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Team:ZJU-China/Modeling
From 2011.igem.org
Project/Modeling/biofilm
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IntroductionCompartment:The biofilm itself is distinguished from the overlying water and the substratum to which it is attached. A mass-transport boundary layer separates the biofilm from the overlying water. Within each compartment are components: include different types of biomass ,substrates , products. biomass is often divided into active microbial species, inert cells, and extracellular polymeric substances(EPS). The components can undergo Heterotrophic growth, Heterotrophic respiration, and Heterotrophic inactivation process. All process affecting each component in each compartment are mathematically linked together into a mass balance equation that contains rate terms and parameters for each process. CompartmentThe biofilm: While it is complex even for a homogeneous biofilm morphology, we assume the biofilm surface is flat and all material below the maximum biofilm thickness as part of the biofilm components, and they have a constant density. The bulk liquid: In our experiments, the bulk liquid is large compared to the biofilm. So the simplest way seems to consider it as a boundary condition of the biofilm compartment and specify the concentrations of dissolved. However, dissolved components can exchange between the biofilm and the bulk liquid, and it has a profound impact on the concentrations in the bulk liquid. Thus we include the bulk liquid not only as a boundary condition, but also as a separate, completely mixed compartment, varying according to the inflow, outflow, and the exchanges with the biofilm. The substratum: In our basic model, the substratum is a separate compartment and impermeable. So it does not have much effect on the biofilm system. However in some bioreactor, the substratum may be permeable, or include organic solids that are biodegraded by attached microorganisms. ComponentDissolved components: There are two kind of dissolved components in our model, one is oxygen, the other is substrates where nutrients are inside. They are expressed by inflow concentration of oxygen, inflow concentration of substrates and monod half saturation constant for substrates, monod half saturation constant for oxygen.Diffusion coefficient of oxygen and diffusion coefficient of substrate are also used to characterize the property of these components. Particulate components: In our model, the particulate components are microbes and EPS. We assume that they are homogeneously mixed in the same proportion in all parts of the biofilm. So can use bacterial density to relate the amount of bacterial and the volume it takes up. And the volume fraction of EPS in Bacterial is specified by a constant. ProcessDefine a dynamic process for growth, a dynamic process for respiration, and a dynamic process for inactivation. The microbial stoichiometric numbers of the processes (referring to substrates) and (referring to Oxygen) and rate of the processes are shown in following table. modelingCalculate growth and oxygen concentration gradient of a biofilm which consists of Heterotrophic bacteria. The water inflow at a constant rate contains substrates and Oxygen. Growth occurs with Monod-type rate laws. Respiration occurs with specific rate. A program variable LF referring to Biofilm Thickness and 3 dynamic volume state variables O_2, S, X referring to oxygen, substrates and the Heterotrophic bacteria are defined. All necessary constants and initial conditions are defined in following table. Some of their values are based on average results provided by IWA. 
Definition of Process: 
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