Skip to main content
Log in

Multistationarity in the Space of Total Concentrations for Systems that Admit a Monomial Parametrization

  • Original Article
  • Published:
Bulletin of Mathematical Biology Aims and scope Submit manuscript

Abstract

We apply tools from real algebraic geometry to the problem of multistationarity of chemical reaction networks. A particular focus is on the case of reaction networks whose steady states admit a monomial parametrization. For such systems, we show that in the space of total concentrations multistationarity is scale invariant: If there is multistationarity for some value of the total concentrations, then there is multistationarity on the entire ray containing this value (possibly for different rate constants)—and vice versa. Moreover, for these networks it is possible to decide about multistationarity independent of the rate constants by formulating semi-algebraic conditions that involve only concentration variables. These conditions can easily be extended to include total concentrations. Hence, quantifier elimination may give new insights into multistationarity regions in the space of total concentrations. To demonstrate this, we show that for the distributive phosphorylation of a protein at two binding sites multistationarity is only possible if the total concentration of the substrate is larger than either the total concentration of the kinase or the total concentration of the phosphatase. This result is enabled by the chamber decomposition of the space of total concentrations from polyhedral geometry. Together with the corresponding sufficiency result of Bihan et al., this yields a characterization of multistationarity up to lower-dimensional regions.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Banaji M, Craciun G (2009) Graph-theoretic approaches to injectivity and multiple equilibria in systems of interacting elements. Commun Math Sci 7(4):867–900

    Article  MathSciNet  MATH  Google Scholar 

  • Banaji M, Craciun G (2010) Graph-theoretic criteria for injectivity and unique equilibria in general chemical reaction systems. Adv Appl Math 44(2):168–184

    Article  MathSciNet  MATH  Google Scholar 

  • Bates DJ, Hauenstein JD, Sommese AJ, Wampler CW (2006) Bertini: Software for Numerical Algebraic Geometry. https://bertini.nd.edu with permanent https://doi.org/10.7274/R0H41PB5

  • Becker E, Neuhaus R (1993) Computation of real radicals of polynomial ideals. Computational algebraic geometry. Springer, Berlin, pp 1–20

    MATH  Google Scholar 

  • Bihan F, Dickenstein A, Giaroli M (2018) Lower bounds for positive roots and regions of multistationarity in chemical reaction networks. preprint, arXiv:1807.05157

  • Bradford R, Davenport J, England M, Errami H, Gerdt VP, Grigoriev D, Hoyt C, Kosta M, Radulescu O, Sturm T, Weber A (2017) A case study on the parametric occurrence of multiple steady states. In: Proceedings of the 42nd international symposium on symbolic and algebraic computation (ISSAC ’17), ACM, pp 45–52

  • Brake D, Niemberg M (2016) Paramotopy. http://paramotopy.com

  • Brown CW (2003) QEPCAD B: a program for computing with semi-algebraic sets using CADs. ACM SIGSAM Bull 37(4):97–108

    Article  MATH  Google Scholar 

  • Brown CW, Strzeboński A (2010) Black-box/white-box simplification and applications to quantifier elimination. In: Proceedings of the 2010 international symposium on symbolic and algebraic computation. ACM, pp 69–76

  • Conradi C, Flockerzi D (2012) Multistationarity in mass action networks with applications to ERK activation. J Math Biol 65(1):107–156

    Article  MathSciNet  MATH  Google Scholar 

  • Conradi C, Mincheva M (2014) Catalytic constants enable the emergence of bistability in dual phosphorylation. J R Soc Interface 11(95):20140158

    Article  Google Scholar 

  • Conradi C, Shiu A (2018) Dynamics of posttranslational modification systems: recent progress and future directions. Biophys J 114(3):507–515

    Article  Google Scholar 

  • Conradi C, Pantea C (2019) Chapter 9–multistationarity in biochemical networks: results, analysis, and examples. In: Robeva R, Macauley M (eds) Algebraic and combinatorial computational biology. Academic Press, Cambridge, pp 279–317

    Chapter  MATH  Google Scholar 

  • Conradi C, Saez-Rodriguez J, Gilles E-D, Raisch J (2005) Using chemical reaction network theory to discard a kinetic mechanism hypothesis, systems biology. IEE Proc (now IET Syst Biol) 152(4):243–248

    Google Scholar 

  • Conradi C, Flockerzi D, Raisch J (2008) Multistationarity in the activation of a MAPK: parametrizing the relevant region in parameter space. Math Biosci 211(1):105–131

    Article  MathSciNet  MATH  Google Scholar 

  • Conradi C, Feliu E, Mincheva M, Wiuf C (2017) Identifying parameter regions for multistationarity. PLOS Comput Biol 13(10):1–25

