TABLE II.

synNotch signaling model.

No.	Equation	Reaction velocities	Parameters	Description
1	$$R+L\hspace{0.17em}\rightleftharpoons \hspace{0.17em}C$$ (1)	$k_{\mathrm{on}}\mathrm{R}\left(t\right)\mathrm{L}\left(t\right),\hspace{0.17em}{\hspace{0.17em}k}_{\mathrm{off}}\mathrm{C}\left(t\right)$	$k_{\mathrm{on}},k_{\mathrm{off}}=$ the same as endogenous receptor	Binding kinetics
2	$$C\to C_{*}+TF$$ (2)	$k_{\mathrm{cleave}}\mathrm{C}\left(t\right)$	$k_{\mathrm{cleave}}=1\hspace{0.17em}{\mathrm{\text{min}}}^{-1}$ (assumed)	Detachment of TF
3	$$C_{*}\to L$$ (3)	$k_{\mathrm{int}}{\mathrm{C}}_{*}\left(t\right)$	$k_{\mathrm{int}}=$ the same as endogenous receptor	Ligand recycling
4	$$TF\to \varnothing$$ (4)	$k_{\mathrm{deg}}\text{TF}\left(t\right)$	$k_{\mathrm{deg}}=$ the same as phospho-protein decay	Degradation of TF
5	$$\varnothing \to \mathrm{RNA}$$ (5)	$k_{\mathrm{trpt}}\mathrm{u}\frac{1}{1+{\left(\frac{K_{\mathrm{M}}}{\mathrm{TF}\left(t\right)}\right)}^n}$	$k_{\mathrm{trpt}}=600\hspace{0.17em}\mathrm{nt}\times {\mathrm{\text{min}}}^{-1}$ (calculated65)	RNA production
			$K_{\mathrm{M}}=1\hspace{0.17em}{\mathrm{\text{min}}}^{-1}$ (assumed)
6	$$\mathrm{RNA}\to \mathrm{RNA}+\mathrm{protein}$$ (6)	$k_{\mathrm{trsl}}\text{RNA}\left(t\right)$	$k_{\mathrm{trsl}}=600\hspace{0.17em}\mathrm{aa}\times {\mathrm{\text{min}}}^{-1}$ (calculated65)	Protein production
7	$$\mathrm{RNA}\to \varnothing$$ (7)	$k_{\mathrm{deg}\hspace{0.17em}\mathrm{RNA}}\text{RNA}\left(t\right)$	$k_{\mathrm{deg}\hspace{0.17em}\mathrm{RNA}}=0.0462\hspace{0.17em}{\mathrm{\text{min}}}^{-1}$ (calculated66,67)	RNA degradation