Chaste functionality
Cardiac Chaste user functionality
- Solution of both the monodomain and bidomain equations (including external baths representation).
- Solution of coupled electro-mechanical problems using stable numerical algorithms.
- Automatic implementation of cellular action potential models from the CellML repository.
- Ability to load any tetrahedral mesh (including anatomically-based meshes of any size) and to automatically generate simple geometry meshes (slabs, etc).
- Automatic generation of mathematical model for fibre orientation associated with both anatomically-based and simple geometry meshes.
- Ability to define tissue properties both globally and locally based on XML files (for instance, to describe heterogeneities in ionic current properties)
- Post-processing of simulation results to calculate electrophysiological properties such as action potential duration, conduction velocity, etc.
- Checkpoint of simulations midway through run and restart with altered parameters
Cell-based Chaste user functionality
- Simulation of both cell-centre- and vertex-based models of cell populations in one, two or three spatial dimensions.
- Ability to define different force laws for cell-cell interactions.
- Ability to define different boundary conditions and geometric domains.
- Ability to define different cell killer objects, which govern the conditions in which cells undergo necrosis/apoptosis.
- Ability to define different cell-cycle models, which govern cell proliferation and quiescence.
- Ability to define different cell proliferative types (stem, transit amplifying and differentiated cells).
- Ability to define different cell mutation states, which can effect cell proliferation, migration and adhesion.
- Ability to define reaction-diffusion equations for key nutrients or signalling molecules, whose concentrations may influence (and in turn be influenced by) any of the above.
- Visualization and post-processing of simulation results.