    Article  Google Scholar 

  • Coste M (2002) An introduction to semialgebraic geometry. RAAG Netw Sch 145:30

    Google Scholar 

  • Cox DA, Little JB, O’Shea D (1996) Ideals, varieties, and algorithms, 2nd edn. Springer, New York

    MATH  Google Scholar 

  • Craciun G, Dickenstein A, Shiu A, Sturmfels B (2009) Toric dynamical systems. J Symb Comput 44(11):1551–1565 Ordner: Gatermann

    Article  MathSciNet  MATH  Google Scholar 

  • Craciun G, Pantea C, Rempala GA (2009) Algebraic methods for inferring biochemical networks: a maximum likelihood approach. Comput Biol Chem 33(5):361–367

    Article  MathSciNet  MATH  Google Scholar 

  • De Loera JA, Kim ED, Onn S, Santos F (2009) Graphs of transportation polytopes. J Comb Theory Ser A 116(8):1306–1325

    Article  MathSciNet  MATH  Google Scholar 

  • Dickenstein A (2016) Biochemical reaction networks: an invitation for algebraic geometers, vol 656. Mathematical congress of the Americas. American Mathematical Society, Providence, pp 65–83

    MATH  Google Scholar 

  • Dickenstein A, Péréz-Millán M, Shiu A, Tang X (2019) Multistationarity in structured reaction networks. Bull Math Biol 81(5):1527–1581

    Article  MathSciNet  MATH  Google Scholar 

  • Dolzmann A, Sturm T (1997) REDLOG: computer algebra meets computer logic. SIGSAM Bull 31(2):2–9

    Article  Google Scholar 

  • Eisenbud D, Sturmfels B (1996) Binomial ideals. Duke Math J 84(1):1–45

    Article  MathSciNet  MATH  Google Scholar 

  • Ellison PR (1998) The Advanced Deficiency Algorithm and its applications to mechanism discrimination, Ph.D. thesis, The University of Rochester

  • Ellison P, Feinberg M (2000) How catalytic mechanisms reveal themselves in multiple steady-state data: I. Basic principles. J Mol Catal A Chem 154(1–2):155–167

    Article  Google Scholar 

  • Ellison P, Feinberg M, Yueb M-H, Saltsburg H (2000) How catalytic mechanisms reveal themselves in multiple steady-state data: II. An ethylene hydrogenation example. J Mol Catal A Chem 154(1–2):169–184

    Article  Google Scholar 

  • Érdi P, Tóth J (1989) Mathematical models of chemical reactions: theory and applications of deterministic and stochastic models. Manchester University Press, Manchester

    MATH  Google Scholar 

  • Feinberg M (1995a) The existence and uniqueness of steady states for a class of chemical reaction networks. Arch Ration Mech Anal 132(4):311–370

    Article  MathSciNet  MATH  Google Scholar 

  • Feinberg M (1995b) Multiple steady states for chemical reaction networks of deficiency one. Arch Ration Mech Anal 132(4):371–406

    Article  MathSciNet  MATH  Google Scholar 

  • Feliu E, Wiuf C (2012) Preclusion of switch behavior in networks with mass-action kinetics. Appl Math Comput 219(4):1449–1467

    MathSciNet  MATH  Google Scholar 

  • Flockerzi D, Holstein K, Conradi C (2014) N-site phosphorylation systems with 2n–1 steady states. Bull Math Biol 76:1–25

    Article  MathSciNet  MATH  Google Scholar 

  • Gawrilow E, Joswig M (2000) polymake: a framework for analyzing convex polytopes, polytopes–combinatorics and computation, vol 29. Birkhäuser, Basel, pp 43–47

    Book  MATH  Google Scholar 

  • Gleixner A, Bastubbe M, Eifler L, Gally T, Gamrath G, Gottwald RL, Hendel G, Hojny C, Koch T, Lübbecke ME, Maher SJ, Miltenberger M, Müller B, Pfetsch ME, Puchert C, Rehfeldt D, Schlösser F, Schubert C, Serrano F, Shinano Y, Viernickel JM, Walter M, Wegscheider F, Witt JT, Witzig J (2018) The SCIP optimization suite 6.0, Technical report, Optimization Online

  • Gross E, Harrington HA, Rosen Z, Sturmfels B (2016) Algebraic systems biology: a case study for the wnt pathway. Bull Math Biol 78(1):21–51

    Article  MathSciNet  MATH  Google Scholar 

  • Holstein K, Flockerzi D, Conradi C (2013) Multistationarity in sequential distributed multisite phosphorylation networks. Bull Math Biol 75(11):2028–2058

    Article  MathSciNet  MATH  Google Scholar 

  • Kahle T, Miller E (2014) Decompositions of commutative monoid congruences and binomial ideals. Algebra Number Theory 8(6):1297–1364

