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Implementation of the case study using the framework

Models for microbial growth and conversion in biofilms can be readily implemented in the framework, provided that they can be described in the form of a stoichiometric table. The process rates and stoichiometries for the case study presented in the article are described in the form of a stoichiometric table in Table 1. The implementation of the net reaction for PHB, a substance involved in one of the 7 processes shown in the stoichiometric table will be used bellow to illustrate the procedure to describe a model in the framework.

Kinetics for the PHB internal storage compound

From Table 1 in the article comes that the net rate for PHB dynamics is:

The rates for each of these three processes in which PHB is involved are



NOTE: in these equations, the factores M and I refer to Monod (saturation) and inhibition factors respectivelly. For a species i the factors Mi and Ii are:


The processes in which PHB is involved are defined in the modelling framework by the following lines of code:

    //Monod and inhibition coefficients
    ProcessFactor mS = new Saturation(substrate, KS);
    ProcessFactor iS = new Inhibition(substrate, KS);
    ProcessFactor mO = new Saturation(oxygen, KO);
    ProcessFactor mO_star = new Saturation(oxygen, KO_star);
    ProcessFactor iPHB = new InhibitionFromFraction(phb, activeHPHB, KP);
    ProcessFactor iEPS = new InhibitionFromFraction(eps, activeHEPS, KP);
    //           ---- Create the reactions ----
    //---carbon source uptake by H-PHB
    Reaction sUptakeHPHB = new Reaction("substrate uptake by H-PHB",
        activeHPHB, qMax, 3);
    sUptakeHPHB.addFactor(mS);
    sUptakeHPHB.addFactor(mO);
    sUptakeHPHB.addFactor(iPHB);
    //---Growth of H-PHB
    Reaction growthHPHB = new Reaction("growth H-PHB", activeHPHB, qMax * YSX,
        2);
    growthHPHB.addFactor(mS);
    growthHPHB.addFactor(mO_star);
    //---PHB consumption
    Reaction phbConsumption = new Reaction("PHB consumption", phb, kPhb, 2);
    phbConsumption.addFactor(iS);
    phbConsumption.addFactor(mO);

Source code for the case study model is contained also in the zip package containing the program (subdirectory nl/tudelft/bt/model/examples/CaseStudyPHBvsEPS.java).

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2004 - Biofilm Modeling group at the TU Delft