Trying to convert fuel cell model to first order rate

Create a Rate Rule for an Exponential Rate of Change

This example shows how to change the amount of a species similar to a first-order reaction using the first-order rate rule. For example, suppose the species x decays exponentially. The rate of change of species x is:

The analytical solution is:

where is the amount of species at time t, and is the initial amount. Use the following commands to set up a SimBiology model accordingly and simulate it.

m = sbiomodel('m');
c = addcompartment(m,'comp');
s = addspecies(m,'x','InitialAmount',2);
p = addparameter(m,'k','Value',1);
r = addrule(m,'x = -k * x','RuleType','rate');
[t,sd,species] = sbiosimulate(m);
plot(t,sd);
legend(species);
xlabel('Time');
ylabel('Species Amount');

So the model I have stated above is a previous simbiolgy model to represent a first order rate. I am trying to convert my fuel cell created attached to this first order model and then incorporate it into the SGLT2 inhibition model. Can anyone help or explain how I can go about this ?

Answer 1

[William Rose]

@Nathaniel Porter,

I ran BFCBirds.m. I don;t see how it applies to modeling SGLT2 inhibition, especially when using the SymBiology environment. I am not familiar with the SimBiology environment. It appears from your code that the SimBio environment allows you to define compartments and rules describing the relaitonships between the quantitities in those compartments. Like the Simulaiton Analysis and Modeling program (SAAM) which I used for compartmental modeling in the 80s or 90s.

Start by writing the rate equations for the quantities of interest (blood glucose, etc). This will include an equation for glucose loss in the urine. This glucose loss is reduced by the sodium-glucose transporter 2 protein (SGLT2). The SGLT2 moves glucose from urine back to the blood, before the urine leaves the body. Inhibition of SGLT2 (by Jardiance or a similar drug) will increase the rate of glucose loss into the urine. YOu will also need to decide how many compartments you want or need in your model to simulate the phenomena of interest to you. The bllod is one compartment. You may want to add the glomerular filtrate (which becomes urine) is another compartment. Use your knowledge of the physiology to write approximate equations. Once you have decided on the compartmnts and equaitons, you can implement them in SimBio.

[Nathaniel Porter]

Okay thank you

[Florian Augustin]

Hi Nathaniel,

I wanted to complement William's answer with a few concepts in SimBiology that may be helpful. If I understand you correctly, you want to combine your fuel cell model with SGLT2? Looking at the file BFCBird.m attached to your question, it seems like you may be able to re-create this code in SimBiology using repeated assignment rules.

You can use the SGLT2 model as a base model, add parameters or species to it as needed, and then define the fuel cell in terms of repeated assignment rules. If you are not already using it, I recommend using the SimBiology Model Builder app (type simbiology on the MATLAB command line to open it). This app allows you to copy/paste parts of one model into another to combine them (in case you already had a SimBiology model of your fuel cell).

If you define your fuel cell model in terms of ODEs, I think there is a conversion tool from MATLAB scripts containing ODEs to SimBiology models. As far as I know, this requires the ODEs to be written in a specific format. Let me know if this is of interest to you and we can follow up on this.

I hope this helps.

Best,

Florian