June  2014, 1(2): 377-389. doi: 10.3934/jcd.2014.1.377

Equation-free computation of coarse-grained center manifolds of microscopic simulators

1. 

School of Applied Mathematics and Physical Sciences, National Technical University of Athens, Athens, GR-157 80, Greece

Received  April 2012 Revised  May 2012 Published  December 2014

An algorithm, based on the Equation-free concept, for the approximation of coarse-grained center manifolds of microscopic simulators is addressed. It is assumed that the macroscopic equations describing the emergent dynamics are not available in a closed form. Appropriately initialized short runs of the microscopic simulators, which are treated as black box input-output maps provide a polynomial estimate of a local coarse-grained center manifold; the coefficients of the polynomial are obtained by wrapping around the microscopic simulator an optimization algorithm. The proposed method is demonstrated through kinetic Monte Carlo simulations, of simple reactions taking place on catalytic surfaces, exhibiting coarse-grained turning points and Andronov-Hopf bifurcations.
Citation: Constantinos Siettos. Equation-free computation of coarse-grained center manifolds of microscopic simulators. Journal of Computational Dynamics, 2014, 1 (2) : 377-389. doi: 10.3934/jcd.2014.1.377
References:
[1]

E. H. Abed, A simple proof of stability on the center manifold for Hopf bifurcation,, SIAM Review, 30 (1988), 487.  doi: 10.1137/1030096.  Google Scholar

[2]

H. Boumediene, K. Wei and A. J. Krener, The controlled center dynamics,, Multiscale Model. Simul., 3 (2005), 838.  doi: 10.1137/040603139.  Google Scholar

[3]

J. Carr, Applications of Center Manifold Theory,, Springer-Verlag, (1981).   Google Scholar

[4]

N. Fenichel, Geometric singular perturbation theory for ordinary differential equations,, J. Diff. Equat., 31 (1979), 53.  doi: 10.1016/0022-0396(79)90152-9.  Google Scholar

[5]

C. W. Gear and I. G. Kevrekidis, Constraint-defined manifolds: A legacy code approach to low-dimensional computation,, J. Scientific Comput., 25 (2005), 17.  doi: 10.1007/s10915-004-4630-x.  Google Scholar

[6]

C. W. Gear, T. J. Kaper, I. G. Kevrekidis and A. Zagaris, Projecting to a slow manifold: Singularly perturbed systems and legacy codes,, SIAM J. Appl. Dyn. Syst., 4 (2005), 711.  doi: 10.1137/040608295.  Google Scholar

[7]

D. T. Gillespie, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions,, J. Comput. Phys., 22 (1976), 403.  doi: 10.1016/0021-9991(76)90041-3.  Google Scholar

[8]

D. T. Gillespie, Exact stochastic simulation of coupled chemical reactions,, J. Phys. Chem., 81 (1977), 2340.  doi: 10.1021/j100540a008.  Google Scholar

[9]

G. Guckenheimer and M. Myers, Computing Hopf bifurcations,, SIAM J. Sci. Comput., 17 (1996), 1275.  doi: 10.1137/S1064827593253495.  Google Scholar

[10]

P. Holmes, Center manifolds, normal forms and bifurcations of vector fields,, Physica 2D, 2 (1981), 449.  doi: 10.1016/0167-2789(81)90022-1.  Google Scholar

[11]

N. Kazantzis and T. Good, Invariant manifolds and the calculation of the long-term asymptotic response of nonlinear processes using singular PDEs,, Comp. Chem. Eng., 26 (2002), 999.  doi: 10.1016/S0098-1354(02)00022-4.  Google Scholar

[12]

C. T. Kelley, Iterative Methods for Linear and Nonlinear Equations,, SIAM series on Frontiers in Applied Mathematics, (1999).  doi: 10.1137/1.9781611970944.  Google Scholar

[13]

C. T. Kelley, Iterative Methods for Optimization,, SIAM series on Frontiers in Applied Mathematics, (1999).  doi: 10.1137/1.9781611970920.  Google Scholar

[14]

I. G. Kevrekidis, C. W. Gear, J. M. Hyman, P. G. Kevrekidis, O. Runborg and C. Theodoropoulos, Equation-free coarse-grained multiscale computation: Enabling microscopic simulators to perform system-level tasks,, Comm. Math. Sciences, 1 (2003), 715.  doi: 10.4310/CMS.2003.v1.n4.a5.  Google Scholar

