How do I optimize my simulation and build in appropriate constraints on values?

Matlab and modeling novice here. My ModelAnalyzer simulation abruptly stops graphing two species (IL-23 and Occupancy) of interest. I'm not sure what is causing this. Additionally, my RO (receptor occupancy) should never be a negative value since it's a %. How do I constrain this to a value from 0-100?

Another question is how do I generate a plot of Free Drug vs. Occupancy values? I have attached my file to this question. Please let me know if I'm making mistakes that are leading to this output.

Answer 1

[Jeremy Huard]

Hi @Ian,

I don't know the original mathematical model but based on the project you shared, I can recommend the following:

1. I recommend you to activate Unit Conversion in the Simulation settings since you use different time units in the model and smiulation program (minute vs second).
2. There seems to be an issue with the ODE driving the concentration of IL-23. The term ParacrineConsumption is currently independent of free drug:

which seems in contradiction with the events.

I assume you didn't set to 0 at t=0 since it would be with the current implementation.

Having ParacrineConsumption being a constant and thus independent of IL-23 can indeed lead to negative values.

3. Once the points above are solved, you could use a scheduled dose instead of multiple events to modify the value of . Schedule doses provide a way to specific each dosing time and dosing amount separately in a schedule table. You can create a schedule dose by clicking in the Type column of the table of doses.

Using a schedule dose is more efficient than events if the triggers occur at a predefined list of timepoints.

By the way, not artificially constraining IL-23 to always be positive makes it possible to see the issue described in point 2.

I hope this helps.

Best regards,

Jérémy

[Priya Moorthy]

Hi, Ian,

It is possible to plot Free Drug vs. Occupancy using the XY plots in the SimBiologyModelAnalyzer. Create an XY plot from the plot gallery, then select both states in the browser and drag and drop them onto the plot. Alternately, you can select both states and then click on XY plot from the plot gallery to create a plot with those states. If you want to swap the X and Y states, right click on the plot and select "Swap X and Y Variables".

Best,

Priya