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MICROBIAL_REACTION Card
Specifies parameters for microbially-mediated reactions
Required Cards:
- REACTION <string>
- Reaction equation. The rate constant is multiplied by the Monod expressions for electron donor and acceptor for select species on the left side of the equation. The reaction may be inhibited by any species in the system.
- RATE_CONSTANT <float>
- rate constant for the reaction.
Optional Cards:
- ACTIVATION_ENERGY <float>
- Activation energy for temperature-dependent rates calculated by the Arrhenius equation [J/mol]
- MONOD
Specifies the Monod equation for the electron donor or acceptor
- SPECIES NAME <string>
- Name of species.
- HALF_SATURATION_CONSTANT <float>
- Half saturation constant for the Monod expression.
- THRESHOLD_CONCENTRATION <float>
- Threshold concentration below which the reaction stops.
- INHIBITION
Specifies inhibition based on species concentration and an inhibition constant(s). Three types of inhibition are currently supported. MONOD, INVERSE_MONOD, THRESHOLD.
- Monod Inhibition:
- INHIBITION
SPECIES_NAME <string>
- TYPE MONOD
- Specifies the type of inhibition to be Monod. The reaction proceeds as long as the species concentration is well below the half saturation constant: inhibition = Cth/ (Cth+ concentration)
- INHIBITION_CONSTANT <float>
- Half saturation constant.
- Inverse Monod Inhibition:
- INHIBITION
SPECIES_NAME <string>
- TYPE INVERSE_MONOD
- Specifies the type of inhibition to be inverse Monod. The reaction proceeds as long as the species concentration is well above the half saturation constant: inhibition = concentration / (Cth+ concentration)
- INHIBITION_CONSTANT <float>
- Half saturation constant.
- Threshold Inhibition:
- INHIBITION
SPECIES_NAME <string>
- TYPE THRESHOLD <float>
- Specifies the type of inhibition to be threshold and the scaling factor to be applied. Inhibition is calculated based on the following equation: inhibition = 0.5 + arctan((concentration - Cth) * f) / PI. Inhibition is above and below Cthwhen the sign of Cthis negative or positive, respectively.
- INHIBITION_CONSTANT <float>
- Threshold concentration
- BIOMASS
- Specifies the immobile biomass species to be included in the rate expression
- SPECIES_NAME <string>
- Name of the species
- YIELD <float>
- Fraction of energy going towared biomass synthesis.
Examples:
CHEMISTRY PRIMARY_SPECIES A(aq) B(aq) C(aq) / MICROBIAL_REACTION REACTION A(aq) + 2 B(aq) <-> 1.5 C(aq) RATE_CONSTANT 1.d-12 MONOD SPECIES_NAME A(aq) ! A is the donor HALF_SATURATION_CONSTANT 1.d-5 / MONOD SPECIES_NAME B(aq) ! B is the acceptor HALF_SATURATION_CONSTANT 1.d-4 / INHIBITION SPECIES_NAME C(aq) TYPE MONOD INHIBITION_CONSTANT 6.d-4 ! C is the product and inhibits when too high / / ...CHEMISTRY PRIMARY_SPECIES A(aq) B(aq) C(aq) / IMMOBILE_SPECIES D(im) / MICROBIAL_REACTION REACTION A(aq) + 2 B(aq) <-> 1.5 C(aq) RATE_CONSTANT 1.d-6 MONOD SPECIES_NAME A(aq) HALF_SATURATION_CONSTANT 1.d-5 ! A is the donor THRESHOLD_CONCENTRATION 1.d-20 / MONOD SPECIES_NAME B(aq) HALF_SATURATION_CONSTANT 1.d-4 ! B is the acceptor THRESHOLD_CONCENTRATION 1.d-11 / INHIBITION SPECIES_NAME C(aq) TYPE INVERSE_MONOD INHIBITION_CONSTANT 6.d-4 ! C is the product and inhibits when too high / BIOMASS SPECIES_NAME D(im) YIELD 0.01d0 / / IMMOBILE_DECAY_REACTION SPECIES_NAME D(im) RATE_CONSTANT 1.d-9 / ... /
Updated