NPZ-model/Biological-Processes.md

@@ -29,7 +29,7 @@ Where $`DIN_{upt,max}`$ is the maximum DIN uptake rate of algae at 10&deg;C [d<s
 
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 # ZooGrazing
-The phytoplankton is grazed by zooplankton in the water column. The rate is depending on the  phytoplankton (Phyto) and zooplankton (Zoo) biomass and is influenced by the water temperature. The grazing rate is calculated from the maximum specific grazing rate ($`ZooGrazing_{max}`$) [d<sup>-1</sup>] at ambient temperature using a Holling type-II functional response for the phytoplankton.
+The phytoplankton is grazed by zooplankton in the water column. The rate is depending on the  phytoplankton (Phyto) and zooplankton (Zoo) biomass and is influenced by the water temperature. The grazing rate is calculated from the maximum specific grazing rate ($`ZooGrazing_{max}`$) [d<sup>-1</sup>] at ambient temperature using a Holling type-II functional response for the phytoplankton, with $`ks_{ZooGrazing}`$ as the half saturation coefficient for zooplankton grazing on phytoplankton (mmolN m<sup>-3</sup>). 
 ```math
 ZooGrazing = ZooGrazing_{max} \cdot T_{fac} \cdot Zoo \cdot (\frac{Phyto}{Phyto+ks_{ZooGrazing}})
 ```
@@ -52,7 +52,7 @@ ZooExcretion = Resp_{Zoo} \cdot Zoo \cdot T_{fac}
 
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 # ZooMortality
-The mortality of the zooplankton is described as a second-order function on the zooplankton biomass. Mortality is also assumed to be temperature-dependent.
+The mortality of the zooplankton is described as a second-order function on the zooplankton biomass. Mortality is also assumed to be temperature-dependent. $`M_{Zoo}`$ is the mortality rate of the zooplankton (mmolN<sup>-1</sup>m<sup>-3</sup>d<sup>-1</sup>).
 
 ```math
 ZooMortality = M_{Zoo} \cdot Zoo^{2} \cdot T_{fac}
@@ -76,33 +76,41 @@ Mort_{i} = M_{i} + DensM_{i} \cdot (\frac {FF_{i}}{CC_{i}}-1)) \cdot FF_{i}
 
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 # Mineralization
-The mineralisation of detritus is described as a first-order function with a first-order rate constant $`r_{Det}`$ The mineralisation rate increases with water temperature.
+The mineralisation of detritus ($`Det_{Min}`$), in units of mmolN m<sup>-3</sup> d<sup>-1</sup>is described as a first-order function with a first-order rate constant $`r_{Det}`$ The mineralisation rate increases with water temperature.
 
 ```math
-Mineralization = r_{Det} \cdot Det \cdot T_{fac}
+Det_{Min} = r_{Det} \cdot Det \cdot T_{fac}
 ```
 
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 # DINupMPB
-DINupMPB is the production of 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, water temperature, the nutrient concentration (DIN) and the microphytobenthos concentration.
+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) 
 
 ```math
 PAR_{b} = 0.5 \cdot I_{0}
 ```
-DINupMPB is calculated from the maximum specific uptake rate [d<sup>-1</sup>] at ambient temperature and the algal concentration. Limitations by light and nutrients are described by Monod formulations. 
+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. 
 
 ```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 _\cdot + 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. 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.
 
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 # BotMin
-The mineralisation of bottom detritus is described as a first-order function with a first-order rate constant $`r_{Bot\_Det}`$. The mineralisation rate increases with water temperature.
+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.
 
 ```math
-Mineralization = r_{Bot\_Det} \cdot Bot\_Det \cdot T_{fac}
+Bot\_Det_{Min}= r_{Bot\_Det} \cdot Bot\_Det \cdot T_{fac}
+```
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+
+# N-loss due to denitrification
+Part of the detritus in the bottom is mineralized by denitrification. As a result part of the nitrogen is lost as N<sub>2</sub> to the atmosphere ($`N_{loss}`$) [mmolN m<sup>-2</sup> d<sup>-1</sup>].
+
+```math
+N_{loss} = p_{Denit}\cdot Bot\_Det_{Min}
 ```
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