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ACTIONS ON EACH INDIVIDUAL

INDISIM - YEAST An individual-based model to study the behaviour of yeast populations in batch cultures. ACTIONS ON EACH INDIVIDUAL. ACTIONS ON EACH INDIVIDUAL. ACTIONS ON EACH INDIVIDUAL. ACTIONS ON EACH INDIVIDUAL. RANDOM MOTION. RANDOM MOTION. RANDOM MOTION. RANDOM MOTION.

vivian-wilkerson
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ACTIONS ON EACH INDIVIDUAL

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

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

  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. SIMULATION RESULTSGlobal Properties Temporal evolution of nutrient and metabolites in the simulated yeast culture

  5. SIMULATION RESULTSGlobal 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. SIMULATION RESULTSIndividual Properties Temporal evolution of the mean biomass of the cell population

  7. SIMULATION RESULTSIndividual Properties Temporal evolution of the average nutrient uptake

  8. SIMULATION RESULTSIndividual 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. SIMULATION RESULTSIndividual Properties Histograms of the distributions of masses in the simulated yeast culture at different steps of the simulated evolution

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

  11. SIMULATION RESULTSIndividual 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. SIMULATION RESULTSIndividual 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. SIMULATION RESULTSIndividual 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. SIMULATION RESULTSIndividual 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. SIMULATION RESULTSIndividual 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. SIMULATION RESULTSIndividual 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. Flow chart of our computer code INDISIMand a detailed flow chart program step, with the tasks implemented at each time step for a bacterial study.

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