%This program calls a function which implements the basic model of the repressilator,
%with one of the repression stages being replaced with mRNA inhibition.

%Close all windows and clear all variables

clear all;
close all;

%Set the rate constant for mRNA/asRNA binding in per transcipt per second

%Set the simulation to run over 3 hours (3*60*60 seconds)
tspan = [0 3*60*60];

%Set the initial conditions of the 5 species in molecules per cell
%[mRNA_cI, mRNA_lacI, mRNA_asRNA, protein_cI, protein_lacI]

IC = [0, 0, 0, 80, 100];

%run the simulation!!
[t result] = ode23s(@repressilator_physical_mRNAi, tspan, IC, [], k_RNAi);

%in figure 1 plot the concentrations of the 3 mRNA species
plot(t/60, result(:,1), 'b-', t/60, result(:,2), 'r-', t/60, result(:,3), 'g-');
title('Oscillation of the 3 mRNA species');
legend('cI', 'lacI', 'asRNA');
xlabel('Time (min)');
ylabel('mRNA per cell');

%in figure 2 plot the concentrations of the 2 protein species
plot(t/60, result(:,4), 'b-', t/60, result(:,5), 'r-');
title('Oscillation of the 2 repressor proteins');
legend('cI', 'lacI');
xlabel('Time (min)');
ylabel('Proteins per cell');

Back to index