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- | [[Image:f3env.png|thumb]] (see [[Team:Paris/Modeling/Oscillations#Biochemical_Assumptions|the considerations on the use of EnvZ]])
| + | {{Paris/Menu}} |
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- | We have [EnvZ]<sub>produced</sub> = {coef<sub>env</sub>}''expr(pTet)'' = {coef<sub>env</sub>} ƒ1([aTc]<sub>i</sub>)
| + | {{Paris/Header|Method & Algorithm : ƒ3bis}} |
| + | <center> = act_''pFlhDC'' </center> |
| + | <br> |
| | | |
- | and [EnvZ]<sub>total</sub> = [EnvZ]<sub>b</sub> + [EnvZ]<sub>produced</sub>
| + | [[Image:f6DCA.png|thumb|Specific Plasmid Characterisation for ƒ3bis]] |
| + | In this experiment, we have |
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- | and [FliA] = {coef<sub>FliA</sub>}''expr(pBad)'' = {coef<sub>FliA</sub>} ƒ2([arab]<sub>i</sub>)
| + | ''' [''EnvZ'']<sub>''real''</sub> = {coef<sub>''envZ''</sub>} ƒ1([aTc]<sub>i</sub>) ''' |
| | | |
- | So, if we denote phosphorylated OmpR by ''OmpR<sup>*</sup>'', we have
| + | but we use ''' [aTc]<sub>i</sub> = Inv_ƒ1( [''EnvZ''] ) ''' |
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- | [[Image:F3ompfromenv.jpg|center]]
| + | so, at steady-states, ''phosphorylated OmpR'' verify : |
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- | that we can then introduce in the previous expression (ƒ 3) :
| + | [[Image:F3b.jpg|center]] |
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- | [[Image:F3ompfinal.jpg|center]] | + | We can then solve it, and reintroduce the result in the previously characterized ''' ƒ3( 0, [OmpR<sup>*</sup>] ) ''', to determine the parameters : |
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- | <br><br> | + | <div style="text-align: center"> |
| + | {{Paris/Toggle|Table of Values|Team:Paris/Modeling/More_f3bis_Table}} |
| + | </div> |
| | | |
- | {|border="1" style="text-align: center"
| + | <div style="text-align: center"> |
- | |param
| + | {{Paris/Toggle|Algorithm|Team:Paris/Modeling/More_f3bis_Algo}} |
- | |signification
| + | </div> |
- | |unit
| + | |
- | |value
| + | |
- | |comments
| + | |
- | |-
| + | |
- | |[expr(pFlhDC)]
| + | |
- | |expression rate of <br> pFlhDC '''with RBS E0032'''
| + | |
- | |nM.min<sup>-1</sup>
| + | |
- | | | + | |
- | |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? | + | |
- | |-
| + | |
- | |γ<sub>GFP</sub>
| + | |
- | |dilution-degradation rate <br> of GFP(mut3b)
| + | |
- | |min<sup>-1</sup>
| + | |
- | |0.0198
| + | |
- | |
| + | |
- | |-
| + | |
- | |[GFP]
| + | |
- | |GFP concentration at steady-state
| + | |
- | |nM
| + | |
- | |
| + | |
- | |need for 20 + 20 measures <br> and 5x5 measures for the relation below?
| + | |
- | |-
| + | |
- | |(''fluorescence'')
| + | |
- | |value of the observed fluorescence
| + | |
- | |au
| + | |
- | |
| + | |
- | |need for 20 + 20 measures <br> and 5x5 measures for the relation below?
| + | |
- | |-
| + | |
- | |''conversion''
| + | |
- | |conversion ratio between <br> fluorescence and concentration
| + | |
- | |nM.au<sup>-1</sup>
| + | |
- | |(1/79.429)
| + | |
- | |
| + | |
- | |}
| + | |
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- | <br><br>
| + | <br> |
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- | {|border="1" style="text-align: center"
| + | <center> |
- | |param
| + | [[Team:Paris/Modeling/Implementation| <Back - to "Implementation" ]]| <br> |
- | |signification <br> corresponding parameters in the [[Team:Paris/Modeling/Oscillations#Resulting_Equations|equations]]
| + | [[Team:Paris/Modeling/Protocol_Of_Characterization| <Back - to "Protocol Of Characterization" ]]| |
- | |unit | + | </center> |
- | |value
| + | |
- | |comments
| + | |
- | |-
| + | |
- | |β<sub>13</sub>
| + | |
- | |production rate of FliA-pFlhDC '''with RBS E0032''' <br> β<sub>13</sub>
| + | |
- | |nM.min<sup>-1</sup>
| + | |
- | |
| + | |
- | |
| + | |
- | |-
| + | |
- | |(K<sub>12</sub>/{coef<sub>fliA</sub>})
| + | |
- | |activation constant of FliA-pFlhDC <br> K<sub>12</sub> | + | |
- | |nM
| + | |
- | |
| + | |
- | |
| + | |
- | |-
| + | |
- | |n<sub>12</sub> | + | |
- | |complexation order of FliA-pFlhDC <br> n<sub>12</sub>
| + | |
- | |no dimension
| + | |
- | |
| + | |
- | |
| + | |
- | |-
| + | |
- | |β<sub>2</sub>
| + | |
- | |production rate of OmpR-pFlhDC '''with RBS E0032''' <br> β<sub>2</sub>
| + | |
- | |nM.min<sup>-1</sup>
| + | |
- | |
| + | |
- | |
| + | |
- | |-
| + | |
- | |(K<sub>22</sub>/{coef<sub>omp</sub>})
| + | |
- | |activation constant of OmpR-pFlhDC <br> K<sub>22</sub>
| + | |
- | |nM
| + | |
- | |
| + | |
- | |
| + | |
- | |-
| + | |
- | |n<sub>22</sub>
| + | |
- | |complexation order of OmpR-pFlhDC <br> n<sub>22</sub>
| + | |
- | |no dimension
| + | |
- | |
| + | |
- | |
| + | |
- | |}
| + | |
Method & Algorithm : 3bis
= act_pFlhDC
Specific Plasmid Characterisation for 3bis
In this experiment, we have
[EnvZ]real = {coefenvZ} 1([aTc]i)
but we use [aTc]i = Inv_1( [EnvZ] )
so, at steady-states, phosphorylated OmpR verify :
We can then solve it, and reintroduce the result in the previously characterized 3( 0, [OmpR*] ) , to determine the parameters :
↓ Algorithm ↑
function optimal_parameters = find_f3_EnvZ(X_data, Y_data, initial_parameters)
global beta17 K15 n15;
function output = act_pFlhDC(parameters, X_data)
for k = 1:length(X_data)
OmpR_P = complexes((parameters(1) + X_data(k)),parameters(2),parameters(3),parameters(4));
output(k) = beta17*(1 - hill( OmpR_P, K15, n15 ));
end
end
options=optimset('LevenbergMarquardt','on','TolX',1e-10,'MaxFunEvals',1e10,'TolFun',1e-10,'MaxIter',1e4);
optimal_parameters = lsqcurvefit( @(parameters, X_data) act_pFlhDC(parameters, X_data), ...
initial_parameters, X_data, Y_data, options );
end
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<Back - to "Protocol Of Characterization" |
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