Model Overview

List of Model Reactions

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

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

^*3 Reactions taking place only in the scenarios which include the activation of scbA by $R_{2}$

Reactions

$O_{R} + R_{2} \rightleftharpoons O_{R} \bullet R_{2}$ $O_{R}\bullet R_{2} + R_{2} \rightleftharpoons O_{R}\bullet 2R_{2}$ $O_{A} + R_{2} \rightleftharpoons O_{A}\bullet R_{2}$ $O_{A}\bullet R_{2} + R_{2} \rightleftharpoons O_{A}\bullet 2R_{2}$ $A + R_{2} \rightleftharpoons AR_{2}$ *1 $2C + R_{2} \rightleftharpoons C_{2}\bullet R_{2}$ $O_{A} + AR_{2} \rightleftharpoons O_{A}\bullet AR_{2}$ *1 $O_{A}\bullet R_{2} + AR_{2} \rightleftharpoons O_{A}\bullet R_{2}\bullet AR_{2}$ *1 $O_{A}\bullet 2R_{2} + AR_{2} \rightleftharpoons O_{A}\bullet 2R_{2}\bullet AR_{2}$ *1 $O_{A}\bullet AR_{2} + R_{2} \rightleftharpoons O_{A}\bullet R_{2}\bullet AR_{2}$ *1 $O_{A}\bullet R_{2}\bullet AR_{2} + R_{2} \rightleftharpoons O_{A}\bullet 2R_{2}\bullet AR_{2}$ *1 $S \xrightarrow{A} C$ $O_{R} \rightarrow O_{R} + r$ $O_{A} \rightarrow O_{A} + a$ $O_{A}\bullet AR_{2} \rightarrow O_{A}\bullet AR_{2} + a$ *1 $O_{A}\bullet R_{2} \rightarrow O_{A}\bullet R_{2} + a$ *3 $O_{A}\bullet 2R_{2} \rightarrow O_{A}\bullet 2R_{2} + a$ *3 $O_{A}\bullet R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet R_{2}\bullet AR_{2} + a$ *3 $O_{A}\bullet 2R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet 2R_{2}\bullet AR_{2} + a$ *3 $a + r \rightleftharpoons r\bullet a$ *2 $r \rightarrow r + R$ $a \rightarrow a + A$ $2R \rightleftharpoons R_{2}$ $C \underset{r \cdot D}{\stackrel{D}{\rightleftharpoons}} C_{e}$ $r\rightarrow \varnothing$ $R\rightarrow \varnothing$ $R_{2}\rightarrow \varnothing$ $a\rightarrow \varnothing$ $A\rightarrow \varnothing$ $C\rightarrow \varnothing$ $C_{2}\bullet R_{2}\rightarrow \varnothing$ $AR_{2}\rightarrow \varnothing$ *1 $r\bullet a\rightarrow \varnothing$ *2 $C_{e}\rightarrow \varnothing$ $O_{R}\bullet R_{2} \rightarrow O_{R}\bullet R_{2} + O_{R}$ $O_{R}\bullet 2R_{2} \rightarrow O_{R}\bullet 2R_{2} + O_{R}$ $O_{A}\bullet R_{2} \rightarrow O_{A}\bullet R_{2} + O_{A}$ $O_{A}\bullet 2R_{2} \rightarrow O_{A}\bullet 2R_{2} + O_{A}$ $O_{A}\bullet AR_{2} \rightarrow O_{A}\bullet AR_{2} + O_{A}$ $O_{A}\bullet R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet R_{2}\bullet AR_{2} + O_{A}$ $O_{A}\bullet 2R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet 2R_{2}\bullet AR_{2} + O_{A}$

