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 = C_th/ (C_th+ 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 / (C_th+ 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 - C_th) * f) / PI. Inhibition is above and below C_thwhen the sign of C_this 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
  /
  ...
/