Chemical data

Chemical data is a set of values for a generalized animal species that is treated as parameters. They are kept fixed (free = 0) by default, but can be released (free = 1) if adequat data exists to estimate them. See addchem, which is called in the pars_init file.

Two groups of chemical compounds are delineated: organic (structure, reserve, food, feces) and mineral (carbon dioxide, water, dioxygen, nitrogen-waste). Chemical data can be classified for these groups of chemical compounds as follows

Specific densities

Specific density is mass per volume; in the standard DEB units: g/cm³. Wet biomass has a specific density of around 1 g/cm³, since water dominates. Dry biomass has a lower specific density, but the water content varies considerably among the taxa; see comments on section 3.2.1 of DEB3 . Function get_D_V associates a typical value to the names of the phylum and class. The specific densities of structure, reserve, food and feces are all set equal; those of the minerals are not specified nor used.

Chemical potentials

The chemical potential of a generalized compound is the free energy per unit of mass; in the standard DEB units: J/C-mol. The bulk of biomass consists of proteins, carbohydrates and lipids and their masses are expressed in C-moles. AmP works in the combustion frame of reference (as opposed to the thermodynamic one), where the chemical potentials of mineral compounds is set to zero. Table 4.2 of DEB3 gives typical values for the chemical potentials of the three dominant chemical groups. Reserve is assumed to be more riche in carbohydrates and/or lipids, relative to structure. Food for animals consists of other organisms, so a mix between reserve and structure, and feces is assumed to have a somewhat lower chemical potential. Needless to say that the actual chemical potentials depend on type of food (as do the digestion and defacation efficiencies, which are parameters)

Chemical indices

A chemical index of a chemical element in a chemical compound is the frequency of atoms of that element, relative to carbon. We only follow the chemical elements C, H, O and N for convenience, but inclusion of other elements is straight forward. Since we work in C-moles, the chemical index of carbon is always 1 per definition. The chemical indices of the 4 dry organic compounds are all taken equal by default; the molecular weights are implied by these settings. They are computed in the function parscomp_st, The composition of nitrogen waste differs between taxa; ammonia (NH₃) is typically used by invertebrates, but is rather toxic when it accumulates. Function get_N_waste associates a typical composition to the names of the phylum and class.