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.
Comte, J C; Marquié, P; Remoissenet, M
1999-12-01
We introduce a nonlinear Klein-Gordon lattice model with specific double-well on-site potential, additional constant external force and dissipation terms, which admits exact discrete kink or traveling wave fronts solutions. In the non-dissipative or conservative regime, our numerical simulations show that narrow kinks can propagate freely, and reveal that static or moving discrete breathers, with a finite but long lifetime, can emerge from kink-antikink collisions. In the general dissipative regime, the lifetime of these breathers depends on the importance of the dissipative effects. In the overdamped or diffusive regime, the general equation of motion reduces to a discrete reaction diffusion equation; our simulations show that, for a given potential shape, discrete wave fronts can travel without experiencing any propagation failure but their collisions are inelastic.
Coarse-graining the calcium dynamics on a stochastic reaction-diffusion lattice model
Shen, Chuansheng
2013-01-01
We develop a coarse grained (CG) approach for efficiently simulating calcium dynamics in the endoplasmic reticulum membrane based on a fine stochastic lattice gas model. By grouping neighboring microscopic sites together into CG cells and deriving CG reaction rates using local mean field approximation, we perform CG kinetic Monte Carlo (kMC) simulations and find the results of CG-kMC simulations are in excellent agreement with that of the microscopic ones. Strikingly, there is an appropriate range of coarse proportion $m$, corresponding to the minimal deviation of the phase transition point compared to the microscopic one. For fixed $m$, the critical point increases monotonously as the system size increases, especially, there exists scaling law between the deviations of the phase transition point and the system size. Moreover, the CG approach provides significantly faster Monte Carlo simulations which are easy to implement and are directly related to the microscopics, so that one can study the system size eff...
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.
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.
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 ...
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.
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...
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.
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.
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.
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.
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.
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
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.
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.
Hybrid approaches for multiple-species stochastic reaction-diffusion models.
Spill, Fabian
2015-10-01
Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.
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.
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.
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.
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.
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.
A GPU Reaction Diffusion Soil-Microbial Model
Falconer, Ruth; Houston, Alasdair; Schmidt, Sonja; Otten, Wilfred
2014-05-01
Parallelised algorithms are frequent in bioinformatics as a consequence of the close link to informatics - however in the field of soil science and ecology they are less prevalent. A current challenge in soil ecology is to link habitat structure to microbial dynamics. Soil science is therefore entering the 'big data' paradigm as a consequence of integrating data pertinent to the physical soil environment obtained via imaging and theoretical models describing growth and development of microbial dynamics permitting accurate analyses of spatio-temporal properties of different soil microenvironments. The microenvironment is often captured by 3D imaging (CT tomography) which yields large datasets and when used in computational studies the physical sizes of the samples that are amenable to computation are less than 1 cm3. Today's commodity graphics cards are programmable and possess a data parallel architecture that in many cases is capable of out-performing the CPU in terms of computational rates. The programmable aspect is achieved via a low-level parallel programming language (CUDA, OpenCL and DirectX). We ported a Soil-Microbial Model onto the GPU using the DirectX Compute API. We noted a significant computational speed up as well as an increase in the physical size that can be simulated. Some of the drawbacks of such an approach were concerned with numerical precision and the steep learning curve associated with GPGPU technologies.
Dynamic Analysis of a Reaction-Diffusion Rumor Propagation Model
Zhao, Hongyong; Zhu, Linhe
2016-06-01
The rapid development of the Internet, especially the emergence of the social networks, leads rumor propagation into a new media era. Rumor propagation in social networks has brought new challenges to network security and social stability. This paper, based on partial differential equations (PDEs), proposes a new SIS rumor propagation model by considering the effect of the communication between the different rumor infected users on rumor propagation. The stabilities of a nonrumor equilibrium point and a rumor-spreading equilibrium point are discussed by linearization technique and the upper and lower solutions method, and the existence of a traveling wave solution is established by the cross-iteration scheme accompanied by the technique of upper and lower solutions and Schauder’s fixed point theorem. Furthermore, we add the time delay to rumor propagation and deduce the conditions of Hopf bifurcation and stability switches for the rumor-spreading equilibrium point by taking the time delay as the bifurcation parameter. Finally, numerical simulations are performed to illustrate the theoretical results.
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.
An exact and efficient first passage time algorithm for reaction-diffusion processes on a 2D-lattice
Bezzola, Andri; Bales, Benjamin B.; Alkire, Richard C.; Petzold, Linda R.
2014-01-01
We present an exact and efficient algorithm for reaction-diffusion-nucleation processes on a 2D-lattice. The algorithm makes use of first passage time (FPT) to replace the computationally intensive simulation of diffusion hops in KMC by larger jumps when particles are far away from step-edges or other particles. Our approach computes exact probability distributions of jump times and target locations in a closed-form formula, based on the eigenvectors and eigenvalues of the corresponding 1D transition matrix, maintaining atomic-scale resolution of resulting shapes of deposit islands. We have applied our method to three different test cases of electrodeposition: pure diffusional aggregation for large ranges of diffusivity rates and for simulation domain sizes of up to 4096×4096 sites, the effect of diffusivity on island shapes and sizes in combination with a KMC edge diffusion, and the calculation of an exclusion zone in front of a step-edge, confirming statistical equivalence to standard KMC simulations. The algorithm achieves significant speedup compared to standard KMC for cases where particles diffuse over long distances before nucleating with other particles or being captured by larger islands.
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.
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.
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.
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.
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
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.
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.
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.
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.
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 ...
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.
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.
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.
Wazwaz, Abdul-Majid
2017-07-01
In this work we address the Lane-Emden boundary value problems which appear in chemical applications, biochemical applications, and scientific disciplines. We apply the variational iteration method to solve two specific models. The first problem models reaction-diffusion equation in a spherical catalyst, while the second problem models the reaction-diffusion process in a spherical biocatalyst. We obtain reliable analytical expressions of the concentrations and the effectiveness factors. Proper graphs will be used to illustrate the obtained results. The proposed analysis demonstrates reliability and efficiency applicability of the employed method.
Deriving reaction-diffusion models in ecology from interacting particle systems.
Cantrell, R S; Cosner, C
2004-02-01
We use a scaling procedure based on averaging Poisson distributed random variables to derive population level models from local models of interactions between individuals. The procedure is suggested by using the idea of hydrodynamic limits to derive reaction-diffusion models for population interactions from interacting particle systems. The scaling procedure is formal in the sense that we do not address the issue of proving that it converges; instead we focus on methods for computing the results of the scaling or deriving properties of rescaled systems. To that end we treat the scaling procedure as a transform, in analogy with the Laplace or Fourier transform, and derive operational formulas to aid in the computation of rescaled systems or the derivation of their properties. Since the limiting procedure is adapted from work by Durrett and Levin, we refer to the transform as the Durrett-Levin transform. We examine the effects of rescaling in various standard models, including Lotka-Volterra models, Holling type predator-prey models, and ratio-dependent models. The effects of scaling are mostly quantitative in models with smooth interaction terms, but ratio-dependent models are profoundly affected by the scaling. The scaling transforms ratio-dependent terms that are singular at the origin into smooth terms. Removing the singularity at the origin eliminates some of the unique dynamics that can arise in ratio-dependent models.
Spatiotemporal Patterns in a Ratio-Dependent Food Chain Model with Reaction-Diffusion
Lei Zhang
2014-01-01
Full Text Available Predator-prey models describe biological phenomena of pursuit-evasion interaction. And this interaction exists widely in the world for the necessary energy supplement of species. In this paper, we have investigated a ratio-dependent spatially extended food chain model. Based on the bifurcation analysis (Hopf and Turing, we give the spatial pattern formation via numerical simulation, that is, the evolution process of the system near the coexistence equilibrium point (u2*,v2*,w2*, and find that the model dynamics exhibits complex pattern replication. For fixed parameters, on increasing the control parameter c1, the sequence “holes → holes-stripe mixtures → stripes → spots-stripe mixtures → spots” pattern is observed. And in the case of pure Hopf instability, the model exhibits chaotic wave pattern replication. Furthermore, we consider the pattern formation in the case of which the top predator is extinct, that is, the evolution process of the system near the equilibrium point (u1*,v1*,0, and find that the model dynamics exhibits stripes-spots pattern replication. Our results show that reaction-diffusion model is an appropriate tool for investigating fundamental mechanism of complex spatiotemporal dynamics. It will be useful for studying the dynamic complexity of ecosystems.
Richter, Otto; Moenickes, Sylvia; Suhling, Frank
2012-02-01
The spatial dynamics of range expansion is studied in dependence of temperature. The main elements population dynamics, competition and dispersal are combined in a coherent approach based on a system of coupled partial differential equations of the reaction-diffusion type. The nonlinear reaction terms comprise population dynamic models with temperature dependent reproduction rates subject to an Allee effect and mutual competition. The effect of temperature on travelling wave solutions is investigated for a one dimensional model version. One main result is the importance of the Allee effect for the crossing of regions with unsuitable habitats. The nonlinearities of the interaction terms give rise to a richness of spatio-temporal dynamic patterns. In two dimensions, the resulting non-linear initial boundary value problems are solved over geometries of heterogeneous landscapes. Geo referenced model parameters such as mean temperature and elevation are imported into the finite element tool COMSOL Multiphysics from a geographical information system. The model is applied to the range expansion of species at the scale of middle Europe.
A nonlocal and periodic reaction-diffusion-advection model of a single phytoplankton species.
Peng, Rui; Zhao, Xiao-Qiang
2016-02-01
In this article, we are concerned with a nonlocal reaction-diffusion-advection model which describes the evolution of a single phytoplankton species in a eutrophic vertical water column where the species relies solely on light for its metabolism. The new feature of our modeling equation lies in that the incident light intensity and the death rate are assumed to be time periodic with a common period. We first establish a threshold type result on the global dynamics of this model in terms of the basic reproduction number R0. Then we derive various characterizations of R0 with respect to the vertical turbulent diffusion rate, the sinking or buoyant rate and the water column depth, respectively, which in turn give rather precise conditions to determine whether the phytoplankton persist or become extinct. Our theoretical results not only extend the existing ones for the time-independent case, but also reveal new interesting effects of the modeling parameters and the time-periodic heterogeneous environment on persistence and extinction of the phytoplankton species, and thereby suggest important implications for phytoplankton growth control.
A reaction-diffusion model for radiation-induced bystander effects.
Olobatuyi, Oluwole; de Vries, Gerda; Hillen, Thomas
2017-08-01
We develop and analyze a reaction-diffusion model to investigate the dynamics of the lifespan of a bystander signal emitted when cells are exposed to radiation. Experimental studies by Mothersill and Seymour 1997, using malignant epithelial cell lines, found that an emitted bystander signal can still cause bystander effects in cells even 60 h after its emission. Several other experiments have also shown that the signal can persist for months and even years. Also, bystander effects have been hypothesized as one of the factors responsible for the phenomenon of low-dose hyper-radiosensitivity and increased radioresistance (HRS/IRR). Here, we confirm this hypothesis with a mathematical model, which we fit to Joiner's data on HRS/IRR in a T98G glioma cell line. Furthermore, we use phase plane analysis to understand the full dynamics of the signal's lifespan. We find that both single and multiple radiation exposure can lead to bystander signals that either persist temporarily or permanently. We also found that, in an heterogeneous environment, the size of the domain exposed to radiation and the number of radiation exposures can determine whether a signal will persist temporarily or permanently. Finally, we use sensitivity analysis to identify those cell parameters that affect the signal's lifespan and the signal-induced cell death the most.
Bifurcation analysis of a delay reaction-diffusion malware propagation model with feedback control
Zhu, Linhe; Zhao, Hongyong; Wang, Xiaoming
2015-05-01
With the rapid development of network information technology, information networks security has become a very critical issue in our work and daily life. This paper attempts to develop a delay reaction-diffusion model with a state feedback controller to describe the process of malware propagation in mobile wireless sensor networks (MWSNs). By analyzing the stability and Hopf bifurcation, we show that the state feedback method can successfully be used to control unstable steady states or periodic oscillations. Moreover, formulas for determining the properties of the bifurcating periodic oscillations are derived by applying the normal form method and center manifold theorem. Finally, we conduct extensive simulations on large-scale MWSNs to evaluate the proposed model. Numerical evidences show that the linear term of the controller is enough to delay the onset of the Hopf bifurcation and the properties of the bifurcation can be regulated to achieve some desirable behaviors by choosing the appropriate higher terms of the controller. Furthermore, we obtain that the spatial-temporal dynamic characteristics of malware propagation are closely related to the rate constant for nodes leaving the infective class for recovered class and the mobile behavior of nodes.
A reaction-diffusion model of the Darien Gap Sterile Insect Release Method
Alford, John G.
2015-05-01
The Sterile Insect Release Method (SIRM) is used as a biological control for invasive insect species. SIRM involves introducing large quantities of sterilized male insects into a wild population of invading insects. A fertile/sterile mating produces offspring that are not viable and the wild insect population will eventually be eradicated. A U.S. government program maintains a permanent sterile fly barrier zone in the Darien Gap between Panama and Columbia to control the screwworm fly (Cochliomyia Hominivorax), an insect that feeds off of living tissue in mammals and has devastating effects on livestock. This barrier zone is maintained by regular releases of massive quantities of sterilized male screwworm flies from aircraft. We analyze a reaction-diffusion model of the Darien Gap barrier zone. Simulations of the model equations yield two types of spatially inhomogeneous steady-state solutions representing a sterile fly barrier that does not prevent invasion and a barrier that does prevent invasion. We investigate steady-state solutions using both phase plane methods and monotone iteration methods and describe how barrier width and the sterile fly release rate affects steady-state behavior.
Accumulations of T-points in a model for solitary pulses in an excitable reaction-diffusion medium.
Homburg, A.J.; Natiello, M.A.
2005-01-01
We consider a family of differential equations that describes traveling waves in a reaction-diffusion equation modeling oxidation of carbon oxide on a platinum surface, near the onset of spatio-temporal chaos. The organizing bifurcation for the bifurcation structure with small carbon oxide
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.
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.
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//
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.
Camley, Brian A.; Zhao, Yanxiang; Li, Bo; Levine, Herbert; Rappel, Wouter-Jan
2017-01-01
We study a minimal model of a crawling eukaryotic cell with a chemical polarity controlled by a reaction-diffusion mechanism describing Rho GTPase dynamics. The size, shape, and speed of the cell emerge from the combination of the chemical polarity, which controls the locations where actin polymerization occurs, and the physical properties of the cell, including its membrane tension. We find in our model both highly persistent trajectories, in which the cell crawls in a straight line, and turning trajectories, where the cell transitions from crawling in a line to crawling in a circle. We discuss the controlling variables for this turning instability and argue that turning arises from a coupling between the reaction-diffusion mechanism and the shape of the cell. This emphasizes the surprising features that can arise from simple links between cell mechanics and biochemistry. Our results suggest that similar instabilities may be present in a broad class of biochemical descriptions of cell polarity.
Camley, Brian A; Li, Bo; Levine, Herbert; Rappel, Wouter-Jan
2016-01-01
We study a minimal model of a crawling eukaryotic cell with a chemical polarity controlled by a reaction-diffusion mechanism describing Rho GTPase dynamics. The size, shape, and speed of the cell emerge from the combination of the chemical polarity, which controls the locations where actin polymerization occurs, and the physical properties of the cell, including its membrane tension. We find in our model both highly persistent trajectories, in which the cell crawls in a straight line, and turning trajectories, where the cell transitions from crawling in a line to crawling in a circle. We discuss the controlling variables for this turning instability, and argue that turning arises from a coupling between the reaction-diffusion mechanism and the shape of the cell. This emphasizes the surprising features that can arise from simple links between cell mechanics and biochemistry. Our results suggest that similar instabilities may be present in a broad class of biochemical descriptions of cell polarity.
Aristotelous, Andreas C; Haider, Mansoor A
2014-08-01
Macroscopic models accounting for cellular effects in natural or engineered tissues may involve unknown constitutive terms that are highly dependent on interactions at the scale of individual cells. Hybrid discrete models, which represent cells individually, were used to develop and apply techniques for modeling diffusive nutrient transport and cellular uptake to identify a nonlinear nutrient loss term in a macroscopic reaction-diffusion model of the system. Flexible and robust numerical methods were used, based on discontinuous Galerkin finite elements in space and a Crank-Nicolson temporal discretization. Scales were bridged via averaging operations over a complete set of subdomains yielding data for identification of a macroscopic nutrient loss term that was accurately captured via a fifth-order polynomial. Accuracy of the identified macroscopic model was demonstrated by direct, quantitative comparisons of the tissue and cellular scale models in terms of three error norms computed on a mesoscale mesh. Copyright © 2014 John Wiley & Sons, Ltd.
Tezuka, Ken-ichi; Wada, Yoshitaka; Takahashi, Akiyuki; Kikuchi, Masanori
2005-01-01
Bone is a complex system with functions including those of adaptation and repair. To understand how bone cells can create a structure adapted to the mechanical environment, we propose a simple bone remodeling model based on a reaction-diffusion system influenced by mechanical stress. Two-dimensional bone models were created and subjected to mechanical loads. The conventional finite element method (FEM) was used to calculate stress distribution. A stress-reactive reaction-diffusion model was constructed and used to simulate bone remodeling under mechanical loads. When an external mechanical stress was applied, stimulated bone formation and subsequent activation of bone resorption produced an efficient adaptation of the internal shape of the model bone to a given stress, and demonstrated major structures of trabecular bone seen in the human femoral neck. The degree of adaptation could be controlled by modulating the diffusion constants of hypothetical local factors. We also tried to demonstrate the deformation of bone structure during osteoporosis by the modulation of a parameter affecting the balance between formation and resorption. This simple model gives us an insight into how bone cells can create an architecture adapted to environmental stress, and will serve as a useful tool to understand both physiological and pathological states of bone based on structural information.
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.
Tsibidis, George D
2008-01-01
Temporally and spatially resolved measurements of protein transport inside cells provide important clues to the functional architecture and dynamics of biological systems. Fluorescence Recovery After Photobleaching (FRAP) technique has been used over the past three decades to measure the mobility of macromolecules and protein transport and interaction with immobile structures inside the cell nucleus. A theoretical model is presented that aims to describe protein transport inside the nucleus, a process which is influenced by the presence of a boundary (i.e. membrane). A set of reaction-diffusion equations is employed to model both the diffusion of proteins and their interaction with immobile binding sites. The proposed model has been designed to be applied to biological samples with a Confocal Laser Scanning Microscope (CLSM) equipped with the feature to bleach regions characterised by a scanning beam that has a radially Gaussian distributed profile. The proposed model leads to FRAP curves that depend on the o...
A time-periodic reaction-diffusion epidemic model with infection period
Zhang, Liang; Wang, Zhi-Cheng
2016-10-01
In this paper, we propose a time-periodic and diffusive SIR epidemic model with constant infection period. By introducing the basic reproduction number R_0 via a next generation operator for this model, we show that the disease goes extinction if R_0 1.
Modeling Morphogenesis with Reaction-Diffusion Equations Using Galerkin Spectral Methods
2007-11-02
Professor Reza Malek-Madani Associate Professor Sonia Garcia 1. Introduction: Modeling Morphogenesis In the context of embryology , morphogenesis is...appreciate the rich pattern formation capabilities of these models. As a general rule , the variability of the initial and boundary conditions as well as...random like chaotic systems, but are intricately structured. However, the eventual organization of a system will not immediately follow from the rules of
Spatially explicit control of invasive species using a reaction-diffusion model
Bonneau, Mathieu; Johnson, Fred A.; Romagosa, Christina M.
2016-01-01
Invasive species, which can be responsible for severe economic and environmental damages, must often be managed over a wide area with limited resources, and the optimal allocation of effort in space and time can be challenging. If the spatial range of the invasive species is large, control actions might be applied only on some parcels of land, for example because of property type, accessibility, or limited human resources. Selecting the locations for control is critical and can significantly impact management efficiency. To help make decisions concerning the spatial allocation of control actions, we propose a simulation based approach, where the spatial distribution of the invader is approximated by a reaction–diffusion model. We extend the classic Fisher equation to incorporate the effect of control both in the diffusion and local growth of the invader. The modified reaction–diffusion model that we propose accounts for the effect of control, not only on the controlled locations, but on neighboring locations, which are based on the theoretical speed of the invasion front. Based on simulated examples, we show the superiority of our model compared to the state-of-the-art approach. We illustrate the use of this model for the management of Burmese pythons in the Everglades (Florida, USA). Thanks to the generality of the modified reaction–diffusion model, this framework is potentially suitable for a wide class of management problems and provides a tool for managers to predict the effects of different management strategies.
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.
A stochastic reaction-diffusion model for protein aggregation on DNA
Voulgarakis, Nikolaos K.
Vital functions of DNA, such as transcription and packaging, depend on the proper clustering of proteins on the double strand. The present study investigates how the interplay between DNA allostery and electrostatic interactions affects protein clustering. The statistical analysis of a simple but transparent computational model reveals two major consequences of this interplay. First, depending on the protein and salt concentration, protein filaments exhibit a bimodal DNA stiffening and softening behavior. Second, within a certain domain of the control parameters, electrostatic interactions can cause energetic frustration that forces proteins to assemble in rigid spiral configurations. Such spiral filaments might trigger both positive and negative supercoiling, which can ultimately promote gene compaction and regulate the promoter. It has been experimentally shown that bacterial histone-like proteins assemble in similar spiral patterns and/or exhibit the same bimodal behavior. The proposed model can, thus, provide computational insights into the physical mechanisms used by proteins to control the mechanical properties of the DNA.
Bifurcation and Turing patterns of reaction-diffusion activator-inhibitor model
Wu, Ranchao; Zhou, Yue; Shao, Yan; Chen, Liping
2017-09-01
Gierer-Meinhardt system is one of prototypical pattern formation models. Turing instability could induce various patterns in this system. Hopf bifurcation analysis and its direction are performed on such diffusive model in this paper, by employing normal form and center manifold reduction. The effects of diffusion on the stability of equilibrium point and the bifurcated limit cycle from Hopf bifurcation are investigated. It is found that under some conditions, diffusion-driven instability, i.e, Turing instability, about the equilibrium point and the bifurcated limit cycle will happen, which are stable without diffusion. Those diffusion-driven instabilities will lead to the occurrence of spatially nonhomogeneous solutions. As a result, some patterns, like stripe and spike solutions, will form. The explicit criteria about the stability and instability of the equilibrium point and the limit cycle in the system are derived, which could be readily applied. Further, numerical simulations are presented to illustrate theoretical analysis.
Modeling dual-scale epidemic dynamics on complex networks with reaction diffusion processes
Xiao-gang JIN; Yong MIN
2014-01-01
The frequent outbreak of severe foodborne diseases (e.g., haemolytic uraemic syndrome and Listeriosis) in 2011 warns of a potential threat that world trade could spread fatal pathogens (e.g., enterohemorrhagic Escherichia coli). The epidemic potential from trade involves both intra-proliferation and inter-diffusion. Here, we present a worldwide vegetable trade network and a stochastic computational model to simulate global trade-mediated epidemics by considering the weighted nodes and edges of the network and the dual-scale dynamics of epidemics. We address two basic issues of network structural impact in global epi-demic patterns:(1) in contrast to the prediction of heterogeneous network models, the broad variability of node degree and edge weights of the vegetable trade network do not determine the threshold of global epidemics;(2) a‘penetration effect’, by which community structures do not restrict propagation at the global scale, quickly facilitates bridging the edges between communities, and leads to synchronized diffusion throughout the entire network. We have also defined an appropriate metric that combines dual-scale behavior and enables quantification of the critical role of bridging edges in disease diffusion from widespread trading. The unusual structure mechanisms of the trade network model may be useful in producing strategies for adaptive immunity and reducing international trade frictions.
A reaction-diffusion system modeling the spread of resistance to an antimalarial drug.
Bacaer, Nicolas; Sokhna, Cheikh
2005-04-01
A mathematical model representing the difusion of resistance to an antimalarial drug is developed. Resistance can spread only when the basic reproduction number of the resistant parasites is bigger than the basic reproduction number of the sensitive parasites (which depends on the fraction of infected people treated with the antimalarial drug). Based on a linearization study and on numerical simulations, an expression for the speed at which resistance spreads is conjectured. It depends on the ratio of the two basic reproduction numbers, on a coefficient representing the difusion of mosquitoes, on the death rate of mosquitoes infected by resistant parasites, and on the recovery rate of nonimmune humans infected by resistant parasites.
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.
Beaghton, Andrea; Beaghton, Pantelis John; Burt, Austin
2016-04-01
Some genes or gene complexes are transmitted from parents to offspring at a greater-than-Mendelian rate, and can spread and persist in populations even if they cause some harm to the individuals carrying them. Such genes may be useful for controlling populations or species that are harmful. Driving-Y chromosomes may be particularly potent in this regard, as they produce a male-biased sex ratio that, if sufficiently extreme, can lead to population elimination. To better understand the potential of such genes to spread over a landscape, we have developed a series of reaction-diffusion models of a driving-Y chromosome in 1-D and radially-symmetric 2-D unbounded domains. The wild-type system at carrying capacity is found to be unstable to the introduction of driving-Y males for all models investigated. Numerical solutions exhibit travelling wave pulses and fronts, and analytical and semi-analytical solutions for the asymptotic wave speed under bounded initial conditions are derived. The driving-Y male invades the wild-type equilibrium state at the front of the wave and completely replaces the wild-type males, leaving behind, at the tail of the wave, a reduced- or zero-population state of females and driving-Y males only. In our simplest model of a population with one life stage and density-dependent mortality, wave speed depends on the strength of drive and the diffusion rate of Y-drive males, and is independent of the population dynamic consequences (suppression or elimination). Incorporating an immobile juvenile stage of fixed duration into the model reduces wave speed approximately in proportion to the relative time spent as a juvenile. If females mate just once in their life, storing sperm for subsequent reproduction, then wave speed depends on the movement of mated females as well as Y-drive males, and may be faster or slower than in the multiple-mating model, depending on the relative duration of juvenile and adult life stages. Numerical solutions are shown for
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.
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.
Chalupecký, Vladimír; Kruschwitz, Jens; Muntean, Adrian
2012-01-01
We consider a two-scale reaction diffusion system able to capture the corrosion of concrete with sulfates. Our aim here is to define and compute two macroscopic corrosion indicators: typical pH drop and gypsum profiles. Mathematically, the system is coupled, endowed with micro-macro transmission conditions, and posed on two different spatially-separated scales: one microscopic (pore scale) and one macroscopic (sewer pipe scale). We use a logarithmic expression to compute values of pH from the volume averaged concentration of sulfuric acid which is obtained by resolving numerically the two-scale system (microscopic equations with direct feedback with the macroscopic diffusion of one of the reactants). Furthermore, we also evaluate the content of the main sulfatation reaction (corrosion) product---the gypsum---and point out numerically a persistent kink in gypsum's concentration profile. Finally, we illustrate numerically the position of the free boundary separating corroded from not-yet-corroded regions.
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.
Scarle, Simon
2009-08-01
In the arsenal of tools that a computational modeller can bring to bare on the study of cardiac arrhythmias, the most widely used and arguably the most successful is that of an excitable medium, a special case of a reaction-diffusion model. These are used to simulate the internal chemical reactions of a cardiac cell and the diffusion of their membrane voltages. Via a number of different methodologies it has previously been shown that reaction-diffusion systems are at multiple levels Turing complete. That is, they are capable of computation in the same manner as a universal Turing machine. However, all such computational systems are subject to a limitation known as the Halting problem. By constructing a universal logic gate using a cardiac cell model, we highlight how the Halting problem therefore could limit what it is possible to predict about cardiac tissue, arrhythmias and re-entry. All simulations for this work were carried out on the GPU of an XBox 360 development console, and we also highlight the great gains in computational power and efficiency produced by such general purpose processing on a GPU for cardiac simulations.
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)
Seirin Lee, S.
2010-03-23
Turing\\'s pattern formation mechanism exhibits sensitivity to the details of the initial conditions suggesting that, in isolation, it cannot robustly generate pattern within noisy biological environments. Nonetheless, secondary aspects of developmental self-organisation, such as a growing domain, have been shown to ameliorate this aberrant model behaviour. Furthermore, while in-situ hybridisation reveals the presence of gene expression in developmental processes, the influence of such dynamics on Turing\\'s model has received limited attention. Here, we novelly focus on the Gierer-Meinhardt reaction diffusion system considering delays due the time taken for gene expression, while incorporating a number of different domain growth profiles to further explore the influence and interplay of domain growth and gene expression on Turing\\'s mechanism. We find extensive pathological model behaviour, exhibiting one or more of the following: temporal oscillations with no spatial structure, a failure of the Turing instability and an extreme sensitivity to the initial conditions, the growth profile and the duration of gene expression. This deviant behaviour is even more severe than observed in previous studies of Schnakenberg kinetics on exponentially growing domains in the presence of gene expression (Gaffney and Monk in Bull. Math. Biol. 68:99-130, 2006). Our results emphasise that gene expression dynamics induce unrealistic behaviour in Turing\\'s model for multiple choices of kinetics and thus such aberrant modelling predictions are likely to be generic. They also highlight that domain growth can no longer ameliorate the excessive sensitivity of Turing\\'s mechanism in the presence of gene expression time delays. The above, extensive, pathologies suggest that, in the presence of gene expression, Turing\\'s mechanism would generally require a novel and extensive secondary mechanism to control reaction diffusion patterning. © 2010 Society for Mathematical Biology.
Basan, Markus; Lenz, Martin; Joanny, Jean-François; Risler, Thomas
2015-01-01
Contact inhibition is the process by which cells switch from a motile growing state to a passive and stabilized state upon touching their neighbors. When two cells touch, an adhesion link is created between them by means of transmembrane E-cadherin proteins. Simultaneously, their actin filaments stop polymerizing in the direction perpendicular to the membrane and reorganize to create an apical belt that colocalizes with the adhesion links. Here, we propose a detailed quantitative model of the role of the cytoplasmic $\\beta$-catenin and $\\alpha$-catenin proteins in this process, treated as a reaction-diffusion system. Upon cell-cell contact, the concentration in $\\alpha$-catenin dimers increases, inhibiting actin branching and thereby reducing cellular motility and expansion pressure. This model provides a mechanism for contact inhibition that could explain previously unrelated experimental findings on the role played by E-cadherin, $\\beta$-catenin and $\\alpha$-catenin in the cellular phenotype and in tumorige...