    Article  MathSciNet  MATH  Google Scholar 

  • Lazard D, Rouillier F (2007) Solving parametric polynomial systems. J Symb Comput 42(6):636–667

    Article  MathSciNet  MATH  Google Scholar 

  • Maplesoft (2017) a division of Waterloo Maple Inc., Waterloo, Ontario, Maple

  • Markevich NI, Hoek JB, Kholodenko BN (2004) Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J Cell Biology 164(3):353–359

    Article  Google Scholar 

  • Müller S, Feliu E, Regensburger G, Conradi C, Shiu A, Dickenstein A (2016) Sign conditions for injectivity of generalized polynomial maps with applications to chemical reaction networks and real algebraic geometry. Found Comput Math 16(1):69–97

    Article  MathSciNet  MATH  Google Scholar 

  • Neuhaus R (1998) Computation of real radicals of polynomial ideals–II. J Pure Appl Algebra 124(1–3):261–280

    Article  MathSciNet  MATH  Google Scholar 

  • Péréz-Millán M, Dickenstein A (2018) The structure of MESSI biological systems. SIAM J Appl Dyn Syst 17(2):1650–1682

    Article  MathSciNet  MATH  Google Scholar 

  • Péréz-Millán M, Dickenstein A, Shiu A, Conradi C (2012) Chemical reaction systems with toric steady states. Bull Math Biol 74(5):1027–1065

    Article  MathSciNet  MATH  Google Scholar 

  • Rambau J (2002) TOPCOM: triangulations of point configurations and oriented matroids. In: Arjeh MC, Xiao-Shan G, Nobuki T (eds) Mathematical software–ICMS 2002. World Scientific, Singapore, pp 330–340

    Google Scholar 

  • Rockafellar RT (1970) Convex analysis. Princeton University Press, Princeton

    Book  MATH  Google Scholar 

  • Sadeghimanesh AH, Feliu E (2019a) Gröbner bases of reaction networks with intermediate species. Adv Appl Math 107:74–101

    Article  MathSciNet  MATH  Google Scholar 

  • Sadeghimanesh AH, Feliu E (2019b) The multistationarity structure of networks with intermediates and a binomial core network. Bull Math Biol 81:2428–2462

    Article  MathSciNet  MATH  Google Scholar 

  • Schlosser PM, Feinberg M (1994) A theory of multiple steady states in isothermal homogeneous CFSTRs with many reactions. Chem Eng Sci 49(11):1749–1767

    Article  Google Scholar 

  • Shinar G, Feinberg M (2012) Concordant chemical reaction networks. Math Biosci 240(2):92–113

    Article  MathSciNet  MATH  Google Scholar 

  • Shinar G, Feinberg M (2013) Concordant chemical reaction networks and the species-reaction graph. Math Biosci 241(1):1–23

    Article  MathSciNet  MATH  Google Scholar 

  • Shiu A (2010) Algebraic methods for biochemical reaction network theory, Ph.D. thesis, University of California, Berkeley

  • Shiu A, Sturmfels B (2010) Siphons in chemical reaction networks. Bull Math Biol 72(6):1448–1463 Ordner: Gatermann

    Article  MathSciNet  MATH  Google Scholar 

  • Wang L, Sontag E (2008) On the number of steady states in a multiple futile cycle. J Math Biol 57:29–52

    Article  MathSciNet  MATH  Google Scholar 

  • Wiuf C, Feliu E (2013) Power-law kinetics and determinant criteria for the preclusion of multistationarity in networks of interacting species. SIAM J Appl Dyn Syst 12(4):1685–1721

    Article  MathSciNet  MATH  Google Scholar 

  • Wolfram Research, Inc., Mathematica, Version 11.2, Champaign, IL (2017)

  • Ziegler Günter M (2012) Lectures on polytopes, GTM, vol 152. Springer, Berlin

    Google Scholar 

Download references

Acknowledgements

This project is funded by the Deutsche Forschungsgemeinschaft, 284057449. Alexandru Iosif and Thomas Kahle are also partially supported by the DFG-RTG “MathCore,” 314838170. We thank the anonymous reviewers for their valuable comments. One reviewer helped to improve the paper by providing a simpler proof of Lemma 3.10, clarifying the statements of Theorems 3.15 and 3.18, and pointing us to Frédéric et al. (2018, Theorem 4.1) which yields Corollary 4.13.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Carsten Conradi.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Conradi, C., Iosif, A. & Kahle, T. Multistationarity in the Space of Total Concentrations for Systems that Admit a Monomial Parametrization. Bull Math Biol 81, 4174–4209 (2019). https://doi.org/10.1007/s11538-019-00639-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11538-019-00639-4

Keywords

Mathematics Subject Classification

Navigation