A brief overview of the code structure is provided in Section 6.2.3 of Dan Harvey's DPhil thesis.

It looks like Dan's approach is to create a class NodeBasedCellPopulationWithSemId inheriting from NodeBasedCellPopulation, where there is a 1-1 correspondence between nodes and cells, but not to actually use any cell functionality like division, growth, or death, so that cells aren't really thought of as 'actual' cells. Two NodeAttributes are then used to keep track of whether each node is actually part of an 'actual' cell's nucleus (mIsParticle) and to keep track of which 'actual' cell it belongs to (mIsRegion).

I guess this was done to limit the amount of new coding required, and because for the use cases considered by Dan Harvey and others, cell behaviours like division weren't necessary. I think a more general approach, allowing for cell division and cell death, will require a new cell population that maintains a correspondence between each cell and multiple nodes (as is the case already in VertexBasedCellPopulation and - once it is in the develop branch - ImmersedBoundaryCellPopulation).

With this new approach, I can see a few minor edits needed to the existing mechanics code, e.g.

• in SemForce::AddForceContribution(), to find which cell owns each node, instead of calling GetRegion() we'd want to get its global index then call GetCellUsingLocationIndex() on the cell population;
• in SemParameterScaler::ScaleSpringConstant(), instead of calling GetNumElements() with an semIndex, we'd instead want to get the number of nodes owned by a cell (elsewhere in the Chaste code, we'd do this by interrogating some kind of mesh element associated with the cell, so it depends on whether we'd want to stick to using NodesOnlyMesh in this new approach).

Then more effort would be required to implement things like cells dividing, growing/shrinking, dying, and interacting with any PDE state variables.

Dan Harvey's full DPhil thesis: https://ora.ox.ac.uk/objects/uuid:95f50f05-9cf5-4c58-9115-aff7aabdfd6f/files/m25393982233b14b3892ac994f014e96e

Original SEM paper: https://iopscience.iop.org/article/10.1088/1478-3975/5/1/015002/meta

Relevant recent paper by Dokmegang et al: https://www.biorxiv.org/content/10.1101/2020.06.08.140269v4

The other SEM paper: https://doi.org/10.1088/1478-3975/8/4/045007