Branes and integrable lattice models
Yagi, Junya
2016-01-01
This is a brief review of my work on the correspondence between four-dimensional $\\mathcal{N} = 1$ supersymmetric field theories realized by brane tilings and two-dimensional integrable lattice models. I explain how to construct integrable lattice models from extended operators in partially topological quantum field theories, and elucidate the correspondence as an application of this construction.
Exact First-Passage Exponents of 1D Domain Growth: Relation to a Reaction-Diffusion Model
Derrida, Bernard; Hakim, Vincent; Pasquier, Vincent
1995-07-01
In the zero temperature Glauber dynamics of the ferromagnetic Ising or q-state Potts model, the size of domains is known to grow like t1/2. Recent simulations have shown that the fraction r\\(q,t\\) of spins, which have never flipped up to time t, decays like the power law r\\(q,t\\)~t-θ\\(q\\) with a nontrivial dependence of the exponent θ\\(q\\) on q and on space dimension. By mapping the problem on an exactly soluble one-species coagulation model ( A+A-->A), we obtain the exact expression of θ\\(q\\) in dimension one.
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 ...
CHEN LaiWen; WANG JingHua; LEE Chun-Hian
2009-01-01
When hyperthermal atomic oxygen collides with a silicon surface, an ultrathin oxidation regime characterized by fractional atomic-oxygen anions having low diffusive and reactive barriers, along with their enhanced diffusion due to both the electric field and image potential, will form on the surface. In accordance with these properties, an attempt was made in the present study to modify the AlmeidaGoncalves-Baumvol (AGB) model by setting the diffusivity and reaction rate constant to be diffusion-length dependence. According to the modified model, numerical parametric studies for oxidation thin growth were performed. The dependencies of the diffusion coefficient, the reaction rate constant,the attenuation length, and the adjustable parameter upon the translational kinetic energy, flux, temperature, and tangential flux of atomic oxygen were analyzed briefly via the fitting of the experimental data given by Tagawa et al. The numerical results confirmed the rationality of the modified diffusion-reaction model. The model together with the computer code developed in this study would be a useful tool for thickness evaluation of the protective film against the oxidation of atomic oxygen toward spacecraft surface materials in LEO environment.
LEE; Chun-Hian
2009-01-01
When hyperthermal atomic oxygen collides with a silicon surface, an ultrathin oxidation regime characterized by fractional atomic-oxygen anions having low diffusive and reactive barriers, along with their enhanced diffusion due to both the electric field and image potential, will form on the surface. In ac- cordance with these properties, an attempt was made in the present study to modify the Almeida- Goncalves-Baumvol (AGB) model by setting the diffusivity and reaction rate constant to be diffu- sion-length dependence. According to the modified model, numerical parametric studies for oxidation thin growth were performed. The dependencies of the diffusion coefficient, the reaction rate constant, the attenuation length, and the adjustable parameter upon the translational kinetic energy, flux, tem- perature, and tangential flux of atomic oxygen were analyzed briefly via the fitting of the experimental data given by Tagawa et al. The numerical results confirmed the rationality of the modified diffu- sion-reaction model. The model together with the computer code developed in this study would be a useful tool for thickness evaluation of the protective film against the oxidation of atomic oxygen toward spacecraft surface materials in LEO environment.
The dynamics of p53 in single cells: physiologically based ODE and reaction-diffusion PDE models
Eliaš, Ján; Dimitrio, Luna; Clairambault, Jean; Natalini, Roberto
2014-08-01
The intracellular signalling network of the p53 protein plays important roles in genome protection and the control of cell cycle phase transitions. Recently observed oscillatory behaviour in single cells under stress conditions has inspired several research groups to simulate and study the dynamics of the protein with the aim of gaining a proper understanding of the physiological meanings of the oscillations. We propose compartmental ODE and PDE models of p53 activation and regulation in single cells following DNA damage and we show that the p53 oscillations can be retrieved by plainly involving p53-Mdm2 and ATM-p53-Wip1 negative feedbacks, which are sufficient for oscillations experimentally, with no further need to introduce any delays into the protein responses and without considering additional positive feedback.
Marco A. Velasco
2016-10-01
Full Text Available Scaffolds are essential in bone tissue engineering, as they provide support to cells and growth factors necessary to regenerate tissue. In addition, they meet the mechanical function of the bone while it regenerates. Currently, the multiple methods for designing and manufacturing scaffolds are based on regular structures from a unit cell that repeats in a given domain. However, these methods do not resemble the actual structure of the trabecular bone which may work against osseous tissue regeneration. To explore the design of porous structures with similar mechanical properties to native bone, a geometric generation scheme from a reaction-diffusion model and its manufacturing via a material jetting system is proposed. This article presents the methodology used, the geometric characteristics and the modulus of elasticity of the scaffolds designed and manufactured. The method proposed shows its potential to generate structures that allow to control the basic scaffold properties for bone tissue engineering such as the width of the channels and porosity. The mechanical properties of our scaffolds are similar to trabecular tissue present in vertebrae and tibia bones. Tests on the manufactured scaffolds show that it is necessary to consider the orientation of the object relative to the printing system because the channel geometry, mechanical properties and roughness are heavily influenced by the position of the surface analyzed with respect to the printing axis. A possible line for future work may be the establishment of a set of guidelines to consider the effects of manufacturing processes in designing stages.
Johnson, Margaret E.; Hummer, Gerhard
2014-07-01
We present a new algorithm for simulating reaction-diffusion equations at single-particle resolution. Our algorithm is designed to be both accurate and simple to implement, and to be applicable to large and heterogeneous systems, including those arising in systems biology applications. We combine the use of the exact Green's function for a pair of reacting particles with the approximate free-diffusion propagator for position updates to particles. Trajectory reweighting in our free-propagator reweighting (FPR) method recovers the exact association rates for a pair of interacting particles at all times. FPR simulations of many-body systems accurately reproduce the theoretically known dynamic behavior for a variety of different reaction types. FPR does not suffer from the loss of efficiency common to other path-reweighting schemes, first, because corrections apply only in the immediate vicinity of reacting particles and, second, because by construction the average weight factor equals one upon leaving this reaction zone. FPR applications include the modeling of pathways and networks of protein-driven processes where reaction rates can vary widely and thousands of proteins may participate in the formation of large assemblies. With a limited amount of bookkeeping necessary to ensure proper association rates for each reactant pair, FPR can account for changes to reaction rates or diffusion constants as a result of reaction events. Importantly, FPR can also be extended to physical descriptions of protein interactions with long-range forces, as we demonstrate here for Coulombic interactions.
Lattice Boltzmann model for nanofluids
Xuan Yimin; Yao Zhengping [Nanjing University of Science and Technology, School of Power Engineering, Nanjing (China)
2005-01-01
A nanofluid is a particle suspension that consists of base liquids and nanoparticles and has great potential for heat transfer enhancement. By accounting for the external and internal forces acting on the suspended nanoparticles and interactions among the nanoparticles and fluid particles, a lattice Boltzmann model is proposed for simulating flow and energy transport processes inside the nanofluids. First, we briefly introduce the conventional lattice Boltzmann model for multicomponent systems. Then, we discuss the irregular motion of the nanoparticles and inherent dynamic behavior of nanofluids and describe a lattice Boltzmann model for simulating nanofluids. Finally, we conduct some calculations for the distribution of the suspended nanoparticles. (orig.)
Williamson, S. Gill
2010-01-01
Will the cosmological multiverse, when described mathematically, have easily stated properties that are impossible to prove or disprove using mathematical physics? We explore this question by constructing lattice multiverses which exhibit such behavior even though they are much simpler mathematically than any likely cosmological multiverse.
De Soto, F; Carbonell, J; Leroy, J P; Pène, O; Roiesnel, C; Boucaud, Ph.
2007-01-01
We present the first results of a quantum field approach to nuclear models obtained by lattice techniques. Renormalization effects for fermion mass and coupling constant in case of scalar and pseudoscalar interaction lagrangian densities are discussed.
Zhao, Qi; Yi, Ming; Liu, Yan
2011-10-01
The mitogen-activated protein kinase (MAPK) cascade plays a critical role in the control of cell growth. Deregulation of this pathway contributes to the development of many cancers. To better understand its signal transduction, we constructed a reaction-diffusion model for the MAPK pathway. We modeled the three layers of phosphorylation-dephosphorylation reactions and diffusion processes from the cell membrane to the nucleus. Based on different types of feedback in the MAPK cascade, four operation modes are introduced. For each of the four modes, spatial distributions and dose-response curves of active kinases (i.e. ppMAPK) are explored by numerical simulation. The effects of propagation length, diffusion coefficient and feedback strength on the pathway dynamics are investigated. We found that intrinsic bistability in the MAPK cascade can generate a traveling wave of ppMAPK with constant amplitude when the propagation length is short. ppMAPK in this mode of intrinsic bistability decays more slowly than it does in all other modes as the propagation length increases. Moreover, we examined the global and local responses to Ras-GTP of these four modes, and demonstrated how the shapes of these dose-response curves change as the propagation length increases. Also, we found that larger diffusion constant gives a higher response level on the zero-order regime and makes the ppMAPK profiles flatter under strong Ras-GTP stimulus. Furthermore, we observed that spatial responses of ppMAPK are more sensitive to negative feedback than to positive feedback in the broader signal range. Finally, we showed how oscillatory signals pass through the kinase cascade, and found that high frequency signals are damped faster than low frequency ones.
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.
Lattice Boltzmann Model for Compressible Fluid on a Square Lattice
SUN Cheng-Hai
2000-01-01
A two-level four-direction lattice Boltzmann model is formulated on a square lattice to simulate compressible flows with a high Mach number. The particle velocities are adaptive to the mean velocity and internal energy. Therefore, the mean flow can have a high Mach number. Due to the simple form of the equilibrium distribution, the 4th order velocity tensors are not involved in the calculations. Unlike the standard lattice Boltzmann model, o special treatment is need for the homogeneity of 4th order velocity tensors on square lattices. The Navier-Stokes equations were derived by the Chapman-Enskog method from the BGK Boltzmann equation. The model can be easily extended to three-dimensional cubic lattices. Two-dimensional shock-wave propagation was simulated
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.
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.
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.
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
Fluctuating multicomponent lattice Boltzmann model.
Belardinelli, D; Sbragaglia, M; Biferale, L; Gross, M; Varnik, F
2015-02-01
Current implementations of fluctuating lattice Boltzmann equations (FLBEs) describe single component fluids. In this paper, a model based on the continuum kinetic Boltzmann equation for describing multicomponent fluids is extended to incorporate the effects of thermal fluctuations. The thus obtained fluctuating Boltzmann equation is first linearized to apply the theory of linear fluctuations, and expressions for the noise covariances are determined by invoking the fluctuation-dissipation theorem directly at the kinetic level. Crucial for our analysis is the projection of the Boltzmann equation onto the orthonormal Hermite basis. By integrating in space and time the fluctuating Boltzmann equation with a discrete number of velocities, the FLBE is obtained for both ideal and nonideal multicomponent fluids. Numerical simulations are specialized to the case where mean-field interactions are introduced on the lattice, indicating a proper thermalization of the system.
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.
A Lattice-Gas Model of Microemulsions
Boghosian, B M; Emerton, A N; Boghosian, Bruce M.; Coveney, Peter V.; Emerton, Andrew N.
1995-01-01
We develop a lattice gas model for the nonequilibrium dynamics of microemulsions. Our model is based on the immiscible lattice gas of Rothman and Keller, which we reformulate using a microscopic, particulate description so as to permit generalisation to more complicated interactions, and on the prescription of Chan and Liang for introducing such interparticle interactions into lattice gas dynamics. We present the results of simulations to demonstrate that our model exhibits the correct phenomenology, and we contrast it with both equilibrium lattice models of microemulsions, and to other lattice gas models.
SIMPLE LATTICE BOLTZMANN MODEL FOR TRAFFIC FLOWS
Yan Guangwu; Hu Shouxin
2000-01-01
A lattice Boltzmann model with 5-bit lattice for traffic flows is proposed.Using the Chapman-Enskog expansion and multi-scale technique,we obtain the higher-order moments of equilibrium distribution function.A simple traffic light problem is simulated by using the present lattice Boltzmann model,and the result agrees well with analytical solution.
王智诚; 王双明
2013-01-01
利用动力系统方法及持久性理论研究了一类时间周期的时滞非局部反应扩散单种群增长模型，建立了解的全局存在性以及一致持久性。%The paper was concerned with a class of delayed nonlocal reaction-diffusion equation with a time period, which modelled the growth of a single species. By using the monotone dynamical system method and practice persistence theory, the global existence and uniform persistence of solutions were established.
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
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.
Lattice Models of Quantum Gravity
Bittner, E R; Holm, C; Janke, W; Markum, H; Riedler, J
1998-01-01
Standard Regge Calculus provides an interesting method to explore quantum gravity in a non-perturbative fashion but turns out to be a CPU-time demanding enterprise. One therefore seeks for suitable approximations which retain most of its universal features. The $Z_2$-Regge model could be such a desired simplification. Here the quadratic edge lengths $q$ of the simplicial complexes are restricted to only two possible values $q=1+\\epsilon\\sigma$, with Ising model. To test whether this simpler model still contains the essential qualities of the standard Regge Calculus, we study both models in two dimensions and determine several observables on the same lattice size. In order to compare expectation values, e.g. of the average curvature or the Liouville field susceptibility, we employ in both models the same functional integration measure. The phase structure is under current investigation using mean field theory and numerical simulation.
Hydrodynamic behaviour of Lattice Boltzmann and Lattice BGK models
Behrend, O; Warren, P
1993-01-01
Abstract: We present a numerical analysis of the validity of classical and generalized hydrodynamics for Lattice Boltzmann Equation (LBE) and Lattice BGK methods in two and three dimensions, as a function of the collision parameters of these models. Our analysis is based on the wave-number dependence of the evolution operator. Good ranges of validity are found for BGK models as long as the relaxation time is chosen smaller than or equal to unity. The additional freedom in the choice of collision parameters for LBE models does not seem to give significant improvement.
谢溪庄
2011-01-01
In this paper, the author proposed and considered a Schoner reaction-diffusion equation in competing model with nonlocal delays . Each species in the discrete delay type model has a corresponding constant maturation time. Only the adult members are involved competition and immature members are in the absence of competition. We established the existence of traveling wave fronts connecting two boundary equilibriums. The approach used in this paper is the upper-lower solutions technique and monotone iteration by Wang, Li and Ruan for reaction-diffusion systems with spatio-temporal delays.%构造并研究了一类具有非局部时滞Schoner竞争反应扩散模型．每一个种群的成熟期是一个常数，而且只有成年种群存在竞争，幼年的种群并不存在竞争，此外种群个体在空间区域中的运动是随机行走的．我们利用Wang，Li和Ruan建立的具有非局部时滞的反应扩散系统的波前解存在性理论，证明了连接两个边界平衡解的行波解的存在性．
田慧洁; 李艳玲; 郭改慧
2016-01-01
研究了具有饱和项和毒素影响的反应扩散模型的平衡态方程,在齐次Neumann边界条件下常数平衡解的分歧与稳定性.利用谱分析和分歧理论的方法,分别以r1、r2为分歧参数,讨论了系统在常数平衡解附近出现分歧现象;同时运用线性算子的扰动理论和分歧解的稳定理论给出分歧解的稳定性.%The steady-states of reaction diffusion model with saturating terms and effects of toxic substances is studied, the bifurcation and the stability of a reaction-diffusion system with homogeneous Neumann boundary are investigated by the method of spectral analysis and bifurcation theory. The bifurcation at the steady-state solutions is acquired by treating r1, r2 as bifurcation parameters. Moreover, some stability results of the bifurcation solutions are obtained by using pertur-bation theory of linear operators and stability theory of bifurcation solutions.
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.
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.
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.
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.
Potts and percolation models on bowtie lattices.
Ding, Chengxiang; Wang, Yancheng; Li, Yang
2012-08-01
We give the exact critical frontier of the Potts model on bowtie lattices. For the case of q = 1, the critical frontier yields the thresholds of bond percolation on these lattices, which are exactly consistent with the results given by Ziff et al. [J. Phys. A 39, 15083 (2006)]. For the q = 2 Potts model on a bowtie A lattice, the critical point is in agreement with that of the Ising model on this lattice, which has been exactly solved. Furthermore, we do extensive Monte Carlo simulations of the Potts model on a bowtie A lattice with noninteger q. Our numerical results, which are accurate up to seven significant digits, are consistent with the theoretical predictions. We also simulate the site percolation on a bowtie A lattice, and the threshold is s(c) = 0.5479148(7). In the simulations of bond percolation and site percolation, we find that the shape-dependent properties of the percolation model on a bowtie A lattice are somewhat different from those of an isotropic lattice, which may be caused by the anisotropy of the lattice.
Lattice models of ionic systems
Kobelev, Vladimir; Kolomeisky, Anatoly B.; Fisher, Michael E.
2002-05-01
A theoretical analysis of Coulomb systems on lattices in general dimensions is presented. The thermodynamics is developed using Debye-Hückel theory with ion-pairing and dipole-ion solvation, specific calculations being performed for three-dimensional lattices. As for continuum electrolytes, low-density results for simple cubic (sc), body-centered cubic (bcc), and face-centered cubic (fcc) lattices indicate the existence of gas-liquid phase separation. The predicted critical densities have values comparable to those of continuum ionic systems, while the critical temperatures are 60%-70% higher. However, when the possibility of sublattice ordering as well as Debye screening is taken into account systematically, order-disorder transitions and a tricritical point are found on sc and bcc lattices, and gas-liquid coexistence is suppressed. Our results agree with recent Monte Carlo simulations of lattice electrolytes.
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.
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...
Disorder solutions of lattice spin models
Batchelor, M. T.; van Leeuwen, J. M. J.
1989-01-01
It is shown that disorder solutions, which have been obtained by different methods, follow from a simple decimation method. The method is put in general form and new disorder solutions are constructed for the Blume-Emery-Griffiths model on a triangular lattice and for Potts and Ising models on square and fcc lattices.
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.
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.
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...
Lattice Model for water-solute mixtures
Furlan, A. P.; Almarza, N. G.; M. C. Barbosa
2016-01-01
A lattice model for the study of mixtures of associating liquids is proposed. Solvent and solute are modeled by adapting the associating lattice gas (ALG) model. The nature of interaction solute/solvent is controlled by tuning the energy interactions between the patches of ALG model. We have studied three set of parameters, resulting on, hydrophilic, inert and hydrophobic interactions. Extensive Monte Carlo simulations were carried out and the behavior of pure components and the excess proper...
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'.
A Solvable Decorated Ising Lattice Model
无
2006-01-01
A decoratedlattice is suggested and the Ising model on it with three kinds of interactions K1, K2, and K3 is studied. Using an equivalent transformation, the square decorated Ising lattice is transformed into a regular square Ising lattice with nearest-neighbor, next-nearest-neighbor, and four-spin interactions, and the critical fixed point is found atK1 = 0.5769, K2 = -0.0671, and K3 = 0.3428, which determines the critical temperature of the system. It is also found that this system and the regular square Ising lattice, and the eight-vertex model belong to the same universality class.
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.
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.
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.
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.
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.
Lattice distortion in disordered antiferromagnetic XY models
Li Peng-Fei; Cao Hai-Jing
2012-01-01
The behavior of lattice distortion in spin 1/2 antiferromagnetic XY models with random magnetic modulation is investigated with the consideration of spin-phonon coupling in the adiabatic limit.It is found that lattice distortion relies on the strength of the random modulation.For strong or weak enough spin-phonon couplings,the average lattice distortion may decrease or increase as the random modulation is strengthened.This may be the result of competition between the random magnetic modulation and the spin-phonon coupling.
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 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.
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.
张忠文
2015-01-01
A nonlocal and time-delayed reaction-diffusion predator-prey model was studied, where prey individuals undergo two stages, i.e. immature and mature, and the conversion of consumed from prey biomass to predator biomass has a retardation. The growth of the prey population obeys general Beverton-Holt function. By discussing the principal eigenvalue of nonlocal elliptic problems, we showed an explicit expression of the principal eigenvalue, the suﬃcient conditions for the uniform persistence and global extinction for the model could be established. By the fluctuation method, the global attractivity of the unique positive constant steady state was obtained.%考虑一类带阶段结构的扩散捕食者食饵模型，其中食饵个体经历两个生命阶段，未成熟和成熟阶段，捕食者生物量的转化有一个延迟，食饵生物量的增长遵循一般化的Beverton-Holt函数。就非局部椭圆特征问题的主特征值，建立一致持久性与全局灭绝性。利用波动方法，给出唯一正常数稳态解的全局吸引性。
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.
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.
Adaptive Lattice Boltzmann Model for Compressible Flows
无
2000-01-01
A new lattice Boltzmann model for compressible flows is presented. The main difference from the standard lattice Boltzmann model is that the particle velocities are no longer constant, but vary with the mean velocity and internal energy. The adaptive nature of the particle velocities permits the mean flow to have a high Mach number. The introduction of a particle potential energy makes the model suitable for a perfect gas with arbitrary specific heat ratio. The Navier-Stokes (N-S) equations are derived by the Chapman-Enskog method from the BGK Boltzmann equation. Two kinds of simulations have been carried out on the hexagonal lattice to test the proposed model. One is the Sod shock-tube simulation. The other is a strong shock of Mach number 5.09 diffracting around a corner.
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
Lattice Boltzmann Model for Numerical Relativity
Ilseven, E
2015-01-01
In the Bona-Masso formulation, Einstein equations are written as a set of flux conservative first order hyperbolic equations that resemble fluid dynamics equations. Based on this formulation, we construct a lattice Boltzmann model for Numerical Relativity. Our model is validated with well-established tests, showing good agreement with analytical solutions. Furthermore, we show that by increasing the relaxation time, we gain stability at the cost of losing accuracy, and by decreasing the lattice spacings while keeping a constant numerical diffusivity, the accuracy and stability of our simulations improves. Finally, in order to show the potential of our approach a linear scaling law for parallelisation with respect to number of CPU cores is demonstrated. Our model represents the first step in using lattice kinetic theory to solve gravitational problems.
Lattice Gauge Theories and Spin Models
Mathur, Manu
2016-01-01
The Wegner $Z_2$ gauge theory-$Z_2$ Ising spin model duality in $(2+1)$ dimensions is revisited and derived through a series of canonical transformations. These $Z_2$ results are directly generalized to SU(N) lattice gauge theory in $(2+1)$ dimensions to obtain a dual SU(N) spin model in terms of the SU(N) magnetic fields and electric scalar potentials. The gauge-spin duality naturally leads to a new gauge invariant disorder operator for SU(N) lattice gauge theory. A variational ground state of the dual SU(2) spin model with only nearest neighbour interactions is constructed to analyze SU(2) lattice gauge theory.
Antiferromagnetic Ising model on the swedenborgite lattice
Buhrandt, Stefan; Fritz, Lars
2014-01-01
Geometrical frustration in spin systems often results in a large number of degenerate ground states. In this work, we study the antiferromagnetic Ising model on the three-dimensional swedenborgite lattice, which is a specific stacking of kagome and triangular layers. The model contains two exchange
Entropic lattice Boltzmann model for Burgers's equation.
Boghosian, Bruce M; Love, Peter; Yepez, Jeffrey
2004-08-15
Entropic lattice Boltzmann models are discrete-velocity models of hydrodynamics that possess a Lyapunov function. This feature makes them useful as nonlinearly stable numerical methods for integrating hydrodynamic equations. Over the last few years, such models have been successfully developed for the Navier-Stokes equations in two and three dimensions, and have been proposed as a new category of subgrid model of turbulence. In the present work we develop an entropic lattice Boltzmann model for Burgers's equation in one spatial dimension. In addition to its pedagogical value as a simple example of such a model, our result is actually a very effective way to simulate Burgers's equation in one dimension. At moderate to high values of viscosity, we confirm that it exhibits no trace of instability. At very small values of viscosity, however, we report the existence of oscillations of bounded amplitude in the vicinity of the shock, where gradient scale lengths become comparable with the grid size. As the viscosity decreases, the amplitude at which these oscillations saturate tends to increase. This indicates that, in spite of their nonlinear stability, entropic lattice Boltzmann models may become inaccurate when the ratio of gradient scale length to grid spacing becomes too small. Similar inaccuracies may limit the utility of the entropic lattice Boltzmann paradigm as a subgrid model of Navier-Stokes turbulence.
Grid refinement for entropic lattice Boltzmann models.
Dorschner, B; Frapolli, N; Chikatamarla, S S; Karlin, I V
2016-11-01
We propose a multidomain grid refinement technique with extensions to entropic incompressible, thermal, and compressible lattice Boltzmann models. Its validity and accuracy are assessed by comparison to available direct numerical simulation and experiment for the simulation of isothermal, thermal, and viscous supersonic flow. In particular, we investigate the advantages of grid refinement for the setups of turbulent channel flow, flow past a sphere, Rayleigh-Bénard convection, as well as the supersonic flow around an airfoil. Special attention is paid to analyzing the adaptive features of entropic lattice Boltzmann models for multigrid simulations.
Grid refinement for entropic lattice Boltzmann models
Dorschner, B; Chikatamarla, S S; Karlin, I V
2016-01-01
We propose a novel multi-domain grid refinement technique with extensions to entropic incompressible, thermal and compressible lattice Boltzmann models. Its validity and accuracy are accessed by comparison to available direct numerical simulation and experiment for the simulation of isothermal, thermal and viscous supersonic flow. In particular, we investigate the advantages of grid refinement for the set-ups of turbulent channel flow, flow past a sphere, Rayleigh-Benard convection as well as the supersonic flow around an airfoil. Special attention is payed to analyzing the adaptive features of entropic lattice Boltzmann models for multi-grid simulations.
Lattice Boltzmann model for numerical relativity.
Ilseven, E; Mendoza, M
2016-02-01
In the Z4 formulation, Einstein equations are written as a set of flux conservative first-order hyperbolic equations that resemble fluid dynamics equations. Based on this formulation, we construct a lattice Boltzmann model for numerical relativity and validate it with well-established tests, also known as "apples with apples." Furthermore, we find that by increasing the relaxation time, we gain stability at the cost of losing accuracy, and by decreasing the lattice spacings while keeping a constant numerical diffusivity, the accuracy and stability of our simulations improve. Finally, in order to show the potential of our approach, a linear scaling law for parallelization with respect to number of CPU cores is demonstrated. Our model represents the first step in using lattice kinetic theory to solve gravitational problems.
Multisite Interactions in Lattice-Gas Models
Einstein, T. L.; Sathiyanarayanan, R.
For detailed applications of lattice-gas models to surface systems, multisite interactions often play at least as significant a role as interactions between pairs of adatoms that are separated by a few lattice spacings. We recall that trio (3-adatom, non-pairwise) interactions do not inevitably create phase boundary asymmetries about half coverage. We discuss a sophisticated application to an experimental system and describe refinements in extracting lattice-gas energies from calculations of total energies of several different ordered overlayers. We describe how lateral relaxations complicate matters when there is direct interaction between the adatoms, an issue that is important when examining the angular dependence of step line tensions. We discuss the connector model as an alternative viewpoint and close with a brief account of recent work on organic molecule overlayers.
A lattice model for influenza spreading.
Antonella Liccardo
Full Text Available We construct a stochastic SIR model for influenza spreading on a D-dimensional lattice, which represents the dynamic contact network of individuals. An age distributed population is placed on the lattice and moves on it. The displacement from a site to a nearest neighbor empty site, allows individuals to change the number and identities of their contacts. The dynamics on the lattice is governed by an attractive interaction between individuals belonging to the same age-class. The parameters, which regulate the pattern dynamics, are fixed fitting the data on the age-dependent daily contact numbers, furnished by the Polymod survey. A simple SIR transmission model with a nearest neighbors interaction and some very basic adaptive mobility restrictions complete the model. The model is validated against the age-distributed Italian epidemiological data for the influenza A(H1N1 during the [Formula: see text] season, with sensible predictions for the epidemiological parameters. For an appropriate topology of the lattice, we find that, whenever the accordance between the contact patterns of the model and the Polymod data is satisfactory, there is a good agreement between the numerical and the experimental epidemiological data. This result shows how rich is the information encoded in the average contact patterns of individuals, with respect to the analysis of the epidemic spreading of an infectious disease.
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...
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.
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.
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.
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.
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...
Quiver gauge theories and integrable lattice models
Yagi, Junya
2015-01-01
We discuss connections between certain classes of supersymmetric quiver gauge theories and integrable lattice models from the point of view of topological quantum field theories (TQFTs). The relevant classes include 4d $\\mathcal{N} = 1$ theories known as brane box and brane tilling models, 3d $\\mathcal{N} = 2$ and 2d $\\mathcal{N} = (2,2)$ theories obtained from them by compactification, and 2d $\\mathcal{N} = (0,2)$ theories closely related to these theories. We argue that their supersymmetric indices carry structures of TQFTs equipped with line operators, and as a consequence, are equal to the partition functions of lattice models. The integrability of these models follows from the existence of extra dimension in the TQFTs, which emerges after the theories are embedded in M-theory. The Yang-Baxter equation expresses the invariance of supersymmetric indices under Seiberg duality and its lower-dimensional analogs.
An Intermolecular Vibration Model for Lattice Ice
Quinn M. Brewster
2010-06-01
Full Text Available Lattice ice with tetrahedral arrangement is studied using a modified Einstein’s model that incorporates the hindered translational and rotational vibration bands into a harmonic oscillation system. The fundamental frequencies for hindered translational and rotational vibrations are assigned based on the intermolecular vibration bands as well as thermodynamic properties from existing experimental data. Analytical forms for thermodynamic properties are available for the modified model, with three hindered translational bands at (65, 229, 229 cm-1 and three effective hindered rotational bands at 560 cm-1. The derived results are good for temperatures higher than 30 K. To improve the model below 30 K, Lorentzian broadening correction is added. This simple model helps unveil the physical picture of ice lattice vibration behavior.
Quiver gauge theories and integrable lattice models
Yagi, Junya [International School for Advanced Studies (SISSA),via Bonomea 265, 34136 Trieste (Italy); INFN - Sezione di Trieste,via Valerio 2, 34149 Trieste (Italy)
2015-10-09
We discuss connections between certain classes of supersymmetric quiver gauge theories and integrable lattice models from the point of view of topological quantum field theories (TQFTs). The relevant classes include 4d N=1 theories known as brane box and brane tilling models, 3d N=2 and 2d N=(2,2) theories obtained from them by compactification, and 2d N=(0,2) theories closely related to these theories. We argue that their supersymmetric indices carry structures of TQFTs equipped with line operators, and as a consequence, are equal to the partition functions of lattice models. The integrability of these models follows from the existence of extra dimension in the TQFTs, which emerges after the theories are embedded in M-theory. The Yang-Baxter equation expresses the invariance of supersymmetric indices under Seiberg duality and its lower-dimensional analogs.
