Testing of the U-2R-RL model
Verify against MuPad "analysis" document: U-2R-RL_analysis.html Run in "Publish" mode to have a report.
Contents
close all clear all
Set input parameters
model_name='U-2R-RL'; % Set some meaningful parameters matching settings of MuPad analysis % document LRratio_array=[0.0001 : 0.05 : 1.5]'; % Array of L/R Rtotal_array=1e-3*ones(length(LRratio_array),1); % Receptor concentration, M K_A = 1e5; K_B_1_s_1 = 2; K_B_1_s_2 = 4; K_B_2 = 2; % 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
Call as non-vectorized:
concentrations_array=[]; tic for counter=1:length(LRratio_array) % compute [concentrations species_names] = equilibrium_thermodynamic_equations.U_2R_RL_model(... Rtotal_array(counter), LRratio_array(counter), K_A, K_B_1_s_1, K_B_1_s_2, K_B_2, ... 'analytical', 'none'); % collect concentrations_array = [concentrations_array ; concentrations]; end toc
Elapsed time is 0.006367 seconds.
Plot
Figure_title= model_name; 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);
Observations The result matches simulations in the 'analysis' MuPad notebook. The code is correct.
% % %% Test vectorization (if analytical model was vectorized!) % % Call as vectorized: % tic % [concentrations_array species_names] = equilibrium_thermodynamic_equations.U_5R_model(... % Rtotal_array, LRratio_array, K_A,... % K_B_s_1, K_B_s_2, K_B_s_3, K_B_s_4, K_B_s_5,... % 'analytical', 'none'); % toc % % Figure_title= sprintf(' %s - vectorized version', model_name); % 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); % % % %% Conclusions % % Both vectorized and non-vectorized calls work well.