can I directly change the ODE?

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Lo
Lo on 20 Jul 2023
Commented: Lo on 2 Aug 2023
I want to ensure that I truly understand how to use Simbiology by reconstructing an old model. I have the diagram, parameters (rates), initial values, ODEs, and result plots. After using this information to rebuild the model, I found that my results differ from the original ones. I would like to know if any other factors can affect the simulation results besides the data mentioned above. Can I directly modify the ODEs?
Thank you!
  8 Comments
Sam Chak
Sam Chak on 20 Jul 2023
Thanks @Lo. Only the ODEs are left.
Can you type out or paste the 12 ODEs like this? It is for testing the ODEs in MATLAB.
dM/dt = - k_payload*M*P - Mdeg*M
dP/dt = - k_payload*M*P
...
Lo
Lo on 21 Jul 2023
like this ways ?
d(M)/dt = -(k_padlock*M*P) - (Mdeg*M)
d(P)/dt = -(k_padlock*M*P)
d(MP)/dt = (k_padlock*M*P) - (Vmcircular*MP/(Kmcircular+MP))
d(SplR)/dt = -(Vmcircular*MP/(Kmcircular+MP))
d([MP-circular])/dt = (Vmcircular*MP/(Kmcircular+MP)) - (Vmphi29*[MP-circular]/(Kmphi29+[MP-circular]))
d(phi29)/dt = -(Vmphi29*[MP-circular]/(Kmphi29+[MP-circular]))
d([R-free])/dt = (Vmphi29*[MP-circular]/(Kmphi29+[MP-circular])) - (RCPdeg*[R-free]) - (k1*[R-free]*[F-free]-k2*RF) - (k3*[R-free]*[Q-free]-k4*RQ)
d([F-free])/dt = -(k1*[R-free]*[F-free]-k2*RF) - (k7*[F-free]*RQ-k8*RFQ)
d(RF)/dt = (k1*[R-free]*[F-free]-k2*RF) - (k5*RF*[Q-free]-k6*RFQ)
d([Q-free])/dt = -(k3*[R-free]*[Q-free]-k4*RQ) - (k5*RF*[Q-free]-k6*RFQ)
d(RQ)/dt = (k3*[R-free]*[Q-free]-k4*RQ) - (k7*[F-free]*RQ-k8*RFQ)
d(RFQ)/dt = (k5*RF*[Q-free]-k6*RFQ) + (k7*[F-free]*RQ-k8*RFQ)

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Answers (2)

Fulden Buyukozturk
Fulden Buyukozturk on 20 Jul 2023
Edited: Walter Roberson on 20 Jul 2023
You cannot edit ODEs directly but you can inspect them using getequations from the command-line or Show model equations option from Model Builder. You can also inspect quantity initial conditions by selecting Initial Conditions option on the Home tab.
Also, please see this page that describes how SimBiology derives ODEs: https://www.mathworks.com/help/simbio/ug/deriving-simbiology-odes-equations-from-reactions.html

Sam Chak
Sam Chak on 21 Jul 2023
Hi @Lo
The initial values for MP0 and MPcircular0 are not provided. So I made up some values and it displays the trend similar to the following:
tspan = [0 600];
M0 = 0.5;
P0 = 0.05;
MP0 = 0.5; % not provided
SplR0 = 25;
MPcircular0 = 0; % not provided
phi290 = 12.5;
Rfree0 = 0;
Ffree0 = 180664245;
RF0 = 0;
Qfree0 = 361328490;
RQ0 = 0;
RFQ0 = 0;
x0 = [M0 P0 MP0 SplR0 MPcircular0 phi290 Rfree0 Ffree0 RF0 Qfree0 RQ0 RFQ0];
% options = odeset('RelTol', 1e-4, 'AbsTol', 1e-6);
[t, x] = ode15s(@odefcn, tspan, x0);
% Solution Plot
plot(t/60, x(:,12), 'linewidth', 1.5),
grid on, xlabel('Time / minutes'), ylabel('RFQ')
function xdot = odefcn(t, x)
xdot = zeros(12, 1);
% definitions
M = x(1);
P = x(2);
MP = x(3);
SplR = x(4);
MPcircular = x(5);
phi29 = x(6);
Rfree = x(7);
Ffree = x(8);
RF = x(9);
Qfree = x(10);
RQ = x(11);
RFQ = x(12);
% parameters
k_padlock = 32000;
Mdeg = 0.000019254;
Vmcircular = 0.008;
Kmcircular = 1;
Vmphi29 = 112;
Kmphi29 = 31;
RCPdeg = 0;
k1 = 1e12;
k2 = 0;
k3 = 1e12;
k4 = 0;
k5 = 1e12;
k6 = 0;
k7 = 1e12;
k8 = 0;
% dynamics
xdot(1) = - k_padlock*M*P - Mdeg*M;
xdot(2) = - k_padlock*M*P;
xdot(3) = k_padlock*M*P - (Vmcircular*MP)/(Kmcircular + MP);
xdot(4) = - (Vmcircular*MP)/(Kmcircular + MP);
xdot(5) = (Vmcircular*MP)/(Kmcircular + MP) - (Vmphi29*MPcircular)/(Kmphi29 + MPcircular);
xdot(6) = - (Vmphi29*MPcircular)/(Kmphi29 + MPcircular);
xdot(7) = (Vmphi29*MPcircular)/(Kmphi29 + MPcircular) - RCPdeg*Rfree - (k1*Rfree*Ffree - k2*RF) - (k3*Rfree*Qfree - k4*RQ);
xdot(8) = - (k1*Rfree*Ffree - k2*RF) - (k7*Ffree*RQ - k8*RFQ);
xdot(9) = (k1*Rfree*Ffree - k2*RF) - (k5*RF*Qfree - k6*RFQ);
xdot(10) = - (k3*Rfree*Qfree - k4*RQ) - (k5*RF*Qfree - k6*RFQ);
xdot(11) = (k3*Rfree*Qfree - k4*RQ) - (k7*Ffree*RQ - k8*RFQ);
xdot(12) = (k5*RF*Qfree - k6*RFQ) + (k7*Ffree*RQ - k8*RFQ);
end
  5 Comments
Sam Chak
Sam Chak on 23 Jul 2023
Hi @Lo
The final value of RFQ in the simulation depends on the initial values of all 12 states. But you only gave 10 initial values (scoll up). The other two initial values of MP0 and MPcircular were not provided. What are they?
Please insert the values in the MATLAB code and run it. Then show your result of the RFQ here.
Lo
Lo on 2 Aug 2023
I apologize for the late response due to being busy. The result I obtained is exactly the same as yours, but I still don't know what caused the difference in results before.

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