The Correlated Kondo-lattice Model
Kienert, J.; Santos, C.; Nolting, W.
2003-01-01
We investigate the ferromagnetic Kondo-lattice model (FKLM) with a correlated conduction band. A moment conserving approach is proposed to determine the electronic self-energy. Mapping the interaction onto an effective Heisenberg model we calculate the ordering of the localized spin system self-consistently. Quasiparticle densities of states (QDOS) and the Curie temperature are calculated. The band interaction leads to an upper Hubbard peak and modifies the magnetic stability of the FKLM.
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,...
A lattice Boltzmann model for adsorption breakthrough
Agarwal, Saurabh; Verma, Nishith [Indian Institute of Technology Kanpur, Department of Chemical Engineering, Kanpur (India); Mewes, Dieter [Universitat Hannover, Institut fur Verfahrenstechnik, Hannover (Germany)
2005-07-01
A lattice Boltzmann model is developed to simulate the one-dimensional (1D) unsteady state concentration profiles, including breakthrough curves, in a fixed tubular bed of non-porous adsorbent particles. The lattice model solves the 1D time dependent convection-diffusion-reaction equation for an ideal binary gaseous mixture, with solute concentrations at parts per million levels. The model developed in this study is also able to explain the experimental adsorption/desorption data of organic vapours (toluene) on silica gel under varying conditions of temperature, concentrations and flowrates. Additionally, the programming code written for simulating the adsorption breakthrough is modified with minimum changes to successfully simulate a few flow problems, such as Poiseuille flow, Couette flow, and axial dispersion in a tube. The present study provides an alternative numerical approach to solving such types of mass transfer related problems. (orig.)
Lattice fermions in the Schwinger model
Bodwin, Geoffrey T.; Kovacs, Eve V.
1987-05-01
We obtain exact solutions for the continuum limit of the lattice Schwinger model, using the Lagrangian formulations of the Wilson, ``naive,'' Kogut-Susskind, and Drell-Weinstein-Yankielowicz (DWY) lattice fermion derivatives. We examine the mass gap, the anomaly, and the chiral order parameter . As expected, our results for the Wilson formulation are consistent with those of the continuum theory and our results for the ``naive'' formulation exhibit spectrum doubling. In the Kogut-Susskind case, the U(1) anomaly is doubled, but vanishes. In solving the DWY version of the model, we make use of a proposal for resumming perturbation theory due to Rabin. The Lagrangian formulation of the DWY Schwinger model displays spectrum doubling and a mass gap that is √2 times the continuum one. The U(1) anomaly graph is nonvanishing and noncovariant in the continuum limit, but has a vanishing divergence. The chiral order parameter also vanishes.
Ising Model on an Infinite Ladder Lattice
无
2007-01-01
In this paper we propose an Ising model on an infinite ladder lattice, which is made of two infinite Ising spin chains with interactions. It is essentially a quasi-one-dimessional Ising model because the length of the ladder lattice is infinite, while its width is finite. We investigate the phase transition and dynamic behavior of Ising model on this quasi-one-dimessional system. We use the generalized transfer matrix method to investigate the phase transition of the system. It is found that there is no nonzero temperature phase transition in this system. At the same time, we are interested in Glauber dynamics. Based on that, we obtain the time evolution of the local spin magnetization by exactly solving a set of master equations.
Extra-dimensional models on the lattice
Knechtli, Francesco
2016-01-01
In this review we summarize the ongoing effort to study extra-dimensional gauge theories with lattice simulations. In these models the Higgs field is identified with extra-dimensional components of the gauge field. The Higgs potential is generated by quantum corrections and is protected from divergencies by the higher dimensional gauge symmetry. Dimensional reduction to four dimensions can occur through compactification or localization. Gauge-Higgs unification models are often studied using perturbation theory. Numerical lattice simulations are used to go beyond these perturbative expectations and to include non-perturbative effects. We describe the known perturbative predictions and their fate in the strongly-coupled regime for various extra-dimensional models.
Costanza, E. F.; Costanza, G.
2016-10-01
Continuum partial differential equations are obtained from a set of discrete stochastic evolution equations of both non-Markovian and Markovian processes and applied to the diffusion within the context of the lattice gas model. A procedure allowing to construct one-dimensional lattices that are topologically equivalent to two-dimensional lattices is described in detail in the case of a rectangular lattice. This example shows the general features that possess the procedure and extensions are also suggested in order to provide a wider insight in the present approach.
Hyper-lattice algebraic model for data warehousing
Sen, Soumya; Chaki, Nabendu
2016-01-01
This book presents Hyper-lattice, a new algebraic model for partially ordered sets, and an alternative to lattice. The authors analyze some of the shortcomings of conventional lattice structure and propose a novel algebraic structure in the form of Hyper-lattice to overcome problems with lattice. They establish how Hyper-lattice supports dynamic insertion of elements in a partial order set with a partial hierarchy between the set members. The authors present the characteristics and the different properties, showing how propositions and lemmas formalize Hyper-lattice as a new algebraic structure.
Gauge theories and integrable lattice models
Witten, Edward
1989-08-01
Investigations of new knot polynomials discovered in the last few years have shown them to be intimately connected with soluble models of two dimensional lattice statistical mechanics. In this paper, these results, which in time may illuminate the whole question of why integrable lattice models exist, are reconsidered from the point of view of three dimensional gauge theory. Expectation values of Wilson lines in three dimensional Chern-Simons gauge theories can be computed by evaluating the partition functions of certain lattice models on finite graphs obtained by projecting the Wilson lines to the plane. The models in question — previously considered in both the knot theory and statistical mechanics — are IRF models in which the local Boltzmann weights are the matrix elements of braiding matrices in rational conformal field theories. These matrix elements, in turn, can be presented in three dimensional gauge theory in terms of the expectation value of a certain tetrahedral configuration of Wilson lines. This representation makes manifest a surprising symmetry of the braiding matrix elements in conformal field theory.
Analysis of quantum spin models on hyperbolic lattices and Bethe lattice
Daniška, Michal; Gendiar, Andrej
2016-04-01
The quantum XY, Heisenberg, and transverse field Ising models on hyperbolic lattices are studied by means of the tensor product variational formulation algorithm. The lattices are constructed by tessellation of congruent polygons with coordination number equal to four. The calculated ground-state energies of the XY and Heisenberg models and the phase transition magnetic field of the Ising model on the series of lattices are used to estimate the corresponding quantities of the respective models on the Bethe lattice. The hyperbolic lattice geometry induces mean-field-like behavior of the models. The ambition to obtain results on the non-Euclidean lattice geometries has been motivated by theoretical studies of the anti-de Sitter/conformal field theory correspondence.
Renormalization of aperiodic model lattices: spectral properties
Kroon, L
2003-01-01
Many of the published results for one-dimensional deterministic aperiodic systems treat rather simplified electron models with either a constant site energy or a constant hopping integral. Here we present some rigorous results for more realistic mixed tight-binding systems with both the site energies and the hopping integrals having an aperiodic spatial variation. It is shown that the mixed Thue-Morse, period-doubling and Rudin-Shapiro lattices can be transformed to on-site models on renormalized lattices maintaining the individual order between the site energies. The character of the energy spectra for these mixed models is therefore the same as for the corresponding on-site models. Furthermore, since the study of electrons on a lattice governed by the Schroedinger tight-binding equation maps onto the study of elastic vibrations on a harmonic chain, we have proved that the vibrational spectra of aperiodic harmonic chains with distributions of masses determined by the Thue-Morse sequence and the period-doubli...
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.
Integrable Lattice Models From Gauge Theory
Witten, Edward
2016-01-01
These notes provide an introduction to recent work by Kevin Costello in which integrable lattice models of classical statistical mechanics in two dimensions are understood in terms of quantum gauge theory in four dimensions. This construction will be compared to the more familiar relationship between quantum knot invariants in three dimensions and Chern-Simons gauge theory. (Based on a Whittaker Colloquium at the University of Edinburgh and a lecture at Strings 2016 in Beijing.)
Multireflection boundary conditions for lattice Boltzmann models.
Ginzburg, Irina; d'Humières, Dominique
2003-12-01
We present a general framework for several previously introduced boundary conditions for lattice Boltzmann models, such as the bounce-back rule and the linear and quadratic interpolations. The objectives are twofold: first to give theoretical tools to study the existing link-type boundary conditions and their corresponding accuracy; second to design boundary conditions for general flows which are third-order kinetic accurate. Using these new boundary conditions, Couette and Poiseuille flows are exact solutions of the lattice Boltzmann models for a Reynolds number Re=0 (Stokes limit) for arbitrary inclination with the lattice directions. Numerical comparisons are given for Stokes flows in periodic arrays of spheres and cylinders, linear periodic array of cylinders between moving plates, and for Navier-Stokes flows in periodic arrays of cylinders for Re<200. These results show a significant improvement of the overall accuracy when using the linear interpolations instead of the bounce-back reflection (up to an order of magnitude on the hydrodynamics fields). Further improvement is achieved with the new multireflection boundary conditions, reaching a level of accuracy close to the quasianalytical reference solutions, even for rather modest grid resolutions and few points in the narrowest channels. More important, the pressure and velocity fields in the vicinity of the obstacles are much smoother with multireflection than with the other boundary conditions. Finally the good stability of these schemes is highlighted by some simulations of moving obstacles: a cylinder between flat walls and a sphere in a cylinder.
The Body Center Cubic Quark Lattice Model
Lin Xu, Jiao
2004-01-01
The Standard Model while successful in many ways is incomplete; many questions remain. The origin of quark masses and hadronization of quarks are awaiting an answer. From the Dirac sea concept, we infer that two kinds of elementary quarks (u(0) and d(0)) constitute a body center cubic (BCC) quark lattice with a lattice constant a < $10^{-18}$m in the vacuum. Using energy band theory and the BCC quark lattice, we can deduce the rest masses and the intrinsic quantum numbers (I, S, C, b and Q) of quarks. With the quark spectrum, we deduce a baryon spectrum. The theoretical spectrum is in agreement well with the experimental results. Not only will this paper provide a physical basis for the Quark Model, but also it will open a door to study the more fundamental nature at distance scales <$10^{-18}$m. This paper predicts some new quarks $u_{c}$(6490) and d$_{b}$(9950), and new baryons $\\Lambda_{c}^{+}$(6500), $\\Lambda_{b}^{0}$(9960).
INTRINSIC INSTABILITY OF THE LATTICE BGK MODEL
熊鳌魁
2002-01-01
Based on the stability analysis with no linearization and expansion,it is argued that instability in the lattice BGK model is originated from the linearrelaxation hypothesis of collision in the model. The hypothesis stands up only whenthe deviation from the local equilibrium is weak. In this case the computation is abso-lutely stable for real fluids. But for flows of high Reynolds number, this hypothesis isviolated and then instability takes place physically. By performing a transformationa quantified stability criteria is put forward without those approximation. From thecriteria a sufficient condition for stability can be obtained and serve as an estimationof the limited Reynolds number as high as possible.
The Nuclear Yukawa Model on a Lattice
de Soto, F; Carbonell, J
2011-01-01
We present the results of the quantum field theory approach to nuclear Yukawa model obtained by standard lattice techniques. We have considered the simplest case of two identical fermions interacting via a scalar meson exchange. Calculations have been performed using Wilson fermions in the quenched approximation. We found the existence of a critical coupling constant above which the model cannot be numerically solved. The range of the accessible coupling constants is below the threshold value for producing two-body bound states. Two-body scattering lengths have been obtained and compared to the non relativistic results.
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.
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.
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.
Ground-state phase diagram of the Kondo lattice model on triangular-to-kagome lattices
Akagi, Yutaka; Motome, Yukitoshi
2012-01-01
We investigate the ground-state phase diagram of the Kondo lattice model with classical localized spins on triangular-to-kagome lattices by using a variational calculation. We identify the parameter regions where a four-sublattice noncoplanar order is stable with a finite spin scalar chirality while changing the lattice structure from triangular to kagome continuously. Although the noncoplanar spin states appear in a wide range of parameters, the spin configurations on the kagome network beco...
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.
Costanza, E. F.; Costanza, G.
2016-12-01
Continuum partial differential equations are obtained from a set of discrete stochastic evolution equations of both non-Markovian and Markovian processes and applied to the diffusion within the context of the lattice gas model. A procedure allowing to construct one-dimensional lattices that are topologically equivalent to two-dimensional lattices is described in detail in the case of a triangular lattice. This example shows the general features that possess the procedure and extensions are also suggested in order to provide a wider insight in the present approach.
Costanza, E. F.; Costanza, G.
2017-02-01
Continuum partial differential equations are obtained from a set of discrete stochastic evolution equations of both non-Markovian and Markovian processes and applied to the diffusion within the context of the lattice gas model. A procedure allowing to construct one-dimensional lattices that are topologically equivalent to two-dimensional lattices is described in detail in the case of a hexagonal lattice which has the particular feature that need four types of dynamical variables. This example shows additional features to the general procedure and some extensions are also suggested in order to provide a wider insight in the present approach.
Michael Bevers; Curtis H. Flather
1999-01-01
We examine habitat size, shape, and arrangement effects on populations using a discrete reaction-diffusion model. Diffusion is modeled passively and applied to a cellular grid of territories forming a coupled map lattice. Dispersal mortality is proportional to the amount of nonhabitat and fully occupied habitat surrounding a given cell, with distance decay. After...
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.
Multispeed models in off-lattice Boltzmann simulations
Bardow, A.; Karlin, I.V.; Gusev, A.A.
2008-01-01
The lattice Boltzmann method is a highly promising approach to the simulation of complex flows. Here, we realize recently proposed multispeed lattice Boltzmann models [S. Chikatamarla et al., Phys. Rev. Lett. 97 190601 (2006)] by exploiting the flexibility offered by off-lattice Boltzmann methods.
Two-dimensional lattice Boltzmann model for magnetohydrodynamics.
Schaffenberger, Werner; Hanslmeier, Arnold
2002-10-01
We present a lattice Boltzmann model for the simulation of two-dimensional magnetohydro dynamic (MHD) flows. The model is an extension of a hydrodynamic lattice Boltzman model with 9 velocities on a square lattice resulting in a model with 17 velocities. Earlier lattice Boltzmann models for two-dimensional MHD used a bidirectional streaming rule. However, the use of such a bidirectional streaming rule is not necessary. In our model, the standard streaming rule is used, allowing smaller viscosities. To control the viscosity and the resistivity independently, a matrix collision operator is used. The model is then applied to the Hartmann flow, giving reasonable results.
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.
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.
Lattice gauge theories and spin models
Mathur, Manu; Sreeraj, T. P.
2016-10-01
The Wegner Z2 gauge theory-Z2 Ising spin model duality in (2 +1 ) dimensions is revisited and derived through a series of canonical transformations. The Kramers-Wannier duality is similarly obtained. The Wegner Z2 gauge-spin duality is directly generalized to SU(N) lattice gauge theory in (2 +1 ) dimensions to obtain the SU(N) spin model in terms of the SU(N) magnetic fields and their conjugate SU(N) electric scalar potentials. The exact and complete solutions of the Z2, U(1), SU(N) Gauss law constraints in terms of the corresponding spin or dual potential operators are given. The gauge-spin duality naturally leads to a new gauge invariant magnetic disorder operator for SU(N) lattice gauge theory which produces a magnetic vortex on the plaquette. A variational ground state of the SU(2) spin model with nearest neighbor interactions is constructed to analyze SU(2) gauge theory.
Lattice Boltzmann model with nearly constant density.
Fang, Hai-ping; Wan, Rong-zheng; Lin, Zhi-fang
2002-09-01
An improved lattice Boltzmann model is developed to simulate fluid flow with nearly constant fluid density. The ingredient is to incorporate an extra relaxation for fluid density, which is realized by introducing a feedback equation in the equilibrium distribution functions. The pressure is dominated by the moving particles at a node, while the fluid density is kept nearly constant and explicit mass conservation is retained as well. Numerical simulation based on the present model for the (steady) plane Poiseuille flow and the (unsteady) two-dimensional Womersley flow shows a great improvement in simulation results over the previous models. In particular, the density fluctuation has been reduced effectively while achieving a relatively large pressure gradient.
Equilibrium statistical mechanics of lattice models
Lavis, David A
2015-01-01
Most interesting and difficult problems in equilibrium statistical mechanics concern models which exhibit phase transitions. For graduate students and more experienced researchers this book provides an invaluable reference source of approximate and exact solutions for a comprehensive range of such models. Part I contains background material on classical thermodynamics and statistical mechanics, together with a classification and survey of lattice models. The geometry of phase transitions is described and scaling theory is used to introduce critical exponents and scaling laws. An introduction is given to finite-size scaling, conformal invariance and Schramm—Loewner evolution. Part II contains accounts of classical mean-field methods. The parallels between Landau expansions and catastrophe theory are discussed and Ginzburg—Landau theory is introduced. The extension of mean-field theory to higher-orders is explored using the Kikuchi—Hijmans—De Boer hierarchy of approximations. In Part III the use of alge...
Lattice Boltzmann model for resistive relativistic magnetohydrodynamics
Mohseni, F; Succi, S; Herrmann, H J
2015-01-01
In this paper, we develop a lattice Boltzmann model for relativistic magnetohydrodynamics (MHD). Even though the model is derived for resistive MHD, it is shown that it is numerically robust even in the high conductivity (ideal MHD) limit. In order to validate the numerical method, test simulations are carried out for both ideal and resistive limits, namely the propagation of Alfv\\'en waves in the ideal MHD and the evolution of current sheets in the resistive regime, where very good agreement is observed comparing to the analytical results. Additionally, two-dimensional magnetic reconnection driven by Kelvin-Helmholtz instability is studied and the effects of different parameters on the reconnection rate are investigated. It is shown that the density ratio has negligible effect on the magnetic reconnection rate, while an increase in shear velocity decreases the reconnection rate. Additionally, it is found that the reconnection rate is proportional to $\\sigma^{-\\frac{1}{2}}$, $\\sigma$ being the conductivity, w...
Fisher zeros and conformality in lattice models
Meurice, Yannick; Berg, Bernd A; Du, Daping; Denbleyker, Alan; Liu, Yuzhi; Sinclair, Donald K; Unmuth-Yockey, Judah; Zou, Haiyuan
2012-01-01
Fisher zeros are the zeros of the partition function in the beta=2N_c/g^2 complex plane. When they pinch the real axis, finite size scaling allows to distinguish between first and second order transition and to estimate exponents. On the other hand, a gap signals confinement and the method can be used to explore the boundary of the conformal window. We present recent numerical results for 2D O(N) sigma models, 4D U(1) and SU(2) pure gauge and SU(3) with N_f=4and 12 flavors. We discuss attempts to understand some of these results using analytical methods. We discuss the 2-lattice matching and qualitative aspects of the renormalization group (RG) flows in the Migdal-Kadanoff approximation. We consider the effects of the boundary conditions on the nonperturbative part of the average energy in the 1D O(2) model
SOME PROGRESS IN THE LATTICE BOLTMANN MODEL
FENG SHI-DE; TSUTAHARA MICHIHISA; JI ZHONG-ZHEN
2001-01-01
A lattice Boltzmann equation model has been developed by using the equilibrium distribution function of the Maxwell-Boltzmann-like form, which is third order in fluid velocity uα. The criteria of energy conservation between the macroscopic physical quantities and the microscopic particles are introduced into the model, thus the thermal hydrodynamic equations containing the effect of buoyancy force can be recovered in terms of the Taylor and ChapmanEnskog asymptotic expansion methods. The two-dimensional thermal convection phenomena in a square cavity and between two concentric cylinders have been calculated by implementing a heat flux boundary condition. Both numerical results are in good agreement with the conventional numerical results.
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.
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.
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 ...
Lattice Boltzmann modelling of intrinsic permeability
Li, Jun; Wu, Lei; Zhang, Yonghao
2016-01-01
Lattice Boltzmann method (LBM) has been applied to predict flow properties of porous media including intrinsic permeability, where it is implicitly assumed that the LBM is equivalent to the incompressible (or near incompressible) Navier-Stokes equation. However, in LBM simulations, high-order moments, which are completely neglected in the Navier-Stokes equation, are still available through particle distribution functions. To ensure that the LBM simulation is correctly working at the Navier-Stokes hydrodynamic level, the high-order moments have to be negligible. This requires that the Knudsen number (Kn) is small so that rarefaction effect can be ignored. In this technical note, we elaborate this issue in LBM modelling of porous media flows, which is particularly important for gas flows in ultra-tight media.
Lattice Boltzmann modeling of water entry problems
Zarghami, A.; Falcucci, G.; Jannelli, E.; Succi, S.; Porfiri, M.; Ubertini, S.
2014-12-01
This paper deals with the simulation of water entry problems using the lattice Boltzmann method (LBM). The dynamics of the free surface is treated through the mass and momentum fluxes across the interface cells. A bounce-back boundary condition is utilized to model the contact between the fluid and the moving object. The method is implemented for the analysis of a two-dimensional flow physics produced by a symmetric wedge entering vertically a weakly-compressible fluid at a constant velocity. The method is used to predict the wetted length, the height of water pile-up, the pressure distribution and the overall force on the wedge. The accuracy of the numerical results is demonstrated through comparisons with data reported in the literature.
Superconductivity in the Kondo lattice model
Bodensiek, Oliver; Pruschke, Thomas [Institute for Theoretical Physics, University of Goettingen, Friedrich-Hund-Platz 1, D-37077 Goettingen (Germany); Zitko, Rok [Institute for Theoretical Physics, University of Goettingen, Friedrich-Hund-Platz 1, D-37077 Goettingen (Germany); Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana (Slovenia)
2011-07-01
We study the Kondo lattice model with an additional attractive interaction among the conduction-band electrons by means of dynamical mean-field theory in combination with the numerical renormalization group method. In the normal phase we observe a strong dependency of the low-energy scale on the attractive interaction. Thus, there exists a delicate interplay between the attractive interaction and the antiferromagnetic Kondo exchange, which results in a critical interaction, above of which the Fermi surface collapses because the spins become effectively decoupled from the conduction electrons. Additionally, we allow for a s-wave superconducting phase, which appears to be split at the point of the underlying Fermi surface collapse. We discuss the interplay between attractive interaction an Kondo exchange and its pertinence to phonons in heavy fermion physics.
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.
A lattice-model representation of continuous-time random walks
Campos, Daniel [School of Mathematics, Department of Applied Mathematics, University of Manchester, Manchester M60 1QD (United Kingdom); Mendez, Vicenc [Grup de Fisica Estadistica, Departament de Fisica, Universitat Autonoma de Barcelona, 08193 Bellaterra (Barcelona) (Spain)], E-mail: daniel.campos@uab.es, E-mail: vicenc.mendez@uab.es
2008-02-29
We report some ideas for constructing lattice models (LMs) as a discrete approach to the reaction-dispersal (RD) or reaction-random walks (RRW) models. The analysis of a rather general class of Markovian and non-Markovian processes, from the point of view of their wavefront solutions, let us show that in some regimes their macroscopic dynamics (front speed) turns out to be different from that by classical reaction-diffusion equations, which are often used as a mean-field approximation to the problem. So, the convenience of a more general framework as that given by the continuous-time random walks (CTRW) is claimed. Here we use LMs as a numerical approach in order to support that idea, while in previous works our discussion was restricted to analytical models. For the two specific cases studied here, we derive and analyze the mean-field expressions for our LMs. As a result, we are able to provide some links between the numerical and analytical approaches studied.
Immersed boundary lattice Boltzmann model based on multiple relaxation times.
Lu, Jianhua; Han, Haifeng; Shi, Baochang; Guo, Zhaoli
2012-01-01
As an alterative version of the lattice Boltzmann models, the multiple relaxation time (MRT) lattice Boltzmann model introduces much less numerical boundary slip than the single relaxation time (SRT) lattice Boltzmann model if some special relationship between the relaxation time parameters is chosen. On the other hand, most current versions of the immersed boundary lattice Boltzmann method, which was first introduced by Feng and improved by many other authors, suffer from numerical boundary slip as has been investigated by Le and Zhang. To reduce such a numerical boundary slip, an immerse boundary lattice Boltzmann model based on multiple relaxation times is proposed in this paper. A special formula is given between two relaxation time parameters in the model. A rigorous analysis and the numerical experiments carried out show that the numerical boundary slip reduces dramatically by using the present model compared to the single-relaxation-time-based model.
Adaptive evolution on a continuous lattice model
Claudino, Elder S.; Lyra, M. L.; Gleria, Iram; Campos, Paulo R. A.
2013-03-01
In the current work, we investigate the evolutionary dynamics of a spatially structured population model defined on a continuous lattice. In the model, individuals disperse at a constant rate v and competition is local and delimited by the competition radius R. Due to dispersal, the neighborhood size (number of individuals competing for reproduction) fluctuates over time. Here we address how these new variables affect the adaptive process. While the fixation probabilities of beneficial mutations are roughly the same as in a panmitic population for small fitness effects s, a dependence on v and R becomes more evident for large s. These quantities also strongly influence fixation times, but their dependencies on s are well approximated by s-1/2, which means that the speed of the genetic wave front is proportional to s. Most important is the observation that the model exhibits a dual behavior displaying a power-law growth for the fixation rate and speed of adaptation with the beneficial mutation rate, as observed in other spatially structured population models, while simultaneously showing a nonsaturating behavior for the speed of adaptation with the population size N, as in homogeneous populations.
Lattice Boltzmann model for resistive relativistic magnetohydrodynamics.
Mohseni, F; Mendoza, M; Succi, S; Herrmann, H J
2015-08-01
In this paper, we develop a lattice Boltzmann model for relativistic magnetohydrodynamics (MHD). Even though the model is derived for resistive MHD, it is shown that it is numerically robust even in the high conductivity (ideal MHD) limit. In order to validate the numerical method, test simulations are carried out for both ideal and resistive limits, namely the propagation of Alfvén waves in the ideal MHD and the evolution of current sheets in the resistive regime, where very good agreement is observed comparing to the analytical results. Additionally, two-dimensional magnetic reconnection driven by Kelvin-Helmholtz instability is studied and the effects of different parameters on the reconnection rate are investigated. It is shown that the density ratio has a negligible effect on the magnetic reconnection rate, while an increase in shear velocity decreases the reconnection rate. Additionally, it is found that the reconnection rate is proportional to σ-1/2, σ being the conductivity, which is in agreement with the scaling law of the Sweet-Parker model. Finally, the numerical model is used to study the magnetic reconnection in a stellar flare. Three-dimensional simulation suggests that the reconnection between the background and flux rope magnetic lines in a stellar flare can take place as a result of a shear velocity in the photosphere.
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.
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...
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
Spin-1 Ising model on tetrahedron recursive lattices: Exact results
Jurčišinová, E.; Jurčišin, M.
2016-11-01
We investigate the ferromagnetic spin-1 Ising model on the tetrahedron recursive lattices. An exact solution of the model is found in the framework of which it is shown that the critical temperatures of the second order phase transitions of the model are driven by a single equation simultaneously on all such lattices. It is also shown that this general equation for the critical temperatures is equivalent to the corresponding polynomial equation for the model on the tetrahedron recursive lattice with arbitrary given value of the coordination number. The explicit form of these polynomial equations is shown for the lattices with the coordination numbers z = 6, 9, and 12. In addition, it is shown that the thermodynamic properties of all possible physical phases of the model are also completely driven by the corresponding single equations simultaneously on all tetrahedron recursive lattices. In this respect, the spontaneous magnetization, the free energy, the entropy, and the specific heat of the model are studied in detail.
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.
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.
Classical Ising Models Realised on Optical Lattices
Cirio, Mauro; Brennen, G. K.; Twamley, J.; Iblisdir, S.; Boada, O.
2012-02-01
We describe a simple quantum algorithm acting on a register of qubits in d spatial dimensions which computes statistical properties of d+1 dimensional classical Ising models. The algorithm works by measuring scattering matrix elements for quantum processes and Wick rotating to provide estimates for real partition functions of classical systems. This method can be implemented in a straightforward way in ensembles of qubits, e.g. three dimensional optical lattices with only nearest neighbor Ising like interactions. By measuring noise in the estimate useful information regarding location of critical points and scaling laws can be extracted for classical Ising models, possibly with inhomogeneity. Unlike the case of quantum simulation of quantum hamiltonians, this algorithm does not require Trotter expansion of the evolution operator and thus has the advantage of being amenable to fault tolerant gate design in a straightforward manner. Through this setting it is possible to study the quantum computational complexity of the estimation of a classical partition function for a 2D Ising model with non uniform couplings and magnetic fields. We provide examples for the 2 dimensional case.
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.
Hart, W E; Istrail, S
1997-01-01
This paper considers the protein energy minimization problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. We consider two side chain models: a lattice model that generalizes the HP model (Dill, 1985) to explicitly represent side chains on the cubic lattice and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. We describe algorithms with mathematically guaranteed error bounds for both of these models. In particular, we describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 86% of optimal in a face-centered cubic lattice, and we demonstrate how this provides a better than 70% performance guarantee for the HP-TSSC model. Our analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Ngo et al. (1994) concerning the complexity of protein folding models that include side chains.
Topological spin models in Rydberg lattices
Kiffner, Martin; Jaksch, Dieter
2016-01-01
We show that resonant dipole-dipole interactions between Rydberg atoms in a triangular lattice can give rise to artificial magnetic fields for spin excitations. We consider the coherent dipole-dipole coupling between $np$ and $ns$ Rydberg states and derive an effective spin-1/2 Hamiltonian for the $np$ excitations. By breaking time-reversal symmetry via external fields we engineer complex hopping amplitudes for transitions between two rectangular sub-lattices. The phase of these hopping amplitudes depends on the direction of the hop. This gives rise to a staggered, artificial magnetic field which induces non-trivial topological effects. We calculate the single-particle band structure and investigate its Chern numbers as a function of the lattice parameters and the detuning between the two sub-lattices. We identify extended parameter regimes where the Chern number of the lowest band is $C=1$ or $C=2$.
Model of pair aggregation on the Bethe lattice
Baillet, M.V.-P.; Pacheco, A.F.; Gómez, J.B.
1997-01-01
We extend a recent model of aggregation of pairs of particles, analyzing the case in which the supporting framework is a Bethe lattice. The model exhibits a critical behavior of the percolation theory type....
An Active Lattice Model in a Bayesian Framework
Carstensen, Jens Michael
1996-01-01
by penalizing deviations in alignment and lattice node distance. The Markov random field represents prior knowledge about the lattice structure, and through an observation model that incorporates the visual appearance of the nodes, we can simulate realizations from the posterior distribution. A maximum...
