Difference between revisions of "Model Overview"

Latest revision as of 17:10, 16 October 2019

Model scripts

The model scripts for the different scenarios can be found in pdf form here: File:GBL Models.pdf

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

Reaction	Parameter	Values in literature	Units	Mode	Spread	Location parameter (μ)	Scale parameter (σ)
Binding of R₂ to OR operator	$K_{d1},K_{d7}$	0.005−5.8	$nM$	0.299	6.8	0.15471	1.1661
Binding of R₂ to OR operator	$k^{-}_{1}, k^{-}_{7}$	0.09−0.846	$min^{-1}$	0.489	1.98	−0.37642	0.58225
Binding of R₂ to OA operator	$K_{d2},K_{d8}$	0.005−5.8	$nM$	0.299	6.8	0.15471	1.1661
Binding of R₂ to OA operator	$k^{-}_{2},k^{-}_{8}$	0.09−0.846	$min^{-1}$	0.489	1.98	−0.37642	0.58225
Binding of R₂ to A	$K_{d3}$	$10^{4}−10^{6}$	$nM$	$9.9 \cdot 10^{4}$	10.02	13.192	1.2977
Binding of R₂ to A	$k^{-}_{3}$	$38.3-4.46 \cdot 10^{6}$	$min^{-1}$	1879.7	23.13	9.9423	1.5503
Binding of R₂ to C	$K_{d4}$	$0.0011-10400$	$nM$	1.58	730.63	5.9389	2.3412
Binding of R₂ to C	$k^{-}_{4}$	$3 \cdot 10^{-4}-126$	$min^{-1}$	0.816	244	4.2872	2.119
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
Binding of A-R₂ to OA' operator	$k^{-}_{5},k^{-}_{9},k^{-}_{10},k^{-}_{11},k^{-}_{12}$	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
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
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
Antisense interaction between r and a	$K_{ar}$	0.4−89	$nM$	7.8	7.27	3.4665	1.1882
Antisense interaction between r and a	$k^{-}_{ar}$	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
Formation of homo-dimer R₂	$K_{d6}$	2.58-42.9	$nM$	3.89	1.9	1.6716	0.55779
Formation of homo-dimer R₂	$k^{-}_{6}$	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
O_R	0.9592	$nM$	Cell
O_A	0.9592	$nM$	Cell
O_R-R₂	0	$nM$	Cell
O_A-R₂	0	$nM$	Cell
O_A'-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
C_e	0	$nM$	Environment

Difference between revisions of "Model Overview"

