Chemical Reaction Network Theory for in-silico Biologists

The second is the chemical reaction network theory (TARC), which …. A chemical reaction network is a finite set of responses from a finite set of ….

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Contents

  1. Introduction
  2. Chemical reaction networks
  3. Linearity in chemical reaction networks
  4. The kernel of Aκ
  5. The deficiency formula and some biological examples
  6. Fixed points for which AκΨ(c)=0
  7. Existence of fixed points

References

  1. J. Ross A. Arkin and H. McAdams. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells. Genetics, 149:1633–48, 1998.
  2. J.-P. Aubin. Optima and Equilibria, volume 140 of Graduate Texts in Mathematics. Springer-Verlag, 1993.
  3. C. P. Bagowski and J. E. Ferrell. Bistability in the JNK cascade. Curr. Biol., 11(15):1176–82, 2001.
  4. J. E. Bailey. Complex biology with no parameters. Nature Biotechnology, 19:503–4, 2001.
  5. N. Barkai and S. Leibler. Robustness in simple biochemical networks. Nature, 387:913–7, 1997.
  6. A. Berman and R. J. Plemmons. Nonnegative Matrices in the Mathematical Sciences. Classics in Applied Mathematics. SIAM, 1994.
  7. U. Bhalla, P. Ram, and R. Iyengar. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science, 297:1018–23, 2002.
  8. A. Cornish-Bowden. Fundamentals of Enzyme Kinetics. Portland Press, 2nd edition, 1995.
  9. M. Delbrück. Discussion. In Unités biologiques douées de continuité génétique, pages 33–34. CNRS, 1949.
  10. M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain. Stochastic gene expression in a single cell. Science, 297:1183–6, 2002.
  11. M. Feinberg. Lectures on chemical reaction networks. Notes of lectures given at the Mathematics Research Centre, University of Wisconsin, in 1979.
  12. M. Feinberg. Chemical reaction network structure and the stability of complex isothermal reactors I. The deficiency zero and deficiency one theorems. Chem. Eng. Sci, 42(10):2229–68, 1987.
  13. M. Feinberg. Chemical reaction network structure and the stability of complex isothermal reactors II. Multiple steady states for networks of deficiency one. Chem. Eng. Sci, 43(1):1–25, 1988.
  14. M. Feinberg. The existence and uniqueness of steady states for a class of chemical reaction networks. Arch. Rational Mech. Anal., 132:311–370, 1995.
  15. M. Feinberg. Multiple steady states for chemical reaction networks of deficiency one. Arch. Rational Mech. Anal., 132:371–406, 1995.
  16. M. Feinberg and F. Horn. Chemical mechanism structure and the coincidence of the stoichio-metric and kinetic subspace. Arch. Rational Mech. Anal., 66:83–97, 1977.
  17. A. Goldbeter and D. E. Koshland. An amplified sensitivity arising from covalent modification in biological systems. PNAS, 78(11):6840–6844, 1981.
  18. A. Goldbetter. Biochemical Oscillations and Cellular Rhythms: the molecular bases of periodic and chaotic behaviour. Cambridge University Press, 1996.
  19. B. D. Gompaerts, L. M. Kramer, and P. E. R. Tatham. Signal Transduction. Academic Press, 2002.
  20. M. W. Hirsch and S. Smale. Differential Equations, Dynamical Systems and Linear Algebra. Pure and Applied Mathematics. Academic Press, 1974.
  21. A. Hoffman, A. Levchenko, M. L. Scott, and D. Baltimore. The IκB-NFκB signalling module: temporal control and selective gene activation. Science, 298:1241–5, 2002.
  22. F. Horn and R. Jackson. General mass action kinetics. Arch. Rational Mech. Anal., 47:81–116, 1972.
  23. D. A. Hume. Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood, 96(7):2323–8, 2000.
  24. M. Laurent and N. Kellershon. Multistability: a major means of differentiation and evolution in biological systems. TIBS, 24:418–22, 1999.
  25. J. M. Levsky and R. H. Singer. Gene expression and the myth of the average cell. Trends in Cell Biology, 13(1):4–6, 2003.
  26. E. N. Lorenz. Deterministic aperiodic flow. J. Atmos. Sci., 20:130–41, 1963.
  27. H. Minc. Nonnegative Matrices. Wiley-Interscience Series in Discrete Mathematics and Optimization. John Wiley, 1988.
  28. S. Pedersen, P. L. Bloch, S. Reeh, and F. C. Neidhardt. Patterns of protein synthesis in E. coli: a catlog of the amount of 140 individual proteins at different growth rates. Cell, 14:179–90, 1978.
  29. P. M. Schlosser. A graphical determination of the possibility of multiple steady states in complex isothermal CFSTRs. PhD thesis, University of Rochester, 1988.
  30. P. M. Schlosser and M. Feinberg. A theory of multiple steady states in isothermal homogeneous CFSTRs with many reactions. Chem. Eng. Sci., 49(11):1749–67, 1994.
  31. C. Soulé. Graphic requirements for multistationarity. Preprint, IHES, February 2003.
  32. R. Thomas. On the relation between the logical structure of systems and their ability to generate multiple steady states or sustained oscillations. Springer Series in Synergetics, 9:180–93, 1981.
  33. R. Thomas. Laws for the dynamics of regulatory networks. Int. Jour. Dev. Biol., 42:479–85, 1998.
  34. G. von Dassow, E. Meir, E. M. Munro, and G. M. Odell. The segment polarity network is a robust developmental module. Nature, 406:188–92, 2000.
  35. J. A. Yorke and E. D. Yorke. Metastable chaos: the transition to sustained chaotic behaviour in the Lorentz model. J. Stat. Phys, 21:263–77, 1979.
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