How to simulte a chemical reaction at different initial concentratios of reactants in the Simbiolgy interfase of Matlab?

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Luis B. Walter 2024-2-10

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评论： Luis B. Walter 2024-2-12

SimbiologyprotocolI.pdf

How to simulate in the Simbiology interfase of Matlab the time course of a reaction such as, for example, A + B <-> C, at different initial concentrations of A, keeping the initial concentration of B constant?

I included in the attach a graphical help of my question.

Thanks a lot

Luis B.

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Answer 1

Priya Moorthy 2024-2-11

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Hi, Luis,

There are three different ways to change the initial values for a quantity (species, parameter or compartment) in your SimBiology model.

1) Variants: You can create variants to define alternate initial values for a quantity. See https://www.mathworks.com/help/simbio/ug/variant-object.html for a detailed description of how to use variants.

2) Sliders: You can explore the effect of changing initial values by creating sliders for a simulation program in the SimBiology Model Analyzer. After creating a simulation program, create a slider by dragging and dropping a model quantity from the Models panel onto the Explorer panel (see first screenshot). When you move the slider, the simulation will re-run with the new initial value. Select the "Keep results from each run" checkbox (circled in yellow in the screenshot) to preserve the previous results and add new lines to the plot with each subsequent run.

3) Scan program: Create a scan program by selecting "Run scan" from the Program button in the toolbar or add a "Generate samples" step using the "+" button in the program tab (see second screenshot). Configure the "Generate samples" step to scan over different initial values for one or more quantities. You can configure plot settings through the Property Editor panel to customize your plot (see third screenshot).