Defining Solutes and Particle Types
The solute mark-ups list and describe all the solute compounds used by the model, along with their molecular diffusivity in water. At this point we do not specify concentration information; that information will be specified in the section for bulk compartments.
The pressure solute is not actually a physical solute, but is used in computing biomass spreading effects. It is best to leave the pressure mark-up as-is. However, during a chemostat run any solutes not involved in the reactions in which the agents participate must not be listed (i.e. do not use the ‘pressure solute’ for chemostat simulations).
The particle mark-ups refer to the different compartments used to describe agent species (which is done later in the protocol file). When defining a species, one has to list which of the possible compartments are used by that species. At this level of the protocol file, the compartments are defined independently of any species and described by their name and density.
These three particle types are very common (active biomass, inert biomass, and capsular compounds, respectively), and most simulations will employ all three.