Biomedical subjects

Joaquim Valls

Publications and source records attributed to Joaquim Valls.

3 recordsLinked to original sources

PubMed2006

Individual-based modelling of bacterial cultures to study the microscopic causes of the lag phase.

The lag phase has been widely studied for years in an effort to contribute to the improvement of food safety. Many analytical models have been built and tested by several authors. The use of Individual-based Modelling (IbM) allows us to probe deeper into the behaviour of individual cells; it is a bridge between theories and experiments when needed. INDividual DIScrete SIMulation (INDISIM) has been developed and coded by our group as an IbM simulator and used to study bacterial growth, including the microscopic causes of the lag phase. First of all, the evolution of cellular masses, specifically the mean mass and biomass distribution, is shown to be a determining factor in the beginning of the exponential phase. Secondly, whenever there is a need for an enzyme synthesis, its rate has a direct effect on the lag duration. The variability of the lag phase with different factors is also studied. The known decrease of the lag phase with an increase in the temperature is also observed in the simulations. An initial study of the relationship between individual and collective lag phases is presented, as a complement to the studies already published. One important result is the variability of the individual lag times and generation times. It has also been found that the mean of the individual lags is greater than the population lag. This is the first in a series of studies of the lag phase that we are carrying out. Therefore, the present work addresses a generic system by making a simple set of assumptions.

Bacteria↗

PubMed2002

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

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.

Bacteria↗

PubMed1992

Nonequilibrium dynamics in lattice ecosystems: Chaotic stability and dissipative structures.

A generalized coupled map lattice (CML) model of ecosystem dynamics is presented. We consider the spatiotemporal behavior of a prey-predator map, a model of host-parasitoid interactions, and two-species competition. The latter model can show phase separation of domains (Turing-like structures) even when chaos is present. We also use this CML model to explore the time evolution and structural properties of ecological networks built with a set of N competing species. The May-Wigner criterion is applied as a measure of stability, and some regularities in the stable networks observed are discussed.

Journal Article↗