Latest revision as of 17:10, 16 October 2019

Contents

Model scripts

List of Model Reactions

Parameters for model reactions

Parameters for cell growth

Initial concentrations of species

Differential equations

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@@ Line 3: / Line 3: @@
 default [[Welcome to the In-Silico Model of γ-butyrolactone regulation in Streptomyces coelicolor|Go back to overview]]
 </imagemap>
+== Model scripts ==
+The model scripts for the different scenarios can be found in pdf form here: [[File:GBL_Models.pdf]]
+== List of Model Reactions ==
+<sup>*1</sup> Reactions taking place only in the scenarios which includes the activating complex <math>AR_{2}</math>
+<sup>*2</sup> Reactions taking place only in the scenarios which includes the antisense RNA interactions
+<sup>*3</sup> Reactions taking place only in the scenarios which include the activation of ''scbA'' by <math>R_{2}</math>
+{|class="wikitable"
+<table border='1' style="text-align:center">
+! Reactions
+|-
+|<math>O_{R} + R_{2} \rightleftharpoons O_{R} \bullet R_{2}</math>
+<math>O_{R}\bullet R_{2} + R_{2} \rightleftharpoons O_{R}\bullet 2R_{2}</math>
+<math>O_{A} + R_{2} \rightleftharpoons O_{A}\bullet R_{2}</math>
+<math>O_{A}\bullet R_{2} + R_{2} \rightleftharpoons O_{A}\bullet 2R_{2}</math>
+<math>A + R_{2} \rightleftharpoons AR_{2}</math> <sup>*1</sup>
+<math>2C + R_{2} \rightleftharpoons C_{2}\bullet R_{2}</math>
+<math>O_{A} + AR_{2} \rightleftharpoons O_{A}\bullet AR_{2}</math> <sup>*1</sup>
+<math>O_{A}\bullet R_{2} + AR_{2} \rightleftharpoons O_{A}\bullet R_{2}\bullet AR_{2}</math> <sup>*1</sup>
+<math>O_{A}\bullet 2R_{2} + AR_{2} \rightleftharpoons O_{A}\bullet 2R_{2}\bullet AR_{2}</math> <sup>*1</sup>
+<math>O_{A}\bullet AR_{2} + R_{2} \rightleftharpoons O_{A}\bullet R_{2}\bullet AR_{2}</math> <sup>*1</sup>
+<math>O_{A}\bullet R_{2}\bullet AR_{2} + R_{2} \rightleftharpoons O_{A}\bullet 2R_{2}\bullet AR_{2}</math> <sup>*1</sup>
+<math>S \xrightarrow{A} C</math>
+<math>O_{R} \rightarrow O_{R} + r</math>
+<math>O_{A} \rightarrow O_{A} + a</math>
+<math>O_{A}\bullet AR_{2} \rightarrow O_{A}\bullet AR_{2} + a</math> <sup>*1</sup>
+<math>O_{A}\bullet R_{2} \rightarrow O_{A}\bullet R_{2} + a</math> <sup>*3</sup>
+<math>O_{A}\bullet 2R_{2} \rightarrow O_{A}\bullet 2R_{2} + a</math> <sup>*3</sup>
+<math>O_{A}\bullet R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet R_{2}\bullet AR_{2} + a</math> <sup>*3</sup>
+<math>O_{A}\bullet 2R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet 2R_{2}\bullet AR_{2} + a</math> <sup>*3</sup>
+<math>a + r \rightleftharpoons r\bullet a</math> <sup>*2</sup>
+<math>r \rightarrow r + R</math>
+<math>a \rightarrow a + A</math>
+<math>2R \rightleftharpoons R_{2}</math>
+<math>C \underset{r \cdot D}{\stackrel{D}{\rightleftharpoons}} C_{e}</math>
+<math>r\rightarrow \varnothing</math>
+<math>R\rightarrow \varnothing</math>
+<math>R_{2}\rightarrow \varnothing</math>
+<math>a\rightarrow \varnothing</math>
+<math>A\rightarrow \varnothing</math>
+<math>C\rightarrow \varnothing</math>
+<math>C_{2}\bullet R_{2}\rightarrow \varnothing</math>
+<math>AR_{2}\rightarrow \varnothing</math> <sup>*1</sup>
+<math>r\bullet a\rightarrow \varnothing</math> <sup>*2</sup>
+<math>C_{e}\rightarrow \varnothing</math>
