1. 1 INDISIM - YEAST An individual-based model to study the behaviour of yeast populations in batch cultures

2. 2 ACTIONS ON EACH INDIVIDUAL RANDOM MOTION UPTAKE OF NUTRIENT PARTICLES DEPENDING ON LOCAL ENVIRONMENT (GLUCOSE AND ETHANOL) AND INDIVIDUAL CHARACTERISTICS (SIZE AND SCARS) INCREASE OF BIOMASS ACCORDING TO THE METABOLIZED NUTRIENT PRODUCTION AND EXCRETION OF RESIDUAL PARTICLES (ETHANOL WITH INHIBITORY EFECTS) BUDDING REPRODUCTION (WITH UNEQUAL DIVISION) BUDDING PHASE? CELL DIVISION? NO YES NEW INDIVIDUAL A YES NEW CONFIGURATION OF POPULATION UNBUDDED PHASE REQUIREMENTS TO BE VIABLE? DEATH AND LYSIS NO YES A ENOUGH NUTRIENT PARTICLES FOR ITS MAINTENANCE ? UPDATE THE NEW INDIVIDUAL CHARACTERISTICS ACTIONS ON EACH INDIVIDUAL RANDOM MOTION UPTAKE OF NUTRIENT PARTICLES DEPENDING ON LOCAL ENVIRONMENT (GLUCOSE AND ETHANOL) AND INDIVIDUAL CHARACTERISTICS (SIZE AND SCARS) INCREASE OF BIOMASS ACCORDING TO THE METABOLIZED NUTRIENT PRODUCTION AND EXCRETION OF RESIDUAL PARTICLES (ETHANOL WITH INHIBITORY EFECTS) BUDDING REPRODUCTION (WITH UNEQUAL DIVISION) BUDDING PHASE? CELL DIVISION? NO YES NEW INDIVIDUAL A YES NEW CONFIGURATION OF POPULATION UNBUDDED PHASE REQUIREMENTS TO BE VIABLE? DEATH AND LYSIS NO YES A ENOUGH NUTRIENT PARTICLES FOR ITS MAINTENANCE ? UPDATE THE NEW INDIVIDUAL CHARACTERISTICS ACTIONS ON EACH INDIVIDUAL RANDOM MOTION UPTAKE OF NUTRIENT PARTICLES DEPENDING ON LOCAL ENVIRONMENT (GLUCOSE AND ETHANOL) AND INDIVIDUAL CHARACTERISTICS (SIZE AND SCARS) INCREASE OF BIOMASS ACCORDING TO THE METABOLIZED NUTRIENT PRODUCTION AND EXCRETION OF RESIDUAL PARTICLES (ETHANOL WITH INHIBITORY EFECTS) BUDDING REPRODUCTION (WITH UNEQUAL DIVISION) BUDDING PHASE? CELL DIVISION? NO YES NEW INDIVIDUAL A YES NEW CONFIGURATION OF POPULATION UNBUDDED PHASE REQUIREMENTS TO BE VIABLE? DEATH AND LYSIS NO YES A ENOUGH NUTRIENT PARTICLES FOR ITS MAINTENANCE ? UPDATE THE NEW INDIVIDUAL CHARACTERISTICS ACTIONS ON EACH INDIVIDUAL RANDOM MOTION UPTAKE OF NUTRIENT PARTICLES DEPENDING ON LOCAL ENVIRONMENT (GLUCOSE AND ETHANOL) AND INDIVIDUAL CHARACTERISTICS (SIZE AND SCARS) INCREASE OF BIOMASS ACCORDING TO THE METABOLIZED NUTRIENT PRODUCTION AND EXCRETION OF RESIDUAL PARTICLES (ETHANOL WITH INHIBITORY EFECTS) BUDDING REPRODUCTION (WITH UNEQUAL DIVISION) BUDDING PHASE? CELL DIVISION? NO YES NEW INDIVIDUAL A YES NEW CONFIGURATION OF POPULATION UNBUDDED PHASE REQUIREMENTS TO BE VIABLE? DEATH AND LYSIS NO YES A ENOUGH NUTRIENT PARTICLES FOR ITS MAINTENANCE ? UPDATE THE NEW INDIVIDUAL CHARACTERISTICS

3. 3 SIMULATION RESULTS The comparison with experimental data is only qualitative at the present level. The first simulations results relate to the development of population descriptors and to the development of variability within the population of cells. The results have been split into two parts: Global Properties These involve population properties parameters, like the change in concentrations of glucose, of ethanol, number of yeast and of the biomass. Individual Properties We are concerned with both time evolving and distributions of population parameters, ……. some of which will become directly comparable with experiment when we overcome the question of scaling to real times and energies. Flow cytometric light scattering experiments are capable to probe the properties of individual yeast cells.

4. 4 SIMULATION RESULTS Global Properties Temporal evolution of nutrient and metabolites in the simulated yeast culture

5. 5 SIMULATION RESULTS Global Properties Temporal evolution Thick line: Total biomass Thin line: Viable biomass Log ( number of yeast cells) Evolution of the yeast population: lag phase (0-40 time step), exponential phase (40-400 time step), linear phase (400–600 time step), metabolic slow down (600–1000 time steps), final phase (1000–1200 time step).

6. 6 SIMULATION RESULTS Individual Properties Temporal evolution of the mean biomass of the cell population

7. 7 SIMULATION RESULTS Individual Properties Temporal evolution of the average nutrient uptake

8. 8 SIMULATION RESULTS Individual Properties Microscopic population parameters, namely distributions of variables controlled at individual level: (a) distribution of masses; (b) distribution of genealogical ages; (c) duration of the two periods of the cellular cycle; (d) distribution of masses at the end of each period of the cellular cycle. These are mainly related to the cellular cycle and reflect the state of the yeast population at given times in the fermentation process.

9. 9 SIMULATION RESULTS Individual Properties Histograms of the distributions of masses in the simulated yeast culture at different steps of the simulated evolution

10. 10 SIMULATION RESULTS Individual Properties Histograms of the distributions of genealogical ages of yeast cells in the simulated yeast culture at different steps of the simulated evolution

11. 11 SIMULATION RESULTS Individual Properties Boxplots of the durations of the unbudded interval (Phase 1) as a function of the genealogical ages of the yeast cells in the simulated yeast culture at different steps of the evolution.

12. 12 SIMULATION RESULTS Individual Properties Temporal evolution of the 95% confidence intervals for the mean duration of the unbudded interval (Phase 1) of the cells in the simulated yeast culture, using separate plots for daughter and parent cells.

13. 13 SIMULATION RESULTS Individual Properties Boxplots of the durations of the budding interval (Phase 2) as a function of the genealogical ages of the yeast cells in the simulated yeast culture at different steps of the evolution.

14. 14 SIMULATION RESULTS Individual Properties Temporal evolution of the 95% confidence intervals for the mean duration of the budding interval (Phase 2) of the cells in the simulated yeast culture, using separate plots for daughter and parent cells.

15. 15 SIMULATION RESULTS Individual Properties Boxplots of the final masses at the end of the unbudded interval (Phase 1), as a function of the genealogical ages of the yeast cells in the simulated yeast culture, at different steps.

16. 16 SIMULATION RESULTS Individual Properties Boxplots of the final masses for parent and daughter cells at the end of the budding interval (Phase 2), as a function of the genealogical ages of the yeast cells in the simulated yeast culture, at different steps.

17. 17 Flow chart of our computer code INDISIM and a detailed flow chart program step, with the tasks implemented at each time step for a bacterial study.