in thin films
Jakob, A.; Stucki, S.; Schnyder, B.; Koetz, R. [Paul Scherrer Inst. (PSI), Villigen (Switzerland)
1997-06-01
Detoxification of fly ash from waste incineration by evaporating harmful heavy metals is limited by the formation of stable heavy metal-matrix compounds. To study the rate of these heavy metal-matrix reactions, experiments were performed with the diffusion couple ZnO (heavy metal)-SiO{sub 2} (matrix). The atomic concentration profiles after different annealing treatments were analysed by X-ray photoelectron spectroscopy (XPS). (author) 3 figs., 4 refs.
Compact-like kink in a real electrical reaction-diffusion chain
Comte, J.C. [Laboratoire de Physiopathologie des Reseaux Neuronaux du Cycle Veille-Sommeil, CNRS UMR 5167, Faculte de Medecine Laennec 7, Rue Guillaume Paradin, 69372 Lyon Cedex 08 (France)]. E-mail: comtejc@sommeil.univ-lyon1.fr; Marquie, P. [Laboratoire d' Electronique, Informatique et Image (LE2i) UMR CNRS 5158, Aile des Sciences de l' Ingenieur, BP 47870, 21078 Dijon Cedex (France)
2006-07-15
We demonstrate experimentally the compact-like kinks existence in a real electrical reaction-diffusion chain. Our measures show that such entities are strictly localized and consequently present a finite spatial extent. We show equally that the kink velocity is threshold-dependent. A theoretical quantification of the critical coupling under which propagation fails is also achieved and reveals that nonlinear coupling leads to a propagation failure reduction.
Traveling Wave Solutions of Reaction-Diffusion Equations Arising in Atherosclerosis Models
Narcisa Apreutesei
2014-05-01
Full Text Available In this short review article, two atherosclerosis models are presented, one as a scalar equation and the other one as a system of two equations. They are given in terms of reaction-diffusion equations in an infinite strip with nonlinear boundary conditions. The existence of traveling wave solutions is studied for these models. The monostable and bistable cases are introduced and analyzed.
Meng-ge Liu; Wei Yu; Chi-xing Zhou
2006-01-01
The kinetic model for diffusion-controlled intermolecular reaction of homogenous polymer under steady shear was theoretically studied. The classic formalism and the concept of conformation ellipsoids were integrated to get a new equation, which directly correlates the rate constant with shear rate. It was found that the rate constant is not monotonic with shear rate. The scale of rate constant is N-1.5 (N is the length of chains), which is in consistent with de Gennes's result.
Xiang-Chao Shi
2016-02-01
Full Text Available The fractional reaction diffusion equation is one of the popularly used fractional partial differential equations in recent years. The fast Adomian decomposition method is used to obtain the solution of the Cauchy problem. Also, the analytical scheme is extended to the fractional one where the Taylor series is employed. In comparison with the classical Adomian decomposition method, the ratio of the convergence is increased. The method is more reliable for the fractional partial differential equations.
Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems
Li, Zhen; Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em
2015-01-01
We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux a...
Chuangxia Huang
2011-01-01
Full Text Available Stability of reaction-diffusion recurrent neural networks (RNNs with continuously distributed delays and stochastic influence are considered. Some new sufficient conditions to guarantee the almost sure exponential stability and mean square exponential stability of an equilibrium solution are obtained, respectively. Lyapunov's functional method, M-matrix properties, some inequality technique, and nonnegative semimartingale convergence theorem are used in our approach. The obtained conclusions improve some published results.
INFLUENCE OF NOISE AND DELAY ON REACTION-DIFFUSION RECURRENT NEURAL NETWORKS
Li Wu
2006-01-01
In this paper, the influence of the noise and delay upon the stability property of reaction-diffusion recurrent neural networks (RNNs) with the time-varying delay is discussed. The new and easily verifiable conditions to guarantee the mean value exponential stability of an equilibrium solution are derived. The rate of exponential convergence can be estimated by means of a simple computation based on these criteria.
Finite Travelling Waves for a Semilinear Degenerate Reaction-Diffusion System
Shu WANG; Cheng Fu WANG; Dang LUO
2001-01-01
In this paper, the existence and nonexistence of finite travelling waves (FTWs) for a semilinear degenerate reaction-diffusion systemis studied, where 0 ＜αi ＜ 1, mij ≥ 0 and ∑nj=1mij ＞ 0, i,j = 1,.. N. Necessary and sufficientconditions on existence and large time behaviours of FTWs of (I) are obtained by using the matrixtheory, Schauder's fixed point theorem, and upper and lower solutions method.
Giammar, Daniel E; Wang, Fei; Guo, Bin; Surface, J Andrew; Peters, Catherine A; Conradi, Mark S; Hayes, Sophia E
2014-12-16
Reactions of CO2 with magnesium silicate minerals to precipitate magnesium carbonates can result in stable carbon sequestration. This process can be employed in ex situ reactors or during geologic carbon sequestration in magnesium-rich formations. The reaction of aqueous CO2 with the magnesium silicate mineral forsterite was studied in systems with transport controlled by diffusion. The approach integrated bench-scale experiments, an in situ spectroscopic technique, and reactive transport modeling. Experiments were performed using a tube packed with forsterite and open at one end to a CO2-rich solution. The location and amounts of carbonate minerals that formed were determined by postexperiment characterization of the solids. Complementing this ex situ characterization, (13)C NMR spectroscopy tracked the inorganic carbon transport and speciation in situ. The data were compared with the output of reactive transport simulations that accounted for diffusive transport processes, aqueous speciation, and the forsterite dissolution rate. All three approaches found that the onset of magnesium carbonate precipitation was spatially localized about 1 cm from the opening of the forsterite bed. Magnesite was the dominant reaction product. Geochemical gradients that developed in the diffusion-limited zones led to locally supersaturated conditions at specific locations even while the volume-averaged properties of the system remained undersaturated.
Generalized monotone method and numerical approach for coupled reaction diffusion systems
Sowmya, M.; Vatsala, Aghalaya S.
2017-01-01
Study of coupled reaction diffusion systems are very useful in various branches of science and engineering. In this paper, we provide a methodology to construct the solution for the coupled reaction diffusion systems, with initial and boundary conditions, where the forcing function is the sum of an increasing and decreasing function. It is known that the generalized monotone method coupled with coupled lower and upper solutions yield monotone sequences which converges uniformly and monotonically to coupled minimal and maximal solutions. In addition, the interval of existence is guaranteed by the lower and upper solutions, which are relatively easy to compute. Using the lower and upper solutions as the initial approximation, we develop a method to compute the sequence of coupled lower and upper solutions on the interval or on the desired interval of existence. Further, if the uniqueness conditions are satisfied, the coupled minimal and maximal solutions converge to the unique solution of the reaction diffusion systems. We will provide some numerical results as an application of our numerical methodology.
Szalai, István; Cuiñas, Daniel; Takács, Nándor; Horváth, Judit; De Kepper, Patrick
2012-08-06
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.
Ram K. Saxena
2015-04-01
Full Text Available This article is in continuation of the authors research attempts to derive computational solutions of an unified reaction-diffusion equation of distributed order associated with Caputo derivatives as the time-derivative and Riesz-Feller derivative as space derivative. This article presents computational solutions of distributed order fractional reaction-diffusion equations associated with Riemann-Liouville derivatives of fractional orders as the time-derivatives and Riesz-Feller fractional derivatives as the space derivatives. The method followed in deriving the solution is that of joint Laplace and Fourier transforms. The solution is derived in a closed and computational form in terms of the familiar Mittag-Leffler function. It provides an elegant extension of results available in the literature. The results obtained are presented in the form of two theorems. Some results associated specifically with fractional Riesz derivatives are also derived as special cases of the most general result. It will be seen that in case of distributed order fractional reaction-diffusion, the solution comes in a compact and closed form in terms of a generalization of the Kampé de Fériet hypergeometric series in two variables. The convergence of the double series occurring in the solution is also given.
Using R-matrix Theory to Analyze Resonant Reactions
Hale, G.M. [Theoretical Division Los Alamos National Laboratory (United States)
2006-07-01
Full text of publication follows: We begin with a summary of R-matrix theory, formulated in terms of Green's functions that include the Bloch operator to apply the boundary conditions. This is a general approach, not restricted to any particular reaction mechanism, that nevertheless is particularly well-suited to describing resonant reactions. We then give a brief description of the capabilities of the general Los Alamos R-matrix code, EDA. This code can fit the data for any type of measurement for a reaction involving any types of two-body channels (including charged particles and photons), using an automated chi-square minimization algorithm that has quadratic convergence and yields the covariance matrix of the fitting parameters at a local chi-square minimum. This allows covariance information to be produced for the calculated (cross-section) data. As time allows, several examples will be given for light systems, including reactions initiated by n+p ({sup 2}H), n+{sup 6}Li ({sup 7}Li), n+{sup 10}B ({sup 11}B), and n+{sup 16}O ({sup 17}O). These systems have varying numbers of visible resonances, ranging from none in the {sup 2}H system up to many in the {sup 17}O system. However, the same R-matrix approach gives a good description of the data in all cases, several of which were used in the recent IAEA standards evaluation, and in Endf/B7 general-purpose files. Some aspects of the output covariances that result from such R-matrix analyses will be discussed. (authors)
Zheng, Jingjing; Truhlar, Donald G
2012-01-01
Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.
Kleinman, Leonid S.; Red, X. B., Jr.