[15]

I. G. Kevrekidis, C. W. Gear and G. Hummer, Equation-free: the computer-assisted analysis of complex, multiscale systems,, A.I.Ch.E.J., 50 (2004), 1346.   Google Scholar

[16]

A. Kolpas, J. Moehlis and I. G. Kevrekidis, Coarse-grained analysis of stochasticity-induced switching between collective motion states,, Proc. Nat. Acad. Sci. USA, 104 (2007), 5931.  doi: 10.1073/pnas.0608270104.  Google Scholar

[17]

Y. A. Kuznetsov, Elements of Applied Bifurcation Theory,, $2^{nd}$ edition, (1998).   Google Scholar

[18]

A. Makeev, D. Maroudas and I. G. Kevrekidis, Coarse stability and biifurcation analysis using stochastic simulators: Kinetic Monte Carlo examples,, J. Chem. Phys., 116 (2002), 10083.  doi: 10.1063/1.1476929.  Google Scholar

[19]

A. H. Nayef, Applied Nonlinear Dynamics,, Wiley-VCH, (2007).  doi: 10.1002/9783527617548.  Google Scholar

[20]

C. I. Siettos, M. Graham and I. G. Kevrekidis, Coarse brownian dynamics for nematic liquid crystals: Bifurcation diagrams via stochastic simulation,, J. Chem. Phys., 118 (2003), 10149.   Google Scholar

[21]

Y. Saad, Numerical Methods for Large Eigenvalue Problems,, Manchester University Press, (1992).   Google Scholar

[22]

R. Seydel, Practical Bifurcation and Stability Analysis,, Springer-Verlag, (1994).   Google Scholar

[23]

C. I. Siettos, R. Rico-Martinez and I. G. Kevrekidis, A systems-based approach to multiscale computation: EquationfFree detection of coarse-grained bifurcations,, Comp. Chem. Eng., 30 (2006), 1632.   Google Scholar

[24]

I. Yammaguchi, Y. Ogawa, Y. Jimbo, H. Nakao and K. Kotani, Reduction theories elucidate the origins of complex biological rhythms generated by interacting delay-indeced oscillations,, PLoS ONE, 6 (2011).   Google Scholar

[25]

A. Zagaris, C. W. Gear, T. J. Kapper and I. G. Kevrekidis, Analysis of the accuracy and convergence of equation-free projection to a slow manifold,, ESAIM: Mathematical Modelling and Numerical Analysis, 43 (2009), 757.  doi: 10.1051/m2an/2009026.  Google Scholar

show all references

References:
[1]

E. H. Abed, A simple proof of stability on the center manifold for Hopf bifurcation,, SIAM Review, 30 (1988), 487.  doi: 10.1137/1030096.  Google Scholar

[2]

H. Boumediene, K. Wei and A. J. Krener, The controlled center dynamics,, Multiscale Model. Simul., 3 (2005), 838.  doi: 10.1137/040603139.  Google Scholar

[3]

J. Carr, Applications of Center Manifold Theory,, Springer-Verlag, (1981).   Google Scholar

[4]

N. Fenichel, Geometric singular perturbation theory for ordinary differential equations,, J. Diff. Equat., 31 (1979), 53.  doi: 10.1016/0022-0396(79)90152-9.  Google Scholar

[5]

C. W. Gear and I. G. Kevrekidis, Constraint-defined manifolds: A legacy code approach to low-dimensional computation,, J. Scientific Comput., 25 (2005), 17.  doi: 10.1007/s10915-004-4630-x.  Google Scholar

[6]

C. W. Gear, T. J. Kaper, I. G. Kevrekidis and A. Zagaris, Projecting to a slow manifold: Singularly perturbed systems and legacy codes,, SIAM J. Appl. Dyn. Syst., 4 (2005), 711.  doi: 10.1137/040608295.  Google Scholar

[7]

D. T. Gillespie, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions,, J. Comput. Phys., 22 (1976), 403.  doi: 10.1016/0021-9991(76)90041-3.  Google Scholar

[8]

