- Author:
- Shelley Fong <sfon036@UoA.auckland.ac.nz>
- Date:
- 2025-04-28 10:50:08+12:00
- Desc:
- Adding expo files
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/b2d/rawfile/7ffdffa3746a5082ac7fe40e9eb41ff3ac238444/exposure/exposure_frontpage.rst
About this model
====================
This is a bond-graph model of the metabolism of generic receptor tyrosine kinase (RTK) in the mammalian cell.
**INPUTS:**
- Ligand (L) stimulus
**OUTPUTS:**
- Change in molar amount of phosphorylated RTK K\ :sub:`2`\ P\ :sub:`n`\
**REACTIONS:**
- Re\ :sub:`1`\ : the binding of L to one RTK (K\ :sub:`1`)
- Re\ :sub:`2`\ : formation of complex of two RTK molecules which have dimerized, with ligand present (LK\ :sub:`1` K\ :sub:`2`).
- Re\ :sub:`3`\ : autophosphorylation of RTKs in the dimer.
Model status
=============
The current CellML implementation runs in OpenCOR.
Model overview
===================
The following model of RTK action is based on what is widely known in literature.
.. figure:: exposure/BG_diagram.png
:width: 100%
:align: center
:alt: BG RTK reaction
Bond-graph formulation of the generic RTK network. E represents the RTK protein. Because this model is generic, :math:`{n}` would change depending on the chosen reaction.
|
.. csv-table:: List of chemical species
:header: "Abbreviation", "Name"
:widths: 5, 15
"K", "Receptor tyrosine kinase (RTK)"
"L", "Ligand"
"P\ :sub:`i`", "Phosphate"
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/b2d/rawfile/fd659c74315399c5874252dbf5f279552c9811ff/parameter_finder/kinetic_parameters_RTK.py>`_.
Here, this solve process is performed in Python.