1995-01-01
An algorithm has been developed for time-dependent forced convective diffusion-reaction having convection by a recirculating flow field within the drop that is hydrodynamically coupled at the interface with a convective external flow field that at infinity becomes a uniform free-streaming flow. The concentration field inside the droplet is likewise coupled with that outside by boundary conditions at the interface. A chemical reaction can take place either inside or outside the droplet, or reactions can take place in both phases. The algorithm has been implemented, and for comparison results are shown here for the case of no reaction in either phase and for the case of an external first order reaction, both for unsteady behavior. For pure interphase mass transfer, concentration isocontours, local and average Sherwood numbers, and average droplet concentrations have been obtained as a function of the physical properties and external flow field. For mass transfer enhanced by an external reaction, in addition to the above forms of results, we present the enhancement factor, with the results now also depending upon the (dimensionless) rate of reaction.
Kleinman, Leonid S.; Reed, X. B., Jr.
1995-01-01
An algorithm has been developed for the forced convective diffusion-reaction problem for convection inside and outside a droplet by a recirculating flow field hydrodynamically coupled at the droplet interface with an external flow field that at infinity becomes a uniform streaming flow. The concentration field inside the droplet is likewise coupled with that outside by boundary conditions at the interface. A chemical reaction can take place either inside or outside the droplet or reactions can take place in both phases. The algorithm has been implemented and results are shown here for the case of no reaction and for the case of an external first order reaction, both for unsteady behavior. For pure interphase mass transfer, concentration isocontours, local and average Sherwood numbers, and average droplet concentrations have been obtained as a function of the physical properties and external flow field. For mass transfer enhanced by an external reaction, in addition to the above forms of results, we present the enhancement factor, with the results now also depending upon the (dimensionless) rate of reaction.
Modeling and finite difference numerical analysis of reaction-diffusion dynamics in a microreactor.
Plazl, Igor; Lakner, Mitja
2010-03-01
A theoretical description with numerical experiments and analysis of the reaction-diffusion processes of homogeneous and non-homogeneous reactions in a microreactor is presented considering the velocity profile for laminar flows of miscible and immiscible fluids in a microchannel at steady-state conditions. A Mathematical model in dimensionless form, containing convection, diffusion, and reaction terms are developed to analyze and to forecast the reactor performance. To examine the performance of different types of reactors, the outlet concentrations for the plug-flow reactor (PFR), and the continuous stirred-tank reactor (CSTR) are also calculated for the case of an irreversible homogeneous reaction of two components. The comparison of efficiency between ideal conventional macroscale reactors and the microreactor is presented for a wide range of operating conditions, expressed as different Pe numbers (0.01 < Pe < 10). The numerical procedure of complex non-linear systems based on an implicit finite-difference method improved by non-equidistant differences is proposed.
On the Finite Line Source Problem in Diffusion Theory
Mikkelsen, Torben; Troen, Ib; Larsen, Søren Ejling
1982-01-01
A simple formula for calculating dispersion from a continuous finite line source, placed at right angles to the mean wind direction, is derived on the basis of statistical theory. Comparison is made with the virtual source concept usually used and this is shown to be correct only in the limit where...
Reactions to others' mistakes: an empirical test of fairness theory.
Williams, Kevin J; Nicklin, Jessica M
2009-10-01
Drawing on fairness theory (R. Folger & R. Cropanzano, 1998, 2001), the authors examined undergraduates' reactions to advisor mistakes made in an academic advisement scenario. The authors hypothesized that perceived fairness, blame, and behavioral intentions to address wrongdoing would be influenced by outcome severity and the nature of the mistake (knowledgeable mistakes vs. ignorant mistakes; errors of commission vs. errors of omission). Results partially supported the hypotheses. Participants perceived scenarios as less fair and expressed higher intent to address the wrongdoing when the consequences were high in severity and when a knowledgeable person made the mistake. Participants attributed significantly more blame to the advisor in the high severity outcome conditions. Counterfactual thoughts mediated the effects of target knowledge but not outcome severity. The authors discuss theoretical and practical implications.
Berlowitz, D.R.
1996-11-01
In the last few decades the negative impact by humans on the thin atmospheric layer enveloping the earth, the basis for life on this planet, has increased steadily. In order to halt, or at least slow down this development, the knowledge and study of these anthropogenic influence has to be increased and possible remedies have to be suggested. An important tool for these studies are computer models. With their help the atmospheric system can be approximated and the various processes, which have led to the current situation can be quantified. They also serve as an instrument to assess short or medium term strategies to reduce this human impact. However, to assure efficiency as well as accuracy, a careful analysis of the numerous processes involved in the dispersion of pollutants in the atmosphere is called for. This should help to concentrate on the essentials and also prevent excessive usage of sometimes scarce computing resources. The basis of the presented work is the EUMAC Zooming Model (ETM), and particularly the component calculating the dispersion of pollutants in the atmosphere, the model MARS. The model has two main parts: an explicit solver, where the advection and the horizontal diffusion of pollutants are calculated, and an implicit solution mechanism, allowing the joint computation of the change of concentration due to chemical reactions, coupled with the respective influence of the vertical diffusion of the species. The aim of this thesis is to determine particularly the influence of the horizontal components of the turbulent diffusion on the existing implicit solver of the model. Suggestions for a more comprehensive inclusion of the full three dimensional diffusion operator in the implicit solver are made. This is achieved by an appropriate operator splitting. A selection of numerical approaches to tighten the coupling of the diffusion processes with the calculation of the applied chemical reaction mechanisms are examined. (author) figs., tabs., refs.
Simulations of pattern dynamics for reaction-diffusion systems via SIMULINK.
Wang, Kaier; Steyn-Ross, Moira L; Steyn-Ross, D Alistair; Wilson, Marcus T; Sleigh, Jamie W; Shiraishi, Yoichi
2014-04-11
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. 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. 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-diagram does not require high-level programming
Evaluating candidate reactions to selection practices using organisational justice theory.
Patterson, Fiona; Zibarras, Lara; Carr, Victoria; Irish, Bill; Gregory, Simon
2011-03-01
This study aimed to examine candidate reactions to selection practices in postgraduate medical training using organisational justice theory. We carried out three independent cross-sectional studies using samples from three consecutive annual recruitment rounds. Data were gathered from candidates applying for entry into UK general practice (GP) training during 2007, 2008 and 2009. Participants completed an evaluation questionnaire immediately after the short-listing stage and after the selection centre (interview) stage. Participants were doctors applying for GP training in the UK. Main outcome measures were participants' evaluations of the selection methods and perceptions of the overall fairness of each selection stage (short-listing and selection centre). A total of 23,855 evaluation questionnaires were completed (6893 in 2007, 10,497 in 2008 and 6465 in 2009). Absolute levels of perceptions of fairness of all the selection methods at both the short-listing and selection centre stages were consistently high over the 3years. Similarly, all selection methods were considered to be job-related by candidates. However, in general, candidates considered the selection centre stage to be significantly fairer than the short-listing stage. Of all the selection methods, the simulated patient consultation completed at the selection centre stage was rated as the most job-relevant. This is the first study to use a model of organisational justice theory to evaluate candidate reactions during selection into postgraduate specialty training. The high-fidelity selection methods are consistently viewed as more job-relevant and fairer by candidates. This has important implications for the design of recruitment systems for all specialties and, potentially, for medical school admissions. Using this approach, recruiters can systematically compare perceptions of the fairness and job relevance of various selection methods. © Blackwell Publishing Ltd 2011.
Wang, Bi-Yao; Li, Ze-Rong; Tan, Ning-Xin; Yao, Qian; Li, Xiang-Yuan
2013-04-25
We present a further interpretation of reaction class transition state theory (RC-TST) proposed by Truong et al. for the accurate calculation of rate coefficients for reactions in a class. It is found that the RC-TST can be interpreted through the isodesmic reaction method, which is usually used to calculate reaction enthalpy or enthalpy of formation for a species, and the theory can also be used for the calculation of the reaction barriers and reaction enthalpies for reactions in a class. A correction scheme based on this theory is proposed for the calculation of the reaction barriers and reaction enthalpies for reactions in a class. To validate the scheme, 16 combinations of various ab initio levels with various basis sets are used as the approximate methods and CCSD(T)/CBS method is used as the benchmarking method in this study to calculate the reaction energies and energy barriers for a representative set of five reactions from the reaction class: R(c)CH(R(b))CR(a)CH2 + OH(•) → R(c)C(•)(R(b))CR(a)CH2 + H2O (R(a), R(b), and R(c) in the reaction formula represent the alkyl or hydrogen). Then the results of the approximate methods are corrected by the theory. The maximum values of the average deviations of the energy barrier and the reaction enthalpy are 99.97 kJ/mol and 70.35 kJ/mol, respectively, before correction and are reduced to 4.02 kJ/mol and 8.19 kJ/mol, respectively, after correction, indicating that after correction the results are not sensitive to the level of the ab initio method and the size of the basis set, as they are in the case before correction. Therefore, reaction energies and energy barriers for reactions in a class can be calculated accurately at a relatively low level of ab initio method using our scheme. It is also shown that the rate coefficients for the five representative reactions calculated at the BHandHLYP/6-31G(d,p) level of theory via our scheme are very close to the values calculated at CCSD(T)/CBS level. Finally, reaction
New theory of diffusive and coherent nature of optical wave via a quantum walk
Ide, Yusuke; Konno, Norio; Matsutani, Shigeki; Mitsuhashi, Hideo
2017-08-01
We propose a new theory on a relation between diffusive and coherent nature in one dimensional wave mechanics based on a quantum walk. It is known that the quantum walk in homogeneous matrices provides the coherent property of wave mechanics. Using the recent result of a localization phenomenon in a one-dimensional quantum walk (Konno, 2010), we numerically show that the randomized localized matrices suppress the coherence and give diffusive nature.
John A. Norton; Frank M. Bass
1987-01-01
This study deals with the dynamic sales behavior of successive generations of high-technology products. New technologies diffuse through a population of potential buyers over time. Therefore, diffusion theory models are related to this demand growth. Furthermore, successive generations of a technology compete with earlier ones, and that behavior is the subject of models of technological substitution. Building upon the Bass (Bass, F. M. 1969. A new-product growth model for consumer durables. M...
