The finite volume spectral element method to solve Turing models in the biological pattern formation

It is well known that reaction-diffusion systems describing Turing models can display very rich pattern formation behavior. Turing systems have been proposed for pattern formation in various biological systems, e.g. patterns in fish, butterflies, lady bugs and etc. A Turing model expresses temporal behavior of the concentrations of two reacting and diffusing chemicals which is represented by coupled reaction-diffusion equations. Since the base of these reaction-diffusion equations arises from the conservation laws, we develop a hybrid finite volume spectral element method for the numerical solution of them and apply the proposed method to Turing system generated by the Schnakenberg model. Also, as numerical simulations, we study the variety of spatio-temporal patterns for various values of diffusion rates in the problem.

[1]  K. S. Erduran,et al.  Performance of finite volume solutions to the shallow water equations with shock‐capturing schemes , 2002 .

[2]  Mehdi Dehghan,et al.  Time-splitting procedures for the solution of the two-dimensional transport equation , 2007, Kybernetes.

[3]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[4]  Manuel Doblaré,et al.  Appearance and location of secondary ossification centres may be explained by a reaction-diffusion mechanism , 2009, Comput. Biol. Medicine.

[5]  G. Dewel,et al.  Fluctuations near nonequilibrium phase transitions to nonuniform states , 1980 .

[6]  E. Marwil,et al.  Convergence Results for Schubert’s Method for Solving Sparse Nonlinear Equations , 1979 .

[7]  P. Oliveira ON THE NUMERICAL IMPLEMENTATION OF NONLINEAR VISCOELASTIC MODELS IN A FINITE-VOLUME METHOD , 2001 .

[8]  P. Maini,et al.  Unravelling the Turing bifurcation using spatially varying diffusion coefficients , 1998 .

[9]  H. Meinhardt,et al.  A theory of biological pattern formation , 1972, Kybernetik.

[10]  V. Selmin,et al.  The node-centred finite volume approach: bridge between finite differences and finite elements , 1993 .

[11]  J. Verwer,et al.  Numerical solution of time-dependent advection-diffusion-reaction equations , 2003 .

[12]  Rui Peng,et al.  Qualitative analysis of steady states to the Sel'kov model , 2007 .

[13]  S. Muzaferija,et al.  NUMERICAL METHOD FOR HEAT TRANSFER, FLUID FLOW, AND STRESS ANALYSIS IN PHASE-CHANGE PROBLEMS , 2002 .

[14]  Richard E. Ewing,et al.  Element Approximations of Nonlocal in Time One � dimensional Flows in Porous Media , 1998 .

[15]  Hans Meinhardt,et al.  The Algorithmic Beauty of Sea Shells , 1998, The Virtual Laboratory.

[16]  C. Canuto Spectral methods in fluid dynamics , 1991 .

[17]  M. Dehghan,et al.  A finite volume spectral element method for solving magnetohydrodynamic (MHD) equations , 2011 .

[18]  Michael J. Ward,et al.  Numerical Challenges for Resolving Spike Dynamics for Two One‐Dimensional Reaction‐Diffusion Systems , 2003 .

[19]  Ya-Xiang Yuan,et al.  On the Quadratic Convergence of the Levenberg-Marquardt Method without Nonsingularity Assumption , 2005, Computing.

[20]  F. S. Prout Philosophical Transactions of the Royal Society of London , 2009, The London Medical Journal.

[21]  H. Meinhardt,et al.  A model for pattern formation on the shells of molluscs , 1987 .

[22]  R. Lazarov,et al.  Finite volume element approximations of nonlocal reactive flows in porous media , 2000 .

[23]  J. Schnakenberg,et al.  Simple chemical reaction systems with limit cycle behaviour. , 1979, Journal of theoretical biology.

[24]  A. M. Turing,et al.  The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

[25]  Chenghu Zhou,et al.  Simulating the hydraulic characteristics of the lower Yellow River by the finite‐volume technique , 2002 .

[26]  P. Maini,et al.  Turing patterns in fish skin? , 1996, Nature.

[27]  D. Marquardt An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .

[28]  J. Boissonade,et al.  Turing-type chemical patterns in the chlorite-iodide-malonic acid reaction , 1991 .

[29]  Zhiqiang Cai,et al.  On the finite volume element method , 1990 .

[30]  N. Rashevsky,et al.  Mathematical biology , 1961, Connecticut medicine.

[31]  Mehdi Dehghan,et al.  On the solution of an initial‐boundary value problem that combines Neumann and integral condition for the wave equation , 2005 .

[32]  Dulos,et al.  Experimental evidence of a sustained standing Turing-type nonequilibrium chemical pattern. , 1990, Physical review letters.

[33]  Jianfeng Zhu,et al.  Application of Discontinuous Galerkin Methods for Reaction-Diffusion Systems in Developmental Biology , 2009, J. Sci. Comput..

[34]  Kenneth Levenberg A METHOD FOR THE SOLUTION OF CERTAIN NON – LINEAR PROBLEMS IN LEAST SQUARES , 1944 .

[35]  J. Brandts [Review of: W. Hundsdorfer, J.G. Verwer (2003) Numerical Solution of Time-Dependent Advection-Diffusion-Reaction Equations] , 2006 .

[36]  Andrew J. Wathen,et al.  A moving grid finite element method applied to a model biological pattern generator , 2003 .

