About this model

This is a bond-graph model of the metabolism of generic receptor tyrosine kinase (RTK) in the mammalian cell.

  • Ligand (L) stimulus
  • Change in molar amount of phosphorylated RTK K2Pn
  • Re1: the binding of L to one RTK (K1)
  • Re2: formation of temporary complex of two RTK molecules which have dimerized, with ligand present (LK1 K2).
  • Re3: autophosphorylation of second RTK in the dimer and simultaneous dissociation of 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.

BG PKACI reaction

Fig. 1. Bond-graph formulation of the generic RTK network. Because this model is generic, n would change depending on the chosen reaction.

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.

List of chemical species
Abbreviation Name
K Receptor tyrosine kinase (RTK)
L Ligand
Pi Phosphate

Parameter finding

A description of the process to find bond-graph parameters is shown in the folder 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.
  1. linear algebra script.

Here, this solve process is performed in Python.

Derived from workspace BG_RTK at changeset 81dae20d940c.
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