Table 1.
Input values used in our iDynoMiCS biofilm simulations.
| Parameter | Values | Description | References |
|---|---|---|---|
| S bulk | 10−3−10−2 g/L | Bulk concentration of limiting nutrient (here assumed to be oxygen). This value is varied to alter biofilm morphology. | Saturation concentration of water at 37oC is 6.6 × 10−3 g/L (Battino et al., 1983) |
| Y | 0.64 g/g | Yield—grams of biomass produced per gram of oxygen consumed | (Beyenal et al., 2003) |
| μmax | 0.1-0.4 /h | Maximum specific growth rate. This value is varied to alter biofilm morphology | (Bakke et al., 1984; Robinson et al., 1984; Beyenal et al., 2003; Kragh et al., 2016) |
| k S | 8.12 × 10−4 g/L | Concentration of oxygen at which the growth is half maximal | (Kragh et al., 2016) |
| D S | 2.3 × 10−4m2/day | Diffusion coefficient of nutrient (oxygen) | (Stewart, 2003) |
| Biofilm diffusivity | 0.8 | Factor multiplying DS to give nutrient diffusion coefficient inside the biofilm | (Rittmann and Manem, 1992; Stewart, 2003) |
| h | 80 μm | Diffusion boundary layer height | (Picioreanu et al., 1998; Xavier et al., 2005; Alpkvist et al., 2006) |
| ρB | 200 g/L | Biomass density of microbes in biofilm | (Xavier et al., 2005; Bjarnsholt et al., 2009) |
| r div | 2 μm | Average radius of microbial agent at division | (Beyenal et al., 2003) |
| k Shov | 1.15 | Factor multiplying the agent's radius to give the shove radius | Default iDynoMiCS value (Lardon et al., 2011) |
| L y | 1,032 μm | Width of the simulation domain | |
| N 0 | 300 | Number of initialized microbial agents |
These values are loosely based on Pseudomonas aeruginosa in a flow cell type set up (Melaugh et al., 2016).