Input Editor Pane Microbial Species

In this pane all properties of microbial species are set.

The names of microbial species can be modified. No two species of any kind can have the same name.

The type of microbial species (aqueous or adsorbed) can not yet be modified after a species was set up.

A species is selected by clicking on the appropriate row of the table.

Adding and removing microbial species

A new microbial species can be added by invoking the "Add new species" button. A dialog box will appear that requires the input of the name and the type (aqueous or adsorbed) of the species. Pressing Cancel or closing the window will abort the addition of the new species.

The selected species can be removed by invoking the "Remove selected species" button when the following condition is met:

The species does not participate in any chemical or microbial reaction. (Chemical reactions are set up in the input panel Chemical reactions, microbial reactions in the input panel Microbial reactions.)
If this conditions is not met, the labeling of the button "Remove selected species" will appear in red. Clicking the button will display a message with a listing of the reasons why this species can not be removed. You need to fix all of these violations of the above listed rule before you can remove the species.
Note: If the selected species can be removed, no confirmation is necessary after clicking the button. All of its data (affected species, initial and boundary conditions etc.) will be lost.

Affected species

Any chemical species can be affected by endogenous respiration of a microbial species. The current number of these affected species is displayed in the table in the top part of the pane. It can be changed by removing the selected affected species - first click on the affected species in the second table of this input pane, then click the button "Remove selected affected species".
Note: Removing an affected species does not remove the species itself from the list of species. This needs to be done in the input pane Chemical species.
Other chemical species can be added to the list of affected species by clicking the button "Add affected species". A dialog will appear that presents the list of possible choices in a combo box and text fields for the stoichiometric coefficient and the half saturation constant. These values can be changed in the table with the affected species. The species itself, however, can not be modified directly. To select a different species, you have to remove and add a new species.

Initial and boundary conditions

Initial concentrations are assigned to all microbial species. Boundary conditions are only assigned to aqueous microbial species.

A more detailed description of initial conditions is here.

A more detailed description of boundary conditions is here.

Last Modified:
Jin-Ping Gwo, email: jgwo@umbc.edu