Nonlinear Theory of Anomalous Diffusion and Application to Fluorescence Correlation Spectroscopy
Boon, Jean Pierre; Lutsko, James F.
2015-12-01
The nonlinear theory of anomalous diffusion is based on particle interactions giving an explicit microscopic description of diffusive processes leading to sub-, normal, or super-diffusion as a result of competitive effects between attractive and repulsive interactions. We present the explicit analytical solution to the nonlinear diffusion equation which we then use to compute the correlation function which is experimentally measured by correlation spectroscopy. The theoretical results are applicable in particular to the analysis of fluorescence correlation spectroscopy of marked molecules in biological systems. More specifically we consider the cases of fluorescently labeled lipids in the plasma membrane and of fluorescent apoferritin (a spherically shaped oligomer) in a crowded dextran solution and we find that the nonlinear correlation spectra reproduce very well the experimental data indicating sub-diffusive molecular motion.
Studies of the accuracy of time integration methods for reaction-diffusion equations
Ropp, David L.; Shadid, John N.; Ober, Curtis C.
2004-03-01
In this study we present numerical experiments of time integration methods applied to systems of reaction-diffusion equations. Our main interest is in evaluating the relative accuracy and asymptotic order of accuracy of the methods on problems which exhibit an approximate balance between the competing component time scales. Nearly balanced systems can produce a significant coupling of the physical mechanisms and introduce a slow dynamical time scale of interest. These problems provide a challenging test for this evaluation and tend to reveal subtle differences between the various methods. The methods we consider include first- and second-order semi-implicit, fully implicit, and operator-splitting techniques. The test problems include a prototype propagating nonlinear reaction-diffusion wave, a non-equilibrium radiation-diffusion system, a Brusselator chemical dynamics system and a blow-up example. In this evaluation we demonstrate a "split personality" for the operator-splitting methods that we consider. While operator-splitting methods often obtain very good accuracy, they can also manifest a serious degradation in accuracy due to stability problems.
Saxena, R. K.; Mathai, A. M.; Haubold, H. J.
2015-10-01
This paper deals with the investigation of the computational solutions of an unified fractional reaction-diffusion equation, which is obtained from the standard diffusion equation by replacing the time derivative of first order by the generalized fractional time-derivative defined by Hilfer (2000), the space derivative of second order by the Riesz-Feller fractional derivative and adding the function ϕ (x, t) which is a nonlinear function governing reaction. The solution is derived by the application of the Laplace and Fourier transforms in a compact and closed form in terms of the H-function. The main result obtained in this paper provides an elegant extension of the fundamental solution for the space-time fractional diffusion equation obtained earlier by Mainardi et al. (2001, 2005) and a result very recently given by Tomovski et al. (2011). Computational representation of the fundamental solution is also obtained explicitly. Fractional order moments of the distribution are deduced. At the end, mild extensions of the derived results associated with a finite number of Riesz-Feller space fractional derivatives are also discussed.
Reaction-diffusion systems in natural sciences and new technology transfer
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.
The DNA Binding Activity of p53 Displays Reaction-Diffusion Kinetics
Hinow, Peter; Rogers, Carl E.; Barbieri, Christopher E.; Pietenpol, Jennifer A.; Kenworthy, Anne K.; DiBenedetto, Emmanuele
2006-01-01
The tumor suppressor protein p53 plays a key role in maintaining the genomic stability of mammalian cells and preventing malignant transformation. In this study, we investigated the intracellular diffusion of a p53-GFP fusion protein using confocal fluorescence recovery after photobleaching. We show that the diffusion of p53-GFP within the nucleus is well described by a mathematical model for diffusion of particles that bind temporarily to a spatially homogeneous immobile structure with binding and release rates k1 and k2, respectively. The diffusion constant of p53-GFP was estimated to be Dp53-GFP = 15.4 μm2 s−1, significantly slower than that of GFP alone, DGFP = 41.6 μm2 s−1. The reaction rates of the binding and unbinding of p53-GFP were estimated as k1 = 0.3 s−1 and k2 = 0.4 s−1, respectively, values suggestive of nonspecific binding. Consistent with this finding, the diffusional mobilities of tumor-derived sequence-specific DNA binding mutants of p53 were indistinguishable from that of the wild-type protein. These data are consistent with a model in which, under steady-state conditions, p53 is latent and continuously scans DNA, requiring activation for sequence-specific DNA binding. PMID:16603489
Yamada, H; Ito, M
1998-01-01
The amoeboid organism, the plasmodium of Physarum polycephalum, behaves on the basis of spatio-temporal pattern formation by local contraction-oscillators. This biological system can be regarded as a reaction-diffusion system which has spatial interaction by active flow of protoplasmic sol in the cell. Paying attention to the physiological evidence that the flow is determined by contraction pattern in the plasmodium, a reaction-diffusion system having self-determined flow arises. Such a coupling of reaction-diffusion-advection is a characteristic of the biological system, and is expected to relate with control mechanism of amoeboid behaviours. Hence, we have studied effects of the self-determined flow on pattern formation of simple reaction-diffusion systems. By weakly nonlinear analysis near a trivial solution, the envelope dynamics follows the complex Ginzburg-Landau type equation just after bifurcation occurs at finite wave number. The flow term affects the nonlinear term of the equation through the critic...
Korneev, V. G.
2016-11-01
Efficiency of the error control of numerical solutions of partial differential equations entirely depends on the two factors: accuracy of an a posteriori error majorant and the computational cost of its evaluation for some test function/vector-function plus the cost of the latter. In the paper consistency of an a posteriori bound implies that it is the same in the order with the respective unimprovable a priori bound. Therefore, it is the basic characteristic related to the first factor. The paper is dedicated to the elliptic diffusion-reaction equations. We present a guaranteed robust a posteriori error majorant effective at any nonnegative constant reaction coefficient (r.c.). For a wide range of finite element solutions on a quasiuniform meshes the majorant is consistent. For big values of r.c. the majorant coincides with the majorant of Aubin (1972), which, as it is known, for relatively small r.c. (< ch -2 ) is inconsistent and looses its sense at r.c. approaching zero. Our majorant improves also some other majorants derived for the Poisson and reaction-diffusion equations.
High Curie temperature Mn5Ge3 thin films produced by non-diffusive reaction
Assaf, E.; Portavoce, A.; Hoummada, K.; Bertoglio, M.; Bertaina, S.
2017-02-01
Polycrystalline Mn5Ge3 thin films were produced on SiO2 using magnetron sputtering and reactive diffusion (RD) or non-diffusive reaction (NDR). In situ X-ray diffraction and atomic force microscopy were used to determine the layer structures, and magnetic force microscopy, superconducting quantum interference device, and ferromagnetic resonance were used to determine their magnetic properties. RD-mediated layers exhibit similar magnetic properties as molecular beam epitaxy-grown monocrystalline Mn5Ge3 thin films, while NDR-mediated layers show magnetic properties similar to monocrystalline C-doped Mn5Ge3Cx thin films with 0.1 ≤ x ≤ 0.2. NDR appears as a complementary metal oxide semi-conductor-compatible efficient method to produce good magnetic quality high-Curie temperature Mn5Ge3 thin films.
A Lagrangian study of scalar diffusion in isotropic turbulence with chemical reaction
Mitarai, S.; Riley, J. J.; Kosály, G.
2003-12-01
Direct numerical simulations are performed of a single-step, nonpremixed, Arrhenius-type reaction developing in isotropic, incompressible, decaying turbulence, for conditions where flame extinction and re-ignition occur. The Lagrangian characteristics of scalar diffusion, information necessary for modeling approaches such as some implementations of probability density function (PDF) methods, are investigated by tracking fluid particles. Focusing on the mixture fraction and temperature as the scalar variables of interest, fluid particles are characterized as continuously burning or noncontinuously burning based upon their recent time history, and noncontinuously burning particles are further characterized based upon their initial regions relative to the flame zone. The behavior of the mixture fraction and temperature fields is contrasted for the different types of particles characterized. Significant differences among these characterized particles are found, for example, in the unclosed conditional expectations of scalar diffusion appearing in the composition PDF equations.
On the Statistics of Reaction-Diffusion Simulations for Molecular Communication
Noel, Adam; Schober, Robert
2015-01-01
A molecule traveling in a realistic propagation environment can experience stochastic interactions with other molecules and the environment boundary. The statistical behavior of some isolated phenomena, such as dilute unbounded molecular diffusion, are well understood. However, the coupling of multiple interactions can impede closed-form analysis, such that simulations are required to determine the statistics. This paper compares the statistics of molecular reaction-diffusion simulation models from the perspective of molecular communication systems. Microscopic methods track the location and state of every molecule, whereas mesoscopic methods partition the environment into virtual containers that hold molecules. The properties of each model are described and compared with a hybrid of both models. Simulation results also assess the accuracy of Poisson and Gaussian approximations of the underlying Binomial statistics.
Critical behavior in reaction-diffusion systems exhibiting absorbing phase transition
Ódor, G
2003-01-01
Phase transitions of reaction-diffusion systems with site occupation restriction and with particle creation that requires n>1 parents and where explicit diffusion of single particles (A) exists are reviewed. Arguments based on mean-field approximation and simulations are given which support novel kind of non-equilibrium criticality. These are in contradiction with the implications of a suggested phenomenological, multiplicative noise Langevin equation approach and with some of recent numerical analysis. Simulation results for the one and two dimensional binary spreading 2A -> 4A, 4A -> 2A model display a new type of mean-field criticality characterized by alpha=1/3 and beta=1/2 critical exponents suggested in cond-mat/0210615.
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.