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.
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.
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.
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
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.
Lattice Entertain You: Paper Modeling of the 14 Bravais Lattices on Youtube
Sein, Lawrence T., Jr.; Sein, Sarajane E.
2015-01-01
A system for the construction of double-sided paper models of the 14 Bravais lattices, and important crystal structures derived from them, is described. The system allows the combination of multiple unit cells, so as to better represent the overall three-dimensional structure. Students and instructors can view the models in use on the popular…
Realizing a lattice spin model with polar molecules
Yan, Bo; Gadway, Bryce; Covey, Jacob P; Hazzard, Kaden R A; Rey, Ana Maria; Jin, Deborah S; Ye, Jun
2013-01-01
With the recent production of polar molecules in the quantum regime, long-range dipolar interactions are expected to facilitate the understanding of strongly interacting many-body quantum systems and to realize lattice spin models for exploring quantum magnetism. In atomic systems, where interactions require wave function overlap, effective spin interactions on a lattice can be realized via superexchange; however, the coupling is weak and limited to nearest-neighbor interactions. In contrast, dipolar interactions exist in the absence of tunneling and extend beyond nearest neighbors. This allows coherent spin dynamics to persist even at high entropy and low lattice filling. Effects of dipolar interactions in ultracold molecular gases have so far been limited to the modification of chemical reactions. We now report the observation of dipolar interactions of polar molecules pinned in a 3D optical lattice. We realize a lattice spin model with spin encoded in rotational states, prepared and probed by microwaves. T...
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.
Hart, W.E.; Istrail, S. [Sandia National Labs., Albuquerque, NM (United States). Algorithms and Discrete Mathematics Dept.
1996-08-09
This paper considers the protein structure prediction problem for lattice and off-lattice protein folding models that explicitly represent side chains. Lattice models of proteins have proven extremely useful tools for reasoning about protein folding in unrestricted continuous space through analogy. This paper provides the first illustration of how rigorous algorithmic analyses of lattice models can lead to rigorous algorithmic analyses of off-lattice models. The authors consider two side chain models: a lattice model that generalizes the HP model (Dill 85) to explicitly represent side chains on the cubic lattice, and a new off-lattice model, the HP Tangent Spheres Side Chain model (HP-TSSC), that generalizes this model further by representing the backbone and side chains of proteins with tangent spheres. They describe algorithms for both of these models with mathematically guaranteed error bounds. In particular, the authors describe a linear time performance guaranteed approximation algorithm for the HP side chain model that constructs conformations whose energy is better than 865 of optimal in a face centered cubic lattice, and they demonstrate how this provides a 70% performance guarantee for the HP-TSSC model. This is the first algorithm in the literature for off-lattice protein structure prediction that has a rigorous performance guarantee. The analysis of the HP-TSSC model builds off of the work of Dancik and Hannenhalli who have developed a 16/30 approximation algorithm for the HP model on the hexagonal close packed lattice. Further, the analysis provides a mathematical methodology for transferring performance guarantees on lattices to off-lattice models. These results partially answer the open question of Karplus et al. concerning the complexity of protein folding models that include side chains.
Diffusive description of lattice gas models
Fiig, T.; Jensen, H.J.
1993-01-01
in time. We have numerically investigated the power spectrum of the density fluctuations, the lifetime distribution, and the spatial correlation function. We discuss the appropriate Langevin-like diffusion equation which can reproduce our numerical findings. Our conclusion is that the deterministic...... lattice gases are described by a diffusion equation without any bulk noise. The open lattice gas exhibits a crossover behavior as the probability for introducing particles at the edge of the system becomes small. The power spectrum changes from a 1/f to a 1/f2 spectrum. The diffusive description, proven...
A new lattice Boltzmann model for incompressible magnetohydrodynamics
Chen Xing-Wang; Shi Bao-Chang
2005-01-01
Most of the existing lattice Boltzmann magnetohydrodynamics (MHD) models can be viewed as compressible schemes to simulate incompressible MHD flows. The compressible effect might lead to some undesired errors in numerical simulations. In this paper a new incompressible lattice Boltzmann MHD model without compressible effect is presented for simulating incompressible MHD flows. Numerical simulations of the Hartmann flow are performed. We do numerous tests and make comparison with Dellar's model in detail. The numerical results are in good agreement with the analytical error.
Central Charge of the Parallelogram Lattice Strong Coupling Schwinger Model
Yee, K
1993-01-01
We put forth a Fierzed hopping expansion for strong coupling Wilson fermions. As an application, we show that the strong coupling Schwinger model on parallelogram lattices with nonbacktracking Wilson fermions span, as a function of the lattice skewness angle, the $\\Delta = -1$ critical line of $6$-vertex models. This Fierzed formulation also applies to backtracking Wilson fermions, which as we describe apparently correspond to richer systems. However, we have not been able to identify them with exactly solved models.
Critical-like behavior in a lattice gas model
Wieloch, A; Lukasik, J; Pawlowski, P; Pietrzak, T; Trautmann, W
2010-01-01
ALADIN multifragmentation data show features characteristic of a critical behavior, which are very well reproduced by a bond percolation model. This suggests, in the context of the lattice gas model, that fragments are formed at nearly normal nuclear densities and temperatures corresponding to the Kertesz line. Calculations performed with a lattice gas model have shown that similarly good reproduction of the data can also be achieved at lower densities, particularly in the liquid-gas coexistence region.
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.
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.
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...
Convergent series for lattice models with polynomial interactions
Ivanov, Aleksandr S.; Sazonov, Vasily K.
2017-01-01
The standard perturbative weak-coupling expansions in lattice models are asymptotic. The reason for this is hidden in the incorrect interchange of the summation and integration. However, substituting the Gaussian initial approximation of the perturbative expansions by a certain interacting model or regularizing original lattice integrals, one can construct desired convergent series. In this paper we develop methods, which are based on the joint and separate utilization of the regularization and new initial approximation. We prove, that the convergent series exist and can be expressed as re-summed standard perturbation theory for any model on the finite lattice with the polynomial interaction of even degree. We discuss properties of such series and study their applicability to practical computations on the example of the lattice ϕ4-model. We calculate expectation value using the convergent series, the comparison of the results with the Borel re-summation and Monte Carlo simulations shows a good agreement between all these methods.
Convergent series for lattice models with polynomial interactions
Ivanov, Aleksandr S
2016-01-01
The standard perturbative weak-coupling expansions in lattice models are asymptotic. The reason for this is hidden in the incorrect interchange of the summation and integration. However, substituting the Gaussian initial approximation of the perturbative expansions by a certain interacting model or regularizing original lattice integrals, one can construct desired convergent series. In this paper we develop methods, which are based on the joint and separate utilization of the regularization and new initial approximation. We prove, that the convergent series exist and can be expressed as the re-summed standard perturbation theory for any model on the finite lattice with the polynomial interaction of even degree. We discuss properties of such series and make them applicable to practical computations. The workability of the methods is demonstrated on the example of the lattice $\\phi^4$-model. We calculate the operator $\\langle\\phi_n^2\\rangle$ using the convergent series, the comparison of the results with the Bo...
Critical Behavior of the Widom-Rowlinson Lattice Model
Dickman, R; Dickman, Ronald; Stell, George
1995-01-01
We report extensive Monte Carlo simulations of the Widom-Rowlinson lattice model in two and three dimensions. Our results yield precise values for the critical activities and densities, and clearly place the critical behavior in the Ising universality class.
Lattice Boltzmann modeling of directional wetting: Comparing simulations to experiments
Jansen, H.P.; Sotthewes, K.; Swigchem, van J.; Zandvliet, H.J.W.; Kooij, E.S.
2013-01-01
Lattice Boltzmann Modeling (LBM) simulations were performed on the dynamic behavior of liquid droplets on chemically striped patterned surfaces, ultimately with the aim to develop a predictive tool enabling reliable design of future experiments. The simulations accurately mimic experimental results,
Kinetic models for irreversible processes on a lattice
Wolf, N.O.
1979-04-01
The development and application of kinetic lattice models are considered. For the most part, the discussions are restricted to lattices in one-dimension. In Chapter 1, a brief overview of kinetic lattice model formalisms and an extensive literature survey are presented. A review of the kinetic models for non-cooperative lattice events is presented in Chapter 2. The development of cooperative lattice models and solution of the resulting kinetic equations for an infinite and a semi-infinite lattice are thoroughly discussed in Chapters 3 and 4. The cooperative models are then applied to the problem of theoretically dtermining the sticking coefficient for molecular chemisorption in Chapter 5. In Chapter 6, other possible applications of these models and several model generalizations are considered. Finally, in Chapter 7, an experimental study directed toward elucidating the mechanistic factors influencing the chemisorption of methane on single crystal tungsten is reported. In this it differs from the rest of the thesis which deals with the statistical distributions resulting from a given mechanism.
Ising model simulation in directed lattices and networks
Lima, F. W. S.; Stauffer, D.
2006-01-01
On directed lattices, with half as many neighbours as in the usual undirected lattices, the Ising model does not seem to show a spontaneous magnetisation, at least for lower dimensions. Instead, the decay time for flipping of the magnetisation follows an Arrhenius law on the square and simple cubic lattice. On directed Barabási-Albert networks with two and seven neighbours selected by each added site, Metropolis and Glauber algorithms give similar results, while for Wolff cluster flipping the magnetisation decays exponentially with time.
O(N) Models with Topological Lattice Actions
Bietenholz, Wolfgang; Gerber, Urs; Niedermayer, Ferenc; Pepe, Michele; Rejón-Barrera, Fernando G; Wiese, Uwe-Jens
2013-01-01
A variety of lattice discretisations of continuum actions has been considered, usually requiring the correct classical continuum limit. Here we discuss "weird" lattice formulations without that property, namely lattice actions that are invariant under most continuous deformations of the field configuration, in one version even without any coupling constants. It turns out that universality is powerful enough to still provide the correct quantum continuum limit, despite the absence of a classical limit, or a perturbative expansion. We demonstrate this for a set of O(N) models (or non-linear $\\sigma$-models). Amazingly, such "weird" lattice actions are not only in the right universality class, but some of them even have practical benefits, in particular an excellent scaling behaviour.
Extended Hubbard models for ultracold atoms in optical lattices
Juergensen, Ole
2015-06-05
In this thesis, the phase diagrams and dynamics of various extended Hubbard models for ultracold atoms in optical lattices are studied. Hubbard models are the primary description for many interacting particles in periodic potentials with the paramount example of the electrons in solids. The very same models describe the behavior of ultracold quantum gases trapped in the periodic potentials generated by interfering beams of laser light. These optical lattices provide an unprecedented access to the fundamentals of the many-particle physics that govern the properties of solid-state materials. They can be used to simulate solid-state systems and validate the approximations and simplifications made in theoretical models. This thesis revisits the numerous approximations underlying the standard Hubbard models with special regard to optical lattice experiments. The incorporation of the interaction between particles on adjacent lattice sites leads to extended Hubbard models. Offsite interactions have a strong influence on the phase boundaries and can give rise to novel correlated quantum phases. The extended models are studied with the numerical methods of exact diagonalization and time evolution, a cluster Gutzwiller approximation, as well as with the strong-coupling expansion approach. In total, this thesis demonstrates the high relevance of beyond-Hubbard processes for ultracold atoms in optical lattices. Extended Hubbard models can be employed to tackle unexplained problems of solid-state physics as well as enter previously inaccessible regimes.
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
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.
Lattice Boltzmann Model for Electronic Structure Simulations
Mendoza, M; Succi, S
2015-01-01
Recently, a new connection between density functional theory and kinetic theory has been proposed. In particular, it was shown that the Kohn-Sham (KS) equations can be reformulated as a macroscopic limit of the steady-state solution of a suitable single-particle kinetic equation. By using a discrete version of this new formalism, the exchange and correlation energies of simple atoms and the geometrical configuration of the methane molecule were calculated accurately. Here, we discuss the main ideas behind the lattice kinetic approach to electronic structure computations, offer some considerations for prospective extensions, and also show additional numerical results, namely the geometrical configuration of the water molecule.
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.
Coupling lattice Boltzmann model for simulation of thermal flows on standard lattices.
Li, Q; Luo, K H; He, Y L; Gao, Y J; Tao, W Q
2012-01-01
In this paper, a coupling lattice Boltzmann (LB) model for simulating thermal flows on the standard two-dimensional nine-velocity (D2Q9) lattice is developed in the framework of the double-distribution-function (DDF) approach in which the viscous heat dissipation and compression work are considered. In the model, a density distribution function is used to simulate the flow field, while a total energy distribution function is employed to simulate the temperature field. The discrete equilibrium density and total energy distribution functions are obtained from the Hermite expansions of the corresponding continuous equilibrium distribution functions. The pressure given by the equation of state of perfect gases is recovered in the macroscopic momentum and energy equations. The coupling between the momentum and energy transports makes the model applicable for general thermal flows such as non-Boussinesq flows, while the existing DDF LB models on standard lattices are usually limited to Boussinesq flows in which the temperature variation is small. Meanwhile, the simple structure and general features of the DDF LB approach are retained. The model is tested by numerical simulations of thermal Couette flow, attenuation-driven acoustic streaming, and natural convection in a square cavity with small and large temperature differences. The numerical results are found to be in good agreement with the analytical solutions and/or other numerical results reported in the literature.
Siebert, Julien; Alonso, Sergio; Bär, Markus; Schöll, Eckehard
2014-05-01
A one-component bistable reaction-diffusion system with asymmetric nonlocal coupling is derived as a limiting case of a two-component activator-inhibitor reaction-diffusion model with differential advection. The effects of asymmetric nonlocal couplings in such a bistable reaction-diffusion system are then compared to the previously studied case of a system with symmetric nonlocal coupling. We carry out a linear stability analysis of the spatially homogeneous steady states of the model and numerical simulations of the model to show how the asymmetric nonlocal coupling controls and alters the steady states and the front dynamics in the system. In a second step, a third fast reaction-diffusion equation is included which induces the formation of more complex patterns. A linear stability analysis predicts traveling waves for asymmetric nonlocal coupling, in contrast to a stationary Turing patterns for a system with symmetric nonlocal coupling. These findings are verified by direct numerical integration of the full equations with nonlocal coupling.
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.
An integrable 3D lattice model with positive Boltzmann weights
Mangazeev, Vladimir V; Sergeev, Sergey M
2013-01-01
In this paper we construct a three-dimensional (3D) solvable lattice model with non-negative Boltzmann weights. The spin variables in the model are assigned to edges of the 3D cubic lattice and run over an infinite number of discrete states. The Boltzmann weights satisfy the tetrahedron equation, which is a 3D generalisation of the Yang-Baxter equation. The weights depend on a free parameter 0model form a two-parameter commutative family. This is the first example of a solvable 3D lattice model with non-negative Boltzmann weights.
New statistical lattice model with double honeycomb symmetry
Naji, S.; Belhaj, A.; Labrim, H.; Bhihi, M.; Benyoussef, A.; El Kenz, A.
2014-04-01
Inspired from the connection between Lie symmetries and two-dimensional materials, we propose a new statistical lattice model based on a double hexagonal structure appearing in the G2 symmetry. We first construct an Ising-1/2 model, with spin values σ = ±1, exhibiting such a symmetry. The corresponding ground state shows the ferromagnetic, the antiferromagnetic, the partial ferrimagnetic and the topological ferrimagnetic phases depending on the exchange couplings. Then, we examine the phase diagrams and the magnetization using the mean field approximation (MFA). Among others, it has been suggested that the present model could be localized between systems involving the triangular and the single hexagonal lattice geometries.
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.
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.
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).
Strong parameter renormalization from optimum lattice model orbitals
Brosco, Valentina; Ying, Zu-Jian; Lorenzana, José
2017-01-01
Which is the best single-particle basis to express a Hubbard-like lattice model? A rigorous variational answer to this question leads to equations the solution of which depends in a self-consistent manner on the lattice ground state. Contrary to naive expectations, for arbitrary small interactions, the optimized orbitals differ from the noninteracting ones, leading also to substantial changes in the model parameters as shown analytically and in an explicit numerical solution for a simple double-well one-dimensional case. At strong coupling, we obtain the direct exchange interaction with a very large renormalization with important consequences for the explanation of ferromagnetism with model Hamiltonians. Moreover, in the case of two atoms and two fermions we show that the optimization equations are closely related to reduced density-matrix functional theory, thus establishing an unsuspected correspondence between continuum and lattice approaches.
Associative Models for Storing and Retrieving Concept Lattices
María Elena Acevedo
2010-01-01
Full Text Available Alpha-beta bidirectional associative memories are implemented for storing concept lattices. We use Lindig's algorithm to construct a concept lattice of a particular context; this structure is stored into an associative memory just as a human being does, namely, associating patterns. Bidirectionality and perfect recall of Alpha-Beta associative model make it a great tool to store a concept lattice. In the learning phase, objects and attributes obtained from Lindig's algorithm are associated by Alpha-Beta bidirectional associative memory; in this phase the data is stored. In the recalling phase, the associative model allows to retrieve objects from attributes or vice versa. Our model assures the recalling of every learnt concept.
Majority-vote model with heterogeneous agents on square lattice
Lima, F W S
2013-01-01
We study a nonequilibrium model with up-down symmetry and a noise parameter $q$ known as majority-vote model of M.J. Oliveira 1992 with heterogeneous agents on square lattice. By Monte Carlo simulations and finite-size scaling relations the critical exponents $\\beta/\
Solitons of a vector model on the honeycomb lattice
Vekslerchik, V. E.
2016-11-01
We study a simple nonlinear vector model defined on the honeycomb lattice. We propose a bilinearization scheme for the field equations and demonstrate that the resulting system is closely related to the well-studied integrable models, such as the Hirota bilinear difference equation and the Ablowitz-Ladik system. This result is used to derive the N-soliton solutions.
A Parallel Lattice Boltzmann Model of a Carotid Artery
Boyd, J.; Ryan, S. J.; Buick, J. M.
2008-11-01
A parallel implementation of the lattice Boltzmann model is considered for a three dimensional model of the carotid artery. The computational method and its parallel implementation are described. The performance of the parallel implementation on a Beowulf cluster is presented, as are preliminary hemodynamic results.
Elimination of Nonlinear Deviations in Thermal Lattice BGK Models
Chen, Y; Hongo, T; Chen, Yu; Ohashi, Hirotada; Akiyam, Mamoru
1993-01-01
Abstracet: We present a new thermal lattice BGK model in D-dimensional space for the numerical calculation of fluid dynamics. This model uses a higher order expansion of equilibrium distribution in Maxwellian type. In the mean time the lattice symmetry is upgraded to ensure the isotropy of 6th order tensor. These manipulations lead to macroscopic equations free from nonlinear deviations. We demonstrate the improvements by conducting classical Chapman-Enskog analysis and by numerical simulation of shear wave flow. The transport coefficients are measured numerically, too.
Efficient Lattice-Based Signcryption in Standard Model
Jianhua Yan
2013-01-01
Full Text Available Signcryption is a cryptographic primitive that can perform digital signature and public encryption simultaneously at a significantly reduced cost. This advantage makes it highly useful in many applications. However, most existing signcryption schemes are seriously challenged by the booming of quantum computations. As an interesting stepping stone in the post-quantum cryptographic community, two lattice-based signcryption schemes were proposed recently. But both of them were merely proved to be secure in the random oracle models. Therefore, the main contribution of this paper is to propose a new lattice-based signcryption scheme that can be proved to be secure in the standard model.
Continuum model for dipolar coupled planar lattices
Costa, Miguel D.; Pogorelov, Yuri G. E-mail: ypogorel@fc.up.pt
2003-03-01
In an effective continuum approach alike the phenomenological Landau theory, we study low energy excitations in a square lattice of dipolar coupled magnetic moments {mu}, over continuously degenerate microvortex (MV) ground states defined by an arbitrary angle 0<{theta}<{pi}/2. We consider two vector order parameters: the MV vector v={mu} (cos {theta}, sin {theta}) and the ferromagnetic (FM) vector f=((1)/(2)) ({partial_derivative}{sub y}v{sub x}, -{partial_derivative}{sub x}v{sub y}). The excitation energy density {approx}f{sup 2} leads to a non-linear Euler equation. It allows, besides common linear waves of small amplitude, also non-linear excitations with unlimited (but slow) variation of {theta}(r). For plane wave excitations {theta}(r)={theta}(n{center_dot}r) propagating along n=(cos phi (cursive,open) Greek, sin phi (cursive,open) Greek), exact integrals of Euler equation are found. The density of excitation states turns anisotropic in {theta}, conforming to the enhanced occurrence of MV-like states with {theta} close to 0 or {pi}/2 in our Monte Carlo simulations of this system at low excitation energies.
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
Lattice Boltzmann Large Eddy Simulation Model of MHD
Flint, Christopher
2016-01-01
The work of Ansumali \\textit{et al.}\\cite{Ansumali} is extended to Two Dimensional Magnetohydrodynamic (MHD) turbulence in which energy is cascaded to small spatial scales and thus requires subgrid modeling. Applying large eddy simulation (LES) modeling of the macroscopic fluid equations results in the need to apply ad-hoc closure schemes. LES is applied to a suitable mesoscopic lattice Boltzmann representation from which one can recover the MHD equations in the long wavelength, long time scale Chapman-Enskog limit (i.e., the Knudsen limit). Thus on first performing filter width expansions on the lattice Boltzmann equations followed by the standard small Knudsen expansion on the filtered lattice Boltzmann system results in a closed set of MHD turbulence equations provided we enforce the physical constraint that the subgrid effects first enter the dynamics at the transport time scales. In particular, a multi-time relaxation collision operator is considered for the density distribution function and a single rel...
Potts model partition functions on two families of fractal lattices
Gong, Helin; Jin, Xian'an
2014-11-01
The partition function of q-state Potts model, or equivalently the Tutte polynomial, is computationally intractable for regular lattices. The purpose of this paper is to compute partition functions of q-state Potts model on two families of fractal lattices. Based on their self-similar structures and by applying the subgraph-decomposition method, we divide their Tutte polynomials into two summands, and for each summand we obtain a recursive formula involving the other summand. As a result, the number of spanning trees and their asymptotic growth constants, and a lower bound of the number of connected spanning subgraphs or acyclic root-connected orientations for each of such two lattices are obtained.
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.
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.
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.
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.
Emergent lattices with geometrical frustration in doped extended Hubbard models
Kaneko, Ryui; Tocchio, Luca F.; Valentí, Roser; Gros, Claudius
2016-11-01
Spontaneous charge ordering occurring in correlated systems may be considered as a possible route to generate effective lattice structures with unconventional couplings. For this purpose we investigate the phase diagram of doped extended Hubbard models on two lattices: (i) the honeycomb lattice with on-site U and nearest-neighbor V Coulomb interactions at 3 /4 filling (n =3 /2 ) and (ii) the triangular lattice with on-site U , nearest-neighbor V , and next-nearest-neighbor V' Coulomb interactions at 3 /8 filling (n =3 /4 ). We consider various approaches including mean-field approximations, perturbation theory, and variational Monte Carlo. For the honeycomb case (i), charge order induces an effective triangular lattice at large values of U /t and V /t , where t is the nearest-neighbor hopping integral. The nearest-neighbor spin exchange interactions on this effective triangular lattice are antiferromagnetic in most of the phase diagram, while they become ferromagnetic when U is much larger than V . At U /t ˜(V/t ) 3 , ferromagnetic and antiferromagnetic exchange interactions nearly cancel out, leading to a system with four-spin ring-exchange interactions. On the other hand, for the triangular case (ii) at large U and finite V', we find no charge order for small V , an effective kagome lattice for intermediate V , and one-dimensional charge order for large V . These results indicate that Coulomb interactions induce [case (i)] or enhance [case(ii)] emergent geometrical frustration of the spin degrees of freedom in the system, by forming charge order.
A Lattice Model of the Development of Reading Comprehension.
Connor, Carol McDonald
2016-12-01
In this article, I present a developmental model of how children learn to comprehend what they read, which builds on current models of reading comprehension and integrates findings from instructional research and evidence-based models of development in early and middle childhood. The lattice model holds that children's developing reading comprehension is a function of the interacting, reciprocal, and bootstrapping effects of developing text-specific, linguistic, and social-cognitive processes, which interact with instruction as child-characteristic-by-instruction (CXI) interaction effects. The processes develop over time and in the context of classroom, home, peer, community, and other influences to affect children's development of proficient reading comprehension. I first describe models of reading comprehension. I then review the basic processes in the model, the role of instruction, and CXI interactions in the context of the lattice model. I then discuss implications for instruction and research.
Fractal properties of the lattice Lotka-Volterra model.
Tsekouras, G A; Provata, A
2002-01-01
The lattice Lotka-Volterra (LLV) model is studied using mean-field analysis and Monte Carlo simulations. While the mean-field phase portrait consists of a center surrounded by an infinity of closed trajectories, when the process is restricted to a two-dimensional (2D) square lattice, local inhomogeneities/fluctuations appear. Spontaneous local clustering is observed on lattice and homogeneous initial distributions turn into clustered structures. Reactions take place only at the interfaces between different species and the borders adopt locally fractal structure. Intercluster surface reactions are responsible for the formation of local fluctuations of the species concentrations. The box-counting fractal dimension of the LLV dynamics on a 2D support is found to depend on the reaction constants while the upper bound of fractality determines the size of the local oscillators. Lacunarity analysis is used to determine the degree of clustering of homologous species. Besides the spontaneous clustering that takes place on a regular 2D lattice, the effects of fractal supports on the dynamics of the LLV are studied. For supports of dimensionality D(s)<2 the lattice can, for certain domains of the reaction constants, adopt a poisoned state where only one of the species survives. By appropriately selecting the fractal dimension of the substrate, it is possible to direct the system into a poisoned or oscillatory steady state at will.
Second order kinetic Kohn-Sham lattice model
Solorzano, Sergio; Herrmann, Hans
2016-01-01
In this work we introduce a new semi-implicit second order correction scheme to the kinetic Kohn-Sham lattice model. The new approach is validated by performing realistic exchange-correlation energy calculations of atoms and dimers of the first two rows of the periodic table finding good agreement with the expected values. Additionally we simulate the ethane molecule where we recover the bond lengths and compare the results with standard methods. Finally, we discuss the current applicability of pseudopotentials within the lattice kinetic Kohn-Sham approach.
Critical Exponents of Ferromagnetic Ising Model on Fractal Lattices
Hsiao, Pai-Yi
2001-04-01
We review the value of the critical exponents ν-1, β/ν, and γ/ν of ferromagnetic Ising model on fractal lattices of Hausdorff dimension between one and three. They are obtained by Monte Carlo simulation with the help of Wolff algorithm. The results are accurate enough to show that the hyperscaling law df = 2β/ν + γ/ν is satisfied in non-integer dimension. Nevertheless, the discrepancy between the simulation results and the γ-expansion studies suggests that the strong universality should be adapted for the fractal lattices.
Trapped ions in optical lattices for probing oscillator chain models
Pruttivarasin, Thaned; Talukdar, Ishan; Kreuter, Axel; Haeffner, Hartmut
2011-01-01
We show that a chain of trapped ions embedded in microtraps generated by an optical lattice can be used to study oscillator models related to dry friction and energy transport. Numerical calculations with realistic experimental parameters demonstrate that both static and dynamic properties of the ion chain change significantly as the optical lattice power is varied. Finally, we lay out an experimental scheme to use the spin degree of freedom to probe the phase space structure and quantum critical behavior of the ion chain.
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/.
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.
Analytical solutions of the lattice Boltzmann BGK model
Zou, Q; Doolen, G D; Zou, Qisu; Hou, Shuling; Doolen, Gary D.
1995-01-01
Abstract: Analytical solutions of the two dimensional triangular and square lattice Boltzmann BGK models have been obtained for the plain Poiseuille flow and the plain Couette flow. The analytical solutions are written in terms of the characteristic velocity of the flow, the single relaxation time representation of these two flows without any approximation.
Convergent series for lattice models with polynomial interactions
Aleksandr S. Ivanov
2017-01-01
Full Text Available The standard perturbative weak-coupling expansions in lattice models are asymptotic. The reason for this is hidden in the incorrect interchange of the summation and integration. However, substituting the Gaussian initial approximation of the perturbative expansions by a certain interacting model or regularizing original lattice integrals, one can construct desired convergent series. In this paper we develop methods, which are based on the joint and separate utilization of the regularization and new initial approximation. We prove, that the convergent series exist and can be expressed as re-summed standard perturbation theory for any model on the finite lattice with the polynomial interaction of even degree. We discuss properties of such series and study their applicability to practical computations on the example of the lattice ϕ4-model. We calculate 〈ϕn2〉 expectation value using the convergent series, the comparison of the results with the Borel re-summation and Monte Carlo simulations shows a good agreement between all these methods.
Kostka polynomials and energy functions in solvable lattice models
Nakayashiki, A; Nakayashiki, Atsushi; Yamada, Yasuhiko
1995-01-01
The relation between the charge of Lascoux-Schuzenberger and the energy function in solvable lattice models is clarified. As an application, A.N.Kirillov's conjecture on the expression of the branching coefficient of {\\widehat {sl_n}}/{sl_n} as a limit of Kostka polynomials is proved.
Yukawa model on a lattice: two body states
De Soto, F; Roiesnel, C; Boucaud, P; Leroy, J P; Pène, O; Boucaud, Ph.
2007-01-01
We present first results of the solutions of the Yukawa model as a Quantum Field Theory (QFT) solved non perturbatively with the help of lattice calculations. In particular we will focus on the possibility of binding two nucleons in the QFT, compared to the non relativistic result.
Filev, Veselin G
2015-01-01
We study the maximally supersymmetric BFFS model at finite temperature and its bosonic relative. For the bosonic model in $p+1$ dimensions, we find that it effectively reduces to a system of gauged Gaussian matrix models. The effective model captures the low temperature regime of the model including the phase transition. The mass becomes $p^{1/3}\\lambda^{1/3}$ for large $p$, with $\\lambda$ the 'tHooft coupling. For $p=9$ simulations of the model give $m=(1.90\\pm.01)\\lambda^{1/3}$, which is also the mass gap of the Hamiltonian. We argue that there is no `sign' problem in the maximally supersymmetric BFSS model and perform detailed simulations of several observables finding excellent agreement with AdS/CFT predictions when $1/\\alpha'$ corrections are included.
Coarse-grained numerical bifurcation analysis of lattice Boltzmann models
Leemput, P. Van; Lust, K.W.A.; Kevrekidis, I.G.
