Team:Paris/Modeling/f4

From 2008.igem.org

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[[Image:f4DCA.png|thumb]]
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{{Paris/Menu}}
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We have [OmpR<sup>*</sup>] = {coef<sub>omp</sub>}''expr(pTet)'' = {coef<sub>omp</sub>} &#131;1([aTc]<sub>i</sub>)
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{{Paris/Header|Method & Algorithm : &#131;4}}
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<center> = act_''pFliA'' </center>
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<br>
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and [FliA] = {coef<sub>FliA</sub>}''expr(pBad)'' = {coef<sub>FliA</sub>} &#131;2([arab]<sub>i</sub>)
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[[Image:f4DCA.png|thumb|Specific Plasmid Characterisation for &#131;4]]
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So, at steady-states,
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According to the characterization plasmid (see right) and to our modeling, in the '''exponential phase of growth''', at the steady state,
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[[Image:F3ompfinal.jpg|center]]
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we have ''' [''FlhDC'']<sub>''real''</sub> = {coef<sub>''flhDC''</sub>} &#131;1([aTc]<sub>i</sub>) '''
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and ''' [''FliA'']<sub>''real''</sub> = {coef<sub>''fliA''</sub>} &#131;2([arab]<sub>i</sub>) '''
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<br><br>
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but we use ''' [aTc]<sub>i</sub> = Inv_&#131;1( [''FlhDC''] ) '''
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and        ''' [arab]<sub>i</sub> = Inv_&#131;2( [''FliA''] ) '''
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{|border="1" style="text-align: center"
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So, at steady-states,
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|param
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|signification
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|unit
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|value
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|comments
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|-
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|[expr(pFlhDC)]
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|expression rate of <br> pFlhDC '''with RBS E0032'''
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|nM.min<sup>-1</sup>
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|need for 20 mesures with well choosen values of [aTc]<sub>i</sub> <br> and for 20 mesures with well choosen values of [arab]<sub>i</sub> <br> and 5x5 measures for the relation below?
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|-
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|γ<sub>GFP</sub>
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|dilution-degradation rate <br> of GFP(mut3b)
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|min<sup>-1</sup>
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|0.0198
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|[GFP]
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|GFP concentration at steady-state
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|nM
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|need for 20 + 20 measures <br> and 5x5 measures for the relation below?
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|-
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|(''fluorescence'')
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|value of the observed fluorescence
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|au
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|need for 20 + 20 measures <br> and 5x5 measures for the relation below?
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|''conversion''
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|conversion ratio between <br> fluorescence and concentration
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|nM.au<sup>-1</sup>
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|(1/79.429)
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|}
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<br><br>
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[[Image:F4.jpg|center]]
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{|border="1" style="text-align: center"
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we use this analytical expression to determine the parameters :
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|param
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|signification <br> corresponding parameters in the [[Team:Paris/Modeling/Oscillations#Resulting_Equations|equations]]
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|unit
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|value
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|comments
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|-
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|β<sub>13</sub>
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|production rate of FliA-pFlhDC '''with RBS E0032''' <br> β<sub>13</sub>
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|nM.min<sup>-1</sup>
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|(K<sub>12</sub>/{coef<sub>fliA</sub>})
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|activation constant of FliA-pFlhDC <br> K<sub>12</sub>
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|nM
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|n<sub>12</sub>
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|complexation order of FliA-pFlhDC <br> n<sub>12</sub>
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|no dimension
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|β<sub>2</sub>
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|production rate of OmpR-pFlhDC '''with RBS E0032''' <br> β<sub>2</sub>
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|nM.min<sup>-1</sup>
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|(K<sub>22</sub>/{coef<sub>omp</sub>})
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|activation constant of OmpR-pFlhDC <br> K<sub>22</sub>
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|nM
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|-
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|n<sub>22</sub>
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|complexation order of OmpR-pFlhDC <br> n<sub>22</sub>
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|no dimension
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|}
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<br><br>
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<div style="text-align: center">
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{{Paris/Toggle|Table of Values|Team:Paris/Modeling/More_f4_Table}}
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</div>
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<div style="text-align: center">
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{{Paris/Toggle|Algorithm|Team:Paris/Modeling/More_f4_Algo}}
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</div>
Then, if we have time, we want to verify the expected relation
Then, if we have time, we want to verify the expected relation
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[[Image:SumpFliA.jpg|center]]
[[Image:SumpFliA.jpg|center]]
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<br>
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<center>
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[[Team:Paris/Modeling/Implementation| <Back - to "Implementation" ]]| <br>
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[[Team:Paris/Modeling/Protocol_Of_Characterization| <Back - to "Protocol Of Characterization" ]]|
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</center>

Latest revision as of 02:07, 30 October 2008

Method & Algorithm : ƒ4


= act_pFliA


Specific Plasmid Characterisation for ƒ4

According to the characterization plasmid (see right) and to our modeling, in the exponential phase of growth, at the steady state,

we have [FlhDC]real = {coefflhDC} ƒ1([aTc]i) and [FliA]real = {coeffliA} ƒ2([arab]i)

but we use [aTc]i = Inv_ƒ1( [FlhDC] ) and [arab]i = Inv_ƒ2( [FliA] )

So, at steady-states,

F4.jpg

we use this analytical expression to determine the parameters :

↓ Table of Values ↑


param signification unit value comments
(fluorescence) value of the observed fluorescence au need for 20 mesures with well choosen values of [aTc]i
and for 20 mesures with well choosen values of [arab]i
and 5x5 measures for the relation below?
conversion conversion ratio between
fluorescence and concentration
↓ gives ↓ 		nM.au-1 (1/79.429)
[GFP] GFP concentration at steady-state nM
γGFP dilution-degradation rate
of GFP(mut3b)
↓ gives ↓ 		min-1 0.0198 Time Cell Division : 35 min.
ƒ4 activity of
pFliA with RBS E0032 		nM.min-1



param signification
corresponding parameters in the equations 		unit value comments
β18 total transcription rate of
FlhDC><pFliA with RBS E0032
β18 		nM.min-1
(K1/{coefflhDC}) activation constant of FlhDC><pFliA
K1 		nM
n1 complexation order of FlhDC><pFliA
n1 		no dimension
β23 total transcription rate of
FliA><pFliA with RBS E0032
β23 		nM.min-1
(K7/{coeffliA}) activation constant of FliA><pFliA
K7 		nM
n10 complexation order of FliA><pFliA
n7 		no dimension
↓ Algorithm ↑


find_ƒ4

Then, if we have time, we want to verify the expected relation

SumpFliA.jpg


<Back - to "Implementation" |
<Back - to "Protocol Of Characterization" |

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