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 cellML repository (using PyCml).
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

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.