2005-01-01
In this paper we study the coarse-grained bifurcation analysis approach proposed by I.G. Kevrekidis and collaborators in PNAS [C. Theodoropoulos, Y.H. Qian, I.G. Kevrekidis, "Coarse" stability and bifurcation analysis using time-steppers: a reaction-diffusion example, Proc. Natl. Acad. Sci. 97 (18)
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.
Beam Diagnosis and Lattice Modeling of the Fermilab Booster
Huang, Xiaobiao [Indiana Univ., Bloomington, IN (United States)
2005-09-01
A realistic lattice model is a fundamental basis for the operation of a synchrotron. In this study various beam-based measurements, including orbit response matrix (ORM) and BPM turn-by-turn data are used to verify and calibrate the lattice model of the Fermilab Booster. In the ORM study, despite the strong correlation between the gradient parameters of adjacent magnets which prevents a full determination of the model parameters, an equivalent lattice model is obtained by imposing appropriate constraints. The fitted gradient errors of the focusing magnets are within the design tolerance and the results point to the orbit offsets in the sextupole field as the source of gradient errors. A new method, the independent component analysis (ICA) is introduced to analyze multiple BPM turn-by-turn data taken simultaneously around a synchrotron. This method makes use of the redundancy of the data and the time correlation of the source signals to isolate various components, such as betatron motion and synchrotron motion, from raw BPM data. By extracting clean coherent betatron motion from noisy data and separates out the betatron normal modes when there is linear coupling, the ICA method provides a convenient means to measure the beta functions and betatron phase advances. It also separates synchrotron motion from the BPM samples for dispersion function measurement. The ICA method has the capability to separate other perturbation signals and is robust over the contamination of bad BPMs. The application of the ICA method to the Booster has enabled the measurement of the linear lattice functions which are used to verify the existing lattice model. The transverse impedance and chromaticity are measured from turn-by-turn data using high precision tune measurements. Synchrotron motion is also observed in the BPM data. The emittance growth of the Booster is also studied by data taken with ion profile monitor (IPM). Sources of emittance growth are examined and an approach to cure
Critical, statistical, and thermodynamical properties of lattice models
Varma, Vipin Kerala
2013-10-15
In this thesis we investigate zero temperature and low temperature properties - critical, statistical and thermodynamical - of lattice models in the contexts of bosonic cold atom systems, magnetic materials, and non-interacting particles on various lattice geometries. We study quantum phase transitions in the Bose-Hubbard model with higher body interactions, as relevant for optical lattice experiments of strongly interacting bosons, in one and two dimensions; the universality of the Mott insulator to superfluid transition is found to remain unchanged for even large three body interaction strengths. A systematic renormalization procedure is formulated to fully re-sum these higher (three and four) body interactions into the two body terms. In the strongly repulsive limit, we analyse the zero and low temperature physics of interacting hard-core bosons on the kagome lattice at various fillings. Evidence for a disordered phase in the Ising limit of the model is presented; in the strong coupling limit, the transition between the valence bond solid and the superfluid is argued to be first order at the tip of the solid lobe.
Thermodynamic properties of lattice hard-sphere models.
Panagiotopoulos, A Z
2005-09-08
Thermodynamic properties of several lattice hard-sphere models were obtained from grand canonical histogram- reweighting Monte Carlo simulations. Sphere centers occupy positions on a simple cubic lattice of unit spacing and exclude neighboring sites up to a distance sigma. The nearestneighbor exclusion model, sigma = radical2, was previously found to have a second-order transition. Models with integer values of sigma = 1 or 2 do not have any transitions. Models with sigma = radical3 and sigma = 3 have weak first-order fluid-solid transitions while those with sigma = 2 radical2, 2 radical3, and 3 radical2 have strong fluid-solid transitions. Pressure, chemical potential, and density are reported for all models and compared to the results for the continuum, theoretical predictions, and prior simulations when available.
A lattice-gas model for amyloid fibril aggregation
Hong, Liu; Qi, Xianghong; Zhang, Yang
2012-01-01
A simple lattice-gas model, with two fundamental energy terms —elongation and nucleation effects, is proposed for understanding the mechanisms of amyloid fibril formation. Based on the analytical solution and Monte Carlo simulation of 1D system, we have thoroughly explored the dependence of mass concentration, number concentration of amyloid filaments and the lag-time on the initial protein concentration, the critical nucleus size, the strengths of nucleation and elongation effects, respectively. We also found that thickening process (self-association of filaments into multi-strand fibrils) is not essential for the modeling of amyloid filaments through simulations on 2D lattice. Compared with the kinetic model recently proposed by Knowles et al., highly quantitative consistency of two models in the calculation of mass fraction of filaments is found. Moreover our model can generate a better prediction on the number fraction, which is closer to experimental values when the elongation strength gets stronger. PMID:23275684
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.
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.
Vertex operators in solvable lattice models
Foda, O E; Miwa, T; Miki, K; Nakayashiki, A; Foda, Omar; Jimbo, Michio; Miwa, Tetsuji; Miki, Kei; Nakayashiki, Atsushi
1994-01-01
We formulate the basic properties of q-vertex operators in the context of the Andrews-Baxter-Forrester (ABF) series, as an example of face-interaction models, derive the q-difference equations satisfied by their correlation functions, and establish their connection with representation theory. We also discuss the q-difference equations of the Kashiwara-Miwa (KM) series, as an example of edge-interaction models. Next, the Ising model--the simplest special case of both ABF and KM series--is studied in more detail using the Jordan-Wigner fermions. In particular, all matrix elements of vertex operators are calculated.
Hormuth, David A., II; Weis, Jared A.; Barnes, Stephanie L.; Miga, Michael I.; Rericha, Erin C.; Quaranta, Vito; Yankeelov, Thomas E.
2015-07-01
Reaction-diffusion models have been widely used to model glioma growth. However, it has not been shown how accurately this model can predict future tumor status using model parameters (i.e., tumor cell diffusion and proliferation) estimated from quantitative in vivo imaging data. To this end, we used in silico studies to develop the methods needed to accurately estimate tumor specific reaction-diffusion model parameters, and then tested the accuracy with which these parameters can predict future growth. The analogous study was then performed in a murine model of glioma growth. The parameter estimation approach was tested using an in silico tumor ‘grown’ for ten days as dictated by the reaction-diffusion equation. Parameters were estimated from early time points and used to predict subsequent growth. Prediction accuracy was assessed at global (total volume and Dice value) and local (concordance correlation coefficient, CCC) levels. Guided by the in silico study, rats (n = 9) with C6 gliomas, imaged with diffusion weighted magnetic resonance imaging, were used to evaluate the model’s accuracy for predicting in vivo tumor growth. The in silico study resulted in low global (tumor volume error 0.92) and local (CCC values >0.80) level errors for predictions up to six days into the future. The in vivo study showed higher global (tumor volume error >11.7%, Dice silico study shows that model parameters can be accurately estimated and used to accurately predict future tumor growth at both the global and local scale. However, the poor predictive accuracy in the experimental study suggests the reaction-diffusion equation is an incomplete description of in vivo C6 glioma biology and may require further modeling of intra-tumor interactions including segmentation of (for example) proliferative and necrotic regions.
Kitaev Lattice Models as a Hopf Algebra Gauge Theory
Meusburger, Catherine
2017-07-01
We prove that Kitaev's lattice model for a finite-dimensional semisimple Hopf algebra H is equivalent to the combinatorial quantisation of Chern-Simons theory for the Drinfeld double D( H). This shows that Kitaev models are a special case of the older and more general combinatorial models. This equivalence is an analogue of the relation between Turaev-Viro and Reshetikhin-Turaev TQFTs and relates them to the quantisation of moduli spaces of flat connections. We show that the topological invariants of the two models, the algebra of operators acting on the protected space of the Kitaev model and the quantum moduli algebra from the combinatorial quantisation formalism, are isomorphic. This is established in a gauge theoretical picture, in which both models appear as Hopf algebra valued lattice gauge theories. We first prove that the triangle operators of a Kitaev model form a module algebra over a Hopf algebra of gauge transformations and that this module algebra is isomorphic to the lattice algebra in the combinatorial formalism. Both algebras can be viewed as the algebra of functions on gauge fields in a Hopf algebra gauge theory. The isomorphism between them induces an algebra isomorphism between their subalgebras of invariants, which are interpreted as gauge invariant functions or observables. It also relates the curvatures in the two models, which are given as holonomies around the faces of the lattice. This yields an isomorphism between the subalgebras obtained by projecting out curvatures, which can be viewed as the algebras of functions on flat gauge fields and are the topological invariants of the two models.
Contact angles in the pseudopotential lattice Boltzmann modeling of wetting
Li, Q; Kang, Q J; Chen, Q
2014-01-01
In this paper, we aim to investigate the implementation of contact angles in the pseudopotential lattice Boltzmann modeling of wetting at a large density ratio. The pseudopotential lattice Boltzmann model [X. Shan and H. Chen, Phys. Rev. E 49, 2941 (1994)] is a popular mesoscopic model for simulating multiphase flows and interfacial dynamics. In this model, the contact angle is usually realized by a fluid-solid interaction. Two widely used fluid-solid interactions: the density-based interaction and the pseudopotential-based interaction, as well as a modified pseudopotential-based interaction formulated in the present paper, are numerically investigated and compared in terms of the achievable contact angles, the maximum and the minimum densities, and the spurious currents. It is found that the pseudopotential-based interaction works well for simulating small static (liquid) contact angles, however, is unable to reproduce static contact angles close to 180 degrees. Meanwhile, it is found that the proposed modif...
Damage spreading in a driven lattice gas model
Rubio Puzzo, M. Leticia; Saracco, Gustavo P.; Albano, Ezequiel V.
2013-06-01
We studied damage spreading in a Driven Lattice Gas (DLG) model as a function of the temperature T, the magnitude of the external driving field E, and the lattice size. The DLG model undergoes an order-disorder second-order phase transition at the critical temperature Tc(E), such that the ordered phase is characterized by high-density strips running along the direction of the applied field; while in the disordered phase one has a lattice-gas-like behavior. It is found that the damage always spreads for all the investigated temperatures and reaches a saturation value D that depends only on T. D increases for TTc(E=∞) and is free of finite-size effects. This behavior can be explained as due to the existence of interfaces between the high-density strips and the lattice-gas-like phase whose roughness depends on T. Also, we investigated damage spreading for a range of finite fields as a function of T, finding a behavior similar to that of the case with E=∞.
Bayesian Analysis of Geostatistical Models With an Auxiliary Lattice
Park, Jincheol
2012-04-01
The Gaussian geostatistical model has been widely used for modeling spatial data. However, this model suffers from a severe difficulty in computation: it requires users to invert a large covariance matrix. This is infeasible when the number of observations is large. In this article, we propose an auxiliary lattice-based approach for tackling this difficulty. By introducing an auxiliary lattice to the space of observations and defining a Gaussian Markov random field on the auxiliary lattice, our model completely avoids the requirement of matrix inversion. It is remarkable that the computational complexity of our method is only O(n), where n is the number of observations. Hence, our method can be applied to very large datasets with reasonable computational (CPU) times. The numerical results indicate that our model can approximate Gaussian random fields very well in terms of predictions, even for those with long correlation lengths. For real data examples, our model can generally outperform conventional Gaussian random field models in both prediction errors and CPU times. Supplemental materials for the article are available online. © 2012 American Statistical Association, Institute of Mathematical Statistics, and Interface Foundation of North America.
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.
Linear lattice modeling of the recycler ring at Fermilab
Xiao, Meiqin; Valishev, Alexander; Nagaslaev, Vladimir P.; /Fermilab; Sajaev, Vadim; /Argonne
2006-06-01
Substantial differences are found in tunes and beta functions between the existing linear model and the real storage ring. They result in difficulties when tuning the machine to new lattice conditions. We are trying to correct the errors by matching the model into the real machine using Orbit Response Matrix (ORM) Fit method. The challenges with ORM particularly in the Recycler ring and the results are presented in this paper.
Vortex Lattice UXO Mobility Model Integration
2015-03-01
16 2.2 ADVANTAGES AND LIMITATIONS OF THE TECHNOLOGY .................... 17 3.0 PERFORMANCE OBJECTIVES...2 Figure 2. SCM for UXO showing the UXO MM analysis (lower left) as part of source quantification efforts...ordnance” (Johnson et al., 2002). A site conceptual model ( SCM ) was developed under this program and is shown schematically in Figure 2. After
A continuum of compass spin models on the honeycomb lattice
Zou, Haiyuan; Liu, Bo; Zhao, Erhai; Liu, W. Vincent
2016-05-01
Quantum spin models with spatially dependent interactions, known as compass models, play an important role in the study of frustrated quantum magnetism. One example is the Kitaev model on the honeycomb lattice with spin-liquid (SL) ground states and anyonic excitations. Another example is the geometrically frustrated quantum 120° model on the same lattice whose ground state has not been unambiguously established. To generalize the Kitaev model beyond the exactly solvable limit and connect it with other compass models, we propose a new model, dubbed ‘the tripod model’, which contains a continuum of compass-type models. It smoothly interpolates the Ising model, the Kitaev model, and the quantum 120° model by tuning a single parameter {θ }\\prime , the angle between the three legs of a tripod in the spin space. Hence it not only unifies three paradigmatic spin models, but also enables the study of their quantum phase transitions. We obtain the phase diagram of the tripod model numerically by tensor networks in the thermodynamic limit. We show that the ground state of the quantum 120° model has long-range dimer order. Moreover, we find an extended spin-disordered (SL) phase between the dimer phase and an antiferromagnetic phase. The unification and solution of a continuum of frustrated spin models as outline here may be useful to exploring new domains of other quantum spin or orbital models.
Lattice Boltzmann model for incompressible flows through porous media.
Guo, Zhaoli; Zhao, T S
2002-09-01
In this paper a lattice Boltzmann model is proposed for isothermal incompressible flow in porous media. The key point is to include the porosity into the equilibrium distribution, and add a force term to the evolution equation to account for the linear and nonlinear drag forces of the medium (the Darcy's term and the Forcheimer's term). Through the Chapman-Enskog procedure, the generalized Navier-Stokes equations for incompressible flow in porous media are derived from the present lattice Boltzmann model. The generalized two-dimensional Poiseuille flow, Couette flow, and lid-driven cavity flow are simulated using the present model. It is found the numerical results agree well with the analytical and/or the finite-difference solutions.
Lattice Modeling of Early-Age Behavior of Structural Concrete
Pan, Yaming; Prado, Armando; Porras, Rocío; Hafez, Omar M.; Bolander, John E.
2017-01-01
The susceptibility of structural concrete to early-age cracking depends on material composition, methods of processing, structural boundary conditions, and a variety of environmental factors. Computational modeling offers a means for identifying primary factors and strategies for reducing cracking potential. Herein, lattice models are shown to be adept at simulating the thermal-hygral-mechanical phenomena that influence early-age cracking. In particular, this paper presents a lattice-based approach that utilizes a model of cementitious materials hydration to control the development of concrete properties, including stiffness, strength, and creep resistance. The approach is validated and used to simulate early-age cracking in concrete bridge decks. Structural configuration plays a key role in determining the magnitude and distribution of stresses caused by volume instabilities of the concrete material. Under restrained conditions, both thermal and hygral effects are found to be primary contributors to cracking potential. PMID:28772590
Simulations of Quantum Spin Models on 2D Frustrated Lattices
Melko, Roger
2006-03-01
Algorithmic advances in quantum Monte Carlo techniques have opened up the possibility of studying models in the general class of the S=1/2 XXZ model (equivalent to hard-core bosons) on frustrated lattices. With an antiferromagnetic diagonal interaction (Jz), these models can be solved exactly with QMC, albeit with some effort required to retain ergodicity in the near-degenerate manifold of states that exists for large Jz. The application of the quantum (ferromagnetic off-diagonal) interaction to this classically degenerate manifold produces a variety of intriguing physics, including an order-by-disorder supersolid phase, novel insulating states, and possible exotic quantum critical phenomena. We discuss numerical results for the triangular and kagome lattices with nearest and next-nearest neighbor exchange interactions, and focus on the relevance of the simulations to related areas of physics, such as experiments of cold trapped atomic gasses and the recent theory of deconfined quantum criticality.
Lattice models of traffic flow considering drivers' delay in response
Zhu Hui-Bing
2009-01-01
This paper proposes two lattice traffic models by taking into account the drivers'delay in response.The lattice versions of the hydrodynamic model are described by the differential-difference equation and difference-difference equation.respectively.The stability conditions for the two models are obtained by using the linear stability theory.The modified KdV equation near the critical point is derived to describe the traffic jam by using the reductive perturbation method,and the kink-antikink soliton solutions related to the traffic density waves are obtained.The results show that the drivers'delay in sensing headway plays an important role in jamming transition.
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.
Mesophyll conductance and reaction-diffusion models for CO
Berghuijs, Herman N.C.; Yin, Xinyou; Tri Ho, Q.; Driever, Steven M.; Retta, Moges A.; Nicolaï, Bart M.; Struik, Paul C.
2016-01-01
One way to increase potential crop yield could be increasing mesophyll conductance g_{m}. This variable determines the difference between the CO_{2} partial pressure in the intercellular air spaces (C_{i}) and that near Rubisco (C_{c}). Various methods can determin
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.
Energy-Dependent Octagonal Lattice Boltzmann Modeling for Compressible Flows
Pavlo, Pavol; Vahala, Linda; Vahala, George
2000-10-01
There has been much interest in thermal lattice Boltzmann modeling (TLBM) for compressible flows because of their inherent parallelizeability. Instead of applying CFD techniques to the nonlinear conservation equations, one instead solves a linear BGK kinetic equation. To reduce storage requirements, the velocity space is discretized and lattice geometries are so chosen to minimize the number of degrees of freedom that must be retained in the Chapman-Enskog recovery of the original macroscopic equations. The simplest (and most efficient) TLBM runs at a CFL=1, so that no numerical diffusion or dissipation is introduced. The algorithm involves Lagrangian streaming (shift operator) and purely local operations. Because of the underlying discrete lattice symmetry, the relaxation distributions cannot be Maxwellian and hence the inherent numerical instability problem in TLBM. We are investigating the use of energy-dependent lattices so as to allow simulation of problems of interest in divertor physics, The appeal of TLBM is that it can provide a unified representation for both strongly collisional (‘fluid’) and weakly collisional (‘Monte Carlo’) regimes. Moreover, our TLBM code is more efficiently solved on mulit-PE platforms than the corresponding CFD codes and is readily extended to 3D. MHD can also be handled by TLBM.
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.
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.
Lapinskas, Saulius; Rosengren, Anders
1994-06-01
Using the cluster-variation method we study the phase diagram of the Blume-Emergy-Griffiths (BEG) model on simple cubic and face-centered cubic lattices. For the simple cubic lattice the main attention is paid to reentrant phenomena and ferrimagnetic phases occurring in a certain range of coupling constants. The results are in close agreement with Monte-Carlo data, available for parts of the phase diagram. Several ferrimagnetic phases are obtained in the vicinity of the line in parameter space, at which the model reduces to the antiferromagnetic three-state Potts model. Our results imply the existence of three phase transitions in the antiferromagnetic Potts model on the simple-cubic lattice. The phase diagrams for the BEG model on the face-centered cubic lattice are obtained in the region of antiquadrupolar ordering. Also the several ordered phases of the antiferromagnetic Potts model on this lattice are discussed.
Simultaneous and non-simultaneous blow-up and uniform blow-up profiles for reaction-diffusion system
Zhengqiu Ling
2012-11-01
Full Text Available This article concerns the blow-up solutions of a reaction-diffusion system with nonlocal sources, subject to the homogeneous Dirichlet boundary conditions. The criteria used to identify simultaneous and non-simultaneous blow-up of solutions by using the parameters p and q in the model are proposed. Also, the uniform blow-up profiles in the interior domain are established.
Lattice-fluid model for gas-liquid chromatography.
Tao, Y; Wells, P S; Yi, X; Yun, K S; Parcher, J F
1999-11-01
Lattice-fluid models describe molecular ensembles in terms of the number of lattice sites occupied by molecular species (r-mers) and the interactions between neighboring molecules. The lattice-fluid model proposed by Sanchez and Lacombe (Macromolecules, 1978;11:1145-1156) was used to model specific retention volume data for a series of n-alkane solutes with n-alkane, polystyrene, and poly(dimethylsiloxane) stationary liquid phases. Theoretical equations were derived for the specific retention volume and also for the temperature dependence and limiting (high temperature) values for the specific retention volume. The model was used to predict retention volumes within 10% for the n-alkanes phases; 22% for polystyrene; and from 20 to 70% for PDMS using no adjustable parameters. The temperature derivative (enthalpy) could be calculated within 5% for all of the solutes in nine stationary liquid phases. The limiting value for the specific retention volume at high temperature (entropy controlled state) could be calculated within 10% for all of the systems. The limiting data also provided a new chromatographic method to measure the size parameter, r, for any chromatographic solute using characteristic and size parameters for the stationary phase only. The calculated size parameters of the solutes were consistent, i.e. independent of the stationary phase and agreed within experimental error with the size parameters previously reported from saturated vapor pressure, latent heat of vaporization or density data.
Simulating Lattice Spin Models on Graphics Processing Units
Levy, Tal; Rabani, Eran; 10.1021/ct100385b
2012-01-01
Lattice spin models are useful for studying critical phenomena and allow the extraction of equilibrium and dynamical properties. Simulations of such systems are usually based on Monte Carlo (MC) techniques, and the main difficulty is often the large computational effort needed when approaching critical points. In this work, it is shown how such simulations can be accelerated with the use of NVIDIA graphics processing units (GPUs) using the CUDA programming architecture. We have developed two different algorithms for lattice spin models, the first useful for equilibrium properties near a second-order phase transition point and the second for dynamical slowing down near a glass transition. The algorithms are based on parallel MC techniques, and speedups from 70- to 150-fold over conventional single-threaded computer codes are obtained using consumer-grade hardware.
Entropy of fermionic models on highly frustrated lattices
A.Honecker
2005-01-01
Full Text Available Spinless fermions on highly frustrated lattices are characterized by the lowest single-particle band which is completely flat. Concrete realizations are provided by the sawtooth chain and the kagom'e lattice. For these models a real-space picture is given in terms of localized states. Furthermore, we find a finite zero-temperature entropy for a suitable choice of the chemical potential. The entropy is computed numerically at finite temperature and one observes a strong cooling effect during adiabatic changes of the chemical potential. We argue that the localized states, the associated zero-temperature entropy as well as the large temperature variations carry over to the repulsive Hubbard model. The relation to flat-band ferromagnetism is also discussed briefly.
LATTICE-BOLTZMANN MODEL FOR COMPRESSIBLE PERFECT GASES
Sun Chenghai
2000-01-01
We present an adaptive lattice Boltzmann model to simulate super sonic flows. The particle velocities are determined by the mean velocity and internal energy. The adaptive nature of particle velocities permits the mean flow to have high Mach number. A particle potential energy is introduced so that the model is suitable for the perfect gas with arbitrary specific heat ratio. The Navier-Stokes equations are derived by the Chapman-Enskog method from the BGK Boltzmann equation.As preliminary tests, two kinds of simulations have been performed on hexagonal lattices. One is the one-dimensional simulation for sinusoidal velocity distributions.The velocity distributions are compared with the analytical solution and the mea sured viscosity is compared with the theoretical values. The agreements are basically good. However, the discretion error may cause some non-isotropic effects. The other simulation is the 29 degree shock reflection.
Effective constraint potential in lattice Weinberg - Salam model
Polikarpov, M I
2011-01-01
We investigate lattice Weinberg - Salam model without fermions for the value of the Weinberg angle $\\theta_W \\sim 30^o$, and bare fine structure constant around $\\alpha \\sim 1/150$. We consider the value of the scalar self coupling corresponding to bare Higgs mass around 150 GeV. The effective constraint potential for the zero momentum scalar field is used in order to investigate phenomena existing in the vicinity of the phase transition between the physical Higgs phase and the unphysical symmetric phase of the lattice model. This is the region of the phase diagram, where the continuum physics is to be approached. We compare the above mentioned effective potential (calculated in selected gauges) with the effective potential for the value of the scalar field at a fixed space - time point. We also calculate the renormalized fine structure constant using the correlator of Polyakov lines and compare it with the one - loop perturbative estimate.
Integrable Lattice Models for Conjugate $A^{(1)}_n$
Behrend, R E; Behrend, Roger E.; Evans, David E.
2004-01-01
A new class of $A^{(1)}_n$ integrable lattice models is presented. These are interaction-round-a-face models based on fundamental nimrep graphs associated with the $A^{(1)}_n$ conjugate modular invariants, there being a model for each value of the rank and level. The Boltzmann weights are parameterized by elliptic theta functions and satisfy the Yang-Baxter equation for any fixed value of the elliptic nome q. At q=0, the models provide representations of the Hecke algebra and are expected to lead in the continuum limit to coset conformal field theories with torus partition functions described by the $A^{(1)}_n$ conjugate modular invariants.
LATTICE BOLTZMANN EQUATION MODEL IN THE CORIOLIS FIELD
FENG SHI-DE; MAO JIANG-YU; ZHANG QIONG
2001-01-01
In a large-scale field of rotational fluid, various unintelligible and surprising dynamic phenomena are produced due to the effect of the Coriolis force. The lattice Boltzmann equation (LBE) model in the Coriolis field is developed based on previous works.[1-4] Geophysical fluid dynamics equations are derived from the model. Numerical simulations have been made on an ideal atmospheric circulation of the Northern Hemisphere by using the model and they reproduce the Rossby wave motion well. Hence the applicability of the model is verified in both theory and experiment.
Critical properties of a dilute O(n) model on the kagome lattice
Li, B.; Guo, W.; Blöte, H.W.J.
2008-01-01
A critical dilute O(n) model on the kagome lattice is investigated analytically and numerically. We employ a number of exact equivalences which, in a few steps, link the critical O(n) spin model on the kagome lattice to the exactly solvable critical q-state Potts model on the honeycomb lattice with
The Potts model on a Bethe lattice with nonmagnetic impurities
Semkin, S. V., E-mail: li15@rambler.ru; Smagin, V. P. [Vladivistok State University of Economics and Service (VSUES) (Russian Federation)
2015-10-15
We have obtained a solution for the Potts model on a Bethe lattice with mobile nonmagnetic impurities. A method is proposed for constructing a “pseudochaotic” impurity distribution by a vanishing correlation in the arrangement of impurity atoms for the nearest sites. For a pseudochaotic impurity distribution, we obtained the phase-transition temperature, magnetization, and spontaneous magnetization jumps at the phase-transition temperature.
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.
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.
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.
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)
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)
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.
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.
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.
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.
Three-dimensional lattice Boltzmann model for electrodynamics.
Mendoza, M; Muñoz, J D
2010-11-01
In this paper we introduce a three-dimensional Lattice-Boltzmann model that recovers in the continuous limit the Maxwell equations in materials. In order to build conservation equations with antisymmetric tensors, like the Faraday law, the model assigns four auxiliary vectors to each velocity vector. These auxiliary vectors, when combined with the distribution functions, give the electromagnetic fields. The evolution is driven by the usual Bhatnager-Gross-Krook (BGK) collision rule, but with a different form for the equilibrium distribution functions. This lattice Bhatnager-Gross-Krook (LBGK) model allows us to consider for both dielectrics and conductors with realistic parameters, and therefore it is adequate to simulate the most diverse electromagnetic problems, like the propagation of electromagnetic waves (both in dielectric media and in waveguides), the skin effect, the radiation pattern of a small dipole antenna and the natural frequencies of a resonant cavity, all with 2% accuracy. Actually, it shows to be one order of magnitude faster than the original Finite-difference time-domain (FDTD) formulation by Yee to reach the same accuracy. It is, therefore, a valuable alternative to simulate electromagnetic fields and opens lattice Boltzmann for a broad spectrum of new applications in electrodynamics.
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 $epsilon_1,epsilon_2o 0$.
Matthew J Simpson
Full Text Available Many processes during embryonic development involve transport and reaction of molecules, or transport and proliferation of cells, within growing tissues. Mathematical models of such processes usually take the form of a reaction-diffusion partial differential equation (PDE on a growing domain. Previous analyses of such models have mainly involved solving the PDEs numerically. Here, we present a framework for calculating the exact solution of a linear reaction-diffusion PDE on a growing domain. We derive an exact solution for a general class of one-dimensional linear reaction-diffusion process on 0
Critical quasiparticles in single-impurity and lattice Kondo models
Vojta, M.; Bulla, R.; Wölfle, P.
2015-07-01
Quantum criticality in systems of local moments interacting with itinerant electrons has become an important and diverse field of research. Here we review recent results which concern (a) quantum phase transitions in single-impurity Kondo and Anderson models and (b) quantum phase transitions in heavy-fermion lattice models which involve critical quasiparticles. For (a) the focus will be on impurity models with a pseudogapped host density of states and their applications, e.g., in graphene and other Dirac materials, while (b) is devoted to strong-coupling behavior near antiferromagnetic quantum phase transitions, with potential applications in a variety of heavy-fermion metals.
Coupling lattice Boltzmann and molecular dynamics models for dense fluids
Dupuis, A.; Kotsalis, E. M.; Koumoutsakos, P.
2007-04-01
We propose a hybrid model, coupling lattice Boltzmann (LB) and molecular dynamics (MD) models, for the simulation of dense fluids. Time and length scales are decoupled by using an iterative Schwarz domain decomposition algorithm. The MD and LB formulations communicate via the exchange of velocities and velocity gradients at the interface. We validate the present LB-MD model in simulations of two- and three-dimensional flows of liquid argon past and through a carbon nanotube. Comparisons with existing hybrid algorithms and with reference MD solutions demonstrate the validity of the present approach.
Stochastic Lattice Gas Model for a Predator-Prey System
Satulovsky, J E; Satulovsky, Javier; Tome, Tania
1994-01-01
We propose a stochastic lattice gas model to describe the dynamics of two animal species population, one being a predator and the other a prey. This model comprehends the mechanisms of the Lotka-Volterra model. Our analysis was performed by using a dynamical mean-field approximation and computer simulations. Our results show that the system exhibits an oscillatory behavior of the population densities of prey and predators. For the sets of parameters used in our computer simulations, these oscillations occur at a local level. Mean-field results predict synchronized collective oscillations.
Nonextensivity of the cyclic lattice Lotka-Volterra model.
