×

A robust and efficient method for steady state patterns in reaction-diffusion systems. (English) Zbl 1250.35017

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

MSC:

35A35 Theoretical approximation in context of PDEs
35K57 Reaction-diffusion equations
65M12 Stability and convergence of numerical methods for initial value and initial-boundary value problems involving PDEs
35K51 Initial-boundary value problems for second-order parabolic systems
35B36 Pattern formations in context of PDEs

Software:

iFEM
Full Text: DOI

References:

[1] Baker, R. E.; Gaffney, E. A.; Maini, P. K., Partial differential equations for self-organization in cellular and developmental biology, Nonlinearity, 21, R251-R290 (2008) · Zbl 1159.35003
[2] Epstein, I. R.; Bansagi, T.; Vanag, V. K., Tomography of reaction-diffusion microemulsions reveals three-dimensional Turing patterns, Science, 331, 1309-1312 (2011) · Zbl 1226.35075
[3] Jilkine, A.; Edelstein-Keshet, L., A comparison of mathematical models for polarization of single eukaryotic cells in response to guided cues, PLoS Computational Biology, 7, e1001121 (2011)
[4] Murray, J. D., Mathematical Biology (2002), Springer Verlag: Springer Verlag New York · Zbl 1006.92001
[5] Park, H. O.; Bi, E. F., Central roles of small GTPases in the development of cell polarity in yeast and beyond, Microbiology and Molecular Biology Reviews, 71, 48-96 (2007)
[6] Pearson, J. E., Complex patterns in a simple system, Science, 261, 189-192 (1993)
[7] Dillon, R.; Maini, P. K.; Othmer, H. G., Pattern formation in generalized Turing systems I. Steady-state patterns in systems with mixed boundary condition, Journal of Mathematical Biology, 32, 345-393 (1994) · Zbl 0829.92001
[8] Maini, P. K.; Myerscough, M. R., Boundary-driven instability, Applied Mathematics Letters, 10, 1, 1-4 (1997) · Zbl 0886.35075
[9] Turing, A. M., The chemical basis of morphogenesis, Philosophical Transactions of the Royal Society of London Series B-Biological Sciences, 237, 37-72 (1952) · Zbl 1403.92034
[10] Goryachev, A. B.; Pokhilko, A. V., Dynamics of Cdc42 network embodies a Turing-type mechanism of yeast cell polarity, FEBS Letters, 582, 1437-1443 (2008)
[11] Lew, D. J.; Howell, A. S.; Savage, N. S.; Johnson, S. A.; Bose, I.; Wagner, A. W.; Zyla, T. R.; Nijhout, H. F.; Reed, M. C.; Goryachev, A. B., Singularity in polarization: rewiring yeast cells to make two buds, Cell, 139, 731-743 (2009)
[12] Meinhardt, H., Models of Biological Pattern Formation (1982), Academic Press: Academic Press London
[13] Stephenson, L. E.; Wolkind, D. J., Weakly nonlinear stability analyses of one-dimensional turing pattern formation in activator-inhibitor/immobilizer model systems, Journal of Mathematical Biology, 33, 771-815 (1995) · Zbl 0832.92003
[14] Kolokolnikov, T.; Wei, J., On ring-like solutions for the Gray-Scott model: existence, instability and self-replicating rings, European Journal of Applied Mathematics, 16, 2, 201-237 (2005) · Zbl 1085.35019
[15] Wei, J.; Winter, M., Stability of spiky solutions in a reaction-diffusion system with four morphogens on the real line, SIAM Journal on Mathematical Analysis, 42, 6, 2818-2841 (2010) · Zbl 1225.35025
[16] Cox, S. M.; Matthews, P. C., Exponential time differencing for stiff systems, Journal of Computational Physics, 176, 2, 430-455 (2002) · Zbl 1005.65069
[17] Kassam, A. K.; Trefethen, L. N., Fourth-order time-stepping for stiff PDEs, SIAM Journal on Scientific Computing, 26, 4, 1214-1233 (2005) · Zbl 1077.65105
[18] Nie, Q.; Wan, F. Y.M.; Zhang, Y. T.; Liu, X. F., Compact integration factor methods in high spatial dimensions, Journal of Computational Physics, 227, 5238-5255 (2008) · Zbl 1142.65072
[19] Nie, Q.; Zhang, Y.; Zhao, R., Efficient semi-implicit schemes for stiff systems, Journal of Computational Physics, 214, 521-537 (2006) · Zbl 1089.65094
[20] Ruuth, S. J., Implicit-explicit methods for reaction-diffusion problems in pattern formation, Journal of Mathematical Biology, 34, 148-176 (1995) · Zbl 0835.92006
[21] Page, K. M.; Maini, P. K.; Monk, N. A.M., Complex pattern formation in reaction-diffusion systems with spatially varying parameters, Physica D, 202, 95-115 (2005) · Zbl 1065.35145
[22] Kelley, C. T., Iterative Methods for Linear and Nonlinear Equations (1995), SIAM: SIAM Philadelphia · Zbl 0832.65046
[23] Brandt, A., Multi-level adaptive solutions, Mathematics of Computation, 31, 138, 333-390 (1977) · Zbl 0373.65054
[24] Briggs, W. L.; Henson, V. E.; McCormick, S. F., A Multigrid Tutorial (1987), SIAM: SIAM Philadelphia, Pennsylvania · Zbl 0659.65095
[25] Xu, J., A novel two-grid method for semilinear elliptic equations, SIAM Journal on Scientific Computing, 15, 231-237 (1994) · Zbl 0795.65077
[26] Morton, K. W.; Mayers, D. F., Numerical Solution of Partial Differential Equations (1995), Cambridge University press · Zbl 0811.65063
[27] Stoer, J.; Bulirsch, R., Introduction to Numerical Analysis (2002), Springer Verlag · Zbl 1004.65001
[28] Nocedal, J.; Wright, S. J., Numerical Optimization (2002), Springer Verlag: Springer Verlag New York
[29] Levenberg, K., A method for the solution of certain non-linear problems in least squares, The Quarterly of Applied Mathematics, 2, 164-168 (1944) · Zbl 0063.03501
[30] Marquardt, D., An algorithm for least-squares estimation of nonlinear parameters, SIAM Journal on Applied Mathematics, 11, 431-441 (1963) · Zbl 0112.10505
[31] L. Chen, An Integrated Finite Element Methods Package in MATLAB, Technical Report, University of California, Irvine, 2009.; L. Chen, An Integrated Finite Element Methods Package in MATLAB, Technical Report, University of California, Irvine, 2009.
[32] Koch, A. J.; Meinhardt, H., Biological pattern formation: from basic mechanisms to complex structures, Reviews of Modern Physics, 66, 1481-1507 (1994)
[33] Bhatia, R., Fourier Series (2004), The Mathematical Association of America
This reference list is based on information provided by the publisher or from digital mathematics libraries. Its items are heuristically matched to zbMATH identifiers and may contain data conversion errors. In some cases that data have been complemented/enhanced by data from zbMATH Open. This attempts to reflect the references listed in the original paper as accurately as possible without claiming completeness or a perfect matching.