function SMGT1();

%-------------- DNA internalization into SP -------------

[t,y] = ode45(@sp,[0 60],[1 0 0 0 0 0]);

subplot(1,2,1)
plot(t,y(:,1),'-r',t,y(:,2),'.b',t,y(:,3),'+g',t,y(:,4),'-.m')
h = legend('free DNA','MHCII/DNA','CD4/DNA','DNA in SP');
set(get(gca,'XLabel'),'String','time, t')
set(get(gca,'YLabel'),'String','DNA content, c')
grid on

subplot(1,2,2)
plot3(y(:,2),y(:,3),y(:,4))
set(get(gca,'XLabel'),'String','MHCII/DNA')
set(get(gca,'YLabel'),'String','CD4/DNA')
set(get(gca,'ZLabel'),'String','DNA in SP')
axis square
grid on

function dy = sp(t,y)
dy = zeros(6,1);  % a column vector

S=1;  % initial condition - free DNA adding

%---------------- PARAMETERS OF THE MODEL ----------------
k1 = 1;     % {0}      MHCII: OFF
km1 = 0.1;
k12 = 0.1;  % {0}      CD4: OFF
k2 = 0.1;   % {0}      MHCII/CD4: OFF
k3 = 0.1;   % {0}      SP: OFF
k4 = 0.1;
k5 = 0;     % {1}      DNase out: ON
k6 = 0;     % {0.1, 1} DNase in: intermediate, ON

%------------------------- MODEL ------------------------
S1=y(1);
S2=y(2);
S3=y(3);
S4=y(4);
S5=y(5);
S6=y(6);

dy(1) = km1*S2 - (k1 + k5 + k12)*S1 + k4*S4;  % free DNA
dy(2) = k1*S1 - (km1 + k2)*S2;                % MHCII/DNA
dy(3) = k12*S1 + k2*S2 - k3*S3;               % CD4/DNA
dy(4) = k3*S3 - (k4 + k6)*S4;                 % DNA in SP
dy(5) = k5*S1;                                % DNase out of SP
dy(6) = k6*S4;                                % DNase in SP

return