Capacities

Reaction bounds

The reactions in the model can be constrained with upper and lower bounds as done typically in FBA, only that here these bounds are specified for each time interval.

Note

Upper and lower bounds can be used to simulate environmental conditions. For example:

  • Ub oxygen uptake = 0; simulates anaerobic conditions.

  • Lb uptake substrate > 1; simulates feeding into the system.

Enzyme capacities

A reaction ‘r’ can be additionally constrained by its upper limit following the relation:

../_images/Methods_img6.jpg

This relation indicates that the fastest rate a reaction can have is limited by the amount of a catalyst (an imbalanced metabolite) and the kcat value of said catalyst. The implementation of said relation is incorporated by using the following matrices:

  • A_cap: Matrix containing the inverse kcat value for each reaction (number of columns) catalyzed by each meatbolite in B_cap (number of rows).

  • B_cap: Matrix indicating which of the imbalanced metabolites (number of columns) serves as a catalyst of a reaction (each row for a reaction).

An example on how to build A_cap and B_cap for a system with multiple enzymes is presented in MinCell 3