+<math>O_{R}\bullet R_{2} \rightarrow O_{R}\bullet R_{2} + O_{R}</math>
+<math>O_{R}\bullet 2R_{2} \rightarrow O_{R}\bullet 2R_{2} + O_{R}</math>
+<math>O_{A}\bullet R_{2} \rightarrow O_{A}\bullet R_{2} + O_{A}</math>
+<math>O_{A}\bullet 2R_{2} \rightarrow O_{A}\bullet 2R_{2} + O_{A}</math>
+<math>O_{A}\bullet AR_{2} \rightarrow O_{A}\bullet AR_{2} + O_{A}</math>
+<math>O_{A}\bullet R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet R_{2}\bullet AR_{2} + O_{A}</math>
+<math>O_{A}\bullet 2R_{2}\bullet AR_{2} \rightarrow O_{A}\bullet 2R_{2}\bullet AR_{2} + O_{A}</math>
+|}
 == Parameters for model reactions ==
@@ Line 10: / Line 110: @@
 ! Reaction
 ! Parameter
-! Value
+! Values in literature
 ! Units
-! Distribution
+! Mode
-Mode
+! Spread
-! Confidence
-Interval Factor
 ! Location
 parameter (μ)
@@ Line 22: / Line 120: @@
 |-
 |rowspan="2" |[[Binding of R2 to OR operator |Binding of R<sub>2</sub> to OR operator]]
-|<math>K_{d1}</math>
+|<math>K_{d1},K_{d7}</math>
 |0.005−5.8
 |<math> nM </math>
-|0.15
+|0.299
-|20
+|6.8
-|−0.72886
+|0.15471
-|1.08086
+|1.1661
 |-
-|<math>k^{-}_{1}</math>
+|<math>k^{-}_{1}, k^{-}_{7}</math>
-|0.09−1.2
+|0.09−0.846
 |<math> min^{-1} </math>
-|0.3
+|0.489
-|3.5
+|1.98
-|−0.89899
+|−0.37642
-|0.55225
+|0.58225
 |-
 |rowspan="2" |[[Binding of R2 to OA operator |Binding of R<sub>2</sub> to OA operator]]
-|<math>K_{d2}</math>
+|<math>K_{d2},K_{d8}</math>
 |0.005−5.8
 |<math> nM </math>
-|0.15
+|0.299
-|20
+|6.8
-|−0.72886
+|0.15471
-|1.08086
+|1.1661
 |-
-|<math>k^{-}_{2}</math>
+|<math>k^{-}_{2},k^{-}_{8}</math>
-|0.09−1.2
+|0.09−0.846
 |<math> min^{-1} </math>
-|0.3
+|0.489
-|3.5
+|1.98
-|−0.89899
+|−0.37642
-|0.55225
+|0.58225
 |-
 |rowspan="2" |[[Binding of R2 to A |Binding of R<sub>2</sub> to A]]
 |<math>K_{d3}</math>
-|<math>10^{3}−10^{6}</math>
+|<math>10^{4}−10^{6}</math>
 |<math> nM </math>
-|<math>7 \cdot 10^{4}</math>
+|<math>9.9 \cdot 10^{4}</math>
-|13
+|10.02
-|12.088
+|13.192
-|0.96535
+|1.2977
 |-
 |<math>k^{-}_{3}</math>
-|<math>60-2.9 \cdot 10^{4}</math>
+|<math>38.3-4.46 \cdot 10^{6}</math>
 |<math> min^{-1} </math>
-|<math>1329.8</math>
+|1879.7
-|21.215
+|23.13
-|8.3942
+|9.9423
-|1.0961
+|1.5503
 |-
 |rowspan="2" |[[Binding of R2 to C |Binding of R<sub>2</sub> to C]]
 |<math>K_{d4}</math>
-|<math>10^{-2}-10^{-4}</math>
+|<math>0.0011-10400</math>
 |<math> nM </math>
-|5
+|1.58
-|1000
+|730.63
-|4.5957
+|5.9389
-|1.65856
+|2.3412
 |-
 |<math>k^{-}_{4}</math>
 |<math>3 \cdot 10^{-4}-126</math>
 |<math> min^{-1} </math>
-|1.3
+|0.816
-|100
+|244
-|2.3977
+|4.2872
-|1.46129
+|2.119
 |-
 |rowspan="2" |[[Binding of A-R2 to OA' operator |Binding of A-R<sub>2</sub> to OA' operator]]
-|<math>K_{d5}</math>
+|<math>K_{d5},K_{d9},K_{d10},K_{d11},K_{d12}</math>
 |0.005−5.8
 |<math> nM </math>
-|0.15
+|0.299
-|30
+|6.8
-|−0.4965
+|0.15471
-|1.1835
+|1.1661
 |-
-|<math>k^{-}_{5}</math>
+|<math>k^{-}_{5},k^{-}_{9},k^{-}_{10},k^{-}_{11},k^{-}_{12}</math>
-|0.09−1.2
+|0.09−0.846
 |<math> min^{-1} </math>
-|0.3
+|0.489
-|4
+|1.98
-|−0.8437
+|−0.37642
-|0.6002
+|0.58225
 |-
 |[[Synthesis of C]]
 |<math>K_{C}</math>
-|0.003−0.01
+|0.00315−85.5
 |<math> min^{-1} </math>
-|0.005
+|0.094
-|10
+|60.49
-|−4.5042
+|0.87914
-|0.8911
+|1.8017
 |-
-|[[Transcription of r]]
+|rowspan="3" |[[Transcription of r]]
-|<math>T_{R}</math>
