Abstract
There exist different schemes of model reduction for parametric ordinary differential systems arising from chemical reaction systems. In this paper, we focus on some schemes which rely on quasi-steady states approximations. We show that these schemes can be formulated by means of differential and algebraic elimination. Our formulation is simpler than the classical ones. It permitted us to obtain an approximation of the basic enzymatic reaction system which is different from those of Henri–Michaëlis–Menten and Briggs–Haldane.
Similar content being viewed by others
References
Bellon, B.: Biochimie structurale: introduction à la cinétique enzymatique (2006) (in French). http://www.up.univ-mrs.fr/wabim/d_agora/d_biochimie/cinetique.pdf
Bennet M.R., Volfson D., Tsimring L., Hasty J.: Transient dynamics of genetic regulatory networks. Biophys. J. 92, 3501–3512 (2007)
Boulier, F.: Réécriture algébrique dans les systèmes d’équations différentielles polynomiales en vue d’applications dans les Sciences du Vivant, May 2006. Mémoire d’habilitation à diriger des recherches. Université Lille I, LIFL, 59655 Villeneuve d’Ascq, France. http://tel.archives-ouvertes.fr/tel-00137153
Boulier, F.: Differential Elimination and Biological Modelling. Radon Series on Computational and Applied Mathematics (Gröbner Bases in Symbolic Analysis) 2, pp. 111–139 (2007). http://hal.archives-ouvertes.fr/hal-00139364
Boulier, F., Lazard, D., Ollivier, F., Petitot, M.: Representation for the radical of a finitely generated differential ideal. In: ISSAC’95: Proceedings of the 1995 International Symposium on Symbolic and Algebraic Computation, pp. 158–166. ACM Press, New York (1995). http://hal.archives-ouvertes.fr/hal-00138020
Boulier F., Lazard D., Ollivier F., Petitot M.: Computing representations for radicals of finitely generated differential ideals. Appl. Algebra Eng. Commun. Comput 20(1), 73–121 (2009) (1997 Techrep. IT306 of the LIFL)
Boulier, F., Lefranc, M., Lemaire, F., Morant, P.-E.: Applying a rigorous quasi-steady state approximation method for proving the absence of oscillations in models of genetic circuits. In: Horimoto, K., et al. (eds.) Proceedings of Algebraic Biology 2008 No. 5147 in LNCS, pp. 56–64. Springer, Berlin (2008)
Boulier, F., Lefranc, M., Lemaire, F., Morant, P.-E., Ürgüplü, A.: On proving the absence of oscillations in models of genetic circuits. In: Anai, K.H.H., Kutsia, T. (eds.) Proceedings of Algebraic Biology, LNCS, vol. 4545, pp. 66–80. Springer, Berlin (2007). http://hal.archives-ouvertes.fr/hal-00139667
Boulier, F., Lemaire, F.: Computing canonical representatives of regular differential ideals. In: ISSAC’00 Proceedings of the 2000 International Symposium on Symbolic and Algebraic Computation, pp. 38–47. ACM Press, New York (2000). http://hal.archives-ouvertes.fr/hal-00139177
Boulier, F., Lemaire, F.: A normal form algorithm for regular differential chains. Math. Comput. Sci. 4(2), 185–201 (2010) doi:10.1007/s11786-010-0060-3
Briggs, G.E., Haldane, J.B.S.: A note on the kinetics of enzyme action. Biochem. J. 19, 338–339 (1925). Available on http://www.biochemj.org/bj/019/0338/bj0190338_browse.htm
Crampin E.J., Schnell S., Mac Sharry P.E.: Mathematical and computational techniques to deduce complex biochemical reaction mechanisms. Prog. Biophys. Mol. Biol. 86, 77–112 (2004)
Hairer E., Wanner G.: Solving ordinary differential equations II Stiff and Differential-Algebraic Problems 2nd edn Springer Series in Computational Mathematics vol 14. Springer, New York (1996)
Henri V.: Lois générales de l’Action des Diastases. Hermann, Paris (1903)
Horn F., Jackson R.: General mass action kinetics. Arch. Ration. Mech. Anal. 47, 81–116 (1972)
Hubert É.: Factorization free decomposition algorithms in differential algebra. J. Symb. Comput. 29(4–5), 641–662 (2000)
Kell D.B., Knowles J.D.: The role of modeling in systems biology. In: Szallasi, Z., Stelling, J., Periwal, V. (eds) System Modeling in Cellular Biology: From Concepts to Nuts and Bolts, pp. 3–18. The MIT Press, Cambridge (2006)
Klamt S., Stelling J.: Stoichiometric and constraint-based modeling. In: Szallasi, Z., Stelling, J., Periwal, V. (eds) System Modeling in Cellular Biology: From Concepts to Nuts and Bolts, pp. 73–96. The MIT Press, Cambridge (2006)
Kolchin E.R.: Differential Algebra and Algebraic Groups. Academic Press, New York (1973)
Lemaire, F., Moreno Maza, M., Xie, Y.: The RegularChains library in MAPLE 10. In: Kotsireas, I.S. (ed.) The MAPLE Conference, pp. 355–368 (2005)
Michaelis, L., Menten M.: Die kinetik der invertinwirkung. Biochemische Zeitschrift 49, 333–369 (1973) (Partial translation in english on http://web.lemoyne.edu/~giunta/menten.html)
Morant, P.-E., Vandermoere, C., Parent, B., Lemaire, F., Corellou, F., Schwartz, C., Bouget, F.-Y., Lefranc, M.: Oscillateurs génétiques simples. Applications à l’horloge circadienne d’une algue unicellulaire. In: Proceedings of the Rencontre du non linéaire Paris (2007). http://nonlineaire.univ-lille1.fr
Niu, W.: Qualitative Analysis of Biological Systems Using Algebraic Methods. PhD thesis, Université Paris VI, Paris, June 2011.
Okino M.S., Mavrovouniotis M.L.: Simplification of mathematical models of chemical reaction systems. Chem. Rev. 98(2), 391–408 (1998)
Ritt J.F.: Differential Algebra. Dover Publications Inc., NewYork (1950)
Sedoglavic, A.: Reduction of Algebraic Parametric Systems by Rectification of their Affine Expanded Lie Symmetries. In: Anai, K.H.H., Kutsia, T. (eds.) Proceedings of Algebraic Biology 2007, LNCS, vol. 4545, pp. 277–291 (2007)
Van Breusegem, V., Bastin, G.: Reduced order dynamical modelling of reaction systems: a singular perturbation approach. In: Proceedings of the 30th IEEE Conference on Decision and Control (Brighton, England, December 1991), pp. 1049–1054
Vilar, J.M.G., Kueh, H.Y., Barkai, N., Leibler, S.: Mechanisms of noise-resistance in genetic oscillators. In: Proceedings of the National Academy of Science of the USA 99, vol. 9, pp. 5988–5992 (2002)
Vora N., Vora N.: Nonlinear model reduction of chemical reaction systems. AIChE J. 45(10), 2320–2332 (2001)
Wang D.: Elimination Practice: Software Tools and Applications. Imperial College Press, London (2003)
Wang, D., Xia, B.: Stability Analysis of Biological Systems with Real Solution Classification. In: Proceedings of ISSAC 2005, pp. 354–361, Beijing (2005)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Boulier, F., Lefranc, M., Lemaire, F. et al. Model Reduction of Chemical Reaction Systems using Elimination. Math.Comput.Sci. 5, 289–301 (2011). https://doi.org/10.1007/s11786-011-0093-2
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s11786-011-0093-2