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Supporting information for Gonze *et al.* (January 15, 2002) *Proc. Natl. Acad. Sci. USA*, 10.1073/pnas.022628299.

Supporting Figure 6
**Fig. 6.** Scheme of the deterministic five-variable core model considered for circadian oscillations, with indication of parameters characterizing the different steps [Goldbeter, A. (1995) *Proc. R. Soc. London Ser. B* **261,** 319–324 and Goldbeter, A. (1996) *Biochemical Oscillations and Cellular Rhythms: The Molecular Bases of Periodic and Chaotic Behavior* (Cambridge Univ. Press, Cambridge, U.K.)]. The model is based on the repression exerted by the nuclear form of a clock protein (P_{N}) on the transcription of its gene into mRNA (M_{P}). mRNA is synthetized in the nucleus and transferred to the cytosol, where it accumulates at a maximum rate *v*_{s}; there it is degraded by an enzyme of maximum rate *v*_{m} and Michaelis constant *K*_{m}. The rate of synthesis of the protein P_{0}, proportional to M_{P}, is characterized by an apparent first-order rate constant *k*_{s}. Parameters *v*_{i} and *K*_{i} (*i* = 1,...,4) denote the maximum rate(s) and Michaelis constant(s) of the kinase and phosphatase involved in the reversible phosphorylation of *P*_{0} into *P*_{1} and *P*_{1} into *P*_{2}, respectively. The fully phosphorylated form *P*_{2} is degraded by an enzyme of maximum rate *v*_{d} and Michaelis constant *K*_{d} and transported into the nucleus at a rate characterized by the apparent first-order rate constant *k*_{1}. Transport of the nuclear form of the clock protein (*P*_{N}) into the cytosol is characterized by the apparent first-order rate constant *k*_{2}. The negative feedback exerted by the nuclear clock protein on gene transcription is described by an equation of the Hill type, in which *n* denotes the degree of cooperativity and *K*_{I} denotes the threshold constant for repression (see *Appendix*, *Kinetic Equations of the Deterministic Model*).

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