🌊 Reactions

The SubDomainReactions trait can model how extracellular resources are transported and how the domain interacts with cells (eg. via secretion and uptake). The get_neighbor_value and get_border_info methods allow multiple subdomains to communicate properly and resolve update steps between them. The get_extracellular_at_pos method allows cells to query for extracellular values at their position in order to calculate their increments. Afterwards, treat_increments function is used for handling of these and other contributions. Finally, the update_fluid_dynamics method advances the simulation of extracellular reactions.

Currently we are still missing fully working building blocks for SubDomainReactions but are in the midst of adding them. The Bacterial Branching showcase is in the middle of being rewritten with the newer chili backend which will use this aspect.