Model Overview

List of Model Reactions

Reaction
$O_{R} + R_{2} \rightleftharpoons O_{R}-R_{2}$	$O_{R}-R_{2} + R_{2} \rightleftharpoons O_{R}-2R_{2}$

Parameters for model reactions

Reaction	Parameter	Value	Units	Distribution Mode	Confidence Interval Factor	Location parameter (μ)	Scale parameter (σ)
Binding of R2 to OR operator	$K_{d1}$	0.005−5.8	$nM$	0.15	20	−0.72886	1.08086
	$k^{-}_{1}$	0.09−1.2	$min^{-1}$	0.3	3.5	−0.89899	0.55225
Binding of R2 to OA operator	$K_{d2}$	0.005−5.8	$nM$	0.15	20	−0.72886	1.08086
	$k^{-}_{2}$	0.09−1.2	$min^{-1}$	0.3	3.5	−0.89899	0.55225
Binding of R2 to A	$K_{d3}$	Failed to parse (Cannot store math image on filesystem.): 10^{3}−10^{6}	$nM$	Failed to parse (Cannot store math image on filesystem.): 7 \cdot 10^{4}	13	12.088	0.96535
	$k^{-}_{3}$	$60-2.9 \cdot 10^{4}$	$min^{-1}$	Failed to parse (Cannot store math image on filesystem.): 1329.8	21.215	8.3942	1.0961
Binding of R2 to C	$K_{d4}$	Failed to parse (Cannot store math image on filesystem.): 10^{-2}-10^{-4}	$nM$	5	1000	4.5957	1.65856
	$k^{-}_{4}$	$3 \cdot 10^{-4}-126$	$min^{-1}$	1.3	100	2.3977	1.46129
Binding of A-R2 to OA' operator	$K_{d5}$	0.005−5.8	$nM$	0.15	30	−0.4965	1.1835
	$k^{-}_{5}$	0.09−1.2	$min^{-1}$	0.3	4	−0.8437	0.6002
Synthesis of C	$K_{C}$	0.003−0.01	$min^{-1}$	0.005	10	−4.5042	0.8911
Transcription of r	$T_{R}$	0.16−8.24	$min^{-1}$	0.88	10	0.66625	0.8911
Transcription of a	$T_{A}$	0.11−5.65	$min^{-1}$	0.60	10	0.28326	0.8911
Antisense interaction between r and a	$K_{ar}$	0.30−60	$min^{-1}$	5	10	2.4035	0.8911
	$k^{-}_{ar}$	0.006−6	$min^{-1}$	0.6	10	0.2833	0.8911
Translation of R	$P_{R}$	0.165−5.86	$min^{-1}$	0.89	10	0.6776	0.8911
Translation of A	$P_{A}$	0.11−4	$min^{-1}$	0.61	10	0.2998	0.8911
Formation of homo-dimer R2	$K_{d6}$	35.3−114	$nM$	30	30	4.8018	1.1835
	$k^{-}_{6}$	2.12−6.84	$min^{-1}$	2	30	2.094	1.1835
Degradation of r	$d_{mR}$	0.03−0.4	$min^{-1}$	0.15	3	−1.6523	0.4947
Degradation of R	$d_{R}$	$8.3 \cdot 10^{-4}- 0.0037$	$min^{-1}$	Failed to parse (Cannot store math image on filesystem.): 1.62 \cdot 10^{-3}	100	−4.28997	1.4613
Degradation of R2	$d_{R_{2}}$	$8.3 \cdot 10^{-4}- 0.0037$	$min^{-1}$	Failed to parse (Cannot store math image on filesystem.): 1.62 \cdot 10^{-3}	100	−4.28997	1.4613
Degradation of a	$d_{mA}$	0.03−0.4	$min^{-1}$	0.15	3	−1.6523	0.4947
Degradation of A	$d_{A}$	$8.3 \cdot 10^{-4}- 0.0037$	$min^{-1}$	Failed to parse (Cannot store math image on filesystem.): 1.62 \cdot 10^{-3}	100	−4.28997	1.4613
Degradation of C	$d_{C}$	Failed to parse (Cannot store math image on filesystem.): 2.86 \cdot 10^{-4}- 2 \cdot 10^{-2}	$min^{-1}$	Failed to parse (Cannot store math image on filesystem.): 2 \cdot 10^{-4}	10	−7.7231	0.8911
Degradation of C2-R2	$d_{CR}$	$8.3 \cdot 10^{-4}- 0.0037$	$min^{-1}$	Failed to parse (Cannot store math image on filesystem.): 1.62 \cdot 10^{-3}	100	−4.28997	1.4613
Degradation of A-R2	$d_{AR}$	$8.3 \cdot 10^{-4}- 0.0037$	$min^{-1}$	Failed to parse (Cannot store math image on filesystem.): 1.62 \cdot 10^{-3}	100	−4.28997	1.4613
Degradation of r-a	$d_{mRA}$	0.35−34.7	$min^{-1}$	5	6	2.1513	0.7361
Diffusion of C and Ce	$D$	0.1−24	$min^{-1}$	8	2	2.188	0.3295
Degradation of Ce	$d_{C}$	Failed to parse (Cannot store math image on filesystem.): 2.86 \cdot 10^{-4}- 2 \cdot 10^{-2}	$min^{-1}$	Failed to parse (Cannot store math image on filesystem.): 2 \cdot 10^{-4}	10	−7.7231	0.8911
Cellular growth	Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): μ	0.0004−0.011	$min^{-1}$	0.001	10	−6.1137	0.8911

Parameters for cell colony growth

Parameter	Value	Units
Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): τ	$63-1732$	$min$
Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): λ	$0.8$	$-$
$V_{0}$	$1.2$	$μm^{3}$
$V_{tot}$	$2 \cdot 10^{−4}$	$μl$

Initial concentrations of species

Species	Initial concentration	Units	Compartment
OR		$nM$	Cell
OA		$nM$	Cell
OA'		$nM$	Cell
OR-R2		$nM$	Cell
OA-R2		$nM$	Cell
OA'-AR2		$nM$	Cell
r		$nM$	Cell
a		$nM$	Cell
r-a		$nM$	Cell
R		$nM$	Cell
R2		$nM$	Cell
A		$nM$	Cell
C		$nM$	Cell
AR2		$nM$	Cell
C2R2		$nM$	Cell
Ce		$nM$	Environment

Differential equations

To be completed.