- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2024-01-16 18:00:06+13:00
- Desc:
- Adding documentation for exposure
- Permanent Source URI:
- https://models.cellml.org/workspace/b5b/rawfile/4136b72c64cf71f36c4c103f7ba19d77246246ff/README.rst
Bond graph example: Steady state for an enzyme-catalyzed reaction with multiple reactants and products
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A common situation is where multiple reactants participate in an enzyme-catalyzed reaction which has multiple products.
For this example, we consider the ‘steady state’ situation in which the amounts of enzyme in the unbound form and the reactant-bound form do not change with time and the enzyme is cycling at a constant rate.
Note that this is different from an ‘equilibrium’ situation in which the flux is actually zero.
We also use this example to introduce another symbol which helps simplify the diagrams as they become more complex.
Since the capacitive storage term :math:`q_c^i` for a chemical species :math:`i` is always associated with its chemical potential :math:`u_c^i` (defined at a 0:node where mass conservation is ensured), it is useful to combine these into one red outline symbol that contains storage term for the chemical species.
The red outline is a reminder that this is also a 0:node for mass conservation.
The reactants :math:`q_c^i`, for :math:`i=1..I`, and products :math:`q_c^j`, for :math:`j=1..J`, are shown below together with the enzyme :math:`q_c^{e0}` and its bound complex :math:`q_c^{e1}`.
.. figure:: fig1.png
:width: 95%
:align: center
:alt: Bond graph of the model
An enzyme-catalyzed reaction with multiple reactants and multiple products.
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
