Fig. 2

Illustration of the spatial modeling framework. Simulated colonies consist of interacting elementary cubes (for illustrative purposes, the cubes are here notably larger than in practise). a Illustration of the elementary cube approximation of a yeast colony. The upper part of the colony (gray elementary cubes) represents the cell mass domain. In these elementary cubes, each microenvironment consists of a mixture of nutrients and cells in different metabolic states. Further, the lower part of the colony (green elementary cubes) represents the nutrient rich agar domain. In the agar domain, each microenvironment can consist of a mixture of nutrients and no cell mass is present. b Mass movement is modeled by considering the fill levels of the elementary cubes. The cell mass is growing in the cubes and once a the fill level threshold is reached, cell mass starts to be move into the neighboring cubes. During the cell mass movement, relative fractions of cells in different metabolic states are moved along