Model Overview

List of Model Reactions

^*1 Reactions taking place only in the scenario which includes the activating complex $AR_{2}$

^*2 Reactions taking place only in the scenario which includes the antisense RNA interactions

Reactions

$O_{R} + R_{2} \rightleftharpoons O_{R}-R_{2}$ $O_{R}-R_{2} + R_{2} \rightleftharpoons O_{R}-2R_{2}$ $O_{A} + R_{2} \rightleftharpoons O_{A}-R_{2}$ $O_{A}-R_{2} + R_{2} \rightleftharpoons O_{A}-2R_{2}$ $A + R_{2} \rightleftharpoons AR_{2}$ *1 $2C + R_{2} \rightleftharpoons C_{2}-R_{2}$ $O_{A} + AR_{2} \rightleftharpoons O_{A}-AR_{2}$ *1 $O_{A}-R_{2} + AR_{2} \rightleftharpoons O_{A}-R_{2}-AR_{2}$ *1 $O_{A}-2R_{2} + AR_{2} \rightleftharpoons O_{A}-2R_{2}-AR_{2}$ *1 $O_{A}-AR_{2} + R_{2} \rightleftharpoons O_{A}-R_{2}-AR_{2}$ *1 $O_{A}-R_{2}-AR_{2} + R_{2} \rightleftharpoons O_{A}-2R_{2}-AR_{2}$ *1 $S \xrightarrow{A} C$ $O_{R} \rightarrow O_{R} + r$ $O_{A} \rightarrow O_{A} + a$ $O_{A}-AR_{2} \rightarrow O_{A}-AR_{2} + a$ *1 $a + r \rightleftharpoons r-a$ *2 $r \rightarrow r + R$ $a \rightarrow a + A$ $2R \rightleftharpoons R_{2}$ $C \underset{r \cdot D}{\stackrel{D}{\rightleftharpoons}} C_{e}$ $r\rightarrow \varnothing$ $R\rightarrow \varnothing$ $R_{2}\rightarrow \varnothing$ $a\rightarrow \varnothing$ $A\rightarrow \varnothing$ $C\rightarrow \varnothing$ $C_{2}-R_{2}\rightarrow \varnothing$ $AR_{2}\rightarrow \varnothing$ *1 $r-a\rightarrow \varnothing$ *2 $C_{e}\rightarrow \varnothing$

