INDISIM-YEAST, an individual-based model to study yeast

Abstract

INDISIM-YEAST, an individual-based simulator, models the evolution of a yeast population by setting up rules of behaviour for each individual cell according to their own biological rules and characteristics. It takes into account the uptake, metabolism, budding reproduction and viability of the yeast cells, over a period of time in the bulk of a liquid medium, occupying a three dimensional closed spatial grid with two kinds of particles (glucose and ethanol). Each microorganism is characterized by its biomass, genealogical age, states in the budding cellular reproduction cycle and position in the space among others. Simulations are carried out for population properties (global properties), as well as for those properties that pertain to individual yeast cells (microscopic properties). The results of the simulations are in good qualitative agreement with established experimental trends.