Define diffusion–mechanics interaction and substrate access across timescales

[joseestragues]

The current implementation does not yet define how the diffusion and mechanics modules should interact when they run at different timescales.

This becomes a blocker for chemotaxis and other mechanics-side behaviors that depend on substrate values or gradients. Right now:

• gradient computation is not included in the diffusion module

• the mechanics module has no clear API to access substrate data

This issue tracks the design needed to support diffusion–mechanics coupling in a consistent way.

Background

you are right. We did not include gradient computation in diffusion module. I wanted to implement it in mechanics, because in physicell it was computed in mechanics dt. Perhaps in the first version, each cell can compute it by itself in the motility code.

Also, its right that now we do not have any way of accessing substrates from mechanics. Lets leave diffusion+mechanics interactions to the next PR since that can get compicated

Originally posted by @asmelko in #110