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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	$K_{d1},K_{d7}$	0.005−5.8	$nM$	0.299	46.7	0.45876	1.2899
	$k^{-}_{1}, k^{-}_{7}$	0.09−0.846	$min^{-1}$	0.489	3.9	−0.36413	0.59272
Binding of R2 to OA operator	$K_{d2},K_{d8}$	0.005−5.8	$nM$	0.299	46.7	0.45876	1.2899
	$k^{-}_{2},k^{-}_{8}$	0.09−0.846	$min^{-1}$	0.489	3.9	−0.36413	0.59272
Binding of R2 to A	$K_{d3}$	$10^{4}−10^{6}$	$nM$	$4.6 \cdot 10^{5}$	100.4	15.184	1.4621
	$k^{-}_{3}$	$38.3-4.46 \cdot 10^{6}$	$min^{-1}$	$13073.73$	341	12.4141	1.7134
Binding of R2 to C	$K_{d4}$	$0.0011-10400$	$nM$	1	100000	7.934	2.7911
	$k^{-}_{4}$	$3 \cdot 10^{-4}-126$	$min^{-1}$	0.82	59545	6.4365	2.5767
Binding of A-R2 to OA' operator	$K_{d5},K_{d9},K_{d10},K_{d11},K_{d12}$	0.005−5.8	$nM$	0.299	46.7	0.45876	1.2899
	$k^{-}_{5},k^{-}_{9},k^{-}_{10},k^{-}_{11},k^{-}_{12}$	0.09−0.846	$min^{-1}$	0.489	3.9	−0.36413	0.59272
Synthesis of C	$K_{C}$	0.0011−0.01	$min^{-1}$	0.0033	3	−5.4531	0.49744
Transcription of r	$\Omega_{R}$	0.16−8.24	$min^{-1}$	0.8346	12.6	0.73383	0.95636
	$k_{F}$	18.2−33	$min^{-1}$	20.4	1.74	3.0886	0.2686
	$k_{onR}$	0.0518-14.5	$min^{-1}$	0.867	16.74	0.92634	1.034
Transcription of a	$\Omega_{A}$	0.11−5.65	$min^{-1}$	0.57	12.5	0.354505	0.95491
	$k_{onA}$	0.039-8.82	$min^{-1}$	0.587	15	0.47762	1.0048
Antisense interaction between r and a	$K_{ar}$	0.4−89	$nM$	7.8	52.8	3.7933	1.3186
	$k^{-}_{ar}$	0.006−6	$min^{-1}$	0.22	23.2	−0.24716	1.1192
Translation of R	$P_{R}$	0.165−5.86	$min^{-1}$	0.74	10.3	0.50964	0.89756
Translation of A	$P_{A}$	0.11−4	$min^{-1}$	0.51	10.3	0.13413	0.89936
Formation of homo-dimer R2	$K_{d6}$	2.58-42.9	$nM$	30	30	4.8018	1.1835
	$k^{-}_{6}$	0.144-51.2	$min^{-1}$	2	30	2.094	1.1835
Degradation of r	$d_{mR}$	0.03−0.365	$min^{-1}$	0.14	4.24	−1.5762	0.62077
Degradation of R	$d_{R}$	$8.3 \cdot 10^{-4}- 0.0037$	$min^{-1}$	$0.0016$	2.5	−6.2752	0.4285
Degradation of R2	$d_{R_{2}}$	$8.3 \cdot 10^{-4}- 0.0037$	$min^{-1}$	$0.0016$	2.5	−6.2752	0.4285
Degradation of a	$d_{mA}$	0.03−0.365	$min^{-1}$	0.14	4.24	−1.5762	0.62077
Degradation of A	$d_{A}$	$8.3 \cdot 10^{-4}- 0.0037$	$min^{-1}$	$0.0016$	2.5	−6.2752	0.4285
Degradation of C	$d_{C}$	$7.68 \cdot 10^{-5}- 2 \cdot 10^{-2}$	$min^{-1}$	$0.003$	25.8	−4.4205	1.1461
Degradation of C2-R2	$d_{CR}$	$8.3 \cdot 10^{-4}- 0.0037$	$min^{-1}$	$0.0016$	2.5	−6.2752	0.4285
Degradation of A-R2	$d_{AR}$	$8.3 \cdot 10^{-4}- 0.0037$	$min^{-1}$	$0.0016$	2.5	−6.2752	0.4285
Degradation of r-a	$d_{mRA}$	0.35−69.3	$min^{-1}$	0.739	200.4	2.2813	1.6074
Diffusion of C and Ce	$D$	0.1−24	$min^{-1}$	2.8	18.2	2.1457	1.0564
Degradation of Ce	$d_{C}$	$7.68 \cdot 10^{-5}- 2 \cdot 10^{-2}$	$min^{-1}$	$0.003$	25.8	−4.4205	1.1461
Cellular growth	Failed to parse (PNG conversion failed; check for correct installation of latex and dvipng (or dvips + gs + convert)): μ	0.0004−0.0107	$min^{-1}$	0.0022	7.5	−5.4517	0.80808

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	0.9592	$nM$	Cell
OA	0.9592	$nM$	Cell
OR-R2	0	$nM$	Cell
OA-R2	0	$nM$	Cell
OA'-AR2	0	$nM$	Cell
r	0	$nM$	Cell
a	0	$nM$	Cell
r-a	0	$nM$	Cell
R	0	$nM$	Cell
R2	0	$nM$	Cell
A	0	$nM$	Cell
C	0	$nM$	Cell
AR2	0	$nM$	Cell
C2R2	0	$nM$	Cell
Ce	0	$nM$	Environment

Differential equations

To be completed.