A Novel Characteristic Expanded Mixed Method for Reaction-Convection-Diffusion Problems
Yang Liu
2013-01-01
Full Text Available A novel characteristic expanded mixed finite element method is proposed and analyzed for reaction-convection-diffusion problems. The diffusion term ∇·(a(x,t∇u is discretized by the novel expanded mixed method, whose gradient belongs to the square integrable space instead of the classical H(div;Ω space and the hyperbolic part d(x(∂u/∂t+c(x,t·∇u is handled by the characteristic method. For a priori error estimates, some important lemmas based on the novel expanded mixed projection are introduced. The fully discrete error estimates based on backward Euler scheme are obtained. Moreover, the optimal a priori error estimates in L2- and H1-norms for the scalar unknown u and a priori error estimates in (L22-norm for its gradient λ and its flux σ (the coefficients times the negative gradient are derived. Finally, a numerical example is provided to verify our theoretical results.
The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules
Seitaridou, Effrosyni
2014-01-01
Simulating the evolution of a chemically reacting system using the bimolecular propensity function, as is done by the stochastic simulation algorithm and its reaction-diffusion extension, entails making statistically inspired guesses as to where the reactant molecules are at any given time. Those guesses will be physically justified if the system is dilute and well-mixed in the reactant molecules. Otherwise, an accurate simulation will require the extra effort and expense of keeping track of the positions of the reactant molecules as the system evolves. One molecule-tracking algorithm that pays careful attention to the physics of molecular diffusion is the enhanced Green's function reaction dynamics (eGFRD) of Takahashi, Tănase-Nicola, and ten Wolde [Proc. Natl. Acad. Sci. U.S.A.141, 2473 (2010)]. We introduce here a molecule-tracking algorithm that has the same theoretical underpinnings and strategic aims as eGFRD, but a different implementation procedure. Called the small-voxel tracking algorithm (SVTA), it combines the well known voxel-hopping method for simulating molecular diffusion with a novel procedure for rectifying the unphysical predictions of the diffusion equation on the small spatiotemporal scale of molecular collisions. Indications are that the SVTA might be more computationally efficient than eGFRD for the problematic class of non-dilute systems. A widely applicable, user-friendly software implementation of the SVTA has yet to be developed, but we exhibit some simple examples which show that the algorithm is computationally feasible and gives plausible results. PMID:25527927
Liming WU; Zhengliang ZHANG
2006-01-01
We establish Talagrand's T2-transportation inequalities for infinite dimensional dissipative diffusions with sharp constants, through Galerkin type's approximations and the known results in the finite dimensional case. Furthermore in the additive noise case we prove also logarithmic Sobolev inequalities with sharp constants. Applications to ReactionDiffusion equations are provided.
BHARDWAJ S B; SINGH RAM MEHAR; SHARMA KUSHAL; MISHRA S C
2016-06-01
Attempts have been made to explore the exact periodic and solitary wave solutions of nonlinear reaction diffusion (RD) equation involving cubic–quintic nonlinearity along with timedependent convection coefficients. Effect of varying model coefficients on the physical parameters of solitary wave solutions is demonstrated. Depending upon the parametric condition, the periodic,double-kink, bell and antikink-type solutions for cubic–quintic nonlinear reaction-diffusion equation are extracted. Such solutions can be used to explain various biological and physical phenomena.
Eskew, Matthew W.; Harrison, Jason; Simoyi, Reuben H.
2016-11-01
Oxidation reactions of thiourea by chlorite in a Hele-Shaw cell are excitable, autocatalytic, exothermic, and generate a lateral instability upon being triggered by the autocatalyst. Reagent concentrations used to develop convective instabilities delivered a temperature jump at the wave front of 2.1 K. The reaction zone was 2 mm and due to normal cooling after the wave front, this generated a spike rather than the standard well-studied front propagation. The reaction front has solutal and thermal contributions to density changes that act in opposite directions due to the existence of a positive isothermal density change in the reaction. The competition between these effects generates thermal plumes. The fascinating feature of this system is the coexistence of plumes and fingering in the same solution which alternate in frequency as the front propagates, generating hot and cold spots within the Hele-Shaw cell, and subsequently spatiotemporal inhomogeneities. The small ΔT at the wave front generated thermocapillary convection which competed effectively with thermogravitational forces at low Eötvös Numbers. A simplified reaction-diffusion-convection model was derived for the system. Plume formation is heavily dependent on boundary effects from the cell dimensions. This work was supported by Grant No. CHE-1056366 from the NSF and a Research Professor Grant from the University of KwaZulu-Natal.
Lacitignola, Deborah; Bozzini, Benedetto; Frittelli, Massimo; Sgura, Ivonne
2017-07-01
The present paper deals with the pattern formation properties of a specific morpho-electrochemical reaction-diffusion model on a sphere. The physico-chemical background to this study is the morphological control of material electrodeposited onto spherical particles. The particular experimental case of interest refers to the optimization of novel metal-air flow batteries and addresses the electrodeposition of zinc onto inert spherical supports. Morphological control in this step of the high-energy battery operation is crucial to the energetic efficiency of the recharge process and to the durability of the whole energy-storage device. To rationalise this technological challenge within a mathematical modeling perspective, we consider the reaction-diffusion system for metal electrodeposition introduced in [Bozzini et al., J. Solid State Electr.17, 467-479 (2013)] and extend its study to spherical domains. Conditions are derived for the occurrence of the Turing instability phenomenon and the steady patterns emerging at the onset of Turing instability are investigated. The reaction-diffusion system on spherical domains is solved numerically by means of the Lumped Surface Finite Element Method (LSFEM) in space combined with the IMEX Euler method in time. The effect on pattern formation of variations in the domain size is investigated both qualitatively, by means of systematic numerical simulations, and quantitatively by introducing suitable indicators that allow to assign each pattern to a given morphological class. An experimental validation of the obtained results is finally presented for the case of zinc electrodeposition from alkaline zincate solutions onto copper spheres.
Breathing spiral waves in the chlorine dioxide-iodine-malonic acid reaction-diffusion system
Berenstein, Igal; Muñuzuri, Alberto P.; Yang, Lingfa; Dolnik, Milos; Zhabotinsky, Anatol M.; Epstein, Irving R.
2008-08-01
Breathing spiral waves are observed in the oscillatory chlorine dioxide-iodine-malonic acid reaction-diffusion system. The breathing develops within established patterns of multiple spiral waves after the concentration of polyvinyl alcohol in the feeding chamber of a continuously fed, unstirred reactor is increased. The breathing period is determined by the period of bulk oscillations in the feeding chamber. Similar behavior is obtained in the Lengyel-Epstein model of this system, where small amplitude parametric forcing of spiral waves near the spiral wave frequency leads to the formation of breathing spiral waves in which the period of breathing is equal to the period of forcing.
Threshold phenomena for symmetric decreasing solutions of reaction-diffusion equations
Muratov, C B
2012-01-01
We study the long time behavior of solutions of the Cauchy problem for nonlinear reaction-diffusion equations in one space dimension with the nonlinearity of bistable, ignition or monostable type. We prove a one-to-one relation between the long time behavior of the solution and the limit value of its energy for symmetric decreasing initial data in $L^2$ under minimal assumptions on the nonlinearities. The obtained relation allows to establish sharp threshold results between propagation and extinction for monotone families of initial data in the considered general setting.
Parabolic inverse convection-diffusion-reaction problem solved using an adaptive parametrization
Deolmi, Giulia
2011-01-01
This paper investigates the solution of a parabolic inverse problem based upon the convection-diffusion-reaction equation, which can be used to estimate both water and air pollution. We will consider both known and unknown source location: while in the first case the problem is solved using a projected damped Gauss-Newton, in the second one it is ill-posed and an adaptive parametrization with time localization will be adopted to regularize it. To solve the optimization loop a model reduction technique (Proper Orthogonal Decomposition) is used.
Vogel, Bernhard; Vogel, Heike; Fiedler, Franz
1994-01-01
A model system is presented that takes into account the main physical and chemical processes on the regional scale here in an area of 100x100 sq km. The horizontal gridsize used is 2x2 sq km. For a case study, it is demonstrated how the model system can be used to separate the contributions of the processes advection, turbulent diffusion, and chemical reactions to the diurnal cycle of ozone. In this way, typical features which are visible in observations and are reproduced by the numerical simulations can be interpreted.
Raftari, Behrouz; Vuik, Kees
2015-01-01
The charging of insulating samples degrades the quality and complicates the interpretation of images in scanning electron microscopy and is important in other applications, such as particle detectors. In this paper we analyze this nontrivial phenomenon on different time scales employing the drift-diffusion-reaction approach augmented with the trapping rate equations and a realistic semi-empirical source function describing the pulsed nature of the electron beam. We consider both the fast processes following the impact of a single primary electron, the slower dynamics resulting from the continuous bombardment of a sample, and the eventual approach to the steady-state regime.
Zoumpanioti, M; Parmaklis, P; de María, P Domínguez; Stamatis, H; Sinisterra, J V; Xenakis, A
2008-09-01
Rhizomucor miehei lipase was immobilized in hydroxy(propylmethyl) cellulose or agar gels containing lecithin or AOT microemulsions. The effect of the diffusion of substrates and products to this catalyst was studied, as well as the effect of temperature on the initial rate of ester synthesis. The composition of the gel affects the reaction rate due to mass transport phenomena. The apparent activation energies were higher for the systems based on agar, independently of the microemulsion used, and lower for the systems based on AOT microemulsions, independently of the polymer used.
Traveling waves in a nonlocal, piecewise linear reaction-diffusion population model
Autry, E. A.; Bayliss, A.; Volpert, V. A.
2017-08-01
We consider an analytically tractable switching model that is a simplification of a nonlocal, nonlinear reaction-diffusion model of population growth where we take the source term to be piecewise linear. The form of this source term allows us to consider both the monostable and bistable versions of the problem. By transforming to a traveling frame and choosing specific kernel functions, we are able to reduce the problem to a system of algebraic equations. We construct solutions and examine the propagation speed and monotonicity of the resulting waves.