+|<math>\Omega_{R}</math>
 |0.16−8.24
 |<math> min^{-1} </math>
-|0.88
+|0.8346
-|10
+|3.55
-|0.66625
+|0.63056
-|0.8911
+|0.90076
+|-
+|<math>k_{F}</math>
+|18.2−33
+|<math> min^{-1} </math>
+|20.7
+|1.34
+|3.1107
+|0.28276
+|-
+|<math>k_{onR}</math>
+|0.0518-14.5
+|<math> min^{-1} </math>
+|0.867
+|4.09
+|0.78694
+|0.96428
 |-
-|[[Transcription of a]]
+|rowspan="3" |[[Transcription of a]]
-|<math>T_{A}</math>
+|<math>\Omega_{A_{basal}}</math>
+|0.001−0.2
+|<math> min^{-1} </math>
+|0.0037
+|10.93
+|−3.8324
+|1.3259
+|-
+|<math>\Omega_{A}</math>
 |0.11−5.65
 |<math> min^{-1} </math>
-|0.60
+|0.572
-|10
+|3.5
-|0.28326
+|0.2514
-|0.8911
+|0.89956
+|-
+|<math>k_{onA}</math>
+|0.039-8.82
+|<math> min^{-1} </math>
+|0.587
+|3.875
+|0.35255
+|0.94054
 |-
 |rowspan="2" |[[Antisense interaction between r and a]]
 |<math>K_{ar}</math>
-|0.30−60
+|0.4−89
-|<math> min^{-1} </math>
+|<math> nM </math>
-|5
+|7.8
-|10
+|7.27
-|2.4035
+|3.4665
-|0.8911
+|1.1882
 |-
 |<math>k^{-}_{ar}</math>
 |0.006−6
 |<math> min^{-1} </math>
-|0.6
+|0.223
-|10
+|4.8
-|0.2833
+|−0.43359
-|0.8911
+|1.0326
 |-
 |[[Translation of R]]
@@ Line 154: / Line 284: @@
 |0.165−5.86
 |<math> min^{-1} </math>
-|0.89
+|0.744
-|10
+|3.2
-|0.6776
+|0.42952
-|0.8911
+|0.85176
 |-
 |[[Translation of A]]
@@ Line 163: / Line 293: @@
 |0.11−4
 |<math> min^{-1} </math>
-|0.61
+|0.5
-|10
+|3.2
-|0.2998
+|0.053356
-|0.8911
+|0.85327
 |-
 |rowspan="2" |[[Formation of homo-dimer R2 |Formation of homo-dimer R<sub>2</sub>]]
 |<math>K_{d6}</math>
-|35.3−114
+|2.58-42.9
 |<math> nM </math>
-|30
+|3.89
-|30
+|1.9
-|4.8018
+|1.6716
-|1.1835
+|0.55779
 |-
 |<math>k^{-}_{6}</math>
-|2.12−6.84
+|0.144-51.2
 |<math> min^{-1} </math>
-|2
+|1.1997
-|30
+|21.7
-|2.094
+|2.5303
-|1.1835
+|1.5324
 |-
 |[[Degradation of r]]
 |<math>d_{mR}</math>
-|0.03−0.4
+|0.03−0.365
 |<math>min^{-1}</math>
-|0.15
+|0.14
-|3
+|2.06
-|−1.6523
+|−1.5916
-|0.4947
+|0.60824
 |-
 |[[Degradation of R]]
 |<math>d_{R}</math>
-|<math>8.3 \cdot 10^{-4}- 0.0037</math>
+|<math>5.02 \cdot 10^{-4}- 0.00578</math>
 |<math>min^{-1}</math>
-|<math>1.62 \cdot 10^{-3}</math>
+|<math>0.00144</math>
-|100
+|1.78
-|−4.28997
+|−6.2837
-|1.4613
+|0.50981
 |-
 |[[Degradation of R2 |Degradation of R<sub>2</sub>]]
 |<math>d_{R_{2}}</math>
-|<math>8.3 \cdot 10^{-4}- 0.0037</math>
+|<math>5.02 \cdot 10^{-4}- 0.00578</math>
 |<math>min^{-1}</math>
-|<math>1.62 \cdot 10^{-3}</math>
+|<math>0.00144</math>
-|100
+|1.78
-|−4.28997
+|−6.2837
-|1.4613
+|0.50981
 |-
 |[[Degradation of a]]
 |<math>d_{mA}</math>
-|0.03−0.4
+|0.03−0.365
 |<math>min^{-1}</math>
-|0.15
+|0.14
-|3
+|2.06
-|−1.6523
+|−1.5916
-|0.4947
+|0.60824
 |-
 |[[Degradation of A]]
 |<math>d_{A}</math>
-|<math>8.3 \cdot 10^{-4}- 0.0037</math>
+|<math>5.02 \cdot 10^{-4}- 0.00578</math>
 |<math>min^{-1}</math>
-|<math>1.62 \cdot 10^{-3}</math>
+|<math>0.00144</math>
-|100
+|1.78
-|−4.28997
+|−6.2837
-|1.4613
+|0.50981
 |-
 |[[Degradation of C]]
 |<math>d_{C}</math>
-|<math>2.86 \cdot 10^{-4}- 2 \cdot 10^{-2}</math>
+|<math>7.68 \cdot 10^{-5}- 2 \cdot 10^{-2}</math>
 |<math>min^{-1}</math>
-|<math>2 \cdot 10^{-4}</math>
+|<math>0.0032</math>
-|10
+|5.1
-|−7.7231
+|−4.6234
-|0.8911
+|1.0539
 |-
 |[[Degradation of C2-R2 |Degradation of C<sub>2</sub>-R<sub>2</sub>]]
 |<math>d_{CR}</math>
