Testing of the U-2R model

Verify against MuPad "analysis" document: U-2R_analysis.html

close all
clear all

Here you will find all figures

figures_folder='U_2R_testing_figures';

TEST COMPUTATION OF EQUILIBRIUM POPULATIONS

Set some meaningful parameters matching settings of MuPad analysis document

LRratio_array=[0 : 0.05 : 1.5]; % Array of L/R

Rtotal_array=1e-3*ones(1,length(LRratio_array)); % Receptor concentration, M


K_A   = 1e6;
K_B_s_1 = 2;
K_B_s_2 = 3;

% Set appropriate options for the model (see model file for details)
% model_numeric_solver='fminbnd'  ;
%
% model_numeric_options=optimset('Diagnostics','off', ...
%                     'Display','off',...
%                     'TolX',1e-9,...
%                     'MaxFunEvals', 1e9);

The important option here is "TolX" that sets termination tolerance on free ligand concentation in molar units. With our solution concentrations in 1e-3 range TolX should be set to some 1e-9.

Compute arrays for populations and plot

concentrations_array=[];
for counter=1:length(LRratio_array)
    % compute
    [concentrations species_names] = equilibrium_thermodynamic_equations.U_2R_model(...
        Rtotal_array(counter), LRratio_array(counter), K_A, K_B_s_1, K_B_s_2,...
        'analytical', 'none');
    % collect
    concentrations_array = [concentrations_array ; concentrations];
end

Plot

Figure_title= 'U_2R';
X_range=[0 max(LRratio_array)+0.1 ]; % extend X just a bit past last point
Y_range=[ ]; % keep automatic scaling for Y
% display figure
figure_handle=equilibrium_thermodynamic_equations.plot_populations(...
    Rtotal_array, LRratio_array, concentrations_array, species_names, Figure_title, X_range, Y_range);
% save it
% results_output.output_figure(figure_handle, figures_folder, 'Concentrations_plot');

Observations The result matches simulations in the 'analysis' MuPad notebook. The code is correct.