Table 1.

Reactions in model A of the Hes1 GRN, their localisation, description and baseline parameter values used

Reaction	Localisation	Description	Parameter values
${\mathit{\text{dimer}}}_{\text{nuc}}+P_f\stackrel{k_1}{\to }{P}_o$	Gene	Promoter occupation	k1 = 1.00 × 109 M−1 min−1 (Tafvizi et al. 2011)
$P_o\stackrel{k_2}{\to }{P}_f$	Gene	Promoter liberation	k2 = 0.10 min−1 (estimate)
$P_f\stackrel{{\alpha }_m}{\to }mRN{A}_{\text{nuc}}$	Gene	mRNA transcription	αm = 3.00 min−1 (Barrio et al. 2006)
$P_o\stackrel{{\alpha }_m/\gamma }{\to }mRN{A}_{\text{nuc}}$	Gene	mRNA transcription (reduced)	αm = 3.00 min−1, γ = 100.00 (Barrio et al. 2006; Takebayashi et al. 1994)
$mRN{A}_{\text{cyt}}\stackrel{{\alpha }_p}{\to }{\mathit{\text{monomer}}}_{\text{cyt}}+mRN{A}_{\text{cyt}}$	Cytoplasm	Protein translation	αp = 1.00 min−1 (Barrio et al. 2006)
$mRN{A}_{\text{cyt}}\stackrel{{\mu }_m}{\to }\varphi$	Cytoplasm	mRNA degradation	μm = 0.031 min−1 (Hirata et al. 2002)
$mRN{A}_{\text{nuc}}\stackrel{{\mu }_m}{\to }\varphi$	Nucleus	mRNA degradation	μm = 0.031 min−1 (Hirata et al. 2002)
${\mathit{\text{monomer}}}_{\text{cyt}}\stackrel{{\mu }_p}{\to }\varphi$	Cytoplasm	Monomer degradation	μp = 0.108 min−1 (Momiji and Monk 2008)
${\mathit{\text{dimer}}}_{\text{cyt}}\stackrel{{\mu }_p/\zeta }{\to }\varphi$	Cytoplasm	Dimer degradation	μp = 0.108 min−1, ζ = 3.00 (Hirata et al. 2002; Momiji and Monk 2008)
${\mathit{\text{dimer}}}_{\text{nuc}}\stackrel{{\mu }_p/\zeta }{\to }\varphi$	Nucleus	Dimer degradation	μp = 0.108 min−1, ζ = 3.00 (Hirata et al. 2002; Momiji and Monk 2008)
${\mathit{\text{monomer}}}_{\text{cyt}}+{\mathit{\text{monomer}}}_{\text{cyt}}\stackrel{{\beta }_1}{\to }{\mathit{\text{dimer}}}_{\text{cyt}}$	Cytoplasm	Monomer dimerisation	β1 = 1.00 × 109 M−1 min−1 (estimate)
${\mathit{\text{dimer}}}_{\text{cyt}}\stackrel{{\beta }_2}{\to }{\mathit{\text{monomer}}}_{\text{cyt}}+{\mathit{\text{monomer}}}_{\text{cyt}}$	Cytoplasm	Dimer detachment	β2 = 0.10 min−1 (estimate)
$mRN{A}_{\text{nuc}}+\mathit{\text{pore}}\stackrel{k_{\text{pore}}}{\to }mRN{A}_{n{m}_p}$	Nuclear membrane	mRNA binding to nuclear pore	kpore = 1.00 × 109 M−1 min−1 (estimate)
$mRN{A}_{n{m}_p}\stackrel{k_{\text{rel}}}{\to }mRN{A}_{\text{cyt}}+\mathit{\text{pore}}$	Nuclear membrane	Release of mRNA to cytoplasm	krel = 6.00 × 103 min−1 (estimate)
${\mathit{\text{dimer}}}_{\text{cyt}}+\mathit{\text{pore}}\stackrel{k_{\text{pore}}}{\to }{\mathit{\text{dimer}}}_{n{m}_p}$	Nuclear membrane	Dimer binding to nuclear pore	kpore = 1.0.0 × 109 M−1 min−1 (estimate)
${\mathit{\text{dimer}}}_{n{m}_p}\stackrel{k_{\text{rel}}}{\to }{\mathit{\text{dimer}}}_{\text{nuc}}+\mathit{\text{pore}}$	Nuclear membrane	Release of dimer to nucleus	krel = 6.00 × 103 min−1 (estimate)