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MICROBIAL_REACTION

Specifies parameters for microbially-mediated reactions.

By default, all aqueous concentrations are in molarity [mol/L]. The units of concentration in the RATE_CONSTANT, HALF_SATURATION, THRESHOLD_CONCENTRATION and INHIBITION_CONSTANT parameters must be consistent throughout all microbial 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, where the units are [mol/L-sec] if no biomass, or [mol/(mol biomass-sec)] if biomass. Here, aqueous concentration units are the default [mol/L].

Optional Cards:

MONOD

Specifies the Monod equation for the electron donor or acceptor.

SPECIES NAME <string>

Name of the species in Monod expression

HALF_SATURATION_CONSTANT <float>

Half saturation constant for the Monod expression

THRESHOLD_CONCENTRATION <float>

Threshold concentration below which the reaction stops

INHIBITION

Specifies inhibition (\(I\)) based on species concentration and inhibition constant(s). Three types of inhibition are currently supported: MONOD, SMOOTHSTEP and THRESHOLD.

TYPE <string>

Type of inhibition: MONOD, SMOOTHSTEP or THRESHOLD

MONOD:

INHIBIT_ABOVE_THRESHOLD: \(I = \frac{C_{th}}{C_{th} + C}\)

INHIBIT_BELOW_THRESHOLD: \(I = \frac{C}{C_{th} + C}\)

SMOOTHSTEP:

\(z = max\left(min\left(\frac{log_{10}(C)-log_{10}(C_{th})}{\eta}+0.5,1\right),0\right)\) where \(\eta\) is the \(\text{log}_{10}\) interval

INHIBIT_ABOVE_THRESHOLD: \(I = 1-(3z^2-2z^3)\)

INHIBIT_BELOW_THRESHOLD: \(I = 3z^2-2z^3\)

THRESHOLD:

INHIBIT_ABOVE_THRESHOLD: \(I = 0.5 - atan((C-C_{th})*f)/\pi\)

INHIBIT_BELOW_THRESHOLD: \(I = 0.5 + atan((C-C_{th})*f)/\pi\)

SPECIES_NAME <string>

Name of the species in the inhibition term

THRESHOLD_CONCENTRATION <float>

Concentration (\(C_{th}\)) at which the inhibition factor is \({\sim}0.5\)

INHIBIT_ABOVE_THESHOLD or INHIBIT_BELOW_THESHOLD

Inhibits the rate when the species concentration is above or below \(C_{th}\).

Other required cards

For SMOOTHSTEP:

SMOOTHSTEP_INTERVAL <float>

Interval \(\eta\) centered on \(C_{th}\) in \(\text{log}_{10}\) space over which \(I\) ranges between 0-1. Default = 3.

For THRESHOLD:

SCALING_FACTOR

Scaling factor \(f\). Default = \(10^5 / C_{th}\).

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.

CONCENTRATION_UNITS <string>

Options include MOLARITY [mol/L], MOLALITY, [mol/kg water] and ACTIVITY. Default = MOLARITY.

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 ! inhibit at high C(aq) concentration
      SPECIES_NAME C(aq)
      TYPE MONOD
      INHIBIT_ABOVE_THRESHOLD
      THRESHOLD_CONCENTRATION 6.d-4
    /
  /
...

CHEMISTRY
  PRIMARY_SPECIES
    A(aq)
    B(aq)
    C(aq)
  /
  IMMOBILE_SPECIES
    D(im)
  /
  MICROBIAL_REACTION
    CONCENTRATION_UNITS ACTIVITY
    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 ! inhibit at low A(aq) concentration
      SPECIES_NAME A(aq)
      TYPE SMOOTHSTEP
      SMOOTHSTEP_INTERVAL 1.
      INHIBIT_BELOW_THRESHOLD
      THRESHOLD_CONCENTRATION 1.d-6
    /
    BIOMASS
      SPECIES_NAME D(im)
      YIELD 0.01d0
    /
  /
  IMMOBILE_DECAY_REACTION
    SPECIES_NAME D(im)
    RATE_CONSTANT 1.d-9
  /
  ...
/