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Update Biological Processes authored by Wijsman, Jeroen's avatar Wijsman, Jeroen
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NPZ-model/Biological-Processes.md
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......@@ -58,14 +58,6 @@ The mortality of the zooplankton is described as a second-order function on the
ZooMortality = M_{Zoo} \cdot Zoo^{2} \cdot T_{fac}
```
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# MortMPB
In the model, the microphytobenthos is not grazed by filterfeeders. The mortality is described as a second-order function on the microphytobenthos biomass. Mortality is also assumed to be temperature-dependent.
```math
Mort_{MPB} = M_{MPB} \cdot MPB^{2} \cdot T_{fac}
```
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# MortShellfish
The mortality rate ($`Mort_{i}`$, mmol N m-2 d<sup>-1</sup>) of shellfish species $`i`$ (Mus, Oys and Coc) assumed to be density dependent, with $`M_{i}`$ is the specific mortality rate when the biomass of the shellfish species equals the carrying capacity ($`CC_{i}`$). $`DensM_{i}`$ indicates the importance of the density dependent mortality and FF_{i} is the density of shellfish species $`i`$.
......@@ -84,21 +76,34 @@ Det_{Min} = r_{Det} \cdot Det \cdot T_{fac}
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# DINupMPB
DINupMPB is the primary production by microphytobenthos [mmolN m<sup>-2</sup> d<sup>-1</sup>]. It is assumed that microphytobenthos only occurs at the intertidal areas. DINupMPB is depending on the irradiation at the surface ($`I_{0}`$), the water temperature, the nutrient concentration (DIN) and the microphytobenthos concentration.
Mean daily irradiation at the water surface [W d<sup>-1</sup>] is derived from the file KNMI measurements (stored in “./DataOS/KNMI/”).
It is assumed that about 50% of the light is photosynthetic active radiation (PAR)
$`DIN_{upt,MPB}`$ is the primary production by microphytobenthos [mmolN m<sup>-2</sup> d<sup>-1</sup>]. It is assumed that production only occurs at the intertidal areas during exposure. $`DIN_{upt,MPB}`$ is depending on the irradiation at the surface ($`I_{0}`$), the water temperature, the nutrient concentration (DIN) and the microphytobenthos concentration. Mean daily irradiation at the water surface [W d<sup>-1</sup>] is derived from the file KNMI measurements (stored in “./DataOS/KNMI/”). It is assumed that about 50% of the light is photosynthetic active radiation (PAR). The photosynthetic active radiation at the intertidal flats ($`PAR_{b}`$) [W d<sup>-1</sup>] can be expressed as:
```math
PAR_{b} = 0.5 \cdot I_{0}
```
DINupMPB is calculated from the maximum specific uptake rate ($`MPB_{upt,max}`$) [d<sup>-1</sup>] at ambient temperature and the algal concentration. Limitations by light and nutrients are described by Monod formulations.
When the local biomass of microphytobenthos at the intertidal flats becomes too high, the primary production can be inhibited. The effective microphytobenthos concentration is calculated by:
```math
MPB_{eff} = MPB \cdot (1 - \frac{PAR_{b}}{PAR_{b} + ks_{PAR,MPB}})
```
$`DIN_{upt,MPB}`$ is calculated from the maximum specific uptake rate ($`MPB_{upt,max}`$) [d<sup>-1</sup>] at ambient temperature and the microphytobenthos biomass. Limitations by light and nutrients are described by Monod formulations.
```math
DIN_{upt,MPB}= MPB_{upt,max} \cdot MPB \cdot (1-\frac{MPB}{CC_{MPB} \cdot f_{int}}) \cdot (\frac{PAR_{b}}{PAR_{b} + ks_{PAR,MPB}}) \cdot (\frac{DIN}{DIN + ks_{DIN,MPB}}) \cdot T_{fac}
DIN_{upt,MPB}= MPB_{upt,max} \cdot Exp \cdot MPB \cdot (\frac{PAR_{b}}{PAR_{b} + ks_{PAR,MPB}}) \cdot (\frac{DIN}{DIN + ks_{DIN,MPB}}) \cdot T_{fac}
```
Where $`MPB_{upt,max} `$ is the maximum DIN uptake rate [d<sup>-1</sup>] of microphytobenthos at 10&deg;C, $`ks_{PAR,MPB}`$ and $`ks_{DIN,MPB}`$ are the half-saturation coefficients for light and DIN, respectively. Production of the microphytobenthos is limited by the carrying capacity ($`CC_{MPB}`$) [mmol N m<sup>-2</sup>] at the intertidal flat. $`T_{fac}`$ is the correction for the ambient water temperature.
Where $`MPB_{upt,max} `$ is the maximum DIN uptake rate [d<sup>-1</sup>] of microphytobenthos at 10&deg;C, $`ks_{PAR,MPB}`$ and $`ks_{DIN,MPB}`$ are the half-saturation coefficients for light and DIN, respectively. $`Exp`$ is the fraction of the time that the intertidal areas are exposed and $`T_{fac}`$ is the correction for the ambient water temperature.
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# MortMPB
In the model, the microphytobenthos is not grazed by filterfeeders. The mortality is described as a second-order function on the microphytobenthos biomass. Mortality is also assumed to be temperature-dependent.
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```math
Mort_{MPB} = M_{MPB} \cdot MPB^{2} \cdot T_{fac}
```
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# BotMin
The mineralization of bottom detritus ($`Bot\_Det_{Min}`$) [mmolN m<sup>-2</sup> d<sup>-1</sup>] is described as a first-order function with constant $`r_{Bot\_Det}`$. The mineralization rate increases with water temperature.
......