Team:Paris/Modeling/f3bis

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Revision as of 14:55, 29 October 2008

Method & Algorithm : ƒ3bis

Specific Plasmid Characterisation for ƒ3bis

We have [EnvZ]_real = {coef_envZ} ƒ1([aTc]_i) ( and [FliA]_real = {coef_fliA} ƒ2([arab]_i) )

but we use [aTc]_i = Inv_ƒ1( [EnvZ] ) ( and [arab]_i = Inv_ƒ2( [FliA] ) )

So, at steady-states,

↓ 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 5: / Line 5: @@
 [[Image:f6DCA.png|thumb|Specific Plasmid Characterisation for &#131;3bis]]
-We have <span style="color:#0000FF;">[''FlhDC'']<sub>''real''</sub> = {coef<sub>''flhDC''</sub>} &#131;1([aTc]<sub>i</sub>)</span>
+We have <span style="color:#0000FF;">[''EnvZ'']<sub>''real''</sub> = {coef<sub>''envZ''</sub>} &#131;1([aTc]<sub>i</sub>)</span>
-and <span style="color:#0000FF;">[''FliA'']<sub>''real''</sub> = {coef<sub>''fliA''</sub>} &#131;2([arab]<sub>i</sub>)</span>
+( and <span style="color:#0000FF;">[''FliA'']<sub>''real''</sub> = {coef<sub>''fliA''</sub>} &#131;2([arab]<sub>i</sub>)</span> )
-but we use <span style="color:#0000FF;">[aTc]<sub>i</sub> = Inv_&#131;1( [''FlhDC''] ) </span>
+but we use <span style="color:#0000FF;">[aTc]<sub>i</sub> = Inv_&#131;1( [''EnvZ''] ) </span>
-and        <span style="color:#0000FF;">[arab]<sub>i</sub> = Inv_&#131;2( [''FliA''] ) </span>
+( and        <span style="color:#0000FF;">[arab]<sub>i</sub> = Inv_&#131;2( [''FliA''] ) </span> )
 So, at steady-states,
-[[Image:F3env.jpg|center]]
+[[Image:F3.jpg|center]]
 <br>