Unfolding-based corrector estimates for a reaction-diffusion system predicting concrete corrosion
Fatima, Tasnim; Ptashnyk, Mariya
2011-01-01
We use the periodic unfolding technique to derive corrector estimates for a reaction-diffusion system describing concrete corrosion penetration in the sewer pipes. The system, defined in a periodically-perforated domain, is semi-linear, partially dissipative, and coupled via a non-linear ordinary differential equation posed on the solid-water interface at the pore level. After discussing the solvability of the pore scale model, we apply the periodic unfolding techniques (adapted to treat the presence of perforations) not only to get upscaled model equations, but also to prepare a proper framework for getting a convergence rate (corrector estimates) of the averaging procedure.
A Reaction-diffusion System with Nonlinear Absorption Terms and Boundary Flux
2008-01-01
This paper deals with a reaction-diffusion system with nonlinear absorption terms and boundary flux. As results of interactions among the six nonlinear terms in the system, some sufficient conditions on global existence and finite time blow-up of the solutions are described via all the six nonlinear exponents appearing in the six nonlinear terms. In addition, we also show the influence of the coefficients of the absorption terms as well as the geometry of the domain to the global existence and finite time blow-up of the solutions for some cases. At last, some numerical results are given.
Positional information and reaction-diffusion: two big ideas in developmental biology combine.
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.
"Depletion": A Game with Natural Rules for Teaching Reaction Rate Theory.
Olbris, Donald J.; Herzfeld, Judith
2002-01-01
Depletion is a game that reinforces central concepts of reaction rate theory through simulation. Presents the game with a set of follow-up questions suitable for either a quiz or discussion. Also describes student reaction to the game. (MM)
Dynamical Analysis of a Delayed Reaction-Diffusion Predator-Prey System
Yanuo Zhu
2012-01-01
Full Text Available This work deals with the analysis of a delayed diffusive predator-prey system under Neumann boundary conditions. The dynamics are investigated in terms of the stability of the nonnegative equilibria and the existence of Hopf bifurcation by analyzing the characteristic equations. The direction of Hopf bifurcation and the stability of bifurcating periodic solution are also discussed by employing the normal form theory and the center manifold reduction. Furthermore, we prove that the positive equilibrium is asymptotically stable when the delay is less than a certain critical value and unstable when the delay is greater than the critical value.
Stability and Bifurcation in a Delayed Reaction-Diffusion Equation with Dirichlet Boundary Condition
Guo, Shangjiang; Ma, Li
2016-04-01
In this paper, we study the dynamics of a diffusive equation with time delay subject to Dirichlet boundary condition in a bounded domain. The existence of spatially nonhomogeneous steady-state solution is investigated by applying Lyapunov-Schmidt reduction. The existence of Hopf bifurcation at the spatially nonhomogeneous steady-state solution is derived by analyzing the distribution of the eigenvalues. The direction of Hopf bifurcation and stability of the bifurcating periodic solution are also investigated by means of normal form theory and center manifold reduction. Moreover, we illustrate our general results by applications to the Nicholson's blowflies models with one- dimensional spatial domain.
Rate of diffusion-limited reactions for a fractal aggregate of reactive spheres
Tseng, Chin-Yao; Tsao, Heng-Kwong
2002-08-01
We study the reaction rate for a fractal cluster of perfectly absorbing, stationary spherical sinks in a medium containing a mobile reactant. The effectiveness factor eta, which is defined as the ratio of the total reaction rate of the cluster to that without diffusional interactions, is calculated. The scaling behavior of eta is derived for arbitrary fractal dimension based on the Kirkwood-Riseman approximation. The asymptotic as well as the finite size scaling of eta are confirmed numerically by the method of multipole expansion, which has been proven to be an excellent approximation. The fractal assembly is made of N spheres with its dimension varying from D1, eta][approx(ln N)-1 for D=1, and eta][approxN0 for D1 the screening effect of diffusive interactions grows with the size, for Ddecays with decreasing D. The conclusion is also applicable to transport phenomena like dissolution, heat conduction, and sedimentation.
Cluster geometry and survival probability in systems driven by reaction-diffusion dynamics
Windus, Alastair; Jensen, Henrik J [The Institute for Mathematical Sciences, 53 Prince' s Gate, South Kensington, London SW7 2PG (United Kingdom)], E-mail: h.jensen@imperial.ac.uk
2008-11-15
We consider a reaction-diffusion model incorporating the reactions A{yields}{phi}, A{yields}2A and 2A{yields}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.
Complex patterns in reaction-diffusion systems a tale of two front instabilities
Hagberg, A; Aric Hagberg; Ehud Meron
1994-01-01
Two front instabilities in a reaction-diffusion system are shown to lead to the formation of complex patterns. The first is an instability to transverse modulations that drives the formation of labyrinthine patterns. The second is a Nonequilibrium Ising-Bloch (NIB) bifurcation that renders a stationary planar front unstable and gives rise to a pair of counterpropagating fronts. Near the NIB bifurcation the relation of the front velocity to curvature is highly nonlinear and transitions between counterpropagating fronts become feasible. Nonuniformly curved fronts may undergo local front transitions that nucleate spiral-vortex pairs. These nucleation events provide the ingredient needed to initiate spot splitting and spiral turbulence. Similar spatio-temporal processes have been observed recently in the ferrocyanide-iodate-sulfite reaction.
Cluster geometry and survival probability in systems driven by reaction diffusion dynamics
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.
Effective field theory as a limit of R-matrix theory for light nuclear reactions
Hale, Gerald M.; Brown, Lowell S.; Paris, Mark W.
2014-01-01
We study the zero channel radius limit of Wigner's R-matrix theory for two cases and show that it corresponds to nonrelativistic effective quantum field theory. We begin with the simple problem of single-channel np elastic scattering in the 1S0 channel. The dependence of the R-matrix width g2 and level energy Eλ on the channel radius a for fixed scattering length a0 and effective range r0 is determined. It is shown that these quantities have a simple pole for a critical value of the channel radius, ap=ap(a0,r0). The 3H(d ,n)4He reaction cross section, analyzed with a two-channel effective field theory in the previous paper [Phys. Rev. C 89, 014622 (2014), 10.1103/PhysRevC.89.014622], is then examined using a two-channel, single-level R-matrix parametrization. The resulting S matrix is shown to be identical in these two representations in the limit that R-matrix channel radii are taken to zero. This equivalence is established by giving the relationship between the low-energy constants of the effective field theory (couplings gc and mass m*) and the R-matrix parameters (reduced width amplitudes γc and level energy Eλ). An excellent three-parameter fit to the observed astrophysical factor S¯ is found for "unphysical" values of the reduced widths, γc2<0.
Effective field theory as a limit of R-matrix theory for light nuclear reactions
Hale, Gerald M; Paris, Mark W
2014-01-01
We study the zero channel radius limit of Wigner's R-matrix theory for two cases, and show that it corresponds to non-relativistic effective quantum field theory. We begin with the simple problem of single-channel n-p elastic scattering in the 1S0 channel. The dependence of the R matrix width and level energy on the channel radius, "a" for fixed scattering length a0 and effective range r0 is determined. It is shown that these quantities have a simple pole for a critical value of the channel radius. The 3H(d,n)4He reaction cross section, analyzed with a two-channel effective field theory in the previous paper, is then examined using a two-channel, single-level R-matrix parametrization. The resulting S matrix is shown to be identical in these two representations in the limit that R-matrix channel radii are taken to zero. This equivalence is established by giving the relationship between the low-energy constants of the effective field theory (couplings and mass) and the R-matrix parameters (reduced width amplitu...
Diffusion theory and knowledge dissemination, utilization, and integration in public health.
Green, Lawrence W; Ottoson, Judith M; García, César; Hiatt, Robert A
2009-01-01
Legislators and their scientific beneficiaries express growing concerns that the fruits of their investment in health research are not reaching the public, policy makers, and practitioners with evidence-based practices. Practitioners and the public lament the lack of relevance and fit of evidence that reaches them and barriers to their implementation of it. Much has been written about this gap in medicine, much less in public health. We review the concepts that have guided or misguided public health in their attempts to bridge science and practice through dissemination and implementation. Beginning with diffusion theory, which inspired much of public health's work on dissemination, we compare diffusion, dissemination, and implementation with related notions that have served other fields in bridging science and practice. Finally, we suggest ways to blend diffusion with other theory and evidence in guiding a more decentralized approach to dissemination and implementation in public health, including changes in the ways we produce the science itself.
Diffusion theory for light propagation in biological tissue : limitations and adaptations
Graaff, R; Hoenders, BJ; Tuchin, VV
2005-01-01
Diffusion theory is an approximation of the equation of radiative transport, that is used to describe light propagation in turbid media. This approximation is very popular because of its simplicity, possibilities to describe time-resolved light propagation, and for its appeal to physical intuition.
Pousttchi, Key; Wiedemann, Dietmar Georg
2005-01-01
An important condition of business profit in mobile commerce offers in the B2C area is the availability of wide accepted mobile payment procedures. The contribution considers mobile payment on the perspective of diffusion theory and analyses which relative advantages could arise by using mobile payment procedures.
Grgurovic, Maja
2014-01-01
This study investigates technology-enhanced blended learning in an English as a Second Language (ESL) program from the theoretical perspective of Diffusion of Innovations theory. The study first established that the use of a learning management system (LMS) in two ESL classes represented an educational innovation. Next, the innovation attributes…
Knuth, Rebecca
1997-01-01
Discusses the appropriateness of applying diffusion theory to the study of five factors that influence school library development globally: (1) the evolution of, acceptance of, and consensus on a viable service-delivery model; (2) influence exercised by professional organizations; (3) generation of acceptable standards; (4) overt government…
Kinetic theory of self-diffusion in a moderately dense one-component plasma
Suttorp, L.G.
