Modelling 2: Introduction to modelling assignment. A basic physical-biological model. Model equations. Model operation. The assignment.
A basic physical-biological model. The IMPRESS model - a recent modification of the Phyto1D model described in: Sharples, J Investigating the seasonal vertical structure of phytoplankton in shelf seas. Marine Models Online, 1, A 1-D (vertical) coupled physical- biological model. Applicable to shelf seas. Uses supplied meteorological and tidal data. Uses a turbulence closure scheme. Cell-quota threshold limitation model of primary production n-2 n-1 n velocities and scalars vertical turbulent mixing coefficients Wind stress Cooling Heating Tidally-oscillating slope z zz Seabed friction and nutrient source z=0 z=h
Model equations. (The Basics) Changes in velocity Oscillating pressure gradient (m tidal constituents) Coriolis force Frictional coupling through water (including wind stress and bottom friction boundary conditions. The structure of the water currents is controlled by the equation of motion: The boundary conditions (friction at the sea surface and the sea bed) shear in the current profile turbulence mixing
Meteorological forcing. The model water column is heated by: Solar irradiance at the surface. Exponential decay of heat down through the water column. Heat losses from the surface caused by infra-red back radiation, conduction, and evaporation. Surface wind stress. Turbulent mixing of the heat through the water.
S N1 N1 X1X1 N2 N2 X2X2 PAR grazing and respiration recycled nutrient uptake sink / swim S = dissolved inorganic nitrogen N = algal internal nutrient X = algal chlorophyll biomass Subscripts 1 and 2 refer to the two possible phytoplankton taxa/ species Schematic diagram of the biological scalars and processes at each grid cell. Vertical turbulent mixing between neighbouring grid cells The biological model. At each grid cell: 1 or 2 species of phytoplankton (we will only use one species). Phytoplankton consist of chlorophyll (or carbon) and an internal nutrient store. Phytoplankton receive light (PAR; solar irradiance from the meteorological data, with an exponential depth profile). Phytoplankton take up nutrients from the surrounding dissolved inorganic nitrogen (S). Phytoplankton and nitrogen are affected by turbulent mixing.
Modelling phytoplankton - chlorophyll biomass X. At each grid cell in the model phytoplankton changes are caused by…... Turbulent mixing through the water column between grid cells Growth within the grid cell (can be positive or negative) Losses to grazers (always negative) Sinking or swimming of the phytoplankton Growth requires sufficient light and a store of nutrients. Sufficient light phytoplankton need to remain above their critical depth.
Modelling turbulent mixing. A key component of the model is the ability to link the ability of turbulence to mix properties vertically through the water to the strength of the stability of the water. At each grid cell in the model, the turbulent diffusivity and turbulent viscosity are related to the gradient Richardson number. K z, N z Ri Ri critical
The Assignment. The aims of this exercise are: Develop an appreciation of how coupled physical-biological models can be used to investigate processes in the ocean. Appreciate the need to make sure a model is applicable to the question you are addressing. Develop an appreciation of how sensitive model results are to the driving parameters. Use the model to develop your understanding of the physics and biology of shelf seas. Use the model as an experimental tool, developing your ability to plan, record, and report on a methodical investigation. You need the documents: model.doc assignment.doc