fix nufeb/growth/nob command

Syntax

fix ID group-ID nufeb/growth/nob o2-ID o2-Ks no2-ID no2-Ks no3-ID keyword value ...

  • ID = user-assigned name for the fix

  • group-ID = ID of the group atoms to apply the fix to

  • o2-ID = substrate ID for oxygen

  • o2-Ks = half-velocity constant (Ks) for oxygen

  • no2-ID = substrate ID for nitrite

  • no2-Ks = half-velocity constant (Ks) for nitrite

  • no3-ID = substrate ID for nitrate

  • zero or more keyword/value pairs may be appended

  • keyword = growth or yield or decay or maintain

    growth value = maximum growth rate
yield value = yield coefficient
decay value = decay rate
maintain value = maintenance coefficient

Examples

#--- examples/biofilm-anammox ---#

group nob type 1
grid_style nufeb/chemostat 3 o2 no2 no3 4e-6

fix f_gnob nob nufeb/growth/nob o2 6.8e-4 no2 1.3e-3 no3 growth 1.6782e-5 yield 0.041 maintain 0.694e-6 decay 1.27e-7

Description

Perform microbial growth to the atoms defined in group-ID. The affected atoms are considered as nitrite-oxidizing bacteria (NOB), which have a spherical shape (see atom_style coccus). The model assumes that NOBs can perform nitrite oxidation to produce nitrate as part of their growth process. Additionally, the model takes into account microbial decay and endogenous respiration processes.

The fix is called at each biological step (see run_style nufeb) to update atom and grid attributes. The value of the substrate ID keyword XX-ID must be consistent with the name defined in the grid_style chemostat command. The following forward Euler method is implemented to update the mass (m) of each atom in the group:

\[ \begin{align}\begin{aligned}m' & = m + \mu \cdot \Delta t\\\hfill\end{aligned}\end{align} \]

The specific growth rates \(\mu\) is calculated based on the equations described in (Ofiteru, I.D., et al, 2013):

\[ \begin{align}\begin{aligned}\mu & = r1 + r2 - b_{decay}\\r1 & = \mu_{max} \cdot \frac{S_{no2}}{S_{no2} + Ks_{no2}} \cdot \frac{S_{o2}}{S_{o2} + Ks_{o2}}\\r2 & = b_{maint} \cdot \frac{S_{o2}}{S_{o2} + Ks_{o2}}\end{aligned}\end{align} \]

where:

  • \(b_{decay}\) is the decay rate (decay)

  • \(\mu_{max}\) is the maximum growth rate (growth)

  • \(S_{no2}, S_{o2}\) are the local concentrations of nitrite and oxygen, respectively, at the grid cell in which atom resides

  • \(Ks_{no2}, Ks_{o2}\) are the half-velocity constants for nitrite (no2-Ks) and oxygen (o2-Ks), respectively

  • \(b_{maint}\) is the maintenance coefficient (maintain)

The new mass is then used to update the diameter of the atom. If fix nufeb/diffusion_reaction is applied, the fix also update substrate utilisation (reaction) rates in all the affected grid cells:

\[ \begin{align}\begin{aligned}R_{no2} & = -\frac{1}{Y} \cdot r1 \cdot X\\R_{o2} & = -(\frac{1.15 - Y}{Y} r1 + r3) \cdot X\\R_{no3} & = \frac{1}{Y} \cdot r1 \cdot X\end{aligned}\end{align} \]

where:

  • \(r_{no2}, r_{o2}, R_{no3}\) are the utilisation rates of nitrite, oxygen, and nitrate in the affected grid cells, respectively

  • \(Y\) is the yield coefficient (yield)

  • \(X\) is the NOB biomass density in grid cell

Restrictions

This fix is not compatible with the following commands:

(Ofiteru, I.D., et al 2013) Ofiteru, I.D., et al., Multi-scale modelling of bioreactor-separator system for wastewater treatment with two-dimensional activated sludge floc dynamics, Water Research (2013)