1980-01-01
A microscopic description of self-diffusion in a moderately dense classical one-component plasma is given on the basis of renormalized kinetic theory. The effects of close binary collisions and of collective interactions in the plasma are taken into account through the use of a composite memory kern
Mothers "Google It Up:" Extending Communication Channel Behavior in Diffusion of Innovations Theory.
Sundstrom, Beth
2016-01-01
This study employed qualitative methods, conducting 44 in-depth interviews with biological mothers of newborns to understand women's perceptions and use of new media, mass media, and interpersonal communication channels in relation to health issues. Findings contribute to theoretical and practical understandings of the role of communication channels in diffusion of innovations theory. In particular, this study provides a foundation for the use of qualitative research to advance applications of diffusion of innovations theory. Results suggest that participants resisted mass media portrayals of women's health. When faced with a health question, participants uniformly started with the Internet to "Google it up." Findings suggest new media comprise a new communication channel with new rules, serving the functions of both personal and impersonal influence. In particular, pregnancy and the postpartum period emerged as a time when campaign planners can access women in new ways online. As a result, campaign planners could benefit from introducing new ideas online and capitalizing on the strength of weak ties favored in new media. Results expand the innovativeness/needs paradox in diffusion of innovations theory by elaborating on the role of new media to reach underserved populations. These findings provide an opportunity to better understand patient information seeking through the lens of diffusion of innovations theory.
Using Diffusion of Innovation Theory to Promote Universally Designed College Instruction
Scott, Sally; McGuire, Joan
2017-01-01
Universal Design applied to college instruction has evolved and rapidly spread on an international scale. Diffusion of Innovation theory is described and used to identify patterns of change in this trend. Implications and strategies are discussed for promoting this inclusive approach to teaching in higher education.
Mahakrishnan, Sathiya; Chakraborty, Subrata; Vijay, Amrendra
2016-09-15
Diffusion, an emergent nonequilibrium transport phenomenon, is a nontrivial manifestation of the correlation between the microscopic dynamics of individual molecules and their statistical behavior observed in experiments. We present a thorough investigation of this viewpoint using the mathematical tools of quantum scattering, within the framework of Boltzmann transport theory. In particular, we ask: (a) How and when does a normal diffusive transport become anomalous? (b) What physical attribute of the system is conceptually useful to faithfully rationalize large variations in the coefficient of normal diffusion, observed particularly within the dynamical environment of biological cells? To characterize the diffusive transport, we introduce, analogous to continuous phase transitions, the curvature of the mean square displacement as an order parameter and use the notion of quantum scattering length, which measures the effective interactions between the diffusing molecules and the surrounding, to define a tuning variable, η. We show that the curvature signature conveniently differentiates the normal diffusion regime from the superdiffusion and subdiffusion regimes and the critical point, η = ηc, unambiguously determines the coefficient of normal diffusion. To solve the Boltzmann equation analytically, we use a quantum mechanical expression for the scattering amplitude in the Boltzmann collision term and obtain a general expression for the effective linear collision operator, useful for a variety of transport studies. We also demonstrate that the scattering length is a useful dynamical characteristic to rationalize experimental observations on diffusive transport in complex systems. We assess the numerical accuracy of the present work with representative experimental results on diffusion processes in biological systems. Furthermore, we advance the idea of temperature-dependent effective voltage (of the order of 1 μV or less in a biological environment, for example
A hybrid multi-scale computational scheme for advection-diffusion-reaction equation
Karimi, S.; Nakshatrala, K. B.
2016-12-01
Simulation of transport and reaction processes in porous media and subsurface science has become more vital than ever. Over the past few decades, a variety of mathematical models and numerical methodologies for porous media simulations have been developed. As the demand for higher accuracy and validity of the models grows, the issue of disparate temporal and spatial scales becomes more problematic. The variety of reaction processes and complexity of pore geometry poses a huge computational burden in a real-world or reservoir scale simulation. Meanwhile, methods based on averaging or up- scaling techniques do not provide reliable estimates to pore-scale processes. To overcome this problem, development of hybrid and multi-scale computational techniques is considered a promising approach. In these methods, pore-scale and continuum-scale models are combined, hence, a more reliable estimate to pore-scale processes is obtained without having to deal with the tremendous computational overhead of pore-scale methods. In this presentation, we propose a computational framework that allows coupling of lattice Boltzmann method (for pore-scale simulation) and finite element method (for continuum-scale simulation) for advection-diffusion-reaction equations. To capture disparate in time and length events, non-matching grid and time-steps are allowed. Apart from application of this method to benchmark problems, multi-scale simulation of chemical reactions in porous media is also showcased.
Zhang, Xianlong; Wang, Xiaoling; Nie, Kai; Li, Mingpeng; Sun, Qingping
2016-08-01
Various species of bacteria form highly organized spatially-structured aggregates known as biofilms. To understand how microenvironments impact biofilm growth dynamics, we propose a diffusion-reaction continuum model to simulate the formation of Bacillus subtilis biofilm on an agar plate. The extended finite element method combined with level set method are employed to perform the simulation, numerical results show the quantitative relationship between colony morphologies and nutrient depletion over time. Considering that the production of polysaccharide in wild-type cells may enhance biofilm spreading on the agar plate, we inoculate mutant colony incapable of producing polysaccharide to verify our results. Predictions of the glutamate source biofilm’s shape parameters agree with the experimental mutant colony better than that of glycerol source biofilm, suggesting that glutamate is rate limiting nutrient for Bacillus subtilis biofilm growth on agar plate, and the diffusion-limited is a better description to the experiment. In addition, we find that the diffusion time scale is of the same magnitude as growth process, and the common-employed quasi-steady approximation is not applicable here.
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.
Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems
Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.; Karniadakis, George E.
2015-07-07
We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic DPD framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between particles, and an analytical formula is proposed to relate the mesoscopic concentration friction to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.
Brownian-motion based simulation of stochastic reaction-diffusion systems for affinity based sensors
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.
Hybrid approaches for multiple-species stochastic reaction-diffusion models
Spill, Fabian; Alarcon, Tomas; Maini, Philip K; Byrne, Helen
2015-01-01
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 ...
Diffusion-influenced reactions in a hollow nano-reactor with a circular hole
Piazza, Francesco; Traytak, Sergey D.
Hollow nanostructures are paid increasing attention in many nanotechnology-related communities in view of their numerous applications in chemistry and biotechnology, e.g. as smart nanoreactors or drug-delivery systems. In this paper we consider irreversible, diffusion-influenced reactions occurring within a hollow spherical cavity endowed with a circular hole on its surface. Importantly, our model is not limited to small sizes of the aperture. In our scheme, reactants can freely diffuse inside and outside the cavity through the hole, and react at a spherical boundary of given size encapsulated in the chamber and endowed with a given intrinsic rate constant. We work out the solution of the above problem, enabling one to compute the reaction rate constant to any desired accuracy. Remarkably, we show that, in the case of narrow holes, the rate constant is extremely well-approximated by a simple formula that can be derived on the basis of simple physical arguments and that can be readily employed to analyze experimental data.
Spatiotemporal patterns in reaction-diffusion system and in a vibrated granular bed
Swinney, H.L.; Lee, K.J.; McCormick, W.D. [Univ. of Texas, Austin, TX (United States)
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.
Maeta, Takahiro [Graduate School of System Engineering, Okayama Prefectural University, 111 Kuboki, Soja, Okayama 719-1197 (Japan); GlobalWafers Japan Co., Ltd., Higashikou, Seirou-machi, Kitakanbara-gun, Niigata 957-0197 (Japan); Sueoka, Koji [Department of Communication Engineering, Okayama Prefectural University, 111 Kuboki, Soja, Okayama 719-1197 (Japan)
2014-08-21
Ge-based substrates are being developed for applications in advanced nano-electronic devices because of their higher intrinsic carrier mobility than Si. The stability and diffusion mechanism of impurity atoms in Ge are not well known in contrast to those of Si. Systematic studies of the stable sites of 2nd to 6th row element impurity atoms in Ge crystal were undertaken with density functional theory (DFT) and compared with those in Si crystal. It was found that most of the impurity atoms in Ge were stable at substitutional sites, while transition metals in Si were stable at interstitial sites and the other impurity atoms in Si were stable at substitutional sites. Furthermore, DFT calculations were carried out to clarify the mechanism responsible for the diffusion of impurity atoms in Ge crystals. The diffusion mechanism for 3d transition metals in Ge was found to be an interstitial-substitutional diffusion mechanism, while in Si this was an interstitial diffusion mechanism. The diffusion barriers in the proposed diffusion mechanisms in Ge and Si were quantitatively verified by comparing them to the experimental values in the literature.
Passive Rocket Diffuser Theory: A Re-Examination of Minimum Second Throat Size
Jones, Daniel R.
2016-01-01
Second-throat diffusers serve to isolate rocket engines from the effects of ambient back pressure during testing without using active control systems. Among the most critical design parameters is the relative area of the diffuser throat to that of the nozzle throat. A smaller second throat is generally desirable because it decreases the stagnation-to-ambient pressure ratio the diffuser requires for nominal operation. There is a limit, however. Below a certain size, the second throat can cause pressure buildup within the diffuser and prevent it from reaching the start condition that protects the nozzle from side-load damage. This paper presents a method for improved estimation of the minimum second throat area which enables diffuser start. The new 3-zone model uses traditional quasi-one-dimensional compressible flow theory to approximate the structure of two distinct diffuser flow fields observed in Computational Fluid Dynamics (CFD) simulations and combines them to provide a less-conservative estimate of the second throat size limit. It is unique among second throat sizing methods in that it accounts for all major conical nozzle and second throat diffuser design parameters within its limits of application. The performance of the 3-zone method is compared to the historical normal shock and force balance methods, and verified against a large number of CFD simulations at specific heat ratios of 1.4 and 1.25. Validation is left as future work, and the model is currently intended to function only as a first-order design tool.