Parameters for model reactions

Failed to parse (lexing error): {|class="wikitable" <table border='1' style="text-align:center"> ! Reaction ! Parameter ! Values in literature ! Units ! Mode ! Spread ! Location parameter (μ) ! Scale parameter (σ) |- |rowspan="2" |[[Binding of R2 to OR operator |Binding of R₂ to OR operator]] |<math>K_{d1},K_{d7} |0.005−5.8 |$nM$ |0.299 |6.8 |0.15471 |1.1661 |- |$k^{-}_{1}, k^{-}_{7}$ |0.09−0.846 |$min^{-1}$ |0.489 |1.98 |−0.37642 |0.58225 |- |rowspan="2" |Binding of R₂ to OA operator |$K_{d2},K_{d8}$ |0.005−5.8 |$nM$ |0.299 |6.8 |0.15471 |1.1661 |- |$k^{-}_{2},k^{-}_{8}$ |0.09−0.846 |$min^{-1}$ |0.489 |1.98 |−0.37642 |0.58225 |- |rowspan="2" |Binding of R₂ to A |$K_{d3}$ |$10^{4}−10^{6}$ |$nM$ |$9.9 \cdot 10^{4}$ |10.02 |13.192 |1.2977 |- |$k^{-}_{3}$ |$38.3-4.46 \cdot 10^{6}$ |$min^{-1}$ |1879.7 |23.13 |9.9423 |1.5503 |- |rowspan="2" |Binding of R₂ to C |$K_{d4}$ |$0.0011-10400$ |$nM$ |1.58 |730.63 |5.9389 |2.3412 |- |$k^{-}_{4}$ |$3 \cdot 10^{-4}-126$ |$min^{-1}$ |0.816 |244 |4.2872 |2.119 |- |rowspan="2" |Binding of A-R₂ to OA' operator |$K_{d5},K_{d9},K_{d10},K_{d11},K_{d12}$ |0.005−5.8 |$nM$ |0.299 |6.8 |0.15471 |1.1661 |- |$k^{-}_{5},k^{-}_{9},k^{-}_{10},k^{-}_{11},k^{-}_{12}$ |0.09−0.846 |$min^{-1}$ |0.489 |1.98 |−0.37642 |0.58225 |- |Synthesis of C |$K_{C}$ |0.00315−85.5 |$min^{-1}$ |0.094 |60.49 |0.87914 |1.8017 |- |rowspan="3" |Transcription of r |$\Omega_{R}$ |0.16−8.24 |$min^{-1}$ |0.8346 |3.55 |0.63056 |0.90076 |- |$k_{F}$ |18.2−33 |$min^{-1}$ |20.7 |1.34 |3.1107 |0.28276 |- |$k_{onR}$ |0.0518-14.5 |$min^{-1}$ |0.867 |4.09 |0.78694 |0.96428 |- |rowspan="3" |Transcription of a |$\Omega_{A_{basal}}$ |0.001−0.2 |$min^{-1}$ |0.0037 |10.93 |−3.8324 |1.3259 |- |$\Omega_{A}$ |0.11−5.65 |$min^{-1}$ |0.572 |3.5 |0.2514 |0.89956 |- |$k_{onA}$ |0.039-8.82 |$min^{-1}$ |0.587 |3.875 |0.35255 |0.94054 |- |rowspan="2" |Antisense interaction between r and a |$K_{ar}$ |0.4−89 |$nM$ |7.8 |7.27 |3.4665 |1.1882 |- |$k^{-}_{ar}$ |0.006−6 |$min^{-1}$ |0.223 |4.8 |−0.43359 |1.0326 |- |Translation of R |$P_{R}$ |0.165−5.86 |$min^{-1}$ |0.744 |3.2 |0.42952 |0.85176 |- |Translation of A |$P_{A}$ |0.11−4 |$min^{-1}$ |0.5 |3.2 |0.053356 |0.85327 |- |rowspan="2" |Formation of homo-dimer R₂ |$K_{d6}$ |2.58-42.9 |$nM$ |3.89 |1.9 |1.6716 |0.55779 |- |$k^{-}_{6}$ |0.144-51.2 |$min^{-1}$ |1.1997 |21.7 |2.5303 |1.5324 |- |Degradation of r |$d_{mR}$ |0.03−0.365 |$min^{-1}$ |0.14 |2.06 |−1.5916 |0.60824 |- |Degradation of R |$d_{R}$ |$5.02 \cdot 10^{-4}- 0.00578$ |$min^{-1}$ |$0.00144$ |1.78 |−6.2837 |0.50981 |- |Degradation of R₂ |$d_{R_{2}}$ |$5.02 \cdot 10^{-4}- 0.00578$ |$min^{-1}$ |$0.00144$ |1.78 |−6.2837 |0.50981 |- |Degradation of a |$d_{mA}$ |0.03−0.365 |$min^{-1}$ |0.14 |2.06 |−1.5916 |0.60824 |- |Degradation of A |$d_{A}$ |$5.02 \cdot 10^{-4}- 0.00578$ |$min^{-1}$ |$0.00144$ |1.78 |−6.2837 |0.50981 |- |Degradation of C |$d_{C}$ |$7.68 \cdot 10^{-5}- 2 \cdot 10^{-2}$ |$min^{-1}$ |$0.0032$ |5.1 |−4.6234 |1.0539 |- |Degradation of C₂-R₂ |$d_{CR}$ |$5.02 \cdot 10^{-4}- 0.00578$ |$min^{-1}$ |$0.00144$ |1.78 |−6.2837 |0.50981 |- |Degradation of A-R₂ |$d_{AR}$ |$5.02 \cdot 10^{-4}- 0.00578$ |$min^{-1}$ |$0.00144$ |1.78 |−6.2837 |0.50981 |- |Degradation of r-a |$d_{mRA}$ |0.35−69.3 |$min^{-1}$ |4.9 |14.1 |2.5669 |0.98835 |- |Diffusion of C and C_e |$D$ |0.1−24 |$min^{-1}$ |2.8 |4.27 |1.9947 |0.98233 |- |Degradation of Ce |$d_{C}$ |$7.68 \cdot 10^{-5}- 2 \cdot 10^{-2}$ |$min^{-1}$ |$0.0032$ |5.1 |−4.6234 |1.0539 |}

Parameters for cell growth

Parameter	Range of values	Units
$K$	$7.14 \cdot 10^{12} - 9\cdot 10^{12}$	cells
$N_0$	$5 \cdot 10^{10} - 2\cdot 10^{11}$	cells
$\mu_{max}$	$0.003368 - 0.007499$	$min^{-1}$
$v$	$0.001482 - 0.5814$	$min^{-1}$
$m$	$0.47 - 2.46$	n.a.
$\lambda$	$330.52 - 883$	$min$

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