Contents

Testing of the U_RL model

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Here you will find all figures

figures_folder='U_RL_testing_figures';

TEST COMPUTATION OF EQUILIBRIUM POPULATIONS

Set some meaningful parameters

Rtotal=1e-3; % Receptor concentration, M
LRratio_array=[0 : 0.02 : 1.45]; % Array of L/R
K_a_A=1e6;  % Binding affinity constant
K_a_B=4;  % Isomerization constant

% Set appropriate options for the model (see model file for details)
model_numeric_solver='analytical'  ;

model_numeric_options='none';

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_RL_model(...
        Rtotal, LRratio_array(counter), K_a_A, K_a_B,...
        model_numeric_solver, model_numeric_options);
    % collect
    concentrations_array = [concentrations_array ; concentrations];
end

Plot

Figure_title= 'U-RL model';
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(...
    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 is exactly what we expect from this model.

As ligand is added, the ligand-receptor complex is formed species is formed at a constant ratio between the two forms, RL and RL*

Conclusion

The model equilibrium_thermodynamic_equations.U_RL_model() works well.

Published with MATLAB® R2013a