-|<math>8.3 \cdot 10^{-4}- 0.0037</math>
+|<math>5.02 \cdot 10^{-4}- 0.00578</math>
 |<math>min^{-1}</math>
-|<math>1.62 \cdot 10^{-3}</math>
+|<math>0.00144</math>
-|100
+|1.78
-|−4.28997
+|−6.2837
-|1.4613
+|0.50981
 |-
 |[[Degradation of A-R2 |Degradation of A-R<sub>2</sub>]]
 |<math>d_{AR}</math>
-|<math>8.3 \cdot 10^{-4}- 0.0037</math>
+|<math>5.02 \cdot 10^{-4}- 0.00578</math>
 |<math>min^{-1}</math>
-|<math>1.62 \cdot 10^{-3}</math>
+|<math>0.00144</math>
-|100
+|1.78
-|−4.28997
+|−6.2837
-|1.4613
+|0.50981
 |-
 |[[Degradation of r-a]]
 |<math>d_{mRA}</math>
-|0.35−34.7
+|0.35−69.3
 |<math>min^{-1}</math>
-|5
+|4.9
-|6
+|14.1
-|2.1513
+|2.5669
-|0.7361
+|0.98835
 |-
 |[[Diffusion of C and Ce |Diffusion of C and C<sub>e</sub>]]
@@ Line 270: / Line 400: @@
 |0.1−24
 |<math>min^{-1}</math>
-|8
+|2.8
-|2
+|4.27
-|2.188
+|1.9947
-|0.3295
+|0.98233
 |-
 |[[Degradation of Ce]]
 |<math>d_{C}</math>
-|<math>2.86 \cdot 10^{-4}- 2 \cdot 10^{-2}</math>
+|<math>7.68 \cdot 10^{-5}- 2 \cdot 10^{-2}</math>
 |<math>min^{-1}</math>
-|<math>2 \cdot 10^{-4}</math>
+|<math>0.0032</math>
-|10
+|5.1
-|−7.7231
+|−4.6234
-|0.8911
+|1.0539
-|-
-|[[Cellular growth]]
-|<math>μ</math>
-|0.0004−0.011
-|<math>min^{-1}</math>
-|0.001
-|10
-|−6.1137
-|0.8911
 |}
-== Parameters for cell colony growth ==
+== Parameters for cell growth ==
 {|class="wikitable"
 <table border='1' style="text-align:center">
 ! Parameter
-! Value
+! Range of values
 ! Units
 |-
-| <math>τ</math>
+|<math>K</math>
-|<math> 63-1732 </math>
+|<math>7.14 \cdot 10^{12} - 9\cdot 10^{12}</math>
-|<math> min </math>
+|cells
 |-
-| <math>λ</math>
+|<math>N_0</math>
-|<math> 0.8 </math>
+|<math>5 \cdot 10^{10} - 2\cdot 10^{11}</math>
-|<math> - </math>
+|cells
 |-
-| <math>V_{0}</math>
+|<math>\mu_{max}</math>
-|<math> 1.2 </math>
+|<math>0.003368 - 0.007499</math>
-|<math> μm^{3}</math>
+|<math>min^{-1}</math>
 |-
-|<math>V_{tot}</math>
+|<math>v</math>
-|<math> 2 \cdot 10^{−4} </math>
+|<math>0.001482 - 0.5814</math>
-|<math> μl</math>
+|<math>min^{-1}</math>
+|-
+|<math>m</math>
+|<math>0.47 - 2.46</math>
+|n.a.
+|-
+|<math>\lambda</math>
+|<math>330.52 - 883</math>
+|<math>min</math>
 |}
@@ Line 329: / Line 458: @@
 |-
 |O<sub>R</sub>
-|
+|0.9592
 |<math> nM </math>
 |Cell
 |-
 | O<sub>A</sub>
-|
+|0.9592
 |<math> nM </math>
 |Cell
-|-
-| O<sub>A</sub>'
-|
-|<math> nM </math>
-| Cell
 |-
 | O<sub>R</sub>-R<sub>2</sub>
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | O<sub>A</sub>-R<sub>2</sub>
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | O<sub>A</sub>'-AR<sub>2</sub>
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | r
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | a
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | r-a
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | R
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | R<sub>2</sub>
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | A
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | C
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | AR<sub>2</sub>
-|
+|0
 |<math> nM </math>
 | Cell
 |-
 | C<sub>2</sub>R<sub>2</sub>
-|
+| 0
 |<math> nM </math>
 | Cell
 |-
 | C<sub>e</sub>
-|
+| 0
 |<math> nM </math>
 | Environment
 |}
 == Differential equations ==
-To be completed.
+[[Image:Diffeq.png|850px]]