- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2024-01-16 17:34:48+13:00
- Desc:
- updates to the model and SED-ML, separate out example 3.7
- Permanent Source URI:
- https://models.physiomeproject.org/workspace/af2/rawfile/b70c68cac4814ff329fa16813fb4b6b93850ae28/README.rst
Bond graph example: An enzyme-catalyzed reaction and Michaelis-Menten kinetics
===============================================================================
Consider the enzymatic reaction shown below, which is often associated with Michaelis-Menten (MM) kinetics.
:math:`q_c^1` is a substrate that binds reversibly to an enzyme :math:`q_c^3` to form the complex :math:`q_c^4`, which breaks down to regenerate the enzyme and yield a product :math:`q_c^2`.
In conventional MM kinetics this last step is treated as irreversible, since :math:`A_2^f ≫ A_2^r`.
.. figure:: fig1.png
:width: 95%
:align: center
:alt: Schematic and bond graph of the model
An enzyme (:math:`q_c^3`)-catalyzed reaction (a), and its bond graph representation (b).
Flux balance is ensured for each of the four species at the 0:nodes, and energy balance at the 1:nodes ensures the correct stoichiometry.
The **Views Available** menu to the right provides various options to explore this model here in the Physiome Model Repository.
Of particular interest is the *Launch with OpenCOR* menu item, which will load the simulation experiment shown below directly into the `OpenCOR`_ desktop application.
.. figure:: fig2.png
:width: 95%
:align: center
:alt: OpenCOR showing simulation experiment.
Showing the result of launching the simulation experiment from this exposure in OpenCOR and executing the simulation.
.. _CellML: https://www.cellml.org/
.. _OpenCOR: https://opencor.ws/
.. _SED-ML: https://sed-ml.org
