From 2006.igem.org
clear all;
close all;
%default:
% n = 3;
% nSa = 3;
% nSr = 3;
% K = 5;
% KSa = 5;
% KSr = 5;
% k = 2;
% kd = 1;
% period = 30;
n = 1; % keine Kooperativität der Zinkfinger -> alle n immer = 1
nSa = 3; % Kooperativität von S (als Aktivator)
nSr = 3; % Kooperativität von S (als Repressor)
K = 120; % Affinität (höheres K = höhere Affinität)
KSa = 5;
KSr = 5;
k = 2;
kd = 0.9; % Degradationsrate der Zinkfinger
para = [n,nSa,nSr,K,KSa,KSr,k,kd,period];
y0 = [2,0,0,0];
opt = odeset('RelTol',1e-3,'AbsTol',1e-6);
% stepsize
tstep = 0.2;
% duration
tfinal = 600;
% run computation
[t,y] = ode15s('ode_counter',[0:tstep:tfinal],y0,opt,para);
s = input_signal([0:tstep:tfinal],period);
%plot 4 concentrations plus S over time
colors = ['k' 'm' 'c' 'g' 'r'];
%colors = ['k' 'k' 'k' 'k' 'k']; %for doing powerpoint presentations
for i = 1:4,
subplot(5,1,i);
plot(t,y(:,i),colors(i));
axis([0 tfinal -0.1 2.1]);
ylabel(sprintf('[R%d]', i))
hold on;
end
subplot(5,1,5);
plot(t,s,colors(5));
axis([0 tfinal -0.1 1.1]);
ylabel('[S]')
xlabel('time')
hold off;
param=[K, kd];
v = jury(y, [0:tstep:tfinal], period, tstep, tfinal, param);