Tsekouras, G A; Provata, A; Tsallis, C
2004-01-01
We numerically show that the lattice Lotka-Volterra model, when realized on a square lattice support, gives rise to a finite production, per unit time, of the nonextensive entropy S(q)=(1- summation operator (i)p(q)(i))/(q-1) (S(1)=- summation operator (i)p(i) ln p(i)). This finiteness only occurs for q=0.5 for the d=2 growth mode (growing droplet), and for q=0 for the d=1 one (growing stripe). This strong evidence of nonextensivity is consistent with the spontaneous emergence of local domains of identical particles with fractal boundaries and competing interactions. Such direct evidence is, to our knowledge, exhibited for the first time for a many-body system which, at the mean field level, is conservative.
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.
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.
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).
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.
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.
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.
Filter-matrix lattice Boltzmann model for microchannel gas flows.
Zhuo, Congshan; Zhong, Chengwen
2013-11-01
The lattice Boltzmann method has been shown to be successful for microscale gas flows, and it has attracted significant research interest. In this paper, the recently proposed filter-matrix lattice Boltzmann (FMLB) model is first applied to study the microchannel gas flows, in which a Bosanquet-type effective viscosity is used to capture the flow behaviors in the transition regime. A kinetic boundary condition, the combined bounce-back and specular-reflection scheme with the second-order slip scheme, is also designed for the FMLB model. By analyzing a unidirectional flow, the slip velocity and the discrete effects related to the boundary condition are derived within the FMLB model, and a revised scheme is presented to overcome such effects, which have also been validated through numerical simulations. To gain an accurate simulation in a wide range of Knudsen numbers, covering the slip and the entire transition flow regimes, a set of slip coefficients with an introduced fitting function is adopted in the revised second-order slip boundary condition. The periodic and pressure-driven microchannel flows have been investigated by the present model in this study. The numerical results, including the velocity profile and the mass flow rate, as well as the nonlinear pressure distribution along the channel, agree fairly well with the solutions of the linearized Boltzmann equation, the direct simulation Monte Carlo results, the experimental data, and the previous results of the multiple effective relaxation lattice Boltzmann model. Also, the present results of the velocity profile and the mass flow rate show that the present model with the fitting function can yield improved predictions for the microchannel gas flow with higher Knudsen numbers in the transition flow regime.
Simulation of rheological behavior of asphalt mixture with lattice model
杨圣枫; 杨新华; 陈传尧
2008-01-01
A three-dimensional(3D) lattice model for predicting the rheological behavior of asphalt mixtures was presented.In this model asphalt mixtures were described as a two-phase composite material consisting of asphalt sand and coarse aggregates distributed randomly.Asphalt sand was regarded as a viscoelastic material and aggregates as an elastic material.The rheological response of asphalt mixture subjected to different constant stresses was simulated.The calibrated overall creep strain shows a good approximation to experimental results.
Lattice Boltzmann model for nonlinear convection-diffusion equations.
Shi, Baochang; Guo, Zhaoli
2009-01-01
A lattice Boltzmann model for convection-diffusion equation with nonlinear convection and isotropic-diffusion terms is proposed through selecting equilibrium distribution function properly. The model can be applied to the common real and complex-valued nonlinear evolutionary equations, such as the nonlinear Schrödinger equation, complex Ginzburg-Landau equation, Burgers-Fisher equation, nonlinear heat conduction equation, and sine-Gordon equation, by using a real and complex-valued distribution function and relaxation time. Detailed simulations of these equations are performed, and it is found that the numerical results agree well with the analytical solutions and the numerical solutions reported in previous studies.
Multicritical tensor models and hard dimers on spherical random lattices
Bonzom, Valentin
2012-01-01
Random tensor models which display multicritical behaviors in a remarkably simple fashion are presented. They come with entropy exponents \\gamma = (m-1)/m, similarly to multicritical random branched polymers. Moreover, they are interpreted as models of hard dimers on a set of random lattices for the sphere in dimension three and higher. Dimers with their exclusion rules are generated by the different interactions between tensors, whose coupling constants are dimer activities. As an illustration, we describe one multicritical point, which is interpreted as a transition between the dilute phase and a crystallized phase, though with negative activities.
Phase transitions in the lattice model of intercalation
T.S. Mysakovych
2008-12-01
Full Text Available The lattice model which can be employed for the description of intercalation of ions in crystals is considered in this work. Pseudospin formalism is used in describing the interaction of electrons with ions. The possibility of hopping of intercalated ions between different positions is taken into account. The thermodynamics of the model is investigated in the mean field approximation. Phase diagrams are built. It is shown that at high values of the parameter of ion transfer, the phase transition to a modulated phase disappears.
A Spatial Lattice Model Applied for Meteorological Visualization and Analysis
Mingyue Lu
2017-03-01
Full Text Available Meteorological information has obvious spatial-temporal characteristics. Although it is meaningful to employ a geographic information system (GIS to visualize and analyze the meteorological information for better identification and forecasting of meteorological weather so as to reduce the meteorological disaster loss, modeling meteorological information based on a GIS is still difficult because meteorological elements generally have no stable shape or clear boundary. To date, there are still few GIS models that can satisfy the requirements of both meteorological visualization and analysis. In this article, a spatial lattice model based on sampling particles is proposed to support both the representation and analysis of meteorological information. In this model, a spatial sampling particle is regarded as the basic element that contains the meteorological information, and the location where the particle is placed with the time mark. The location information is generally represented using a point. As these points can be extended to a surface in two dimensions and a voxel in three dimensions, if these surfaces and voxels can occupy a certain space, then this space can be represented using these spatial sampling particles with their point locations and meteorological information. In this case, the full meteorological space can then be represented by arranging numerous particles with their point locations in a certain structure and resolution, i.e., the spatial lattice model, and extended at a higher resolution when necessary. For practical use, the meteorological space is logically classified into three types of spaces, namely the projection surface space, curved surface space, and stereoscopic space, and application-oriented spatial lattice models with different organization forms of spatial sampling particles are designed to support the representation, inquiry, and analysis of meteorological information within the three types of surfaces. Cases
Lattice location of dopant atoms: An -body model calculation
N K Deepak
2010-03-01
The channelling and scattering yields of 1 MeV -particles in the $\\langle 1 0 0 \\rangle$, $\\langle 1 1 0 \\rangle and $\\langle 1 1 1 \\rangle$ directions of silicon implanted with bismuth and ytterbium have been simulated using -body model. The close encounter yield from dopant atoms in silicon is determined from the flux density, using the Bontemps and Fontenille method. All previous works reported in literature so far have been done with computer programmes using a statistical analytical expression or by a binary collision model or a continuum model. These results at the best gave only the transverse displacement of the lattice site from the concerned channelling direction. Here we applied the superior -body model to study the yield from bismuth in silicon. The finding that bismuth atom occupies a position close to the silicon substitutional site is new. The transverse displacement of the suggested lattice site from the channelling direction is consistent with the experimental results. The above model is also applied to determine the location of ytterbium in silicon. The present values show good agreement with the experimental results.
Quadrature-based Lattice Boltzmann Model for Relativistic Flows
Blaga, Robert
2016-01-01
A quadrature-based finite-difference lattice Boltzmann model is developed that is suitable for simulating relativistic flows of massless particles. We briefly review the relativistc Boltzmann equation and present our model. The quadrature is constructed such that the stress-energy tensor is obtained as a second order moment of the distribution function. The results obtained with our model are presented for a particular instance of the Riemann problem (the Sod shock tube). We show that the model is able to accurately capture the behavior across the whole domain of relaxation times, from the hydrodynamic to the ballistic regime. The property of the model of being extendable to arbitrarily high orders is shown to be paramount for the recovery of the analytical result in the ballistic regime.
Contact angles in the pseudopotential lattice Boltzmann modeling of wetting
Li, Qing; Luo, K. H.; Kang, Q. J.; Chen, Q.
2014-11-01
In this paper we investigate the implementation of contact angles in the pseudopotential lattice Boltzmann modeling of wetting at a large density ratio ρL/ρV=500 . The pseudopotential lattice Boltzmann model [X. Shan and H. Chen, Phys. Rev. E 49, 2941 (1994), 10.1103/PhysRevE.49.2941] is a popular mesoscopic model for simulating multiphase flows and interfacial dynamics. In this model the contact angle is usually realized by a fluid-solid interaction. Two widely used fluid-solid interactions, the density-based interaction and the pseudopotential-based interaction, as well as a modified pseudopotential-based interaction formulated in the present paper are numerically investigated and compared in terms of the achievable contact angles, the maximum and the minimum densities, and the spurious currents. It is found that the pseudopotential-based interaction works well for simulating small static (liquid) contact angles θ static contact angles close to 180∘. Meanwhile, it is found that the proposed modified pseudopotential-based interaction performs better in light of the maximum and the minimum densities and is overall more suitable for simulating large contact angles θ >90∘ as compared with the two other types of fluid-solid interactions. Furthermore, the spurious currents are found to be enlarged when the fluid-solid interaction force is introduced. Increasing the kinematic viscosity ratio between the vapor and liquid phases is shown to be capable of reducing the spurious currents caused by the fluid-solid interactions.
Lattice modeling of fracture processes in numerical concrete with irregular shape aggregates
Qian, Z.; Schlangen, H.E.J.G.
2013-01-01
The fracture processes in concrete can be simulated by lattice fracture model [1]. A lattice network is usually constructed on top of the material structure of concrete, and then the mechanical properties of lattice elements are assigned, corresponding with the phases they represent. The material st
Monte Carlo Simulation of Kinesin Movement with a Lattice Model
WANG Hong; DOU Shuo-Xing; WANG Peng-Ye
2005-01-01
@@ Kinesin is a processive double-headed molecular motor that moves along a microtubule by taking about 8nm steps. It generally hydrolyzes one ATP molecule for taking each forward step. The processive movement of the kinesin molecular motors is numerically simulated with a lattice model. The motors are considered as Brownian particles and the ATPase processes of both heads are taken into account. The Monte Carlo simulation results agree well with recent experimental observations, especially on the relation of velocity versus ATP and ADP concentrations.
Testing the hadro-quarkonium model on the lattice
Knechtli, Francesco; Bali, Gunnar S; Collins, Sara; Moir, Graham; Söldner, Wolfgang
2016-01-01
Recently the LHCb experiment found evidence for the existence of two exotic resonances consisting of $c\\bar{c}uud$ quarks. Among the possible interpretations is the hadro-charmonium model, in which charmonium is bound "within" a light hadron. We test this idea on CLS $N_f$=2+1 lattices using the static formulation for the heavy quarks. We find that the static potential is modified by the presence of a hadron such that it becomes more attractive. The effect is of the order of a few MeV.
Thrombosis modeling in intracranial aneurysms: a lattice Boltzmann numerical algorithm
Ouared, R.; Chopard, B.; Stahl, B.; Rüfenacht, D. A.; Yilmaz, H.; Courbebaisse, G.
2008-07-01
The lattice Boltzmann numerical method is applied to model blood flow (plasma and platelets) and clotting in intracranial aneurysms at a mesoscopic level. The dynamics of blood clotting (thrombosis) is governed by mechanical variations of shear stress near wall that influence platelets-wall interactions. Thrombosis starts and grows below a shear rate threshold, and stops above it. Within this assumption, it is possible to account qualitatively well for partial, full or no occlusion of the aneurysm, and to explain why spontaneous thrombosis is more likely to occur in giant aneurysms than in small or medium sized aneurysms.
Kinetic Relations for a Lattice Model of Phase Transitions
Schwetlick, Hartmut; Zimmer, Johannes
2012-11-01
The aim of this article is to analyse travelling waves for a lattice model of phase transitions, specifically the Fermi-Pasta-Ulam chain with piecewise quadratic interaction potential. First, for fixed, sufficiently large subsonic wave speeds, we rigorously prove the existence of a family of travelling wave solutions. Second, it is shown that this family of solutions gives rise to a kinetic relation which depends on the jump in the oscillatory energy in the solution tails. Third, our constructive approach provides a very good approximate travelling wave solution.
Quantum chaos in the nuclear collective model. II. Peres lattices.
Stránský, Pavel; Hruska, Petr; Cejnar, Pavel
2009-06-01
This is a continuation of our paper [Phys. Rev. E 79, 046202 (2009)] devoted to signatures of quantum chaos in the geometric collective model of atomic nuclei. We apply the method by Peres to study ordered and disordered patterns in quantum spectra drawn as lattices in the plane of energy vs average of a chosen observable. Good qualitative agreement with standard measures of chaos is manifested. The method provides an efficient tool for studying structural changes in eigenstates across quantum spectra of general systems.
The strong coupling Kondo lattice model as a Fermi gas
Östlund, S
2007-01-01
The strong coupling half-filled Kondo lattice model is an important example of a strongly interacting dense Fermi system for which conventional Fermi gas analysis has thus far failed. We remedy this by deriving an exact transformation that maps the model to a dilute gas of weakly interacting electron and hole quasiparticles that can then be analyzed by conventional dilute Fermi gas methods. The quasiparticle vacuum is a singlet Mott insulator for which the quasiparticle dynamics are simple. Since the transformation is exact, the electron spectral weight sum rules are obeyed exactly. Subtleties in understanding the behavior of electrons in the singlet Mott insulator can be reduced to a fairly complicated but precise relation between quasiparticles and bare electrons. The theory of free quasiparticles can be interpreted as an exactly solvable model for a singlet Mott insulator, providing an exact model in which to explore the strong coupling regime of a singlet Kondo insulator.
Lattice Boltzmann modeling an introduction for geoscientists and engineers
Sukop, Michael C
2005-01-01
Lattice Boltzmann models have a remarkable ability to simulate single- and multi-phase fluids and transport processes within them. A rich variety of behaviors, including higher Reynolds numbers flows, phase separation, evaporation, condensation, cavitation, buoyancy, and interactions with surfaces can readily be simulated. This book provides a basic introduction that emphasizes intuition and simplistic conceptualization of processes. It avoids the more difficult mathematics that underlies LB models. The model is viewed from a particle perspective where collisions, streaming, and particle-particle/particle-surface interactions constitute the entire conceptual framework. Beginners and those with more interest in model application than detailed mathematical foundations will find this a powerful "quick start" guide. Example simulations, exercises, and computer codes are included. Working code is provided on the Internet.
Phase Diagram for Ashkin-Teller Model on Bethe Lattice
LE Jian-Xin; YANG Zhan-Ru
2005-01-01
Using the recursion method, we study the phase transitions of the Ashkin-Teller model on the Bethe lattice,restricting ourselves to the case of ferromagnetic interactions. The isotropic Ashkin-Teller model and the anisotropic one are respectively investigated, and exact expressions for the free energy and the magnetization are obtained. It can be found that each of the three varieties of phase diagrams, for the anisotropic Ashkin-Teller model, consists of four phases, I.e., the fully disordered paramagnetic phase Para, the fully ordered ferromagnetic phase Ferro, and two partially ordered ferromagnetic phases and , while the phase diagram, for the isotropic Ashkin-Teller model,contains three phases, I.e., the fully disordered paramagnetic phase Para, the fully ordered ferromagnetic phase Baxter Phase, and the partially ordered ferromagnetic phase .
Lattice Boltzmann model for a steady radiative transfer equation.
Yi, Hong-Liang; Yao, Feng-Ju; Tan, He-Ping
2016-08-01
A complete lattice Boltzmann model (LBM) is proposed for the steady radiative transfer equation (RTE). The RTE can be regarded as a pure convection equation with a source term. To derive the expressions for the equilibrium distribution function and the relaxation time, an artificial isotropic diffusion term is introduced to form a convection-diffusion equation. When the dimensionless relaxation time has a value of 0.5, the lattice Boltzmann equation (LBE) is exactly applicable to the original steady RTE. We also perform a multiscale analysis based on the Chapman-Enskog expansion to recover the macroscopic RTE from the mesoscopic LBE. The D2Q9 model is used to solve the LBE, and the numerical results obtained by the LBM are comparable to the results obtained by other methods or analytical solutions, which demonstrates that the proposed model is highly accurate and stable in simulating multidimensional radiative transfer. In addition, we find that the convergence rate of the LBM depends on the transport properties of RTE: for diffusion-dominated RTE with a large optical thickness, the LBM shows a second-order convergence rate in space, while for convection-dominated RTE with a small optical thickness, a lower convergence rate is observed.
Non-String Pursuit towards Unified Model on the Lattice
Kawamoto, N
1999-01-01
Non-standard overview on the possible formulation towards a unified model on the lattice is presented. It is based on the generalized gauge theory which is formulated by differential forms and thus expected to fit in a simplicial manifold. We first review suggestive known results towards this direction. As a small step of concrete realization of the program, we propose a lattice Chern-Simons gravity theory which leads to the Chern-Simons gravity in the continuum limit via Ponzano-Regge model. We then summarize the quantization procedure of the generalized gauge theory and apply the formulation to the generalized topological Yang-Mills action with instanton gauge fixing. We find N=2 super Yang-Mills theory with Dirac-K{ä}hler fermions which are generated from ghosts via twisting mechanism. The Weinberg-Salam model is formulated by the generalized Yang-Mills action which includes Connes's non-commutative geometry formulation as a particular case. In the end a possible scenario to realize the program is propose...
Frustrated square lattice Heisenberg model and magnetism in Iron Telluride
Zaliznyak, Igor; Xu, Zhijun; Gu, Genda; Tranquada, John; Stone, Matthew
2011-03-01
We have measured spin excitations in iron telluride Fe1.1Te, the parent material of (1,1) family of iron-based superconductors. It has been recognized that J1-J2-J3 frustrated Heisenberg model on a square lattice might be relevant for the unusual magnetism and, perhaps, the superconductivity in cuprates [1,2]. Recent neutron scattering measurements show that similar frustrated model might also provide reasonable account for magnetic excitations in iron pnictide materials. We find that it also describes general features of spin excitations in FeTe parent compound observed in our recent neutron measurements, as well as in those by other groups. Results imply proximity of magnetic system to the limit of extreme frustration. Selection of spin ground state under such conditions could be driven by weak extrinsic interactions, such as lattice distortion, or strain. Consequently, different nonuniversal types of magnetic order could arise, both commensurate and incommensurate. These are not necessarily intrinsic to an ideal J1-J2-J3 model, but might result from lifting of its near degeneracy by weak extrinsic perturbations.
Statistical mechanics of directed models of polymers in the square lattice
Rensburg, J V
2003-01-01
Directed square lattice models of polymers and vesicles have received considerable attention in the recent mathematical and physical sciences literature. These are idealized geometric directed lattice models introduced to study phase behaviour in polymers, and include Dyck paths, partially directed paths, directed trees and directed vesicles models. Directed models are closely related to models studied in the combinatorics literature (and are often exactly solvable). They are also simplified versions of a number of statistical mechanics models, including the self-avoiding walk, lattice animals and lattice vesicles. The exchange of approaches and ideas between statistical mechanics and combinatorics have considerably advanced the description and understanding of directed lattice models, and this will be explored in this review. The combinatorial nature of directed lattice path models makes a study using generating function approaches most natural. In contrast, the statistical mechanics approach would introduce...
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.
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.
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.
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.
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.
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.
Zhang, Yufeng; Zhang, Xiangzhi; Wang, Yan; Liu, Jiangen
2017-01-01
With the help of R-matrix approach, we present the Toda lattice systems that have extensive applications in statistical physics and quantum physics. By constructing a new discrete integrable formula by R-matrix, the discrete expanding integrable models of the Toda lattice systems and their Lax pairs are generated, respectively. By following the constructing formula again, we obtain the corresponding (2+1)-dimensional Toda lattice systems and their Lax pairs, as well as their (2+1)-dimensional discrete expanding integrable models. Finally, some conservation laws of a (1+1)-dimensional generalised Toda lattice system and a new (2+1)-dimensional lattice system are generated, respectively.
A Unified Theory of Non-Ideal Gas Lattice Boltzmann Models
Luo, Li-Shi
1998-01-01
A non-ideal gas lattice Boltzmann model is directly derived, in an a priori fashion, from the Enskog equation for dense gases. The model is rigorously obtained by a systematic procedure to discretize the Enskog equation (in the presence of an external force) in both phase space and time. The lattice Boltzmann model derived here is thermodynamically consistent and is free of the defects which exist in previous lattice Boltzmann models for non-ideal gases. The existing lattice Boltzmann models for non-ideal gases are analyzed and compared with the model derived here.
Yamagata, Atsushi
1994-01-01
We perform the Monte Carlo simulations of the hard-sphere lattice gas on the simple cubic lattice with nearest neighbour exclusion. The critical activity is estimated, $z_{\\rm c} = 1.0588 \\pm 0.0003$. Using a relation between the hard-sphere lattice gas and the antiferromagnetic Ising model in an external magnetic field, we conclude that there is no re-entrant phase transition of the latter on the simple cubic lattice.
Topological defects on the lattice: I. The Ising model
Aasen, David; Mong, Roger S. K.; Fendley, Paul
2016-09-01
In this paper and its sequel, we construct topologically invariant defects in two-dimensional classical lattice models and quantum spin chains. We show how defect lines commute with the transfer matrix/Hamiltonian when they obey the defect commutation relations, cousins of the Yang-Baxter equation. These relations and their solutions can be extended to allow defect lines to branch and fuse, again with properties depending only on topology. In this part I, we focus on the simplest example, the Ising model. We define lattice spin-flip and duality defects and their branching, and prove they are topological. One useful consequence is a simple implementation of Kramers-Wannier duality on the torus and higher genus surfaces by using the fusion of duality defects. We use these topological defects to do simple calculations that yield exact properties of the conformal field theory describing the continuum limit. For example, the shift in momentum quantization with duality-twisted boundary conditions yields the conformal spin 1/16 of the chiral spin field. Even more strikingly, we derive the modular transformation matrices explicitly and exactly.
Overview: Understanding nucleation phenomena from simulations of lattice gas models
Binder, Kurt; Virnau, Peter
2016-12-01
Monte Carlo simulations of homogeneous and heterogeneous nucleation in Ising/lattice gas models are reviewed with an emphasis on the general insight gained on the mechanisms by which metastable states decay. Attention is paid to the proper distinction of particles that belong to a cluster (droplet), that may trigger a nucleation event, from particles in its environment, a problem crucial near the critical point. Well below the critical point, the lattice structure causes an anisotropy of the interface tension, and hence nonspherical droplet shapes result, making the treatment nontrivial even within the conventional classical theory of homogeneous nucleation. For temperatures below the roughening transition temperature facetted crystals rather than spherical droplets result. The possibility to find nucleation barriers from a thermodynamic analysis avoiding a cluster identification on the particle level is discussed, as well as the question of curvature corrections to the interfacial tension. For the interpretation of heterogeneous nucleation at planar walls, knowledge of contact angles and line tensions is desirable, and methods to extract these quantities from simulations will be mentioned. Finally, also the problem of nucleation near the stability limit of metastable states and the significance of the spinodal curve will be discussed, in the light of simulations of Ising models with medium range interactions.
Lattice Boltzmann modeling of water-like fluids
Sauro eSucci
2014-04-01
Full Text Available We review recent advances on the mesoscopic modeling of water-like fluids,based on the lattice Boltzmann (LB methodology.The main idea is to enrich the basic LB (hydro-dynamics with angular degrees of freedom responding to suitable directional potentials between water-like molecules.The model is shown to reproduce some microscopic features of liquid water, such as an average number of hydrogen bonds per molecules (HBs between $3$ and $4$, as well as a qualitatively correctstatistics of the hydrogen bond angle as a function of the temperature.Future developments, based on the coupling the present water-like LB model with the dynamics of suspended bodies,such as biopolymers, may open new angles of attack to the simulation of complex biofluidic problems, such as protein folding and aggregation, and the motion of large biomolecules in complex cellular environments.
Free Surface Lattice Boltzmann with Enhanced Bubble Model
Anderl, Daniela; Rauh, Cornelia; Rüde, Ulrich; Delgado, Antonio
2016-01-01
This paper presents an enhancement to the free surface lattice Boltzmann method (FSLBM) for the simulation of bubbly flows including rupture and breakup of bubbles. The FSLBM uses a volume of fluid approach to reduce the problem of a liquid-gas two-phase flow to a single-phase free surface simulation. In bubbly flows compression effects leading to an increase or decrease of pressure in the suspended bubbles cannot be neglected. Therefore, the free surface simulation is augmented by a bubble model that supplies the missing information by tracking the topological changes of the free surface in the flow. The new model presented here is capable of handling the effects of bubble breakup and coalesce without causing a significant computational overhead. Thus, the enhanced bubble model extends the applicability of the FSLBM to a new range of practically relevant problems, like bubble formation and development in chemical reactors or foaming processes.
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.
HTR Spherical Super Lattice Model for Equilibrium Fuel Cycle Analysis
Gray S. Cahng
2005-09-01
Advanced High Temperature gas-cooled Reactors (HTR) currently being developed (GFR, VHTR - Very High Temperature gas-cooled Reactor, PBMR, and GT-MHR) are able to achieve a simplification of safety through reliance on innovative features and passive systems. One of the innovative features in these HTRs is reliance on ceramic-coated fuel particles to retain the fission products even under extreme accident conditions. The effect of the random fuel kernel distribution in the fuel pebble / block is addressed through the use of the Dancoff correction factor in the resonance treatment. In addition, the Dancoff correction factor is a function of burnup and fuel kernel packing factor, which requires that the Dancoff correction factor be updated during Equilibrium Fuel Cycle (EqFC) analysis. Although HTR fuel is rather homogeneously dispersed in the fuel graphite matrix, the heterogeneity effects in between fuel kernels and pebbles cannot be ignored. The double-heterogeneous lattice model recently developed at the Idaho National Engineering and Environmental Laboratory (INEEL) contains tens of thousands of cubic fuel kernel cells, which makes it very difficult to deplete the fuel, kernel by kernel (KbK), for the EqFC analysis. In addition, it is not possible to preserve the cubic size and packing factor in a spherical fuel pebble. To avoid these difficulties, a newly developed and validated HTR pebble-bed Kernel-by-Kernel spherical (KbK-sph) model, has been developed and verified in this study. The objective of this research is to introduce the KbK-sph model and super whole Pebble lattice model (PLM). The verified double-heterogeneous KbK-sph and pebble homogeneous lattice model (HLM) are used for the fuel burnup chracteristics analysis and important safety parameters validation. This study summarizes and compares the KbK-sph and HLM burnup analyzed results. Finally, we discus the Monte-Carlo coupling with a fuel depletion and buildup code - Origen-2 as a fuel burnup
Self-similarity of phase-space networks of frustrated spin models and lattice gas models
Peng, Yi; Wang, Feng; Han, Yilong
2013-03-01
We studied the self-similar properties of the phase-spaces of two frustrated spin models and two lattice gas models. The frustrated spin models included (1) the anti-ferromagnetic Ising model on a two-dimensional triangular lattice (1a) at the ground states and (1b) above the ground states and (2) the six-vertex model. The two lattice gas models were (3) the one-dimensional lattice gas model and (4) the two-dimensional lattice gas model. The phase spaces were mapped to networks so that the fractal analysis of complex networks could be applied, i.e. the box-covering method and the cluster-growth method. These phase spaces, in turn, establish new classes of networks with unique self-similar properties. Models 1a, 2, and 3 with long-range power-law correlations in real space exhibit fractal phase spaces, while models 1b and 4 with short-range exponential correlations in real space exhibit nonfractal phase spaces. This behavior agrees with one of untested assumptions in Tsallis nonextensive statistics. Hong Kong GRC grants 601208 and 601911
Multiple flux difference effect in the lattice hydrodynamic model
Wang Tao; Gao Zi-You; Zhao Xiao-Mei
2012-01-01
Considering the effect of multiple flux difference,an extended lattice model is proposed to improve the stability of traffic flow.The stability condition of the new model is obtained by using linear stability theory.The theoretical analysis result shows that considering the flux difference effect ahead can stabilize traffic flow.The nonlinear analysis is also conducted by using a reductive perturbation method.The modified KdV (mKdV) equation near the critical point is derived and the kink-antikink solution is obtained from the mKdV equation.Numerical simulation results show that the multiple flux difference effect can suppress the traffic jam considerably,which is in line with the analytical result.
Lattice percolation approach to 3D modeling of tissue aging
Gorshkov, Vyacheslav; Privman, Vladimir; Libert, Sergiy
2016-11-01
We describe a 3D percolation-type approach to modeling of the processes of aging and certain other properties of tissues analyzed as systems consisting of interacting cells. Lattice sites are designated as regular (healthy) cells, senescent cells, or vacancies left by dead (apoptotic) cells. The system is then studied dynamically with the ongoing processes including regular cell dividing to fill vacant sites, healthy cells becoming senescent or dying, and senescent cells dying. Statistical-mechanics description can provide patterns of time dependence and snapshots of morphological system properties. The developed theoretical modeling approach is found not only to corroborate recent experimental findings that inhibition of senescence can lead to extended lifespan, but also to confirm that, unlike 2D, in 3D senescent cells can contribute to tissue's connectivity/mechanical stability. The latter effect occurs by senescent cells forming the second infinite cluster in the regime when the regular (healthy) cell's infinite cluster still exists.
Full Eulerian lattice Boltzmann model for conjugate heat transfer.
Hu, Yang; Li, Decai; Shu, Shi; Niu, Xiaodong
2015-12-01
In this paper a full Eulerian lattice Boltzmann model is proposed for conjugate heat transfer. A unified governing equation with a source term for the temperature field is derived. By introducing the source term, we prove that the continuity of temperature and its normal flux at the interface is satisfied automatically. The curved interface is assumed to be zigzag lines. All physical quantities are recorded and updated on a Cartesian grid. As a result, any complicated treatment near the interface is avoided, which makes the proposed model suitable to simulate the conjugate heat transfer with complex interfaces efficiently. The present conjugate interface treatment is validated by several steady and unsteady numerical tests, including pure heat conduction, forced convection, and natural convection problems. Both flat and curved interfaces are also involved. The obtained results show good agreement with the analytical and/or finite volume results.
Lattice model of reduced jamming by a barrier
Cirillo, Emilio N. M.; Krehel, Oleh; Muntean, Adrian; van Santen, Rutger
2016-10-01
We study an asymmetric simple exclusion process in a strip in the presence of a solid impenetrable barrier. We focus on the effect of the barrier on the residence time of the particles, namely, the typical time needed by the particles to cross the whole strip. We explore the conditions for reduced jamming when varying the environment (different drifts, reservoir densities, horizontal diffusion walks, etc.). In particular, we discover an interesting nonmonotonic behavior of the residence time as a function of the barrier length. Besides recovering by means of both the lattice dynamics and the mean-field model well-known aspects like the faster-is-slower effect and the intermittence of the flow, we propose also a birth-and-death process and a reduced one-dimensional (1D) model with variable barrier permeability to capture the behavior of the residence time with respect to the parameters.
