- Author:
- Shelley Fong <s.fong@auckland.ac.nz>
- Date:
- 2022-01-14 11:31:10+13:00
- Desc:
- updating rst
- Permanent Source URI:
- https://models.cellml.org/workspace/674/rawfile/ea49f618e0f66f0b21b447df47b043704f53773e/exposure/exposure_frontpage.rst
About this model
====================
This is a bond-graph model of cyclic AMP (cAMP) metabolism in the cardiac cell.
**INPUTS:**
- ATP stimulus
**OUTPUTS:**
- Change in molar amounts of adenylyl cyclase (AC), cAMP
**REACTIONS:**
- Re1: Conversion of ATP into cAMP via AC
- Re2: Conversion of ATP into cAMP via the Gs:math:`{\alpha}`\ :sub:`GTP`\:AC complex
- Re3: Conversion of ATP into cAMP via the FSK:AC complex
- Re4: Cleavage of cAMP into 5-AMP via PDE
- Re5:
- Re6:
- Re7:
- Re8:
Model status
=============
The current CellML implementation runs in OpenCOR.
Model overview
===================
This model is made by from an existing kinetic model, where the mathematics are translated into the bond-graph formalism. This describes the model in energetic terms and forces adherence to the laws of thermodynamics.
The creation of the composite LR and LRG species are not included in this module. See the `module for L, R, and G binding for these. <https://models.physiomeproject.org/workspace/6f7>`_
For the following figure, all enzymes are shown in maroon.
.. figure:: exposure/BG_cAMP_network.png
:width: 100%
:align: center
:alt: BG cAMP
Fig. 1. Bond graph formulation of the cAMP network
|
For the above bond-graphs, a '0' node refers to a junction where all chemical potentials are the same. A '1' node refers to all fluxes being the same going in and out of the junction.
Parameter finding
~~~~~~~~~~~~~~~~~
A description of the process to find bond-graph parameters 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/6ba/file/c32be022513dc4b620d74803a6ace6ca2d817e11/parameter_finder/find_BG_parameters.py>`_.
Here, this solve process is performed in Python.
Original kinetic model
======================
Saucerman et al: `Modeling beta-adrenergic control of cardiac myocyte contractility in silico. <https://models.physiomeproject.org/exposure/9766d9bd0325c31e47a31b291e26ccad>`_
