Model

This is the main model in this example, and it simulates glycolytic oscillations in Saccharomyces cerevisiae (yeast cells) as described in F. Hynne, S. Danø, and P. G. Sørensen, "Full-Scale Model of Glycolysis in Saccharomyces cerevisiae," Biophysical Chemistry, 94(1–2), 2001 pp. 121–163.

The model has been imported from the BioModels Database using the SBML importer in Wolfram System Modeler and designed using the BioChem library.

View the model diagram for this model.

Simulation

Simulate the model by clicking the Simulate button:

In its default configuration, the model produces a stable limit cycle. Look at, for instance, the variable cytosol.ATP.c to study the oscillations. Plot the variable by expanding the tree in the Plot view in the Simulation Center. First expand the cytosol branch, then the ATP branch, and finally select the c variable by checking the box next to it.

The plot of the variable will appear in a plot window to the right.

To simulate the model on the other side of the bifurcation point, update the initial conditions of the model by choosing Tools ▶ Initialize ▶ From Experiment. This sets the initial state for the next simulation to be the final state of the previous simulation.

Select your current experiment, for instance GlycolysisModel 1, and click OK.

Finally, change the initial value of GlcX0.c from 0.020 to 0.0175 in the Variables tab in Simulation Center.

Simulating again, the variable cytosol.ATP.c will now converge back to a steady state.

As you can see, small changes in a bifurcation parameter can qualitatively change the oscillations of protein and molecule concentrations.