- Author:
- smeans <s.means@auckland.ac.nz>
- Date:
- 2025-11-05 15:56:07+13:00
- Desc:
- added cellml dependencies
- Permanent Source URI:
- https://staging.physiomeproject.org/workspace/d7e/rawfile/b8a595ae6aec59de8bee1394ede307a7b478b7dc/README.rst
About this model
=====================
The bond-graph conversion of a 4-state kinetic sarco-endoplasmic reticulum calcium-ATP-ase model as described in Higgins, 2006
:Original Publication: A Buffering SERCA Pump in Models of Calcium Dynamics, Higgins, Erin R. et al., Biophysical Journal, Volume 91, Issue 1, 151 - 163
:DOI: https://doi.org/10.1529/biophysj.105.075747
Model derivation
=====================
See schematic from original Higgins, 2006 paper and its bond-graph
.. figure:: higgins2006_serca_bg_schematic1
:width: 85%
:align: center
:alt: Schematic of the model
Running the model
=====================
CellML implementation is provided in the file higgins2006_serca_wphosphate.cellml and executable with the simulation environment OpenCOR. Tests reproducing the analytical steady-state as derived for the 4-state model are provided in the CellML file, as well as matlab codes (in parameter_fit_n_find) for computing the analytical steady-state flux. Running the simulation should reproduce the ratio of intracellular to extracellular Ca2+ in the variable 'q_Ca_ratio_analytic' with the numerical solution in variable 'q_Ca_ratio.' Note, simulation time may be quite long out to 60,000 seconds or more.
.. _OpenCOR: https://opencor.ws/
