Http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M3/Modelling/matlabcode
Function code
function dy=ty_celldeath(t,y)
%%
global T km1 km2 k1 k2 k11 n1 n2 de dm growth death
%% %equations
activating_hill_temperature =(k1*(T^n1))/(T^n1+km1^n1); %activating
dy(1)= activating_hill_temperature - dm*y(1); %mRNA concentration
dy(2)= k2*y(1) - de*y(2); %enzyme concentration
hill_function_death = (k11*(y(2)^n2))/(y(2)^n2+km2^n2); %activating
dy(3)= growth*y(3) - death * hill_function_death * y(3); %total cell poulation
dy(4)= death * hill_function_death * y(3); % dead cell population
dy=[dy(1);dy(2);dy(3);dy(4)];
Function call
%function call
clear all;
clc;
%%
global T km1 km2 k1 k2 k11 n1 n2 de dm death growth E
%T=1
km1 =1;
km2 =1;
k1 =0.5;
k2 =1;
k11 =1;
n1 =1;
n2 =1;
de =1;
dm =1;
growth=5;
E =1; %enzyme
%death=3;
i=1;
%%
death=20;
for T=[0:1:4]
[T,Y]=ode45(@ty_celldeath,[7:0.01:10], [0 0 10000 10000]); %initially, has population of 1000
A12(:,i) = Y(:,1); %mRNA conc
A22(:,i) = Y(:,2); %killing enzyme conc
A32(:,i) = Y(:,3); %population
A42(:,i) = Y(:,4); %dead cell population
i=i+1;
end
figure(2);subplot(1,4,1);plot(T,A12); TITLE('mRNA');xlabel('time');legend('T=0','T=1','T=2','T=3','T=4');
figure(2);subplot(1,4,2);plot(T,A22); TITLE('Enzyme');xlabel('time');legend('T=0','T=1','T=2','T=3','T=4');
figure(2);subplot(1,4,3);plot(T,A32); TITLE('Cell population');xlabel('time'); legend('T=0','T=1','T=2','T=3','T=4');
figure(2);subplot(1,4,4);plot(T,A42); TITLE('Dead cell population');xlabel('time'); legend('T=0','T=1','T=2','T=3','T=4');
%%
death=20;
for T=[5:1:9]
[T,Y]=ode45(@ty_celldeath,[0:0.1:10], [0 0 10000 10000]); %initially, has population of 10000
A13(:,i) = Y(:,1); %mRNA conc
A23(:,i) = Y(:,2); %killing enzyme conc
A33(:,i) = Y(:,3); %population
A43(:,i) = Y(:,4); %dead cell population
i=i+1;
end
figure(3);subplot(1,4,1);plot(T,A13); TITLE('mRNA');xlabel('time');legend('T=5','T=6','T=7','T=8','T=9');
figure(3);subplot(1,4,2);plot(T,A23); TITLE('Enzyme');xlabel('time');legend('T=5','T=6','T=7','T=8','T=9');
figure(3);subplot(1,4,3);plot(T,A33); TITLE('Cell population');xlabel('time'); legend('T=5','T=6','T=7','T=8','T=9');
figure(3);subplot(1,4,4);plot(T,A43); TITLE('Dead cell population');xlabel('time'); legend('T=5','T=6','T=7','T=8','T=9');