Hi i am working with ODE45 and i have a issue that it noi t give us a variables in the workspace and also guíve a bump in the downward phase kindlydo guide me what i have to

Hi i am working with ODE45 and i have a issue that it noi t give us a variables in the workspace and also guíve a bump in the downward phase kindlydo  guide me what i have to 

function  Phase_1LIGAND_INTERACTION() 
    % Parameters
    timespan = 0:0.01:100;  % Time vector
    Receptor_concentration = 100;  % Concentration of Receptor
    
    % Initial conditions
    C_LigandReceptor_0 = 0;  % Initial concentration of complex of ligand and receptor
 
    % Time-dependent forward reaction rate constants (anonymous functions)
    Kf1t_start = 5;   % Start time of receptor pulse
    Kf1t_end = 20;     % Duration of receptor pulse
    Kf1Max_rate = 200;
    Kf1Min_rate = 1;
    Kf1growth = -0.1;
  
 % Time-dependent backward reaction rate constants (anonymous functions)
    Kb1t_start =5;   % Start time of Complex  pulse
    Kb1t_end = 20;     % Duration of Complex pulse
    Kb1Max_rate = 20;
    Kb1Min_rate = 10;
    Kb1growth = -1;
   

    kf_1 = @(t) calculate_kf(t, Kf1t_start, Kf1t_end, Kf1Max_rate, Kf1Min_rate, Kf1growth );
     kb_1 = @(t) calculate_kb(t, Kb1t_start, Kb1t_end, Kb1Max_rate, Kb1Min_rate, Kb1growth);
    % Solving the ODE system
    [t, y] = ode45(@(t, y) ode_LR(t, y, kf_1, kb_1), timespan, [Receptor_concentration; C_LigandReceptor_0]);

% Extract the concentrations
receptor_concentration = y(:, 1);
ligand_Receptor_concentration = y(:, 2);  % Now this represents the ligand-receptor complex concentration

% Calculate kf and kb values at each time point
kf_values = zeros(size(t));
kb_values = zeros(size(t));
kf_growth_values = zeros(size(t));
kb_growth_values = zeros(size(t));

for i = 1:length(t)
    kf_values(i) = kf_1(t(i));
    kb_values(i) = kb_1(t(i));
    kf_growth_values(i) = Kf1growth;
    kb_growth_values(i) = Kb1growth;
end

% Create a table for the data
data_table = table(t, kf_values, kb_values, kf_growth_values, kb_growth_values, timespan', ligand_Receptor_concentration, receptor_concentration, ...
    'VariableNames', {'Time', 'kf', 'kb', 'kf_growth', 'kb_growth', 'TimeSpan', 'Ligand_Receptor_Concentration', 'Receptor_Concentration'});

% Write the data table to a CSV file
csv_filename = 'interaction_data.csv';
writetable(data_table, csv_filename);

% ...
    % Plotting the results
    figure;
    plot(t, receptor_concentration, '-o', 'LineWidth', 2);
    hold on;
    plot(t, kf_1(t), '-', 'LineWidth', 2);
    hold on;
    plot(t, kb_1(t), 'o:', 'LineWidth', 3);
    hold on;
    plot(t, ligand_Receptor_concentration, '-k', 'LineWidth', 3);
    hold on;
    xlabel('Time');
    ylabel('Concentration');
    legend('Receptor',  'kf', 'kb' ,'Activated Receptor (Complex)');
end

function kf_1 = calculate_kf(t, Kf1t_start, Kf1t_end, Kf1Max_rate, Kf1Min_rate, Kf1growth )
    kf_1 = zeros(size(t));
    for i = 1:length(t)
        if t(i) < Kf1t_start
            kf_1(i) = Kf1Min_rate;
        elseif t(i) >= Kf1t_start && t(i) < Kf1t_end
            kf_1(i) = Kf1Max_rate - (Kf1Max_rate - Kf1Min_rate) * exp(Kf1growth * (t(i) - Kf1t_start));
        else
            kf_end = Kf1Max_rate - (Kf1Max_rate - Kf1Min_rate) * exp(Kf1growth * (Kf1t_end - Kf1t_start));
            kf_1(i) =  Kf1Min_rate + ( kf_end - Kf1Min_rate) * exp(Kf1growth * (t(i) - Kf1t_end));  
        end
    end
end

function kb_1 = calculate_kb(t, Kb1t_start, Kb1t_end, Kb1Max_rate, Kb1Min_rate, Kb1growth)
    kb_1 = zeros(size(t));
    for i = 1:length(t)
        if t(i) < Kb1t_start
            kb_1(i) = Kb1Min_rate;
        elseif t(i) >= Kb1t_start && t(i) < Kb1t_end
            kb_1(i) = Kb1Max_rate - (Kb1Max_rate - Kb1Min_rate) * exp(Kb1growth * (t(i) - Kb1t_start));
        else
            kb_end = Kb1Max_rate - (Kb1Max_rate - Kb1Min_rate) * exp(Kb1growth * (Kb1t_end - Kb1t_start));
            kb_1(i) = Kb1Min_rate + ( kb_end - Kb1Min_rate) * exp(Kb1growth * (t(i) - Kb1t_end));
        end
    end
end

function dydt = ode_LR(t, y, kf_1, kb_1)
    % Unpack the concentrations
     Receptor_concentration = y(1);
     C_LigandReceptor = y(2);
     


    % Define the ODE system
    dReceptor_dt = -kf_1(t)  * Receptor_concentration + kb_1(t) * C_LigandReceptor;
    d_CLigandReceptor_dt = kf_1(t)  * Receptor_concentration - kb_1(t) * C_LigandReceptor;

    % Pack the derivatives into a column vector
    dydt = [dReceptor_dt; d_CLigandReceptor_dt];
end


   

[Dyuman Joshi]

Convert the function Phase_1LIGAND_INTERACTION to a script and then run the code.

Answer 1

[Abderrahim. B]

Hi!

Functions do not use the base workspace. Every function has its own function workspace. Read more here.

Use assignin function and set the first input argument to 'base' to send variables in a function to the base workspace.

Nothe that there might be other ways to do this.

hope this helps

Abderrahim