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Thermodynamic behavior-rules for a bacterial individual-based model to study the denitrification process

Abstract:

The individual's adaptive behavior to environmental conditions through different behavior-rules is one of the strongest aspects of an individual-based model (IBM). Microbial IBMs consider individuals as discrete entities that follow behavior-rules that dictate how microorganisms interact with their surrounding environment and other microbes, so that the microorganisms and the environment can change their characteristics. This makes it possible to explore connections between micro-level microorganism behaviors and macro-level patterns that emerge from their interactions. INDISIM-Paracoccus is a bacterial IBM used to model the growth and development of the bacteria Paracoccus denitrificans in batch and continuous cultures under aerobic and anaerobic conditions. It embeds thermodynamic properties in individual cells, which can simulate the behavior of the cell population more realistically and mechanistically than other approaches. The IBM's development and application with some intracellular detail and complexity constitute a key advantage in the investigation and understanding of the different steps of denitrification carried out by a denitrifying bacterium.