INDISIM-Paracoccus, an individual-based and thermodynamic model for a denitrifying bacterium

JOURNAL OF THEORETICAL BIOLOGY

卷:403

Article

Araujo Granda, Pablo^1,2  Gras, Anna²  Ginovart, Marta³  Moulton, Vincent⁴ 

[1] Cent Univ Ecuador, Fac Chem Engn, Ciudad Univ Ritter S-N & Bolivia,POB 17-01-3972, Quito, Ecuador

[2] Univ Politecn Cataluna, Dept Agri Food Engn & Biotechnol, Edifici D4,Esteve Terradas 8, Barcelona 08860, Spain

[3] Univ Politecn Cataluna, Dept Math, Edifici D4,Esteve Terradas 8, Barcelona 08860, Spain

[4] Univ E Anglia, Sch Comp Sci, Norwich Res Pk, Norwich NR4 7TJ, Norfolk, England

关键词: Denitrification;    Paracoccus denitrificans;    Bacterial yield prediction;    Individual-based model;    Thermodynamic Electron Equivalents;    Model;    NetLogo;    INDISIM;   

DOI  :  10.1016/j.jtbi.2016.05.017

来源: Elsevier

【 摘 要 】

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 R 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. (C) 2016 Elsevier Ltd. All rights reserved.

【 授权许可】

Free