TU Delft

Monospecies 2D biofilm model

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This applet is a demonstration of the framework for biofilm modeling developed at the TU Delft. The model shown represents a single species biofilm with a single solute species (oxygen) being considered. Biomass detachment is also included in the model, which allows simulations to reach a steady state whenever growth is balanced by detachment.


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Trying out the model

Follow these instructions to reproduce some results obtained previously using biofilm modelling simulations:

Experiment 1: Roughness development in unstressed biofilms
Early multidimensional biofilm studies have shown that roughness of biofilms growing in the absence of detachment forces depends on the mass transport regime of a growth limiting solute. Biofilms grown in conditions where diffusion limitation of the growth limiting solute is not significant will develop a flat morphology. Biofilms in the presence of significant diffusion limitation tend to develop finger like structures that are resultant of the sharp concentration gradients of the growth limiting solute.
This experiment will show you how to reproduce these results for a biofilm grown in oxygen limited conditions. For both cases shown, 1 - smooth biofilm, 2 - rough biofilm, you will need to turn of detachment completely, i.e. set the value of kdet to 0.

1 - Smooth biofilm
Before pressing 'run' do the following:

Run the simulation. At about 30 days you will observe that the biofilm developed a smooth morphology.

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Note: When the number of biomass particles in the simulation becomes large, the spreading step becomes the limiting step of the simulation. In this case, at about day 30 the simulation will become significantly slower, please be patient.

2 - Rough biofilm
Before pressing 'run' do the following:

Run the simulation. The biofilm developed a rough morphology.

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This roughness of the biofilm will be more pronounced the higher you set the values of the boundary layer thickness and the qMaxS.
Experiment 2: Steady state of biofilm under oxygen limitation
Biofilms grown in the presence of detachment forces may be subject to sloughing events, i.e. detachment of large clusters of biomass. Multidimensional biofilm modelling studies have shown that erosion, i.e. continuous detachment of biomass, and sloughing may be explained as resulting from the same mechanism. Further modeling studies have shown how that a "noisy" steady state can exist for biofilms when sloughing events are present. For biofilms grown under the same conditions, applying increased detachment forces may induce in the occurrence of sloughing events and the formation of a smooth biofilm. In this experiment will demonstrate how to create a biofilm showing a rough morphology and a "noisy" steady state where sloughing events occur. After that, detachment forces will be increase to cause a morphology change to a smooth biofilm, removing the occurrence of sloughing events.

Before pressing 'run' do the following:

Run the simulation. Soon in the simulation, the biofilm will start developing fingering instabilities. At about day 25 the first sloughing event will occur. Observe how, after that, the biofilm structure shows a "noisy" steady state, in which tall clusters will rise and collapse in a cyclic fashion.

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When you wish, increase the value of the detachment rate constant to about kdet = 8x10-4 with the simulation running. You will observe the collapse of the tall biofilm clusters as detachment increases. After that, the a steady state will be reached where the biofilm is thin and smooth, and no sloughing events further occur.

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Model kinetics

The system modeled here is very simple: A monospecies biofilm with a single solute species (oxygen). The expressions that define kinetics for the model are the following:
Biomass growth rate:
Oxygen consumption rate:
For references on the symbology used see the notation table in the article.
Although the rates are defined in terms of the maximum substrate uptake rate (qmaxS), the substrate concentration is assumed not to be rate limitting and, therefore, does not appear in the model equations. The value used for the yield of biomass on substrate (YSX), the only parameter not controllable using sliders, is 0.495 gCOD_X/gCOS_S.

Detachment is applied to the surface of the biofilm following a detachment spped function that is proportional to the distance to the solid surface:


2004 - Biofilm Modeling group at the TU Delft