Http://openwetware.org/wiki/IGEM:IMPERIAL/2009/M3/Modelling/matlabcode

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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');