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[[_TOC_]]
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# DINuptake
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DINuptake is the production of phytoplankton (primary production) [mmolN m<sup>-3</sup> d<sup>-1</sup>] and is depending on the underwater-light conditions, water temperature, the nutrient concentration (DIN) and the phytoplankton concentration.
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DINuptake is the production of phytoplankton (primary production) [mmol-N m<sup>-3</sup> d<sup>-1</sup>] and is depending on the underwater-light conditions, water temperature, the nutrient concentration (DIN) and the phytoplankton concentration.
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Mean daily irradiation at the water surface ($`I_{0}`$) [W d<sup>-1</sup>] is derived from the file KNMI measurements (stored in “./DataOS/KNMI/”). The underwater-light conditions are calculated from the daily irradiation at the water surface and the extinction coefficient ($`k_{d}`$):
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| ... | ... | @@ -30,7 +30,7 @@ Where $`DIN_{upt,max}`$ is the maximum DIN uptake rate of algae at 10°C [d<s |
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[top](NPZ model/Biological Processes)
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# ZooGrazing
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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>).
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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 (mmol-N m<sup>-3</sup>).
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```math
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ZooGrazing = ZooGrazing_{max} \cdot T_{fac} \cdot Zoo \cdot \left(\frac{Phyto}{Phyto+ks_{ZooGrazing}}\right)
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```
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| ... | ... | @@ -53,7 +53,7 @@ ZooExcretion = Resp_{Zoo} \cdot Zoo \cdot T_{fac} |
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[top](NPZ model/Biological Processes)
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# ZooMortality
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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>).
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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 (mmol-N<sup>-1</sup>m<sup>-3</sup>d<sup>-1</sup>).
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```math
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ZooMortality = M_{Zoo} \cdot Zoo^{2} \cdot T_{fac}
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| ... | ... | @@ -61,7 +61,7 @@ ZooMortality = M_{Zoo} \cdot Zoo^{2} \cdot T_{fac} |
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[top](NPZ model/Biological Processes)
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# MortShellfish
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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 $`i`$.
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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 $`i`$.
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```math
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Mort_{i} = M_{i} + DensM_{i} \cdot \left(\frac {FF_{i}}{CC_{i}}-1\right) \cdot FF_{i}
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| ... | ... | @@ -69,7 +69,7 @@ Mort_{i} = M_{i} + DensM_{i} \cdot \left(\frac {FF_{i}}{CC_{i}}-1\right) \cdot F |
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[top](NPZ model/Biological Processes)
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# Mineralization
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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.
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The mineralisation of detritus ($`Det_{Min}`$), in units of mmol-N 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.
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```math
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Det_{Min} = r_{Det} \cdot Det \cdot T_{fac}
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[top](NPZ model/Biological Processes)
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# DINupMPB
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$`DIN_{upt,MPB}`$ 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:
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$`DIN_{upt,MPB}`$ is the primary production by microphytobenthos [mmol-N 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:
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```math
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PAR_{b} = 0.5 \cdot I_{0}
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```
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When the local biomass of microphytobenthos at the intertidal flats becomes too high, the primary production can be inhibited. The effective microphytobenthos concentration ($`MPB_{eff}`$)[mmolN m<sup>-2</sup>] is calculated by:
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When the local biomass of microphytobenthos at the intertidal flats becomes too high, the primary production can be inhibited. The effective microphytobenthos concentration ($`MPB_{eff}`$)[mmol-N m<sup>-2</sup>] is calculated by:
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```math
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MPB_{eff} = \left(1 - \frac{MPB}{CC_{MPB} \cdot f_{int}} \right) \cdot MPB
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```
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where $`CC_{MPB}`$ is the maximum concentration of microphytobenthos at the intertidal area [molN m<sup>-2</sup>] and $`f_{int}`$ is the fraction of intertidal area within a compartment [-].
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where $`CC_{MPB}`$ is the maximum concentration of microphytobenthos at the intertidal area [mol-N m<sup>-2</sup>] and $`f_{int}`$ is the fraction of intertidal area within a compartment [-].
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$`DIN_{upt,MPB}`$ is calculated from the maximum specific uptake rate ($`MPB_{upt,max}`$) [d<sup>-1</sup>] at ambient temperature and the effective microphytobenthos biomass. Limitations by light and nutrients are described by Monod formulations. Primary production of the microphytobenthos only takes place when mudflat is exposed (fraction $`Exp `$ of the time). $`DIN_{upt,MPB}`$ is described by:
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| ... | ... | @@ -106,7 +106,7 @@ Mort_{MPB} = M_{MPB} \cdot MPB^{2} \cdot T_{fac} |
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[top](NPZ model/Biological Processes)
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# BotMin
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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.
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The mineralization of bottom detritus ($`Bot\_Det_{Min}`$) [mmol-N 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.
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```math
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Bot\_Det_{Min}= r_{Bot\_Det} \cdot Bot\_Det \cdot T_{fac}
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| ... | ... | @@ -114,7 +114,7 @@ Bot\_Det_{Min}= r_{Bot\_Det} \cdot Bot\_Det \cdot T_{fac} |
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[top](NPZ model/Biological Processes)
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# N-loss due to denitrification
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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>].
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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 ($`N_{loss}`$) [mmol-N m<sup>-2</sup> d<sup>-1</sup>].
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```math
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N_{loss} = p_{Denit}\cdot Bot\_Det_{Min}
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