Species properties

The next step is to define the chemical species present in the system. To do this, click on the species tab. On the left, you see a list of compartments in the model geometry. Select the one for which you want to define species. This species will only exist in this compartment. As a consequence, even if the species in all compartments are chemically the same, you still have to define them separately. Species only exist in the bulk volume of the compartments, i.e., species cannot be present only on the membranes.

To create a new species, click the Add button, select a suitable name, and hit enter. The new species will appear below the compartment name.

On the right hand side, you see the Species Settings menu. Here you can define all relevant properties of the species.

At the top, you can rename the species or assign it to a different compartment. You can also select whether it should be constant for the whole simulation or be variable. A constant species is fixed in time, but it can still be spatially varying if the Spatial option is enabled and the initial concentration is defined analytically or from an image. Constancy may be a useful simplifying assumption in some models if, for example, the species is produced far more quickly than the characteristic simulation timescale.

video showing species settings — How to define a new species in a compartment together with its initial conditions and diffusion constant

Two more properties of a species are of primary importance.

Initial concentration:

This can be set in three ways:

Uniform: a single scalar value everywhere in the compartment.
Analytic: an expression in the spatial coordinates (x, y, and z for 3D models).
Image: a sampled field loaded from image data, giving a per-voxel value.

Diffusion constant:

The presence of a diffusion term

\[\nabla \cdot \left( D \nabla c_{i} \right)\]

is assumed by default (see the documentation on the mathematical formulation for more details). The diffusion constant can also be set in three ways:

Uniform: a single scalar value everywhere in the compartment.
Analytic: an expression in the spatial coordinates (x, y, and z for 3D models).
Image: a sampled field loaded from image data, giving a per-voxel value.

In all cases, D is isotropic (scalar, not tensor). If you don’t want diffusion to be present, set D = 0.

With the definition of these two elements, the species is fully defined and can be used in the next steps of the model definition.

Storage coefficient (Advanced):

In the species Advanced section, you can set a non-negative, dimensionless storage coefficient \(S\). This scales the species time derivative in the PDE:

\[S_i \frac{\partial c_i}{\partial t} = \nabla \cdot \left( D_i \nabla c_i \right) + R_i\]

The default is \(S=1\), which gives the standard reaction-diffusion form. Larger \(S\) values make concentration changes slower in time, while values between 0 and 1 make them faster.

Setting \(S=0\) converts the equation into an algebraic constraint \(0 = \nabla \cdot (D \nabla c) + R\), meaning the species concentration is determined by satisfying this constraint at each timestep rather than being integrated in time.

Note

Take care to get the units correct. All quantities are assumed to have certain SI units, which are noted next to the input field for the respective quantity. For example, the diffusion constant could have units of :math: cm^2/s. For more on units, see here.