Lie algebraic similarity transformed Hamiltonians for lattice model systems
Wahlen-Strothman, Jacob M.; Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Scuseria, Gustavo E.
2015-01-01
We present a class of Lie algebraic similarity transformations generated by exponentials of two-body on-site Hermitian operators whose Hausdorff series can be summed exactly without truncation. The correlators are defined over the entire lattice and include the Gutzwiller factor ni ↑ni ↓ , and two-site products of density (ni ↑+ni ↓) and spin (ni ↑-ni ↓) operators. The resulting non-Hermitian many-body Hamiltonian can be solved in a biorthogonal mean-field approach with polynomial computational cost. The proposed similarity transformation generates locally weighted orbital transformations of the reference determinant. Although the energy of the model is unbound, projective equations in the spirit of coupled cluster theory lead to well-defined solutions. The theory is tested on the one- and two-dimensional repulsive Hubbard model where it yields accurate results for small and medium sized interaction strengths.
Wall Orientation and Shear Stress in the Lattice Boltzmann Model
Matyka, Maciej; Mirosław, Łukasz
2013-01-01
The wall shear stress is a quantity of profound importance for clinical diagnosis of artery diseases. The lattice Boltzmann is an easily parallelizable numerical method of solving the flow problems, but it suffers from errors of the velocity field near the boundaries which leads to errors in the wall shear stress and normal vectors computed from the velocity. In this work we present a simple formula to calculate the wall shear stress in the lattice Boltzmann model and propose to compute wall normals, which are necessary to compute the wall shear stress, by taking the weighted mean over boundary facets lying in a vicinity of a wall element. We carry out several tests and observe an increase of accuracy of computed normal vectors over other methods in two and three dimensions. Using the scheme we compute the wall shear stress in an inclined and bent channel fluid flow and show a minor influence of the normal on the numerical error, implying that that the main error arises due to a corrupted velocity field near ...
Variable-lattice model of multi-component systems. 1. General consideration
Zakharov, A. Yu.; Schneider, A. A.; Udovsky, A. L.
2010-01-01
The paper contains a development of the previously proposed generalized lattice model (GLM). In contrast to usual lattice models, the difference of the specific atomic volumes of the components is taken in account in GLM. In addition to GLM, the dependence of the specific atomic volumes on local atomic environments taken into account in new variable-lattice model (VLM). Thermodynamic functions of multi-component homogeneous phases in the VLM are obtained. Equations of equilibrium between gase...
Contact angles in the pseudopotential lattice Boltzmann modeling of wetting.
Li, Qing; Luo, K H; Kang, Q J; Chen, Q
2014-11-01
In this paper we investigate the implementation of contact angles in the pseudopotential lattice Boltzmann modeling of wetting at a large density ratio ρ_{L}/ρ_{V}=500. The pseudopotential lattice Boltzmann model [X. Shan and H. Chen, Phys. Rev. E 49, 2941 (1994)10.1103/PhysRevE.49.2941] is a popular mesoscopic model for simulating multiphase flows and interfacial dynamics. In this model the contact angle is usually realized by a fluid-solid interaction. Two widely used fluid-solid interactions, the density-based interaction and the pseudopotential-based interaction, as well as a modified pseudopotential-based interaction formulated in the present paper are numerically investigated and compared in terms of the achievable contact angles, the maximum and the minimum densities, and the spurious currents. It is found that the pseudopotential-based interaction works well for simulating small static (liquid) contact angles θstatic contact angles close to 180^{∘}. Meanwhile, it is found that the proposed modified pseudopotential-based interaction performs better in light of the maximum and the minimum densities and is overall more suitable for simulating large contact angles θ>90^{∘} as compared with the two other types of fluid-solid interactions. Furthermore, the spurious currents are found to be enlarged when the fluid-solid interaction force is introduced. Increasing the kinematic viscosity ratio between the vapor and liquid phases is shown to be capable of reducing the spurious currents caused by the fluid-solid interactions.
Lattice Boltzmann modeling of three-phase incompressible flows
Liang, H.; Shi, B. C.; Chai, Z. H.
2016-01-01
In this paper, based on multicomponent phase-field theory we intend to develop an efficient lattice Boltzmann (LB) model for simulating three-phase incompressible flows. In this model, two LB equations are used to capture the interfaces among three different fluids, and another LB equation is adopted to solve the flow field, where a new distribution function for the forcing term is delicately designed. Different from previous multiphase LB models, the interfacial force is not used in the computation of fluid velocity, which is more reasonable from the perspective of the multiscale analysis. As a result, the computation of fluid velocity can be much simpler. Through the Chapman-Enskog analysis, it is shown that the present model can recover exactly the physical formulations for the three-phase system. Numerical simulations of extensive examples including two circular interfaces, ternary spinodal decomposition, spreading of a liquid lens, and Kelvin-Helmholtz instability are conducted to test the model. It is found that the present model can capture accurate interfaces among three different fluids, which is attributed to its algebraical and dynamical consistency properties with the two-component model. Furthermore, the numerical results of three-phase flows agree well with the theoretical results or some available data, which demonstrates that the present LB model is a reliable and efficient method for simulating three-phase flow problems.
Lattice hydrodynamic model based traffic control: A transportation cyber-physical system approach
Liu, Hui; Sun, Dihua; Liu, Weining
2016-11-01
Lattice hydrodynamic model is a typical continuum traffic flow model, which describes the jamming transition of traffic flow properly. Previous studies in lattice hydrodynamic model have shown that the use of control method has the potential to improve traffic conditions. In this paper, a new control method is applied in lattice hydrodynamic model from a transportation cyber-physical system approach, in which only one lattice site needs to be controlled in this control scheme. The simulation verifies the feasibility and validity of this method, which can ensure the efficient and smooth operation of the traffic flow.
A (reactive) lattice-gas approach to economic cycles
Ausloos, Marcel; Clippe, Paulette; Miśkiewicz, Janusz; Peķalski, Andrzej
2004-12-01
A microscopic approach to macroeconomic features is intended. A model for macroeconomic behavior under heterogeneous spatial economic conditions is reviewed. A birth-death lattice gas model taking into account the influence of an economic environment on the fitness and concentration evolution of economic entities is numerically and analytically examined. The reaction-diffusion model can also be mapped onto a high-order logistic map. The role of the selection pressure along various dynamics with entity diffusion on a square symmetry lattice has been studied by Monte-Carlo simulation. The model leads to a sort of phase transition for the fitness gap as a function of the selection pressure and to cycles. The control parameter is a (scalar) “business plan”. The business plan(s) allows for spin-offs or merging and enterprise survival evolution law(s), whence bifurcations, cycles and chaotic behavior.
Lattice Boltzmann models for the grain growth in polycrystalline systems
Yonggang Zheng
2016-08-01
Full Text Available In the present work, lattice Boltzmann models are proposed for the computer simulation of normal grain growth in two-dimensional systems with/without immobile dispersed second-phase particles and involving the temperature gradient effect. These models are demonstrated theoretically to be equivalent to the phase field models based on the multiscale expansion. Simulation results of several representative examples show that the proposed models can effectively and accurately simulate the grain growth in various single- and two-phase systems. It is found that the grain growth in single-phase polycrystalline materials follows the power-law kinetics and the immobile second-phase particles can inhibit the grain growth in two-phase systems. It is further demonstrated that the grain growth can be tuned by the second-phase particles and the introduction of temperature gradient is also an effective way for the fabrication of polycrystalline materials with grained gradient microstructures. The proposed models are useful for the numerical design of the microstructure of materials and provide effective tools to guide the experiments. Moreover, these models can be easily extended to simulate two- and three-dimensional grain growth with considering the mobile second-phase particles, transient heat transfer, melt convection, etc.
Lattice Boltzmann models for the grain growth in polycrystalline systems
Zheng, Yonggang; Chen, Cen; Ye, Hongfei; Zhang, Hongwu
2016-08-01
In the present work, lattice Boltzmann models are proposed for the computer simulation of normal grain growth in two-dimensional systems with/without immobile dispersed second-phase particles and involving the temperature gradient effect. These models are demonstrated theoretically to be equivalent to the phase field models based on the multiscale expansion. Simulation results of several representative examples show that the proposed models can effectively and accurately simulate the grain growth in various single- and two-phase systems. It is found that the grain growth in single-phase polycrystalline materials follows the power-law kinetics and the immobile second-phase particles can inhibit the grain growth in two-phase systems. It is further demonstrated that the grain growth can be tuned by the second-phase particles and the introduction of temperature gradient is also an effective way for the fabrication of polycrystalline materials with grained gradient microstructures. The proposed models are useful for the numerical design of the microstructure of materials and provide effective tools to guide the experiments. Moreover, these models can be easily extended to simulate two- and three-dimensional grain growth with considering the mobile second-phase particles, transient heat transfer, melt convection, etc.
Ghosh, Pushpita; Sen, Shrabani; Riaz, Syed Shahed; Ray, Deb Shankar
2009-05-01
The photosensitive chlorine dioxide-iodine-malonic acid reaction-diffusion system has been an experimental paradigm for the study of Turing pattern over the last several years. When subjected to illumination of varied intensity by visible light the patterns undergo changes from spots to stripes, vice versa, and their mixture. We carry out a nonlinear analysis of the underlying model in terms of a Galerkin scheme with finite number of modes to explore the nature of the stability and existence of various modes responsible for the type and crossover of the light-induced patterns.
Dongfang Li
2014-01-01
Full Text Available This paper is concerned with the stability of non-Fickian reaction-diffusion equations with a variable delay. It is shown that the perturbation of the energy function of the continuous problems decays exponentially, which provides a more accurate and convenient way to express the rate of decay of energy. Then, we prove that the proposed numerical methods are sufficient to preserve energy stability of the continuous problems. We end the paper with some numerical experiments on a biological model to confirm the theoretical results.
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.
Felicia Shirly Peace
2014-01-01
Full Text Available A mathematical model of the dynamics of the self-ignition of a reaction-diffusion system is studied in this paper. An approximate analytical method (modified Adomian decomposition method is used to solve nonlinear differential equations under steady-state condition. Analytical expressions for concentrations of the gas reactant and the temperature have been derived for Lewis number (Le and parameters β, γ, and ϕ2. Furthermore, in this work, the numerical simulation of the problem is also reported using MATLAB program. An agreement between analytical and numerical results is noted.
Turing pattern formation in the chlorine dioxide-iodine- malonic acid reaction-diffusion system
Setayeshgar, Sima
The formation of localized structures in the chlorine dioxide-idodine-malonic acid (CDIMA) reaction-diffusion system is investigated numerically using a realistic model of this system. We analyze the one-dimensional patterns formed along the gradients imposed by boundary feeds, and study their linear stability to symmetry- breaking perturbations (the Turing instability) in the plane transverse to these gradients. We establish that an often-invoked simple local linear analysis which neglects longitudinal diffusion is inappropriate for predicting the linear stability of these patterns. Using a fully nonuniform analysis, we investigate the structure of the patterns formed along the gradients and their stability to transverse Turing pattern formation as a function of the values of two control parameters: the malonic acid feed concentration and the size of the reactor in the dimension along the gradients. The results from this investigation are compared with existing experimental results. We also verify that the two-variable reduction of the chemical model employed in the linear stability analysis is justified. Finally, we present numerical solution of the CDIMA system in two dimensions which is in qualitative agreement with experiments. This result also confirms our linear stability analysis, while demonstrating the feasibility of numerical exploration of realistic chemical models.
The two-regime method for optimizing stochastic reaction-diffusion simulations
Flegg, M. B.
2011-10-19
Spatial organization and noise play an important role in molecular systems biology. In recent years, a number of software packages have been developed for stochastic spatio-temporal simulation, ranging from detailed molecular-based approaches to less detailed compartment-based simulations. Compartment-based approaches yield quick and accurate mesoscopic results, but lack the level of detail that is characteristic of the computationally intensive molecular-based models. Often microscopic detail is only required in a small region (e.g. close to the cell membrane). Currently, the best way to achieve microscopic detail is to use a resource-intensive simulation over the whole domain. We develop the two-regime method (TRM) in which a molecular-based algorithm is used where desired and a compartment-based approach is used elsewhere. We present easy-to-implement coupling conditions which ensure that the TRM results have the same accuracy as a detailed molecular-based model in the whole simulation domain. Therefore, the TRM combines strengths of previously developed stochastic reaction-diffusion software to efficiently explore the behaviour of biological models. Illustrative examples and the mathematical justification of the TRM are also presented.
Fourier spectral methods for fractional-in-space reaction-diffusion equations
Bueno-Orovio, Alfonso
2014-04-01
© 2014, Springer Science+Business Media Dordrecht. Fractional differential equations are becoming increasingly used as a powerful modelling approach for understanding the many aspects of nonlocality and spatial heterogeneity. However, the numerical approximation of these models is demanding and imposes a number of computational constraints. In this paper, we introduce Fourier spectral methods as an attractive and easy-to-code alternative for the integration of fractional-in-space reaction-diffusion equations described by the fractional Laplacian in bounded rectangular domains of ℝ. The main advantages of the proposed schemes is that they yield a fully diagonal representation of the fractional operator, with increased accuracy and efficiency when compared to low-order counterparts, and a completely straightforward extension to two and three spatial dimensions. Our approach is illustrated by solving several problems of practical interest, including the fractional Allen–Cahn, FitzHugh–Nagumo and Gray–Scott models, together with an analysis of the properties of these systems in terms of the fractional power of the underlying Laplacian operator.
Topological Lattice Actions for the 2d XY Model
Bietenholz, W; Niedermayer, F; Pepe, M; Rejón-Barrera, F G; Wiese, U -J
2012-01-01
We consider the 2d XY Model with topological lattice actions, which are invariant against small deformations of the field configuration. These actions constrain the angle between neighbouring spins by an upper bound, or they explicitly suppress vortices (and anti-vortices). Although topological actions do not have a classical limit, they still lead to the universal behaviour of the Berezinskii-Kosterlitz-Thouless (BKT) phase transition - at least up to moderate vortex suppression. Thus our study underscores the robustness of universality, which persists even when basic principles of classical physics are violated. In the massive phase, the analytically known Step Scaling Function (SSF) is reproduced in numerical simulations. In the massless phase, the BKT value of the critical exponent eta_c is confirmed. Hence, even though for some topological actions vortices cost zero energy, they still drive the standard BKT transition. In addition we identify a vortex-free transition point, which deviates from the BKT be...
Superconductivity of heavy fermions in the Kondo lattice model
Sykora, Steffen [IFW Dresden (Germany); Becker, Klaus W. [Institut fuer Theoretische Physik, Technische Universitaet Dresden (Germany)
2015-07-01
Understanding of the origin of superconductivity in strongly correlated electron systems is one of the basic unresolved problems in physics. Examples for such systems are the cuprates and also the heavy-fermion metals, which are compounds with 4f and 5f electrons. In all these materials the superconducting pairing interaction is often believed to be predominantly mediated by spin fluctuations and not by phonons as in normal metals. For the Kondo-lattice model we present results, which are derived within the Projective Renormalization Method (PRM). Based on a recent study of the one-particle spectral function for the normal state we first derive an effective Hamiltonian which describes heavy fermion quasiparticle bands close to the Fermi surface. An extension to the superconducting phase leads to d-wave solutions for the superconducting order parameter in agreement with recent STM measurements.
Modeling of metal foaming with lattice Boltzmann automata
Koerner, C.; Thies, M.; Singer, R.F. [WTM Institute, Department of Materials Science, University of Erlangen, Martensstrasse 5, D-91058 Erlangen (Germany)
2002-10-01
The formation and decay of foams produced by gas bubble expansion in a molten metal is numerically simulated with the Lattice Boltzmann Method (LBM) which belongs to the cellular automaton techniques. The present state of the two dimensional model allows the investigation of the foam evolution process comprising bubble expansion, bubble coalescence, drainage, and eventually foam collapse. Examples demonstrate the influence of the surface tension, viscosity and gravity on the foaming process and the resulting cell structure. In addition, the potential of the LBM to solve problems with complex boundary conditions is illustrated by means of a foam developing within the constraints of a mould as well as a foaming droplet exposed to gravity. (Abstract Copyright [2002], Wiley Periodicals, Inc.)
Phase transition with an isospin dependent lattice gas model
Gulminelli, F. [Caen Univ., 14 (France). Lab. de Physique Corpusculaire; Chomaz, Ph. [Grand Accelerateur National d`Ions Lourds (GANIL), 14 - Caen (France)
1998-10-01
The nuclear liquid-gas phase transition is studied within an isospin dependent Lattice Gas Model in the canonical ensemble. Finite size effects on thermodynamical variables are analyzed by a direct calculation of the partition function, and it is shown that phase coexistence and phase transition are relevant concepts even for systems of a few tens of particles. Critical exponents are extracted from the behaviour of the fragment production yield as a function of temperature by means of a finite size scaling. The result is that in a finite system well defined critical signals can be found at supercritical (Kertesz line) as well as subcritical densities. For isospin asymmetric systems it is shown that, besides the modification of the critical temperature, isotopic distributions can provide an extra observable to identify and characterize the transition. (author) 21 refs.
Exact diagonalization of quantum lattice models on coprocessors
Siro, T.; Harju, A.
2016-10-01
We implement the Lanczos algorithm on an Intel Xeon Phi coprocessor and compare its performance to a multi-core Intel Xeon CPU and an NVIDIA graphics processor. The Xeon and the Xeon Phi are parallelized with OpenMP and the graphics processor is programmed with CUDA. The performance is evaluated by measuring the execution time of a single step in the Lanczos algorithm. We study two quantum lattice models with different particle numbers, and conclude that for small systems, the multi-core CPU is the fastest platform, while for large systems, the graphics processor is the clear winner, reaching speedups of up to 7.6 compared to the CPU. The Xeon Phi outperforms the CPU with sufficiently large particle number, reaching a speedup of 2.5.
Quantum Monte Carlo methods algorithms for lattice models
Gubernatis, James; Werner, Philipp
2016-01-01
Featuring detailed explanations of the major algorithms used in quantum Monte Carlo simulations, this is the first textbook of its kind to provide a pedagogical overview of the field and its applications. The book provides a comprehensive introduction to the Monte Carlo method, its use, and its foundations, and examines algorithms for the simulation of quantum many-body lattice problems at finite and zero temperature. These algorithms include continuous-time loop and cluster algorithms for quantum spins, determinant methods for simulating fermions, power methods for computing ground and excited states, and the variational Monte Carlo method. Also discussed are continuous-time algorithms for quantum impurity models and their use within dynamical mean-field theory, along with algorithms for analytically continuing imaginary-time quantum Monte Carlo data. The parallelization of Monte Carlo simulations is also addressed. This is an essential resource for graduate students, teachers, and researchers interested in ...
Lattice gauge theory of three dimensional Thirring model
Kim, S; Kim, Seyong; Kim, Yoonbai
1999-01-01
Three dimensional Thirring model with N four-component Dirac fermions, reformulated as a lattice gauge theory, is studied by computer simulation. According to an 8^{3} data and preliminary 16^3 data, chiral symmetry is found to be spontaneously broken for N=2,\\;4 and 6. N=2 data exhibits long tail of the non-vanishing chiral condensate into weak coupling region, and N=6 case shows phase separation between the strong coupling region and the weak coupling region. Although the comparison between 8^3 data and 16^3 data shows large finite volume effects, an existence of the critical fermion flavor number N_{{\\rm cr}} (2
A new approach for modelling lattice energy in finite crystal domains
Bilotsky, Y.; Gasik, M.
2015-09-01
Evaluation of internal energy in a crystal lattice requires precise calculation of lattice sums. Such evaluation is a problem in the case of small (nano) particles because the traditional methods are usually effective only for infinite lattices and are adapted to certain specific potentials. In this work, a new method has been developed for calculation of lattice energy. The method is a generalisation of conventional geometric probability techniques for arbitrary fixed lattices in a finite crystal domain. In our model, the lattice energy for wide range of two- body central interaction potentials (including long-range Coulomb potential) has been constructed using absolutely convergent sums. No artificial cut-off potential or periodical extension of the domain (which usually involved for such calculations) have been made for calculation of the lattice energy under this approach. To exemplify the applications of these techniques, the energy of Coulomb potential has been plotted as the function of the domain size.
Critical phenomena in the majority voter model on two-dimensional regular lattices.
Acuña-Lara, Ana L; Sastre, Francisco; Vargas-Arriola, José Raúl
2014-05-01
In this work we studied the critical behavior of the critical point as a function of the number of nearest neighbors on two-dimensional regular lattices. We performed numerical simulations on triangular, hexagonal, and bilayer square lattices. Using standard finite-size scaling theory we found that all cases fall in the two-dimensional Ising model universality class, but that the critical point value for the bilayer lattice does not follow the regular tendency that the Ising model shows.
Critical Behavior of Gaussian Model on X Fractal Lattices in External Magnetic Fields
LI Ying; KONG Xiang-Mu; HUANG Jia-Yin
2003-01-01
Using the renormalization group method, the critical behavior of Gaussian model is studied in external magnetic fields on X fractal lattices embedded in two-dimensional and d-dimensional (d ＞ 2) Euclidean spaces, respectively. Critical points and exponents are calculated. It is found that there is long-range order at finite temperature for this model, and that the critical points do not change with the space dimensionality d (or the fractal dimensionality dr). It is also found that the critical exponents are very different from results of Ising model on the same lattices, and that the exponents on X lattices are different from the exact results on translationally symmetric lattices.
Kumada, H; Saito, K; Nakamura, T; Sakae, T; Sakurai, H; Matsumura, A; Ono, K
2011-12-01
Treatment planning for boron neutron capture therapy generally utilizes Monte-Carlo methods for calculation of the dose distribution. The new treatment planning system JCDS-FX employs the multi-purpose Monte-Carlo code PHITS to calculate the dose distribution. JCDS-FX allows to build a precise voxel model consisting of pixel based voxel cells in the scale of 0.4×0.4×2.0 mm(3) voxel in order to perform high-accuracy dose estimation, e.g. for the purpose of calculating the dose distribution in a human body. However, the miniaturization of the voxel size increases calculation time considerably. The aim of this study is to investigate sophisticated modeling methods which can perform Monte-Carlo calculations for human geometry efficiently. Thus, we devised a new voxel modeling method "Multistep Lattice-Voxel method," which can configure a voxel model that combines different voxel sizes by utilizing the lattice function over and over. To verify the performance of the calculation with the modeling method, several calculations for human geometry were carried out. The results demonstrated that the Multistep Lattice-Voxel method enabled the precise voxel model to reduce calculation time substantially while keeping the high-accuracy of dose estimation.
Classical Logic and Quantum Logic with Multiple and Common Lattice Models
Mladen Pavičić
2016-01-01
Full Text Available We consider a proper propositional quantum logic and show that it has multiple disjoint lattice models, only one of which is an orthomodular lattice (algebra underlying Hilbert (quantum space. We give an equivalent proof for the classical logic which turns out to have disjoint distributive and nondistributive ortholattices. In particular, we prove that both classical logic and quantum logic are sound and complete with respect to each of these lattices. We also show that there is one common nonorthomodular lattice that is a model of both quantum and classical logic. In technical terms, that enables us to run the same classical logic on both a digital (standard, two-subset, 0-1-bit computer and a nondigital (say, a six-subset computer (with appropriate chips and circuits. With quantum logic, the same six-element common lattice can serve us as a benchmark for an efficient evaluation of equations of bigger lattice models or theorems of the logic.
Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems
Daniele D’Agostino
2014-01-01
Full Text Available There is an increasing awareness of the pivotal role of noise in biochemical processes and of the effect of molecular crowding on the dynamics of biochemical systems. This necessity has given rise to a strong need for suitable and sophisticated algorithms for the simulation of biological phenomena taking into account both spatial effects and noise. However, the high computational effort characterizing simulation approaches, coupled with the necessity to simulate the models several times to achieve statistically relevant information on the model behaviours, makes such kind of algorithms very time-consuming for studying real systems. So far, different parallelization approaches have been deployed to reduce the computational time required to simulate the temporal dynamics of biochemical systems using stochastic algorithms. In this work we discuss these aspects for the spatial TAU-leaping in crowded compartments (STAUCC simulator, a voxel-based method for the stochastic simulation of reaction-diffusion processes which relies on the Sτ-DPP algorithm. In particular we present how the characteristics of the algorithm can be exploited for an effective parallelization on the present heterogeneous HPC architectures.
Parallel solutions for voxel-based simulations of reaction-diffusion systems.
D'Agostino, Daniele; Pasquale, Giulia; Clematis, Andrea; Maj, Carlo; Mosca, Ettore; Milanesi, Luciano; Merelli, Ivan
2014-01-01
There is an increasing awareness of the pivotal role of noise in biochemical processes and of the effect of molecular crowding on the dynamics of biochemical systems. This necessity has given rise to a strong need for suitable and sophisticated algorithms for the simulation of biological phenomena taking into account both spatial effects and noise. However, the high computational effort characterizing simulation approaches, coupled with the necessity to simulate the models several times to achieve statistically relevant information on the model behaviours, makes such kind of algorithms very time-consuming for studying real systems. So far, different parallelization approaches have been deployed to reduce the computational time required to simulate the temporal dynamics of biochemical systems using stochastic algorithms. In this work we discuss these aspects for the spatial TAU-leaping in crowded compartments (STAUCC) simulator, a voxel-based method for the stochastic simulation of reaction-diffusion processes which relies on the Sτ-DPP algorithm. In particular we present how the characteristics of the algorithm can be exploited for an effective parallelization on the present heterogeneous HPC architectures.
Parallel Solutions for Voxel-Based Simulations of Reaction-Diffusion Systems
D'Agostino, Daniele; Pasquale, Giulia; Clematis, Andrea; Maj, Carlo; Mosca, Ettore; Milanesi, Luciano; Merelli, Ivan
2014-01-01
There is an increasing awareness of the pivotal role of noise in biochemical processes and of the effect of molecular crowding on the dynamics of biochemical systems. This necessity has given rise to a strong need for suitable and sophisticated algorithms for the simulation of biological phenomena taking into account both spatial effects and noise. However, the high computational effort characterizing simulation approaches, coupled with the necessity to simulate the models several times to achieve statistically relevant information on the model behaviours, makes such kind of algorithms very time-consuming for studying real systems. So far, different parallelization approaches have been deployed to reduce the computational time required to simulate the temporal dynamics of biochemical systems using stochastic algorithms. In this work we discuss these aspects for the spatial TAU-leaping in crowded compartments (STAUCC) simulator, a voxel-based method for the stochastic simulation of reaction-diffusion processes which relies on the Sτ-DPP algorithm. In particular we present how the characteristics of the algorithm can be exploited for an effective parallelization on the present heterogeneous HPC architectures. PMID:25045716
李新政; 白占国; 李燕; 贺亚峰; 赵昆
2015-01-01
The resonance interaction between two modes is investigated using a two-layer coupled Brusselator model. When two different wavelength modes satisfy resonance conditions, new modes will appear, and a variety of superlattice patterns can be obtained in a short wavelength mode subsystem. We find that even though the wavenumbers of two Turing modes are fixed, the parameter changes have infl uences on wave intensity and pattern selection. When a hexagon pattern occurs in the short wavelength mode layer and a stripe pattern appears in the long wavelength mode layer, the Hopf instability may happen in a nonlinearly coupled model, and twinkling-eye hexagon and travelling hexagon patterns will be obtained. The symmetries of patterns resulting from the coupled modes may be different from those of their parents, such as the cluster hexagon pattern and square pattern. With the increase of perturbation and coupling intensity, the nonlinear system will con-vert between a static pattern and a dynamic pattern when the Turing instability and Hopf instability happen in the nonlinear system. Besides the wavenumber ratio and intensity ratio of the two different wavelength Turing modes, perturbation and coupling intensity play an important role in the pattern formation and selection. According to the simulation results, we find that two modes with different symmetries can also be in the spatial resonance under certain conditions, and complex patterns appear in the two-layer coupled reaction diffusion systems.
Highly covariant quantum lattice gas model of the Dirac equation
Yepez, Jeffrey
2011-01-01
We revisit the quantum lattice gas model of a spinor quantum field theory-the smallest scale particle dynamics is partitioned into unitary collide and stream operations. The construction is covariant (on all scales down to a small length {\\ell} and small time {\\tau} = c {\\ell}) with respect to Lorentz transformations. The mass m and momentum p of the modeled Dirac particle depend on {\\ell} according to newfound relations m = mo cos (2{\\pi}{\\ell}/{\\lambda}) and p = (h/2{\\pi}{\\ell}) sin(2{\\pi}{\\ell}/{\\lambda}), respectively, where {\\lambda} is the Compton wavelength of the modeled particle. These relations represent departures from a relativistically invariant mass and the de Broglie relation-when taken as quantifying numerical errors the model is physically accurate when {\\ell} {\\ll} {\\lambda}. Calculating the vacuum energy in the special case of a massless spinor field, we find that it vanishes (or can have a small positive value) for a sufficiently large wave number cutoff. This is a marked departure from th...
MILES FORMULAE FOR BOOLEAN MODELS OBSERVED ON LATTICES
Joachim Ohser
2011-05-01
Full Text Available The densities of the intrinsic volumes – in 3D the volume density, surface density, the density of the integral of the mean curvature and the density of the Euler number – are a very useful collection of geometric characteristics of random sets. Combining integral and digital geometry we develop a method for efficient and simultaneous calculation of the intrinsic volumes of random sets observed in binary images in arbitrary dimensions. We consider isotropic and reflection invariant Boolean models sampled on homogeneous lattices and compute the expectations of the estimators of the intrinsic volumes. It turns out that the estimator for the surface density is proved to be asymptotically unbiased and thusmultigrid convergent for Boolean models with convex grains. The asymptotic bias of the estimators for the densities of the integral of the mean curvature and of the Euler number is assessed for Boolean models of balls of random diameters. Miles formulae with corresponding correction terms are derived for the 3D case.
Bursting regimes in a reaction-diffusion system with action potential-dependent equilibrium.
Stephen R Meier
Full Text Available The equilibrium Nernst potential plays a critical role in neural cell dynamics. A common approximation used in studying electrical dynamics of excitable cells is that the ionic concentrations inside and outside the cell membranes act as charge reservoirs and remain effectively constant during excitation events. Research into brain electrical activity suggests that relaxing this assumption may provide a better understanding of normal and pathophysiological functioning of the brain. In this paper we explore time-dependent ionic concentrations by allowing the ion-specific Nernst potentials to vary with developing transmembrane potential. As a specific implementation, we incorporate the potential-dependent Nernst shift into a one-dimensional Morris-Lecar reaction-diffusion model. Our main findings result from a region in parameter space where self-sustaining oscillations occur without external forcing. Studying the system close to the bifurcation boundary, we explore the vulnerability of the system with respect to external stimulations which disrupt these oscillations and send the system to a stable equilibrium. We also present results for an extended, one-dimensional cable of excitable tissue tuned to this parameter regime and stimulated, giving rise to complex spatiotemporal pattern formation. Potential applications to the emergence of neuronal bursting in similar two-variable systems and to pathophysiological seizure-like activity are discussed.