D. T. Gillespie, Exact stochastic simulation of coupled chemical reactions,, J. Phys. Chem., 81 (1977), 2340.  doi: 10.1021/j100540a008.  Google Scholar

[9]

G. Guckenheimer and M. Myers, Computing Hopf bifurcations,, SIAM J. Sci. Comput., 17 (1996), 1275.  doi: 10.1137/S1064827593253495.  Google Scholar

[10]

P. Holmes, Center manifolds, normal forms and bifurcations of vector fields,, Physica 2D, 2 (1981), 449.  doi: 10.1016/0167-2789(81)90022-1.  Google Scholar

[11]

N. Kazantzis and T. Good, Invariant manifolds and the calculation of the long-term asymptotic response of nonlinear processes using singular PDEs,, Comp. Chem. Eng., 26 (2002), 999.  doi: 10.1016/S0098-1354(02)00022-4.  Google Scholar

[12]

C. T. Kelley, Iterative Methods for Linear and Nonlinear Equations,, SIAM series on Frontiers in Applied Mathematics, (1999).  doi: 10.1137/1.9781611970944.  Google Scholar

[13]

C. T. Kelley, Iterative Methods for Optimization,, SIAM series on Frontiers in Applied Mathematics, (1999).  doi: 10.1137/1.9781611970920.  Google Scholar

[14]

I. G. Kevrekidis, C. W. Gear, J. M. Hyman, P. G. Kevrekidis, O. Runborg and C. Theodoropoulos, Equation-free coarse-grained multiscale computation: Enabling microscopic simulators to perform system-level tasks,, Comm. Math. Sciences, 1 (2003), 715.  doi: 10.4310/CMS.2003.v1.n4.a5.  Google Scholar

[15]

I. G. Kevrekidis, C. W. Gear and G. Hummer, Equation-free: the computer-assisted analysis of complex, multiscale systems,, A.I.Ch.E.J., 50 (2004), 1346.   Google Scholar

[16]

A. Kolpas, J. Moehlis and I. G. Kevrekidis, Coarse-grained analysis of stochasticity-induced switching between collective motion states,, Proc. Nat. Acad. Sci. USA, 104 (2007), 5931.  doi: 10.1073/pnas.0608270104.  Google Scholar

[17]

Y. A. Kuznetsov, Elements of Applied Bifurcation Theory,, $2^{nd}$ edition, (1998).   Google Scholar

[18]

A. Makeev, D. Maroudas and I. G. Kevrekidis, Coarse stability and biifurcation analysis using stochastic simulators: Kinetic Monte Carlo examples,, J. Chem. Phys., 116 (2002), 10083.  doi: 10.1063/1.1476929.  Google Scholar

[19]

A. H. Nayef, Applied Nonlinear Dynamics,, Wiley-VCH, (2007).  doi: 10.1002/9783527617548.  Google Scholar

[20]

C. I. Siettos, M. Graham and I. G. Kevrekidis, Coarse brownian dynamics for nematic liquid crystals: Bifurcation diagrams via stochastic simulation,, J. Chem. Phys., 118 (2003), 10149.   Google Scholar

[21]

Y. Saad, Numerical Methods for Large Eigenvalue Problems,, Manchester University Press, (1992).   Google Scholar

[22]

R. Seydel, Practical Bifurcation and Stability Analysis,, Springer-Verlag, (1994).   Google Scholar

[23]

C. I. Siettos, R. Rico-Martinez and I. G. Kevrekidis, A systems-based approach to multiscale computation: EquationfFree detection of coarse-grained bifurcations,, Comp. Chem. Eng., 30 (2006), 1632.   Google Scholar

[24]

I. Yammaguchi, Y. Ogawa, Y. Jimbo, H. Nakao and K. Kotani, Reduction theories elucidate the origins of complex biological rhythms generated by interacting delay-indeced oscillations,, PLoS ONE, 6 (2011).   Google Scholar

[25]

A. Zagaris, C. W. Gear, T. J. Kapper and I. G. Kevrekidis, Analysis of the accuracy and convergence of equation-free projection to a slow manifold,, ESAIM: Mathematical Modelling and Numerical Analysis, 43 (2009), 757.  doi: 10.1051/m2an/2009026.  Google Scholar

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