Method & Algorithm : 3
Specific Plasmid Characterisation for 3
According to the characterization plasmid (see right) and to our modeling, in the exponential phase of growth, at the steady state, we have [OmpR*]real = {coefompR} 1([aTc]i)
and [FliA]real = {coefFliA} 2([arab]i)
but we use [aTc]i = Inv_1( [OmpR*] )
and [arab]i = Inv_2( [FliA] )
So, at steady-states,
↓ Table ↑
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.
|
3
| activity of pFlhDC with RBS E0032
| nM.min-1
|
|
|
param
| signification corresponding parameters in the equations
| unit
| value
| comments
|
β22
| total transcription rate of FliA><pFlhDC with RBS B0034 β22
| nM.min-1
|
|
|
(K6/{coeffliA})
| activation constant of FliA><pFlhDC K6
| nM
|
|
|
n6
| complexation order of FliA><pFlhDC n6
| no dimension
|
|
|
β17
| basal activity of pFlhDC with RBS B0034 β17
| nM.min-1
|
|
|
(K15/{coefompR})
| activation constant of OmpR><pFlhDC K15
| nM
|
|
|
n15
| complexation order of OmpR><pFlhDC n15
| no dimension
|
|
|
|
↓ Algorithm ↑
find_3 ( FliA )
function optimal_parameters = find_f3_FliA(X_data, Y_data, initial_parameters)
global beta17;
function output = act_pFlhDC(parameters, X_data)
for k = 1:length(X_data)
output(k) = beta17*(1 - hill( X_data(k), parameters(2), parameters(3))) ...
+ parameters(1)*hill(X_data(k), parameters(2), parameters(3));
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
find_3 ( OmpR* )
function optimal_parameters = find_f3_OmpR(X_data, Y_data, initial_parameters)
function output = act_pFlhDC(parameters, X_data)
for k = 1:length(X_data)
output(k) =(1 - hill( X_data(k), parameters(2), parameters(3) )) * parameters(1);
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
|
Then, if we have time, we want to verify the expected relation
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