INDISIM, an individual-based discrete simulation model to study bacterial cultures
Authored by Marta Ginovart, D Lopez, J Valls
Date Published: 2002
DOI: 10.1006/jtbi.2001.2466
Sponsors:
Spanish government
Platforms:
INDISIM
Model Documentation:
Other Narrative
Flow charts
Mathematical description
Model Code URLs:
Model code not found
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 defined by a set of random, time-dependent
variables. These variables may include concentrations of different 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. (C) 2002
Academic Press.
Tags
Chaos
Temperature
Escherichia-coli
Growth-rate