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Oscillations and multiscale dynamics in a closed chemical reaction system: Second law of thermodynamics and temporal complexity

J. Chem. Phys. 129, 154505 (2008); doi:10.1063/1.2995855

Published 16 October 2008

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Yongfeng Li,1 Hong Qian,2 and Yingfei Yi3
1School of Mathematics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
2Department of Applied Mathematics, University of Washington, Seattle, Washington 98195, USA
3School of Mathematics, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and College of Mathematics, Jilin University, Changchun 130012, People's Republic of China

We investigate the oscillatory reaction dynamics in a closed isothermal chemical system: the reversible Lotka–Volterra model. The second law of thermodynamics dictates that the system ultimately reaches an equilibrium. Quasistationary oscillations are analyzed while the free energy of the system serves as a global Lyapunov function of the dissipative dynamics. A natural distinction between regions near and far from equilibrium in terms of the free energy can be established. The dynamics is analogous to a nonlinear mechanical system with time-dependent increasing damping. Near equilibrium, no oscillation is possible as dictated by Onsager's reciprocal symmetry relation. We observe that while the free energy decreases in the closed system's dynamics, it does not follow the steepest descending path. ©2008 American Institute of Physics
History: Received 15 May 2008; accepted 15 September 2008; published 16 October 2008
Permalink: http://link.aip.org/link/?JCPSA6/129/154505/1
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KEYWORDS and PACS

Keywords
PACS
  • 82.60.Hc
    Chemical equilibria and equilibrium constants
  • 82.20.-w
    Chemical kinetics and dynamics
  • YEAR: 2008

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PUBLICATION DATA

ISSN:
0021-9606 (print)   1089-7690 (online)
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REFERENCES (36)

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  1. A. Goldbeter, Biochemical Oscillations and Cellular Rhythms: The Molecular Bases of Periodic and Chaotic Behavior (Cambridge University Press, New York, 1996).
  2. J. D. Murray, Mathematical Biology I: An Introduction, 3rd ed. (Springer, New York, 2002).
  3. H. Qian, J. Phys. Chem. B 110, 15063 (2006).
  4. R. M. Noyes and R. J. Field, Annu. Rev. Phys. Chem. 25, 95 (1974).
  5. J. J. Tyson, in Non-Equilibrium Dynamics in Chemical Systems, edited by C. Vidal and A. Pacault (Springer-Verlag, Berlin, 1981).
  6. I. R. Epstein and J. A. Pojman, An Introduction to Nonlinear Chemical Dynamics: Oscillations, Waves, Patterns, and Chaos (Oxford University Press, London, 1998).
  7. G. Nicolis and I. Prigogine, Self-Organization in Nonequilibrium Systems (Wiley, New York, 1977).
  8. P. Bak and K. Chen, Sci. Am. 264, 46 (1991).
  9. E. Karsenti, Nat. Rev. Mol. Cell Biol. 9, 255 (2008).
  10. O. Benini, R. Cervellati, and P. Fetto, J. Chem. Educ. 73, 865 (1996).
  11. M. Dolnik, A. S. Banks, and I. R. Epstein, J. Phys. Chem. A 101, 5148 (1997).
  12. J. D. Sheppard and P. S. S. Dawson, Can. J. Chem. Eng. 77, 893 (1999).
  13. C. D. Helgason and C. L. Miller, Basic Cell Culture Protocols, 3rd ed. (Humana, Totowa, NJ, 2004).
  14. H. Qian, J. Phys.: Condens. Matter 17, S3783 (2005).
  15. L. G. Ngo and M. R. Roussel, Eur. J. Biochem. 245, 182 (1997).
  16. D. Q. Jiang, M. Qian, and M. P. Qian, Mathematical Theory of Nonequilibrium Steady States: On the Frontier of Probability and Dynamical Systems (Springer-Verlag, New York, 2004).
  17. H. Qian, Annu. Rev. Phys. Chem. 58, 113 (2007).
  18. J. L. Lebowitz, Rev. Mod. Phys. 71, S346 (1999).
  19. M. R. Roussel and S. J. Fraser, J. Chem. Phys. 94, 7106 (1991).
  20. L. Segel and J. J. Tyson, Nature (London) 357, 106 (1992).
  21. L. Jullien and H. Lemarchand, J. Chem. Educ. 78, 803 (2001).
  22. A. N. Gorban and I. V. Karlin, in Invariant Manifolds for Physical and Chemical Kinetics, Lecture Notes in Physics Vol. 660 (Springer, New York, 2005).
  23. W. Liu, D. Xiao, and Y. Yi, J. Differ. Equations 188, 306 (2003).
  24. R. E. O'Malley, Singular Perturbation Methods for Ordinary Differential Equations (Springer-Verlag, Berlin, 1991).
  25. N. G. van Kampen, Phys. Rep. 124, 69 (1985).
  26. G. Moore, Appl. Numer. Math. 17, 319 (1995).
  27. In current mathematical literature, the perturbation theory in Hamiltonian systems has been established within the Hamiltonian framework, i.e., the perturbed system remains Hamiltonian. In the present model, the perturbation is dissipative. As far as we know, no previous study has investigated such a problem rigorously. The mathematical analysis of the present model by the authors will be published elsewhere. The basic idea is similar to the center manifold reduction: reducing a high-dimensional dynamical system into a lower-dimensional form. In Ref. 25, singular perturbation method is employed to approximate the center manifold by assuming the existence of such a manifold. Our mathematical analysis proves its existence.
  28. See D. Walz and S. R. Caplan, Biophys. J. 69, 1698 (1995). In this paper, the authors have shown that a chemical reaction system with every individual reaction being reversible can exhibit oscillatory dynamics. This is in complete agreement with the present study. However, the previous authors identified the reversible system with “near equilibrium.” Even though it is mainly semantics, we believe that their terminology is misleading. As we have shown in the present paper, a reversible system can be either near or far from equilibrium depending on how severe the chemical driving force is.
  29. Strictly speaking, the LV system is a anharmonic oscillation since the frequencies of different periodic orbits vary in the system. In mechanics, harmonic oscillators are usually referred to linear oscillation whose frequencies are the same irrespective of the amplitudes of the oscillation. In the reversible LV system, not only the amplitudes of oscillation change but also its frequencies. The unperturbed Hamiltonian is nonlinear and frequencies for periodic orbits lying in different energy levels are not the same. Even though nonlinear transformations exist between the traditional LV system and a harmonic oscillator (e.g., Refs. 30,31), it is the nonlinear aspect of the LV system that gives rise to the transition between near to far from equilibrium.
  30. N. Samardzija, L. D. Greller, and E. Wasserman, J. Chem. Phys. 90, 2296 (1989).
  31. P. E. Strizhak, Chem. Phys. Lett. 197, 243 (1992).
  32. L. Jullien, A. Lemarchand, S. Charier, O. Ruel, and J. -B. Baudin, J. Phys. Chem. B 107, 9905 (2003).
  33. A. J. Lotka, Proc. Natl. Acad. Sci. U.S.A. 6, 410 (1920).
  34. D. A. Beard and H. Qian, Chemical Biophysics: Quantitative Analysis of Cellular Systems (Cambridge University Press, Cambridge, England, 2008).
  35. C. Abad-Zapatero, Acta Crystallogr., Sect. D: Biol. Crystallogr. 63, 660 (2007).
  36. H. Qian and T. C. Reluga, Phys. Rev. Lett. 94, 028101 (2005).

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