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The generic, quantitative, spatially explicit, individual-based model BacSim was developed to simulate growth and behaviour of bacteria. The potential of this approach is in relating the properties of microscopic entities - cells - to the properties of macroscopic, complex systems such as biofilms. Here, the growth of a single Escherichia coli cell into a(More)
In this paper we describe a spatially multidimensional (two-dimensional [2-D] and three-dimensional [3-D]) particle-based approach for modeling the dynamics of multispecies biofilms growing on multiple substrates. The model is based on diffusion-reaction mass balances for chemical species coupled with microbial growth and spreading of biomass represented by(More)
The origin of altruism is a fundamental problem in evolution, and the maintenance of biodiversity is a fundamental problem in ecology. These two problems combine with the fundamental microbiological question of whether it is always advantageous for a unicellular organism to grow as fast as possible. The common basis for these three themes is a trade-off(More)
Understanding the emergence of the complex organization of biofilms from the interactions of its parts, individual cells and their environment, is the aim of the individual-based modelling (IbM) approach. This IbM is version 2 of BacSim, a model of Escherichia coli colony growth, which was developed into a two-dimensional multi-substrate, multi-species(More)
A computational model explaining formation of mushroom-like biofilm colonies is proposed in this study. The biofilm model combines for the first time cell growth with twitching motility in a three-dimensional individual-based approach. Model simulations describe the tendency of motile cells to form flat biofilms spreading out on the substratum, in contrast(More)
Quorum sensing faces evolutionary problems from non-producing or over-producing cheaters. Such problems are circumvented in diffusion sensing, an alternative explanation for quorum sensing. However, both explanations face the problems of signalling in complex environments such as the rhizosphere where, for example, the spatial distribution of cells can be(More)
We have simulated a nitrifying biofilm with one ammonia and one nitrite oxidising species in order to elucidate the effect of various extracellular polymeric substance (EPS) production scenarios on biofilm structure and function. The individual-based model (IbM) BacSim simulates diffusion of all substrates on a two-dimensional lattice. Each bacterium is(More)
Progress in microbiology has always been driven by technological advances, ever since Antonie van Leeuwenhoek discovered bacteria by making an improved compound microscope. However, until very recently we have not been able to identify microbes and record their mostly invisible activities, such as nutrient consumption or toxin production on the level of the(More)
Biochemical studies on anaerobic phenylme-thylether cleavage by homoacetogenic bacteria have been hampered so far by the complexity of the reaction chain involving methyl transfer to acetyl-CoA synthase and subsequent methyl group carbonylation to acetyl-CoA. Strain TMBS 4 differs from other demethylating homo-acetogenic bacteria in using sulfide as a(More)
Evolutionary game theory can be considered as an extension of the theory of evolutionary optimisation in that two or more organisms (or more generally, units of replication) tend to optimise their properties in an interdependent way. Thus, the outcome of the strategy adopted by one species (e.g., as a result of mutation and selection) depends on the(More)