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.
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.
Bau, Haim; Liu, Changchun; Killawala, Chitvan; Sadik, Mohamed; Mauk, Michael
2014-11-01
Real-time amplification and quantification of specific nucleic acid sequences plays a major role in many medical and biotechnological applications. In the case of infectious diseases, quantification of the pathogen-load in patient specimens is critical to assessing disease progression, effectiveness of drug therapy, and emergence of drug-resistance. Typically, nucleic acid quantification requires sophisticated and expensive instruments, such as real-time PCR machines, which are not appropriate for on-site use and for low resource settings. We describe a simple, low-cost, reactiondiffusion based method for end-point quantification of target nucleic acids undergoing enzymatic amplification. The number of target molecules is inferred from the position of the reaction-diffusion front, analogous to reading temperature in a mercury thermometer. We model the process with the Fisher Kolmogoroff Petrovskii Piscounoff (FKPP) Equation and compare theoretical predictions with experimental observations. The proposed method is suitable for nucleic acid quantification at the point of care, compatible with multiplexing and high-throughput processing, and can function instrument-free. C.L. was supported by NIH/NIAID K25AI099160; M.S. was supported by the Pennsylvania Ben Franklin Technology Development Authority; C.K. and H.B. were funded, in part, by NIH/NIAID 1R41AI104418-01A1.
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.
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.
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.
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...
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.
Normal thermal conduction in lattice models with asymmetric harmonic interparticle interactions
Zhong Yi; Zhang Yong; Wang Jiao; Zhao Hong
2013-01-01
We study the thermal conduction behaviors of one-dimensional lattice models with asymmetric harmonic interparticle interactions.Normal thermal conductivity that is independent of system size is observed when the lattice chains are long enough.Because only the harmonic interactions are involved,the result confirms,without ambiguity,that asymmetry plays a key role in normal thermal conduction in one-dimensional momentum conserving lattices.Both equilibrium and nonequilibrium simulations are performed to support the conclusion.
Different models of gravitating Dirac fermions in optical lattices
Celi, Alessio
2017-07-01
In this paper I construct the naive lattice Dirac Hamiltonian describing the propagation of fermions in a generic 2D optical metric for different lattice and flux-lattice geometries. First, I apply a top-down constructive approach that we first proposed in [Boada et al., New J. Phys. 13, 035002 (2011)] to the honeycomb and to the brickwall lattices. I carefully discuss how gauge transformations that generalize momentum (and Dirac cone) shifts in the Brillouin zone in the Minkowski homogeneous case can be used in order to change the phases of the hopping. In particular, I show that lattice Dirac Hamiltonian for Rindler spacetime in the honeycomb and brickwall lattices can be realized by considering real and isotropic (but properly position dependent) tunneling terms. For completeness, I also discuss a suitable formulation of Rindler Dirac Hamiltonian in semi-synthetic brickwall and π-flux square lattices (where one of the dimension is implemented by using internal spin states of atoms as we originally proposed in [Boada et al., Phys. Rev. Lett. 108, 133001 (2012)] and [Celi et al., Phys. Rev. Lett. 112, 043001 (2014)]).
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.
Lattice Boltzmann modeling of directional wetting: Comparing simulations to experiments
Jansen, H. Patrick; Sotthewes, Kai; van Swigchem, Jeroen; Zandvliet, Harold J. W.; Kooij, E. Stefan
2013-07-01
Lattice Boltzmann Modeling (LBM) simulations were performed on the dynamic behavior of liquid droplets on chemically striped patterned surfaces, ultimately with the aim to develop a predictive tool enabling reliable design of future experiments. The simulations accurately mimic experimental results, which have shown that water droplets on such surfaces adopt an elongated shape due to anisotropic preferential spreading. Details of the contact line motion such as advancing of the contact line in the direction perpendicular to the stripes exhibit pronounced similarities in experiments and simulations. The opposite of spreading, i.e., evaporation of water droplets, leads to a characteristic receding motion first in the direction parallel to the stripes, while the contact line remains pinned perpendicular to the stripes. Only when the aspect ratio is close to unity, the contact line also starts to recede in the perpendicular direction. Very similar behavior was observed in the LBM simulations. Finally, droplet movement can be induced by a gradient in surface wettability. LBM simulations show good semiquantitative agreement with experimental results of decanol droplets on a well-defined striped gradient, which move from high- to low-contact angle surfaces. Similarities and differences for all systems are described and discussed in terms of the predictive capabilities of LBM simulations to model direction wetting.
Multiple-relaxation-time lattice Boltzmann kinetic model for combustion.
Xu, Aiguo; Lin, Chuandong; Zhang, Guangcai; Li, Yingjun
2015-04-01
To probe both the hydrodynamic nonequilibrium (HNE) and thermodynamic nonequilibrium (TNE) in the combustion process, a two-dimensional multiple-relaxation-time (MRT) version of lattice Boltzmann kinetic model (LBKM) for combustion phenomena is presented. The chemical energy released in the progress of combustion is dynamically coupled into the system by adding a chemical term to the LB kinetic equation. Aside from describing the evolutions of the conserved quantities, the density, momentum, and energy, which are what the Navier-Stokes model describes, the MRT-LBKM presents also a coarse-grained description on the evolutions of some nonconserved quantities. The current model works for both subsonic and supersonic flows with or without chemical reaction. In this model, both the specific-heat ratio and the Prandtl number are flexible, the TNE effects are naturally presented in each simulation step. The model is verified and validated via well-known benchmark tests. As an initial application, various nonequilibrium behaviors, including the complex interplays between various HNEs, between various TNEs, and between the HNE and TNE, around the detonation wave in the unsteady and steady one-dimensional detonation processes are preliminarily probed. It is found that the system viscosity (or heat conductivity) decreases the local TNE, but increases the global TNE around the detonation wave, that even locally, the system viscosity (or heat conductivity) results in two kinds of competing trends, to increase and to decrease the TNE effects. The physical reason is that the viscosity (or heat conductivity) takes part in both the thermodynamic and hydrodynamic responses.
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.
Van Enter, A C D
2003-01-01
We consider various sufficiently nonlinear sigma models for nematic ordering of RP^{N-1} type and of lattice gauge type with continous symmetries. We rigorously show that they exhibit a first-order transition in the temperature. The result holds in dimension 2 or more for the RP{N-1} models and in dimension 3 or more for the lattice gauge models. In the two-dimensional case our results clarify and solve a recent controversy about the possibilty of such transitions. For lattice gauge models our methods provide the first prof of a first-order transition in a model with a continous gauge symmetry.
Exact Maps in Density Functional Theory for Lattice Models
Dimitrov, Tanja; Fuks, Johanna I; Rubio, Angel
2015-01-01
In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and for the first time the exact density-to-wavefunction map that underly the Hohenberg-Kohn theorem in density functional theory. Having the explicit wavefunction-to- density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragmen...
Random surfaces, solvable lattice models and discrete quantum gravity in two dimensions
Kostov, I.K. (CEA Centre d' Etudes Nucleaires de Saclay, 91 - Gif-sur-Yvette (France). Service de Physique Theorique)
1989-07-01
We give a review of the analytical results concerning dynamically triangulated surfaces and statistical models on a planar random lattice. The critical behaviour of these models is described by conformal field theories coupled to 2d quantum gravity. (orig.).
Spin-flux phase in the Kondo lattice model with classical localized spins
Agterberg, DF; Yunoki, S
2000-01-01
We provide numerical evidence that a spin-flux phase exists as a ground state of the Kondo lattice model with classical local spins on a square lattice. This state manifests itself as a double-e magnetic order in the classical spins with spin density at both (0, pi) and (pi ,0) and further exhibits
Ruban, Andrei; Simak, S.I.; Shallcross, S.;
2003-01-01
We present a simple effective tetrahedron model for local lattice relaxation effects in random metallic alloys on simple primitive lattices. A comparison with direct ab initio calculations for supercells representing random Ni0.50Pt0.50 and Cu0.25Au0.75 alloys as well as the dilute limit of Au...
Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations
Flegga, Mark B.; Hellander, Stefan; Erban, Radek
2015-01-01
In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is called the ghost cell method (GCM), since it works by constructing a “ghost cell” in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step Δt (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter h, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: (i) Δt → 0 and h is fixed; (ii) Δt → 0 and h → 0 such that √Δt/h is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model. PMID:26568640
New mechanism of spiral wave initiation in a reaction-diffusion-mechanics system.
Louis D Weise
Full Text Available Spiral wave initiation in the heart muscle is a mechanism for the onset of dangerous cardiac arrhythmias. A standard protocol for spiral wave initiation is the application of a stimulus in the refractory tail of a propagating excitation wave, a region that we call the "classical vulnerable zone." Previous studies of vulnerability to spiral wave initiation did not take the influence of deformation into account, which has been shown to have a substantial effect on the excitation process of cardiomyocytes via the mechano-electrical feedback phenomenon. In this work we study the effect of deformation on the vulnerability of excitable media in a discrete reaction-diffusion-mechanics (dRDM model. The dRDM model combines FitzHugh-Nagumo type equations for cardiac excitation with a discrete mechanical description of a finite-elastic isotropic material (Seth material to model cardiac excitation-contraction coupling and stretch activated depolarizing current. We show that deformation alters the "classical," and forms a new vulnerable zone at longer coupling intervals. This mechanically caused vulnerable zone results in a new mechanism of spiral wave initiation, where unidirectional conduction block and rotation directions of the consequently initiated spiral waves are opposite compared to the mechanism of spiral wave initiation due to the "classical vulnerable zone." We show that this new mechanism of spiral wave initiation can naturally occur in situations that involve wave fronts with curvature, and discuss its relation to supernormal excitability of cardiac tissue. The concept of mechanically induced vulnerability may lead to a better understanding about the onset of dangerous heart arrhythmias via mechano-electrical feedback.
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....
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.
Study of the Antiferromagnetic Blume-Capel Model on kagomé Lattice
Hwang, Chi-Ok; Park, Sojeong; Kwak, Wooseop
2016-09-01
We study the anti-ferromagnetic (AF) Ising model and the AF Blume-Capel (BC) model on the kagomé lattice. Using the Wang-Landau sampling method, we estimate the joint density functions for both models on the lattice, and we obtain the exact critical magnetic fields at zero temperature by using the micro-canonical analysis. We also show the patterns of critical lines for the models from micro-canonical analysis.
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.
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.
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.
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].
Immiscible multicomponent lattice Boltzmann model for fluids with high relaxation time ratio
Tao Jiang; Qiwei Gong; Ruofan Qiu; Anlin Wang
2014-10-01
An immiscible multicomponent lattice Boltzmann model is developed for fluids with high relaxation time ratios, which is based on the model proposed by Shan and Chen (SC). In the SC model, an interaction potential between particles is incorporated into the discrete lattice Boltzmann equation through the equilibrium velocity. Compared to the SC model, external forces in our model are discretized directly into the discrete lattice Boltzmann equation, as proposed by Guo et al. We develop it into a new multicomponent lattice Boltzmann (LB) model which has the ability to simulate immiscible multicomponent fluids with relaxation time ratio as large as 29.0 and to reduce `spurious velocity’. In this work, the improved model is validated and studied using the central bubble case and the rising bubble case. It finds good applications in both static and dynamic cases for multicomponent simulations with different relaxation time ratios.
Heat Transport Behaviour in One-Dimensional Lattice Models with Damping
ZHU Heng-Jiang; ZHANG Yong; ZHAO Hong
2004-01-01
@@ We investigate the heat transport behaviours of two typical lattice models, the Fermi-Pasta-Ulam-β model and the φ4 lattice model, in the presence of damping which imitates the effect of the thermal radiation and the thermal diffusion to the surroundings through the sample boundary. It is found that the damping does not affect the thermal conductivity, but can change the heat flux dumped into the lattice chain. We also discuss possible applications under the heuristic guidance of our numerical results. In particular, we suggest a way to measure the thermal conductivity experimentally in the presence of large energy loss arisen from the radiation and the diffusion.
Symmetries of 2-lattices and second order accuracy of the Cauchy--Born Model
Van Koten, Brian
2012-01-01
We show that the Cauchy--Born model of a single-species 2-lattice is second order if the atomistic and continuum kinematics are connected in a novel way. Our proof uses a generalization to 2-lattices of the point symmetry of Bravais lattices. Moreover, by identifying similar symmetries in multi-species pair interaction models, we construct a new stored energy density, using shift-gradients but not strain gradients, that is also second order accurate. These results can be used to develop highly accurate continuum models and atomistic/continuum coupling methods for materials such as graphene, hcp metals, and shape memory alloys.
Lund, Halvor; Simonsen, Ingve
2012-01-01
We review and introduce a generalized reaction-diffusion approach to epidemic spreading in a metapopulation modeled as a complex network. The metapopulation consists of susceptible and infected individuals that are grouped in subpopulations symbolising cities and villages that are coupled by human travel in a transportation network. By analytic methods and numerical simulations we calculate the fraction of infected people in the metaopoluation in the long time limit, as well as the relevant parameters characterising the epidemic threshold that separates an epidemic from a non-epidemic phase. Within this model, we investigate the effect of a heterogeneous network topology and a heterogeneous subpopulation size distribution. Such a system is suited for epidemic modeling where small villages and big cities exist simultaneously in the metapopulation. We find that the heterogeneous conditions cause the epidemic threshold to be a non-trivial function of the reaction rates (local parameters), the network's topology ...
Adam, A. M. A.; Bashier, E. B. M.; Hashim, M. H. A.; Patidar, K. C.
2017-07-01
In this work, we design and analyze a fitted numerical method to solve a reaction-diffusion model with time delay, namely, a delayed version of a population model which is an extension of the logistic growth (LG) equation for a food-limited population proposed by Smith [F.E. Smith, Population dynamics in Daphnia magna and a new model for population growth, Ecology 44 (1963) 651-663]. Seeing that the analytical solution (in closed form) is hard to obtain, we seek for a robust numerical method. The method consists of a Fourier-pseudospectral semi-discretization in space and a fitted operator implicit-explicit scheme in temporal direction. The proposed method is analyzed for convergence and we found that it is unconditionally stable. Illustrative numerical results will be presented at the conference.
Protein-lipid interactions in bilayer membranes: a lattice model.
Pink, D A; Chapman, D
1979-04-01
A lattice model has been developed to study the effects of intrinsic membrane proteins upon the thermodynamic properties of a lipid bilayer membrane. We assume that only nearest-neighbor van der Waals and steric interactions are important and that the polar group interactions can be represented by effective pressure-area terms. Phase diagrams, the temperature T(0), which locates the gel-fluid melting, the transition enthalpy, and correlations were calculated by mean field and cluster approximations. Average lipid chain areas and chain areas when the lipid is in a given protein environment were obtained. Proteins that have a "smooth" homogeneous surface ("cholesterol-like") and those that have inhomogeneous surfaces or that bind lipids specifically were considered. We find that T(0) can vary depending upon the interactions and that another peak can appear upon the shoulder of the main peak which reflects the melting of a eutectic mixture. The transition enthalpy decreases generally, as was found before, but when a second peak appears departures from this behavior reflect aspects of the eutectic mixture. We find that proteins have significant nonzero probabilities for being adjacent to one another so that no unbroken "annulus" of lipid necessarily exists around a protein. If T(0) does not increase much, or decreases, with increasing c, then lipids adjacent to a protein cannot all be all-trans on the time scale (10(-7) sec) of our system. Around a protein the lipid correlation depth is about one lipid layer, and this increases with c. Possible consequences of ignoring changes in polar group interactions due to clustering of proteins are discussed.
Exact maps in density functional theory for lattice models
Dimitrov, Tanja; Appel, Heiko; Fuks, Johanna I.; Rubio, Angel
2016-08-01
In the present work, we employ exact diagonalization for model systems on a real-space lattice to explicitly construct the exact density-to-potential and graphically illustrate the complete exact density-to-wavefunction map that underly the Hohenberg-Kohn theorem in density functional theory. Having the explicit wavefunction-to-density map at hand, we are able to construct arbitrary observables as functionals of the ground-state density. We analyze the density-to-potential map as the distance between the fragments of a system increases and the correlation in the system grows. We observe a feature that gradually develops in the density-to-potential map as well as in the density-to-wavefunction map. This feature is inherited by arbitrary expectation values as functional of the ground-state density. We explicitly show the excited-state energies, the excited-state densities, and the correlation entropy as functionals of the ground-state density. All of them show this exact feature that sharpens as the coupling of the fragments decreases and the correlation grows. We denominate this feature as intra-system steepening and discuss how it relates to the well-known inter-system derivative discontinuity. The inter-system derivative discontinuity is an exact concept for coupled subsystems with degenerate ground state. However, the coupling between subsystems as in charge transfer processes can lift the degeneracy. An important conclusion is that for such systems with a near-degenerate ground state, the corresponding cut along the particle number N of the exact density functionals is differentiable with a well-defined gradient near integer particle number.
Masuda, Hiroshi; Okubo, Tsuyoshi; Kawamura, Hikaru
2012-08-03
Motivated by the recent experiment on kagome-lattice antiferromagnets, we study the zero-field ordering behavior of the antiferromagnetic classical Heisenberg model on a uniaxially distorted kagome lattice by Monte Carlo simulations. A first-order transition, which has no counterpart in the corresponding undistorted model, takes place at a very low temperature. The origin of the transition is ascribed to a cooperative proliferation of topological excitations inherent to the model.
Hallock, Michael J; Stone, John E; Roberts, Elijah; Fry, Corey; Luthey-Schulten, Zaida
2014-05-01
Simulation of in vivo cellular processes with the reaction-diffusion master equation (RDME) is a computationally expensive task. Our previous software enabled simulation of inhomogeneous biochemical systems for small bacteria over long time scales using the MPD-RDME method on a single GPU. Simulations of larger eukaryotic systems exceed the on-board memory capacity of individual GPUs, and long time simulations of modest-sized cells such as yeast are impractical on a single GPU. We present a new multi-GPU parallel implementation of the MPD-RDME method based on a spatial decomposition approach that supports dynamic load balancing for workstations containing GPUs of varying performance and memory capacity. We take advantage of high-performance features of CUDA for peer-to-peer GPU memory transfers and evaluate the performance of our algorithms on state-of-the-art GPU devices. We present parallel e ciency and performance results for simulations using multiple GPUs as system size, particle counts, and number of reactions grow. We also demonstrate multi-GPU performance in simulations of the Min protein system in E. coli. Moreover, our multi-GPU decomposition and load balancing approach can be generalized to other lattice-based problems.
Ma, Y.G.
2000-01-01
The emission of clusters in the nuclear disassembly is investigated within the framework of isospin dependent lattice gas model and classical molecular dynamics model. As observed in the recent experimental data, it is found that the emission of individual cluster is poissonian and thermal scaling is observed in the linear Arrhenius plots made from the average multiplicity of each cluster. The mass, isotope and charge dependent "emission barriers" are extracted from the slopes of the Arrheniu...
Monte Carlo simulation of quantum statistical lattice models
Raedt, Hans De; Lagendijk, Ad
1985-01-01
In this article we review recent developments in computational methods for quantum statistical lattice problems. We begin by giving the necessary mathematical basis, the generalized Trotter formula, and discuss the computational tools, exact summations and Monte Carlo simulation, that will be used t
Li, Xiaoqin; Fang, Kangling; Peng, Guanghan
2017-02-01
In real traffic, aggressive driving behaviors often occurs by anticipating the front density of the next-nearest lattice site at next time step to adjust their acceleration in advance. Therefore, a new lattice model is put forward by considering the driver's aggressive effect (DAE). The linear stability condition is derived from the linear stability theory and the modified KdV equation near the critical point is obtained through nonlinear analysis with the consideration of aggressive driving behaviors, respectively. Both the analytical results and numerical simulation indicate that the driver's aggressive effect can increase the traffic stability. Thus driver's aggressive effect should be considered in traffic lattice model.
Molecular mobility with respect to accessible volume in Monte Carlo lattice model for polymers
Diani, J.; Gilormini, P.
2017-02-01
A three-dimensional cubic Monte Carlo lattice model is considered to test the impact of volume on the molecular mobility of amorphous polymers. Assuming classic polymer chain dynamics, the concept of locked volume limiting the accessible volume around the polymer chains is introduced. The polymer mobility is assessed by its ability to explore the entire lattice thanks to reptation motions. When recording the polymer mobility with respect to the lattice accessible volume, a sharp mobility transition is observed as witnessed during glass transition. The model ability to reproduce known actual trends in terms of glass transition with respect to material parameters, is also tested.
ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.
Johannes Schöneberg
Full Text Available We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.
Finite Lattice Hamiltonian Computations in the P-Representation the Schwinger Model
Aroca, J M; Alvarez-Campot, G; Alvarez-Campot, Gonzalo
1999-01-01
The Schwinger model is studied in a finite lattice by means of the P-representation. The vacuum energy, mass gap and chiral condensate are evaluated showing good agreement with the expected values in the continuum limit.
Finite Lattice Hamiltonian Computations in the P-Representation: the Schwinger Model
1997-01-01
The Schwinger model is studied in a finite lattice by means of the P-representation. The vacuum energy, mass gap and chiral condensate are evaluated showing good agreement with the expected values in the continuum limit.
Lattice Boltzmann model for the perfect gas flows with near-vacuum region
GuangwuYAN; LiYUAN
2000-01-01
It is known that the standard lattice Boltzmann method has near-vacuum limit,i. e., when the density is near zero, this method is invalid. In this letter, we propose a simple lattice Boltzmann model for one-dimensional flows. It possesses the ability of simulating nearvacuum area by setting a limitation of the relaxation factor. Thus, the model overcomes the disadvantage of non-physical pressure and the density. The numerical examples show these results are satisfactory.
An exact solution on the ferromagnetic Face-Cubic spin model on a Bethe lattice
Ohanyan, V. R.; Ananikyan, L. N.; Ananikian, N. S.
2006-01-01
The lattice spin model with $Q$--component discrete spin variables restricted to have orientations orthogonal to the faces of $Q$-dimensional hypercube is considered on the Bethe lattice, the recursive graph which contains no cycles. The partition function of the model with dipole--dipole and quadrupole--quadrupole interaction for arbitrary planar graph is presented in terms of double graph expansions. The latter is calculated exactly in case of trees. The system of two recurrent relations wh...
A nonlinear lattice model for Heisenberg helimagnet and spin wave instabilities
Ludvin Felcy, A.; Latha, M. M.; Christal Vasanthi, C.
2016-10-01
We study the dynamics of a Heisenberg helimagnet by presenting a square lattice model and proposing the Hamiltonian associated with it. The corresponding equation of motion is constructed after averaging the Hamiltonian using a suitable wavefunction. The stability of the spin wave is discussed by means of Modulational Instability (MI) analysis. The influence of various types of inhomogeneities in the lattice is also investigated by improving the model.
Tensor renormalization group approach to two-dimensional classical lattice models.
Levin, Michael; Nave, Cody P
2007-09-21
We describe a simple real space renormalization group technique for two-dimensional classical lattice models. The approach is similar in spirit to block spin methods, but at the same time it is fundamentally based on the theory of quantum entanglement. In this sense, the technique can be thought of as a classical analogue of the density matrix renormalization group method. We demonstrate the method - which we call the tensor renormalization group method - by computing the magnetization of the triangular lattice Ising model.
A Lattice Boltzmann Model and Simulation of KdV-Burgers Equation
ZHANGChao-Ying; TANHui-Li; LIUMu-Ren; KONGLing-Jiang
2004-01-01
A lattice Boltzmann model of KdV-Burgers equation is derived by using the single-relaxation form of the lattice Boltzmann equation. With the present model, we simulate the traveling-wave solutions, the solitary-wave solutions, and the sock-wave solutions of KdV-Burgers equation, and calculate the decay factor and the wavelength of the sock-wave solution, which has exponential decay. The numerical results agree with the analytical solutions quite well.
A New Lattice Boltzmann Model for KdV-Burgers Equation
MA Chang-Feng
2005-01-01
@@ A new lattice Boltzmann model with amending-function for KdV-Burgers equation, ut +uux - αuxx +βuxxx = 0,is presented by using the single-relaxation form of the lattice Boltzmann equation. Applying the proposed model,we simulate the solutions ofa kind of KdV-Burgers equations, and the numerical results agree with the analytical solutions quite well.
Ground-state diagrams for lattice-gas models of catalytic CO oxidation
I.S.Bzovska
2007-01-01
Full Text Available Based on simple lattice models of catalytic carbon dioxide synthesis from oxygen and carbon monoxide, phase diagrams are investigated at temperature T=0 by incorporating the nearest-neighbor interactions on a catalyst surface. The main types of ground-state phase diagrams of two lattice models are classified describing the cases of clean surface and surface containing impurities. Nonuniform phases are obtained and the conditions of their existence dependent on the interaction parameters are established.
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.
Gray S. Chang
2005-11-01
The currently being developed advanced High Temperature gas-cooled Reactors (HTR) is able to achieve a simplification of safety through reliance on innovative features and passive systems. One of the innovative features in these HTRs is reliance on ceramic-coated fuel particles to retain the fission products even under extreme accident conditions. Traditionally, the effect of the random fuel kernel distribution in the fuel pebble / block is addressed through the use of the Dancoff correction factor in the resonance treatment. However, the Dancoff correction factor is a function of burnup and fuel kernel packing factor, which requires that the Dancoff correction factor be updated during Equilibrium Fuel Cycle (EqFC) analysis. An advanced KbK-sph model and whole pebble super lattice model (PSLM), which can address and update the burnup dependent Dancoff effect during the EqFC analysis. The pebble homogeneous lattice model (HLM) is verified by the burnup characteristics with the double-heterogeneous KbK-sph lattice model results. This study summarizes and compares the KbK-sph lattice model and HLM burnup analyzed results. Finally, we discuss the Monte-Carlo coupling with a fuel depletion and buildup code - ORIGEN-2 as a fuel burnup analysis tool and its PSLM calculated results for the HTR EqFC burnup analysis.
The high density phase of the k-NN hard core lattice gas model
Nath, Trisha; Rajesh, R.
2016-07-01
The k-NN hard core lattice gas model on a square lattice, in which the first k next nearest neighbor sites of a particle are excluded from being occupied by another particle, is the lattice version of the hard disc model in two dimensional continuum. It has been conjectured that the lattice model, like its continuum counterpart, will show multiple entropy-driven transitions with increasing density if the high density phase has columnar or striped order. Here, we determine the nature of the phase at full packing for k up to 820 302 . We show that there are only eighteen values of k, all less than k = 4134, that show columnar order, while the others show solid-like sublattice order.
Pattern formation in a two-component reaction-diffusion system with delayed processes on a network
Petit, Julien; Asllani, Malbor; Fanelli, Duccio; Lauwens, Ben; Carletti, Timoteo
2016-11-01
Reaction-diffusion systems with time-delay defined on complex networks have been studied in the framework of the emergence of Turing instabilities. The use of the Lambert W-function allowed us to get explicit analytic conditions for the onset of patterns as a function of the main involved parameters, the time-delay, the network topology and the diffusion coefficients. Depending on these parameters, the analysis predicts whether the system will evolve towards a stationary Turing pattern or rather to a wave pattern associated to a Hopf bifurcation. The possible outcomes of the linear analysis overcome the respective limitations of the single-species case with delay, and that of the classical activator-inhibitor variant without delay. Numerical results gained from the Mimura-Murray model support the theoretical approach.
Fernandes, Ryan I
2012-01-01
An alternating direction implicit (ADI) orthogonal spline collocation (OSC) method is described for the approximate solution of a class of nonlinear reaction-diffusion systems. Its efficacy is demonstrated on the solution of well-known examples of such systems, specifically the Brusselator, Gray-Scott, Gierer-Meinhardt and Schnakenberg models, and comparisons are made with other numerical techniques considered in the literature. The new ADI method is based on an extrapolated Crank-Nicolson OSC method and is algebraically linear. It is efficient, requiring at each time level only $O({\\cal N})$ operations where ${\\cal N}$ is the number of unknowns. Moreover,it is shown to produce approximations which are of optimal global accuracy in various norms, and to possess superconvergence properties.
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.
Sato, Makoto; Yasugi, Tetsuo; Minami, Yoshiaki; Miura, Takashi; Nagayama, Masaharu
2016-08-30
Notch-mediated lateral inhibition regulates binary cell fate choice, resulting in salt and pepper patterns during various developmental processes. However, how Notch signaling behaves in combination with other signaling systems remains elusive. The wave of differentiation in the Drosophila visual center or "proneural wave" accompanies Notch activity that is propagated without the formation of a salt and pepper pattern, implying that Notch does not form a feedback loop of lateral inhibition during this process. However, mathematical modeling and genetic analysis clearly showed that Notch-mediated lateral inhibition is implemented within the proneural wave. Because partial reduction in EGF signaling causes the formation of the salt and pepper pattern, it is most likely that EGF diffusion cancels salt and pepper pattern formation in silico and in vivo. Moreover, the combination of Notch-mediated lateral inhibition and EGF-mediated reaction diffusion enables a function of Notch signaling that regulates propagation of the wave of differentiation.
A Lattice Boltzmann Model of Binary Fluid Mixture
Orlandini, E; Yeomans, J M; Orlandini, Enzo; Swift, Michael R.
1995-01-01
We introduce a lattice Boltzmann for simulating an immiscible binary fluid mixture. Our collision rules are derived from a macroscopic thermodynamic description of the fluid in a way motivated by the Cahn-Hilliard approach to non-equilibrium dynamics. This ensures that a thermodynamically consistent state is reached in equilibrium. The non-equilibrium dynamics is investigated numerically and found to agree with simple analytic predictions in both the one-phase and the two-phase region of the phase diagram.
Efficient Lattice-Based Signcryption in Standard Model
Jianhua Yan; Licheng Wang; Lihua Wang; Yixian Yang; Wenbin Yao
2013-01-01
Signcryption is a cryptographic primitive that can perform digital signature and public encryption simultaneously at a significantly reduced cost. This advantage makes it highly useful in many applications. However, most existing signcryption schemes are seriously challenged by the booming of quantum computations. As an interesting stepping stone in the post-quantum cryptographic community, two lattice-based signcryption schemes were proposed recently. But both of them were merely proved to b...
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.
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.
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.