Wiberg, Gustav Karl Henrik; Arenz, Matthias
2015-01-01
We present a study concerning the influence of the diffusion of H+ and OH- ions on the hydrogen and oxygen evolution reactions (HER and OER) in aqueous electrolyte solutions. Using a rotating disk electrode (RDE), it is shown that at certain conditions the observed current, i.e., the reaction rate...
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.
Nicola Ernesto M
2010-11-01
Full Text Available Abstract Background A central question for the understanding of biological reaction networks is how a particular dynamic behavior, such as bistability or oscillations, is realized at the molecular level. So far this question has been mainly addressed in well-mixed reaction systems which are conveniently described by ordinary differential equations. However, much less is known about how molecular details of a reaction mechanism can affect the dynamics in diffusively coupled systems because the resulting partial differential equations are much more difficult to analyze. Results Motivated by recent experiments we compare two closely related mechanisms for the product activation of allosteric enzymes with respect to their ability to induce different types of reaction-diffusion waves and stationary Turing patterns. The analysis is facilitated by mapping each model to an associated complex Ginzburg-Landau equation. We show that a sequential activation mechanism, as implemented in the model of Monod, Wyman and Changeux (MWC, can generate inward rotating spiral waves which were recently observed as glycolytic activity waves in yeast extracts. In contrast, in the limiting case of a simple Hill activation, the formation of inward propagating waves is suppressed by a Turing instability. The occurrence of this unusual wave dynamics is not related to the magnitude of the enzyme cooperativity (as it is true for the occurrence of oscillations, but to the sensitivity with respect to changes of the activator concentration. Also, the MWC mechanism generates wave patterns that are more stable against long wave length perturbations. Conclusions This analysis demonstrates that amplitude equations, which describe the spatio-temporal dynamics near an instability, represent a valuable tool to investigate the molecular effects of reaction mechanisms on pattern formation in spatially extended systems. Using this approach we have shown that the occurrence of inward
Production method of raw material dispersion liquid for reaction layer of gas diffusion electrode
Furuya, Choichi; Motoo, Satoshi
1987-10-13
Heretofore, in order to make a raw material dispersion liquid of a reaction layer of a gas diffusion electrode, water repellent carbon, polytetrafluoroethylene, water and a surface active agent are mixed, then a cake is made by filtering this mixed liquid and afterwards the cake is heated and dried before being crushed. Since this crushing is done mechanically, homogeneous fine raw material powders cannot be obtained. Accordingly, even when a reaction layer is made by sintering a mixture of this powder, hydrophilic carbon black or hydrophilic carbon black carrying catalyst, and polytetrafluoroethylene, the hydrophilic part and the water repellent part are not distributed homogeneously and the catalytic performance of the reaction layer declines. In order to solve this, this invention proposes a production method that water repellent carbon black, polyterafluoroethylene, water and a surface active agent are mixed, then this mixture is frozen so that the surface active agent may not become active and homogeneous condensed cores of water repellent carbon black and polytetrafluoroethylene powders may be formed, and afterwards a homogeneous fine raw material dispersion liquid is made from thawing the condensed cores without change by thawing the above frozen mixture.
Stamova, Ivanka; Stamov, Gani
2017-09-08
In this paper, we propose a fractional-order neural network system with time-varying delays and reaction-diffusion terms. We first develop a new Mittag-Leffler synchronization strategy for the controlled nodes via impulsive controllers. Using the fractional Lyapunov method sufficient conditions are given. We also study the global Mittag-Leffler synchronization of two identical fractional impulsive reaction-diffusion neural networks using linear controllers, which was an open problem even for integer-order models. Since the Mittag-Leffler stability notion is a generalization of the exponential stability concept for fractional-order systems, our results extend and improve the exponential impulsive control theory of neural network system with time-varying delays and reaction-diffusion terms to the fractional-order case. The fractional-order derivatives allow us to model the long-term memory in the neural networks, and thus the present research provides with a conceptually straightforward mathematical representation of rather complex processes. Illustrative examples are presented to show the validity of the obtained results. We show that by means of appropriate impulsive controllers we can realize the stability goal and to control the qualitative behavior of the states. An image encryption scheme is extended using fractional derivatives. Copyright © 2017 Elsevier Ltd. All rights reserved.
Kondrashova, Daria; Valiullin, Rustem; Kärger, Jörg; Bunde, Armin
2017-07-01
Nanoporous silicon consisting of tubular pores imbedded in a silicon matrix has found many technological applications and provides a useful model system for studying phase transitions under confinement. Recently, a model for mass transfer in these materials has been elaborated [Kondrashova et al., Sci. Rep. 7, 40207 (2017)], which assumes that adjacent channels can be connected by "bridges" (with probability pbridge) which allows diffusion perpendicular to the channels. Along the channels, diffusion can be slowed down by "necks" which occur with probability pneck. In this paper we use Monte-Carlo simulations to study diffusion along the channels and perpendicular to them, as a function of pbridge and pneck, and find remarkable correlations between the diffusivities in longitudinal and radial directions. For clarifying the diffusivity in radial direction, which is governed by the concentration of bridges, we applied percolation theory. We determine analytically how the critical concentration of bridges depends on the size of the system and show that it approaches zero in the thermodynamic limit. Our analysis suggests that the critical properties of the model, including the diffusivity in radial direction, are in the universality class of two-dimensional lattice percolation, which is confirmed by our numerical study.
The science of making more torque from wind: Diffuser experiments and theory revisited.
van Bussel, Gerard J. W., , Dr
2007-07-01
History of the development of DAWT's stretches a period of more than 50 years. So far without any commercial success. In the initial years of development the conversion process was not understood very well. Experimentalists strived at maximising the pressure drop over the rotor disk, but lacked theoretical insight into optimising the performance. Increasing the diffuser area as well as the negative back pressure at the diffuser exit was found profitable in the experiments. Claims were made that performance augmentations with a factor of 4 or more were feasible, but these claims were not confirmed experimentally. With a simple momentum theory, developed along the lines of momentum theory for bare windturbines, it was shown that power augmentation is proportional to the mass flow increase generated at the nozzle of the DAWT. Such mass flow augmentation can be achieved through two basic principles: increase in the diffuser exit ratio and/or by decreasing the negative back pressure at the exit. The theory predicts an optimal pressure drop of 8/9 equal to the pressure drop for bare windturbines independent from the mass flow augmentation obtained. The maximum amount of energy that can be extracted per unit of volume with a DAWT is also the same as for a bare wind turbine. Performance predictions with this theory show good agreement with a CFD calculation. Comparison with a large amount of experimental data found in literature shows that in practice power augmentation factors above 3 have never been achieved. Referred to rotor power coefficients values of CP,rotort= 2.5 might be achievable according to theory, but to the cost of fairly large diffuser area ratio's, typically values of β>4.5.
A Two-grid Method with Expanded Mixed Element for Nonlinear Reaction-diffusion Equations
Wei Liu; Hong-xing Rui; Hui Guo
2011-01-01
Expanded mixed finite element approximation of nonlinear reaction-diffusion equations is discussed. The equations considered here are used to model the hydrologic and bio-geochemical phenomena. To linearize the mixed-method equations, we use a two-grid method involving a small nonlinear system on a coarse gird of size H and a linear system on a fine grid of size h. Error estimates are derived which demonstrate that the error is O(△t + hk+1 + H2k+2-d/2) (k ≥ 1), where k is the degree of the approximating space for the primary variable and d is the spatial dimension. The above estimates are useful for determining an appropriate H for the coarse grid problems.
Reply to Comment on "Enhanced diffusion of enzymes that catalyze exothermic reactions"
Golestanian, Ramin
2016-01-01
Catalytically active enzymes have recently been observed to exhibit enhanced diffusion. In a recent work [C. Riedel et al., Nature 517, 227 (2015)], it has been suggested that this phenomenon is correlated with the degree of exothermicity of the reaction, and a mechanism was proposed to explain the phenomenon based on channeling the released heat into the center of mass kinetic energy of the enzyme. I addressed this question by comparing four different mechanisms, and concluded that collective heating is the strongest candidate out of those four to explain the phenomenon, and in particular, several orders of magnitude stronger than the mechanism proposed by Riedel et al. In a recent preprint (arXiv:1608.05433), K. Tsekouras, C. Riedel, R. Gabizon, S. Marqusee, S. Presse, and C. Bustamante present a comment on my paper [R. Golestanian, Phys. Rev. Lett. 115, 108102 (2015); arXiv:1508.03219], which I address here in this reply.
The dynamics of nonlinear reaction-diffusion equations with small Lévy noise
Debussche, Arnaud; Imkeller, Peter
2013-01-01
This work considers a small random perturbation of alpha-stable jump type nonlinear reaction-diffusion equations with Dirichlet boundary conditions over an interval. It has two stable points whose domains of attraction meet in a separating manifold with several saddle points. Extending a method developed by Imkeller and Pavlyukevich it proves that in contrast to a Gaussian perturbation, the expected exit and transition times between the domains of attraction depend polynomially on the noise intensity in the small intensity limit. Moreover the solution exhibits metastable behavior: there is a polynomial time scale along which the solution dynamics correspond asymptotically to the dynamic behavior of a finite-state Markov chain switching between the stable states.
Existence and convergence to a propagating terrace in one-dimensional reaction-diffusion equations
Ducrot, Arnaud; Matano, Hiroshi
2012-01-01
We consider one-dimensional reaction-diffusion equations for a large class of spatially periodic nonlinearities (including multistable ones) and study the asymptotic behavior of solutions with Heaviside type initial data. Our analysis reveals some new dynamics where the profile of the propagation is not characterized by a single front, but by a layer of several fronts which we call a terrace. Existence and convergence to such a terrace is proven by using an intersection number argument, without much relying on standard linear analysis. Hence, on top of the peculiar phenomenon of propagation that our work highlights, several corollaries will follow on the existence and convergence to pulsating traveling fronts even for highly degenerate nonlinearities that have not been treated before.
