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Table 1 Nominal parameter values for the multispecies biofilm model

From: Microbiota dysbiosis in inflammatory bowel diseases: in silico investigation of the oxygen hypothesis

Symbol Parameter Value Units Source
L Biofilm thickness 40 μm [44]
D X Biomass diffusion coefficients 1x10 −10 cm2/s [41]
k X Biomass mass transfer coefficients 1x10 −7 cm/s [41]
X b Biomass bulk concentrations 0 g/L [41]
D N Carbohydrate diffusion coefficients 2x10 −6 cm2/s [43]
  Amino acid diffusion coefficients 2x10 −6 cm2/s [43]
  Oxygen diffusion coefficient 8x10 −6 cm2/s [43]
k N Nutrient mass transfer coefficients 2x10 −4 cm/s [41]
  Amino acid mass transfer coefficients 2x10 −4 cm/s [41]
  Oxygen mass transfer coefficient 2x10 −2 cm/s Specified
O b Oxygen bulk concentration 0 mM Specified
D P Byproduct diffusion coefficients 2x10 −6 cm2/s [43]
k P Byproduct mass transfer coefficients 5x10 −6 cm/s [41]
  Butyrate mass transfer coefficient 5x10 −5 cm/s Tuned
  Propionate mass transfer coefficient 1x10 −5 cm/s Tuned
P b Byproduct bulk concentrations 0 mM [41]
v max Carbohydrate maximum uptake rates 10 mmol/gDW/h [45]
  Amino acid maximum uptake rates 1 mmol/gDW/h [45]
  Oxygen maximum uptake rate 20 mmol/gDW/h [45]
  Byproduct maximum uptake rates 10 mmol/gDW/h [41]
K m Carbohydrate Michaelis-Menten constants 0.5 mM [45]
  Amino acids Michaelis-Menten constants 0.1 mM [45]
  Oxygen Michaelis-Menten constant 0.003 mM [45]
  Byproduct Michaelis-Menten constants 0.5 mM [41]
ATPM B. thetaiotaomicron ATP maintenance 8.43 mmol/gDW/h [35]
  F. prausnitzii ATP maintenance 4.75 mmol/gDW/h Tuned
  E. coli ATP maintenance 5.5 mmol/gDW/h Tuned