Team:Paris/Modeling/f3bis

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Revision as of 17:59, 29 October 2008

Method & Algorithm : ƒ3bis

Specific Plasmid Characterisation for ƒ3bis

In this experiment, we have [EnvZ]_real = {coef_envZ} ƒ1([aTc]_i)

but we use [aTc]_i = Inv_ƒ1( [EnvZ] )

so, at steady-states, phosphorylated OmpR verify :

We can then solve it and use it in ƒ3( 0, [OmpR^*] )

↓ Table ↑

Team:Paris/Modeling/More f3bis Table

↓ Algorithm ↑

function optimal_parameters = find_f3_EnvZ(X_data, Y_data, initial_parameters)
% gives the 'best parameters' involved in f3 with OmpR = 0 by least-square optimisation
% -> USE IT AFTER find_f3_OmpR
 
% X_data = vector of given values of ( [EnvZ]i ) (experimentally
% controled)
% Y_data = vector of experimentally measured values f3 corresponding of
% the X_data
% initial_parameters = values of the parameters proposed by the literature
%                       or simply guessed
%                    = [EnvZ_b, OmpR_b, K14, n14]
 
global beta17 K15 n15; % parameters GIVEN BY find_f3_OmpR
 
     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));
                 % complexes is a function that solve the "basical
                 % complexation equation"
             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);
% options for the function lsqcurvefit
 
optimal_parameters = lsqcurvefit( @(parameters, X_data) act_pFlhDC(parameters, X_data), ...
     initial_parameters, X_data, Y_data, options );
% search for the fittest parameters, between 1/10 and 10 times the initial
% parameters
 
end

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

@@ Line 4: / Line 4: @@
 [[Image:f6DCA.png|thumb|Specific Plasmid Characterisation for &#131;3bis]]
-''' [''EnvZ'']<sub>''real''</sub> = {coef<sub>''envZ''</sub>} &#131;1([aTc]<sub>i</sub>) '''
+In this experiment, we have ''' [''EnvZ'']<sub>''real''</sub> = {coef<sub>''envZ''</sub>} &#131;1([aTc]<sub>i</sub>) '''
 but we use ''' [aTc]<sub>i</sub> = Inv_&#131;1( [''EnvZ''] ) '''
-so, at steady-states, phosphorylated ''OmpR'' verify :
+so, at steady-states, ''phosphorylated OmpR'' verify :
 [[Image:F3b.jpg|center]]
-We can then solve it and use it in &#131;3( 0, [OmpR<sup>*</sup>] )
+We can then solve it and use it in ''' &#131;3( 0, [OmpR<sup>*</sup>] ) '''
 <br>