INDISIM, an individual based discrete simulation model to study bacterial cultures

Abstract

An individual-based model has been developed and designed to simulate the growth and behaviour of bacterial colonies. The simulator is called INDISIM, which stands for INDividual DIScrete SIMulations. INDISIM is discrete in space and time, and controls a group of bacterial cells at each time step, using a set of random, time-dependent variables for each bacterium. These variables are used to characterize its position in space, biomass, state in the cellular reproduction cycle as well as other individual properties. The space where the bacterial colony evolves is also discrete. A physical lattice is introduced, subject to the appropriate boundary conditions. The lattice is subdivided into spatial cells, also de"ned by a set of random, time-dependent variables. These variables may include concentrations of di!erent types of particles, nutrients, reaction products and residual products. Random variables are used to characterize the individual bacterium and the individual particle, as well as the updating of individual rules. Thus, the simulations are stochastic rather than deterministic. The whole set of variables, those that characterize the bacterial population and the environment where they evolve, enables the simulator to study the behaviour of each microorganism *such as its motion, uptake, metabolism, and viability*according to given rules suited for the system under study. These rules require the input of only a few parameters. Once this information is inputted, INDISIM simulates the behaviour of the system providing insights into the global properties of the system from the assumptions made on the properties of the individual bacteria. The relation between microscopic and global properties of the bacterial colony is obtained by using statistical averaging. In this work INDISIM has been used to study (a) biomass distributions, (b) the relationship between the rate of growth of a bacterial colony and the nutrient concentration and temperature, and (c) metabolic oscillations in batch bacterial colonies. The simulation results are found to be in very good qualitative agreement with available experimental data, and provide useful insights into the mechanisms involved in each case.