[37]  Ian Turner,et al.  A heterogeneous wood drying computational model that accounts for material property variation across growth rings , 2002 .

[38]  Guy Dewel,et al.  Three-dimensional dissipative structures in reaction-diffusion systems , 1992 .

[39]  Edmund J. Crampin,et al.  Mode Transitions in a Model Reaction–Diffusion System Driven by Domain Growth and Noise , 2006, Bulletin of mathematical biology.

[40]  Ian Turner,et al.  A SECOND ORDER CONTROL-VOLUME FINITE-ELEMENT LEAST-SQUARES STRATEGY FOR SIMULATING DIFFUSION IN STRONGLY ANISOTROPIC MEDIA 1) , 2005 .

[41]  I. Prigogine,et al.  Symmetry Breaking Instabilities in Dissipative Systems. II , 1968 .

[42]  I. Epstein,et al.  Modeling of Turing Structures in the Chlorite—Iodide—Malonic Acid—Starch Reaction System , 1991, Science.

[43]  Mehdi Dehghan,et al.  Finite difference procedures for solving a problem arising in modeling and design of certain optoelectronic devices , 2006, Math. Comput. Simul..

[44]  Ching-Long Lin,et al.  An Unstructured Finite Volume Approach for Structural Dynamics in Response to Fluid Motions. , 2008, Computers & structures.

[45]  Stephen K. Scott,et al.  Autocatalytic reactions in the isothermal, continuous stirred tank reactor: Isolas and other forms of multistability , 1983 .

[46]  B. R. Baliga,et al.  Evaluation and Enhancements of Some Control Volume Finite-Element Methods - Part 2. Incompressible Fluid Flow Problems , 1988 .

[47]  Carl Tim Kelley,et al.  Iterative methods for optimization , 1999, Frontiers in applied mathematics.

[48]  Weeratunge Malalasekera,et al.  An introduction to computational fluid dynamics - the finite volume method , 2007 .

[49]  Teemu Leppänen,et al.  Computational studies of pattern formation in Turing systems , 2004 .

[50]  H. Meinhardt Models of biological pattern formation , 1982 .

[51]  S. Kondo,et al.  A reaction–diffusion wave on the skin of the marine angelfish Pomacanthus , 1995, Nature.

[52]  J. Murray,et al.  A minimal mechanism for bacterial pattern formation , 1999, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[53]  Andrew J. Wathen,et al.  A Moving Grid Finite Element Method for the Simulation of Pattern Generation by Turing Models on Growing Domains , 2005, J. Sci. Comput..

[54]  William F. Mitchell,et al.  Optimal Multilevel Iterative Methods for Adaptive Grids , 1992, SIAM J. Sci. Comput..

[55]  M. Fukushima,et al.  On the Rate of Convergence of the Levenberg-Marquardt Method , 2001 .

[56]  W. C. Gardiner,et al.  Transition from Branching‐Chain Kinetics to Partial Equilibrium in the Combustion of Lean Hydrogen‐Oxygen Mixtures in Shock Waves , 1968 .

[57]  C. Bailey,et al.  Discretisation procedures for multi-physics phenomena , 1999 .

[58]  Panagiotis Chatzipantelidis,et al.  A finite volume method based on the Crouzeix–Raviart element for elliptic PDE's in two dimensions , 1999, Numerische Mathematik.

[59]  Endre Süli Convergence of finite volume schemes for Poisson's equation on nonuniform meshes , 1991 .

[60]  C. Chan,et al.  Solution of incompressible flows with or without a free surface using the finite volume method on unstructured triangular meshes , 1999 .

[61]  Mehdi Dehghan,et al.  A numerical method for solution of the two-dimensional sine-Gordon equation using the radial basis functions , 2008, Math. Comput. Simul..

[62]  Vaughan R Voller,et al.  Streamline Upwind Scheme for Control-Volume Finite Elements, Part II. Implementation and Comparison with the Supg Finite-Element Scheme , 1992 .

[63]  M. Rodriguez-Ricard,et al.  Multiscale analysis for diffusion-driven neutrally stable states , 2009, Math. Comput. Model..

[64]  JayanthaPasdunkoraleA. A SECOND ORDER CONTROL-VOLUME FINITE-ELEMENT LEAST-SQUARES STRATEGY FOR SIMULATING DIFFUSION IN STRONGLY ANISOTROPIC MEDIA , 2005 .

[65]  A two-dimensional finite volume method for transient simulation of time- and scale-dependent transport in heterogeneous aquifer systems , 2003 .

[66]  E. Sel'kov,et al.  Self-oscillations in glycolysis. 1. A simple kinetic model. , 1968, European journal of biochemistry.

[67]  B. R. Baliga,et al.  EVALUATION AND ENHANCEMENTS OF SOME CONTROL VOLUME FINITE-ELEMENT METHODS—PART 1. CONVECTION-DIFFUSION PROBLEMS , 1988 .

[68]  T. Vicsek,et al.  Generic modelling of cooperative growth patterns in bacterial colonies , 1994, Nature.

[69]  Vaughan R Voller,et al.  STREAMLINE UPWIND SCHEME FOR CONTROL-VOLUME FINITE ELEMENTS, PART I. FORMULATIONS , 1992 .

[70]  Guy Dewel,et al.  Competition in ramped Turing structures , 1992 .

[71]  J. Murray,et al.  On pattern formation mechanisms for lepidopteran wing patterns and mammalian coat markings. , 1981, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.