Location: FCU_ExcitationContraction_Coupling @ 99ed1a945c23 / exposure / exposure_frontpage.rst

Shelley Fong <sfon036@UoA.auckland.ac.nz>
2022-06-07 15:23:26+12:00
Updating exposure rst and cellml files
Permanent Source URI:

About this Functional Cell Unit

This model is a Functional Cell Unit for excitation-contraction coupling in the cardiac cell. 

This is a composite module, composed of several individual modules, and merged together in a modular fashion.

        - Stimulus current or action potential.
        - Change in number of myosin binding sites on cross-bridges.
Model status

The current CellML implementation compiles in OpenCOR.

Model overview
All components are presented in `bond-graph` form.
Components are made by converting an existing kinetic model and translating into bond-graph form. 

.. figure:: exposure/FCU_picture.png
   :width: 70%
   :align: center
   :alt: Components of the model

   Components of the model.
A description of the process to find bond-graph parameter is shown in the folder    `parameter_finder <parameter_finder>`_, which relies on the:

1. stoichiometry of system

2. kinetic constants for forward/reverse reactions

  - If not already, all reactions are made reversible by assigning a small value to the reverse  direction.
3. `linear algebra script <https://models.physiomeproject.org/workspace/7a8/rawfile/4ae281c45fbbd7c0a2be6c86eb946a84c35f0f70/parameter_finder/find_BG_parameters_composite.py>`_, which outputs the bond-graph parameters K and :math:`{\kappa}`.

Here, this solve process is performed in Python.

Modular description


CellML divides the mathematical model into distinct components, which are able to be re-used in other composite models.
These CellML components are:

- `Sarcoplasmic/endoplasmic Ca2+ ATPase <https://models.physiomeproject.org/workspace/7a5>`_ (SERCA)
- `Phospholamban regulation <https://models.physiomeproject.org/workspace/6d1>`_ (PLB)
- `Ryanodine receptor <https://models.physiomeproject.org/workspace/6e3>`_ (RyR)
- `L-type calcium channel <https://models.physiomeproject.org/workspace/6d7>`_ (LCC)
- `Crossbridge Troponin-C <https://models.physiomeproject.org/e/800>`_ (Crossbridge_TnC)
.. csv-table:: Origin of kinetic model components
   :header: "Source", "Components"
   :widths: 15, 30   
   "`Saucerman et al. (2003) <https://models.physiomeproject.org/exposure/9766d9bd0325c31e47a31b291e26ccad>`_", "PLB"
   "`Luo and Rudy (1994) <https://models.physiomeproject.org/e/81>`_", "LCC"
   "`Tran et al. (2009) <https://models.physiomeproject.org/exposure/815f3cb51960e9c9855e66996c1d1a4c>`_", "SERCA"
   "`Stern et al. (1999) <https://models.physiomeproject.org/exposure/b060fdbcfae8c7d85e595c24d36ab11b>`_", "RyR"
   "`Niederer et al. (2006) <https://models.physiomeproject.org/exposure/97fb1de5199b1a74c89281db97aecc13>`_ , `Land et. al. <http://dx.doi.org/10.1016/j.yjmcc.2017.03.008>`_", "Crossbridge_TnC"
Each of these blocks is itself a CellML model, complete with bond-graph parameters appropriate for the isolated system.