title: INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium.
abstract: We have developed an individual-based model for denitrifying bacteria. The model, called INDISIM-Paracoccus, embeds a thermodynamic model for bacterial yield prediction inside the individual-based model INDISIM, and is designed to simulate the bacterial cell population behavior and the product dynamics within the culture. The INDISIM-Paracoccus model assumes a culture medium containing succinate as a carbon source, ammonium as a nitrogen source and various electron acceptors such as oxygen, nitrate, nitrite, nitric oxide and nitrous oxide to simulate in continuous or batch culture the different nutrient-dependent cell growth kinetics of the bacterium Paracoccus denitrificans. The individuals in the model represent microbes and the individual-based model INDISIM gives the behavior-rules that they use for their nutrient uptake and reproduction cycle. Three previously described metabolic pathways for P. denitrificans were selected and translated into balanced chemical equations using a thermodynamic model. These stoichiometric reactions are an intracellular model for the individual behavior-rules for metabolic maintenance and biomass synthesis and result in the release of different nitrogen oxides to the medium. The model was implemented using the NetLogo platform and it provides an interactive tool to investigate the different steps of denitrification carried out by a denitrifying bacterium. The simulator can be obtained from the authors on request.
authors.affiliation: Chemical Engineering Faculty, Central University of Ecuador, Ciudad Universitaria - Ritter s/n y Bolivia, P.O. Box. 17-01-3972, Quito - Ecuador; Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Edifici D4, Esteve Terradas 8, 08860 Castelldefels, Barcelona - Spain. Electronic address: pablo@araujo.ec.
authors.forename: Pablo
authors.initials: P
authors.lastname: Araujo Granda
authors.affiliation: Department of Agri-Food Engineering and Biotechnology, Universitat Politècnica de Catalunya, Edifici D4, Esteve Terradas 8, 08860 Castelldefels, Barcelona - Spain. Electronic address: anna.gras@upc.edu.
authors.forename: Anna
authors.initials: A
authors.lastname: Gras
authors.affiliation: Department of Mathematics, Universitat Politència de Catalunya, Edifici D4, Esteve Terradas 8, 08860 Castelldefels, Barcelona - Spain. Electronic address: marta.ginovart@upc.edu.
authors.forename: Marta
authors.initials: M
authors.lastname: Ginovart
authors.affiliation: School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ - United Kingdom. Electronic address: v.moulton@uea.ac.uk.
authors.forename: Vincent
authors.initials: V
authors.lastname: Moulton
mesh_terms: D000332:Aerobiosis; D000693:Anaerobiosis; D018533:Biomass; D002138:Calibration; D058440:Denitrification; D008962:Models, Theoretical; D010231:Paracoccus denitrificans / Q000502:physiology*; D013269:Stochastic Processes; D013816:Thermodynamics
keywords: Bacterial yield prediction; Denitrification; INDISIM; Individual-based model; NetLogo; Paracoccus denitrificans; Thermodynamic Electron Equivalents Model