THE EXTINCTION BEHAVIOR OF THE SOLUTIONS FOR A CLASS OF REACTION-DIFFUSION EQUATIONS
陈松林
2001-01-01
The methods of Lp estimation are used to discuss the extinction phenomena of the solutions to the following reaction-diffusion equations with initial-boudnary values u/ t = Au-λ |u|γ-1u-βu ((x,t) ∈Ω×(0,+∞)),u(x,t) | Ω×(0.+∞) = 0,u(x,0) = uo(x) ∈ H1 0(Ω) ∩ L1+γ(Ω) (x ∈Ω).Sufficient and necessary conditions about the extinction of the solutions is given Here λ＞0, γ＞ 0, β＞ 0 are constants, Ω∈ RN is bounded with smooth boundary Ω At last,it is simulated with a higher order equation by using the present methods.
Numerical method using cubic B-spline for a strongly coupled reaction-diffusion system.
Muhammad Abbas
Full Text Available In this paper, a numerical method for the solution of a strongly coupled reaction-diffusion system, with suitable initial and Neumann boundary conditions, by using cubic B-spline collocation scheme on a uniform grid is presented. The scheme is based on the usual finite difference scheme to discretize the time derivative while cubic B-spline is used as an interpolation function in the space dimension. The scheme is shown to be unconditionally stable using the von Neumann method. The accuracy of the proposed scheme is demonstrated by applying it on a test problem. The performance of this scheme is shown by computing L∞ and L2 error norms for different time levels. The numerical results are found to be in good agreement with known exact solutions.
Numerical method using cubic B-spline for a strongly coupled reaction-diffusion system.
Abbas, Muhammad; Majid, Ahmad Abd; Md Ismail, Ahmad Izani; Rashid, Abdur
2014-01-01
In this paper, a numerical method for the solution of a strongly coupled reaction-diffusion system, with suitable initial and Neumann boundary conditions, by using cubic B-spline collocation scheme on a uniform grid is presented. The scheme is based on the usual finite difference scheme to discretize the time derivative while cubic B-spline is used as an interpolation function in the space dimension. The scheme is shown to be unconditionally stable using the von Neumann method. The accuracy of the proposed scheme is demonstrated by applying it on a test problem. The performance of this scheme is shown by computing L∞ and L2 error norms for different time levels. The numerical results are found to be in good agreement with known exact solutions.
STEPS: modeling and simulating complex reaction-diffusion systems with Python
Stefan Wils
2009-06-01
Full Text Available We describe how the use of the Python language improved the user interface of the program STEPS. STEPS is a simulation platform for modeling and stochastic simulation of coupled reaction-diffusion systems with complex 3-dimensional boundary conditions. Setting up such models is a complicated process that consists of many phases. Initial versions of STEPS relied on a static input format that did not cleanly separate these phases, limiting modelers in how they could control the simulation and becoming increasingly complex as new features and new simulation algorithms were added. We solved all of these problems by tightly integrating STEPS with Python, using SWIG to expose our existing simulation code.
Preconditioned time-difference methods for advection-diffusion-reaction equations
Aro, C.; Rodrigue, G. [Lawrence Livermore National Lab., CA (United States); Wolitzer, D. [California State Univ., Hayward, CA (United States)
1994-12-31
Explicit time differencing methods for solving differential equations are advantageous in that they are easy to implement on a computer and are intrinsically very parallel. The disadvantage of explicit methods is the severe restrictions placed on stepsize due to stability. Stability bounds for explicit time differencing methods on advection-diffusion-reaction problems are generally quite severe and implicit methods are used instead. The linear systems arising from these implicit methods are large and sparse so that iterative methods must be used to solve them. In this paper the authors develop a methodology for increasing the stability bounds of standard explicit finite differencing methods by combining explicit methods, implicit methods, and iterative methods in a novel way to generate new time-difference schemes, called preconditioned time-difference methods.
An observer for an occluded reaction-diffusion system with spatially varying parameters
Kramer, Sean; Bollt, Erik M.
2017-03-01
Spatially dependent parameters of a two-component chaotic reaction-diffusion partial differential equation (PDE) model describing ocean ecology are observed by sampling a single species. We estimate the model parameters and the other species in the system by autosynchronization, where quantities of interest are evolved according to misfit between model and observations, to only partially observed data. Our motivating example comes from oceanic ecology as viewed by remote sensing data, but where noisy occluded data are realized in the form of cloud cover. We demonstrate a method to learn a large-scale coupled synchronizing system that represents the spatio-temporal dynamics and apply a network approach to analyze manifold stability.
KPP reaction-diffusion equations with a non-linear loss inside a cylinder
Giletti, Thomas
2010-01-01
We consider in this paper a reaction-diffusion system in presence of a flow and under a KPP hypothesis. While the case of a single-equation has been extensively studied since the pioneering Kolmogorov-Petrovski-Piskunov paper, the study of the corresponding system with a Lewis number not equal to 1 is still quite open. Here, we will prove some results about the existence of travelling fronts and generalized travelling fronts solutions of such a system with the presence of a non-linear spacedependent loss term inside the domain. In particular, we will point out the existence of a minimal speed, above which any real value is an admissible speed. We will also give some spreading results for initial conditions decaying exponentially at infinity.
KPP reaction-diffusion system with a nonlinear loss inside a cylinder
Giletti, Thomas
2010-09-01
We consider in this paper a reaction-diffusion system in the presence of a flow and under a KPP hypothesis. While the case of a single-equation has been extensively studied since the pioneering Kolmogorov-Petrovski-Piskunov paper, the study of the corresponding system with a Lewis number not equal to 1 is still quite open. Here, we will prove some results about the existence of travelling fronts and generalized travelling fronts solutions of such a system with the presence of a nonlinear space-dependent loss term inside the domain. In particular, we will point out the existence of a minimal speed, above which any real value is an admissible speed. We will also give some spreading results for initial conditions decaying exponentially at infinity.
TRAVELING WAVE SPEED AND SOLUTION IN REACTION-DIFFUSION EQUATION IN ONE DIMENSION
周天寿; 张锁春
2001-01-01
By Painlevé analysis, traveling wave speed and solution of reaction-diffusion equations for the concentration of one species in one spatial dimension are in detail investigated. When the exponent of the creation term is larger than the one of the annihilation term, two typical cases are studied, one with the exact traveling wave solutions, yielding the values of speeds, the other with the series expansion solution, also yielding the value of speed. Conversely, when the exponent of creation term is smaller than the one of the annihilation term, two typical cases are also studied, but only for one of them, there is a series development solution, yielding the value of speed, and for the other, traveling wave solution cannot exist. Besides, the formula of calculating speeds and solutions of planar wave within the thin boundary layer are given for a class of typical excitable media.
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.
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.
A reaction-diffusion-based coding rate control mechanism for camera sensor networks.
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.
Robustness of the Critical Behaviour in a Discrete Stochastic Reaction-Diffusion Medium
Fatès, Nazim; Berry, Hugues
We study the steady states of a reaction-diffusion medium modelled by a stochastic 2D cellular automaton. We consider the Greenberg-Hastings model where noise and topological irregularities of the grid are taken into account. The decrease of the probability of excitation changes qualitatively the behaviour of the system from an "active" to an "extinct" steady state. Simulations show that this change occurs near a critical threshold; it is identified as a nonequilibrium phase transition which belongs to the directed percolation universality class. We test the robustness of the phenomenon by introducing persistent defects in the topology : directed percolation behaviour is conserved. Using experimental and analytical tools, we suggest that the critical threshold varies as the inverse of the average number of neighbours per cell.
Xu Rui [Department of Applied Mathematics, Xi' an Jiaotong University, Xi' an 710049 (China)]. E-mail: rxu88@yahoo.com.cn; Chaplain, M.A.J. [Department of Mathematics, University of Dundee, Dundee DD1 4HN (United Kingdom); Davidson, F.A. [Department of Mathematics, University of Dundee, Dundee DD1 4HN (United Kingdom)
2006-11-15
In this paper, we first investigate a stage-structured competitive model with time delays, harvesting, and nonlocal spatial effect. By using an iterative technique recently developed by Wu and Zou (Wu J, Zou X. Travelling wave fronts of reaction-diffusion systems with delay. J Dynam Differen Equat 2001;13:651-87), sufficient conditions are established for the existence of travelling front solution connecting the two boundary equilibria in the case when there is no positive equilibrium. The travelling wave front corresponds to an invasion by a stronger species which drives the weaker species to extinction. Secondly, we consider a stage-structured competitive model with time delays and nonlocal spatial effect when the domain is finite. We prove the global stability of each of the nonnegative equilibria and demonstrate that the more complex model studied here admits three possible long term behaviors: coexistence, bistability and dominance as is the case for the standard Lotka-Voltera competitive model.
Scalable implicit methods for reaction-diffusion equations in two and three space dimensions
Veronese, S.V.; Othmer, H.G. [Univ. of Utah, Salt Lake City, UT (United States)
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.
Di Giacomo, Francesco
2015-01-01
The RRKM Theory of Unimolecular Reactions and Marcus Theory of Electron Transfer are here briefly discussed in a historical perspective. In the final section, after a general discussion on the educational usefulness of teaching chemistry in a historical framework, hints are given on how some characteristics of Marcus' work could be introduced in…
Di Giacomo, Francesco
2015-01-01
The RRKM Theory of Unimolecular Reactions and Marcus Theory of Electron Transfer are here briefly discussed in a historical perspective. In the final section, after a general discussion on the educational usefulness of teaching chemistry in a historical framework, hints are given on how some characteristics of Marcus' work could be introduced in…