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Complexity of Solving Systems with Few Independent Monomials and Applications to Mass-Action Kinetics

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Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 7442))

Abstract

We design an algorithm for finding solutions with nonzero coordinates of systems of polynomial equations which has a better complexity bound than for known algorithms when a system contains a few linearly independent monomials. For parametric binomial systems we construct an algorithm of polynomial complexity. We discuss the applications of these algorithms in the context of chemical reaction systems.

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References

  1. Bihan, F., Sottile, F.: Fewnomial bounds for completely mixed polynomial systems. Advances in Geometry 11(3), 541–556 (2011)

    Article  MathSciNet  MATH  Google Scholar 

  2. Gatermann, K., Huber, B.: A family of sparse polynomial systems arising in chemical reaction systems. Journal of Symbolic Computation 33(3), 275–305 (2002)

    Article  MathSciNet  MATH  Google Scholar 

  3. Gatermann, K., Wolfrum, M.: Bernstein’s second theorem and Viro’s method for sparse polynomial systems in chemistry. Advances in Applied Mathematics 34(2), 252–294 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  4. Gatermann, K., Eiswirth, M., Sensse, A.: Toric ideals and graph theory to analyze Hopf bifurcations in mass action systems. Journal of Symbolic Computation 40(6), 1361–1382 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  5. Domijan, M., Kirkilionis, M.: Bistability and oscillations in chemical reaction networks. Journal of Mathematical Biology 59(4), 467–501 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  6. Craciun, G., Dickenstein, A., Shiu, A., Sturmfels, B.: Toric dynamical systems. Journal of Symbolic Computation 44(11), 1551–1565 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  7. Sturm, T., Weber, A., Abdel-Rahman, E.O., El Kahoui, M.: Investigating algebraic and logical algorithms to solve Hopf bifurcation problems in algebraic biology. Mathematics in Computer Science 2(3), 493–515 (2009)

    Article  MathSciNet  MATH  Google Scholar 

  8. Chistov, A.L.: Algorithm of polynomial complexity for factoring polynomials and finding the components of varieties in subexponential time. Journal of Soviet Mathematics 34(4), 1838–1882 (1986)

    Article  MATH  Google Scholar 

  9. Grigoriev, D.: Factorization of polynomials over a finite field and the solution of systems of algebraic equations. Journal of Soviet Mathematics 34(4), 1762–1803 (1986)

    Article  Google Scholar 

  10. Grigoriev, D., Vorobjov, N.N.: Solving systems of polynomial inequalities in subexponential time. Journal of Symbolic Computation 5(1-2), 37–64 (1988)

    Article  MathSciNet  Google Scholar 

  11. Sturmfels, B.: Grobner bases and convex polytopes. University Lecture Series, vol. 8. American Mathematical Society, Providence (1996)

    Google Scholar 

  12. Gerdt, V.: Involutive methods applied to algebraic and differential systems. Constructive algebra and systems theory. Verh. Afd. Natuurkd. 1. Reeks. K. Ned. Akad. Wet., R. Neth. Acad. Arts Sci. 53, 245–250 (2006)

    MathSciNet  Google Scholar 

  13. Mayr, E., Meyer, A.: The complexity of the word problems for commutative semigroups and polynomial ideals. Adv. in Math 46, 305–329 (1982)

    Article  MathSciNet  MATH  Google Scholar 

  14. Cattani, E., Dickenstein, A.: Counting solutions to binomial complete intersections. Journal of Complexity, 1–25 (2007)

    Google Scholar 

  15. Grigoriev, D., Pasechnik, D.V.: Polynomial-time computing over quadratic maps. I. sampling in real algebraic sets. Comput. Complexity 14, 20–52 (2005)

    Article  MathSciNet  MATH  Google Scholar 

  16. Frumkin, M.: An application of modular arithmetic to the construction of algorithms for solving systems of linear equations. Soviet Math. Dokl 229, 1067–1070 (1976)

    MathSciNet  Google Scholar 

  17. Dumas, J.G., Saunders, B.D.: On efficient sparse integer matrix Smith normal form computations. Journal of Symbolic Computation 32, 71–99 (2001)

    Article  MathSciNet  MATH  Google Scholar 

  18. Pérez Millán, M., Dickenstein, A., Shiu, A., Conradi, C.: Chemical reaction systems with toric steady states. Bulletin of Mathematical Biology, 1–29 (October 2011)

    Google Scholar 

  19. Gatermann, K., Huber, B.: A family of sparse polynomial systems arising in chemical reaction systems. Technical Report Preprint SC 99-27, Konrad-Zuse-Zentrum für Informationstechnik Berlin (1999)

    Google Scholar 

  20. El Kahoui, M., Weber, A.: Deciding Hopf bifurcations by quantifier elimination in a software-component architecture. Journal of Symbolic Computation 30(2), 161–179 (2000)

    Article  MathSciNet  MATH  Google Scholar 

  21. Shinar, G., Feinberg, M.: Structural sources of robustness in biochemical reaction networks. Science 327(5971), 1389–1391 (2010)

    Article  Google Scholar 

  22. Shinar, G., Feinberg, M.: Structural sources of robustness in biochemical reaction networks. supporting online material. Science 327(5971), 1389–1391 (2010)

    Article  Google Scholar 

  23. Li, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., Li, L., He, E., Henry, A., Stefan, M.I., Snoep, J.L., Hucka, M., Le Novère, N., Laibe, C.: BioModels database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Systems Biology 4, 92 (2010)

    Article  Google Scholar 

  24. Feinberg, M.: Stability of complex isothermal reactors–I. the deficiency zero and deficiency one theorems. Chemical Engineering Science 42(10), 2229–2268 (1987)

    Google Scholar 

  25. Proctor, C.: Explaining oscillations and variability in the p53-Mdm2 system. BMC Systems Biology 2, 75 (2008)

    Article  Google Scholar 

  26. Clarke, B.L.: Complete set of steady states for the general stoichiometric dynamical system. The Journal of Chemical Physics 75(10), 4970–4979 (1981)

    Article  MathSciNet  Google Scholar 

  27. Samal, S.S., Errami, H., Weber, A.: A Software Infrastructure to Explore Algebraic Methods for Bio-Chemical Reaction Networks. In: Gerdt, V.P., et al. (eds.) CASC 2012, LNCS, vol. 7442, pp. 294–307. Springer, Heidelberg (2012)

    Google Scholar 

  28. 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., Regensburger, G., Rosenkranz, M., Yoshida, H. (eds.) AB 2008. LNCS, vol. 5147, pp. 56–64. Springer, Heidelberg (2008)

    Chapter  Google Scholar 

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Grigoriev, D., Weber, A. (2012). Complexity of Solving Systems with Few Independent Monomials and Applications to Mass-Action Kinetics. In: Gerdt, V.P., Koepf, W., Mayr, E.W., Vorozhtsov, E.V. (eds) Computer Algebra in Scientific Computing. CASC 2012. Lecture Notes in Computer Science, vol 7442. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32973-9_12

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  • DOI: https://doi.org/10.1007/978-3-642-32973-9_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-32972-2

  • Online ISBN: 978-3-642-32973-9

  • eBook Packages: Computer ScienceComputer Science (R0)

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