Photosynthesis

About

Photosynthesis models for C3 and C4 photosynthesis. Photosynthesis.jl supports three photosynthesis models and two fluorescence models. The photosynthesis models are

C3VJP model based on classic C3 model, which is known as FvCB model (Farquhar et al. 1980)
C4VJP model based on classic C4 model, which is known as Collaz model (Collaz et al. 1992)
C3Cytochrome model based on a new C3 model developed by Johnson and Berry (2021)

We, however, made some modifications by adding a product limited photosynthetic rate to the C3 models, and a Rubisco limited photosynthetic rate to the C4 model.

Besides the tranditional photosynthesis model, we also included functions to compute fluorescence related parameters, such as fluorescence quantum yield and non-photochemical quenching. he two implemented fluorescence models are

Van der Tol et al. (2013) fluorescence model to use with C3VJP and C4VJP models
Johnson and Berry (2021) fluorescence model to use with C3Cytochrome model

We aim to make Photosynthesis.jl a standalone package rather than just part of the CliMA Land model. Thus, in the documentations below, we will present examples of how to use Photosynthesis.jl at the leaf level. Same logic applies to canopy scale simulations.

Model Selection

Starting from v0.3, photosynthesis and fluorescence model selection is done by setting up the fields of a leaf. There are three types of leaf in Photosynthesis (all the structures are defined in ClimaCache.jl and shared among all CliMA Land submodules), and they are

Leaf for a single leaf to use in leaf level research
Leaves1D for a vector of leaves to use in big leaf models
Leaves2D for a matrix of sunlit fractions and a shaded fraction to use along with canopy with leaf angular distribution

For all of the three leaf structs, there are two fields named

PSM for photosynthesis model
PRC for photosynthesis reaction center

A C3VJPModel type PSM along with a VJPReactionCenter type PRC defines the C3VJP model; a C4VJPModel type PSM along with a VJPReactionCenter type PRC defines the C4VJP model; and a C3CytochromeModel type PSM along with a CytochromeReactionCenter type PRC defines the C3Cytochrome model. For instance, leaf_c3, leaf_c4, and leaf_cy each defines a model to use the three predefined photosynthesis models:

using ClimaCache;
FT = Float64;

leaf_c3 = ClimaCache.Leaf{FT}();
leaf_c4 = ClimaCache.Leaf{FT}(PSM = ClimaCache.C4VJPModel{FT}());
leaf_cy = ClimaCache.Leaf{FT}(PSM = ClimaCache.C3CytochromeModel{FT}(), PRC = ClimaCache.CytochromeReactionCenter{FT}());

# users can define the same fields for Leaves1D and Leaves2D to custoimize photosynthesis model
leaf_d3 = ClimaCache.Leaves1D{FT}();
leaf_d4 = ClimaCache.Leaves1D{FT}(PSM = ClimaCache.C4VJPModel{FT}());
leaf_dy = ClimaCache.Leaves1D{FT}(PSM = ClimaCache.C3CytochromeModel{FT}(), PRC = ClimaCache.CytochromeReactionCenter{FT}());
leaf_e3 = ClimaCache.Leaves2D{FT}();
leaf_e4 = ClimaCache.Leaves2D{FT}(PSM = ClimaCache.C4VJPModel{FT}());
leaf_ey = ClimaCache.Leaves2D{FT}(PSM = ClimaCache.C3CytochromeModel{FT}(), PRC = ClimaCache.CytochromeReactionCenter{FT}());

Photosynthesis Model Procedure

For all three photosynthesis+fluorescence combo models, photosynthetic rates are computed using the following procedure:

Update temperature dependent variables using photosystem_temperature_dependence!
Calculate electron transport rate using photosystem_electron_transport!
Calculate RubisCO limited rate using rubisco_limited_rate!
Calculate light limited rate using light_limited_rate!
Calculate product limited rate using product_limited_rate!
Calculate gross and net rates using colimit_photosynthesis!
Update fluorescence related variables using photosystem_coefficients!

Yet, for convenience, all the listed steps are combined in one function leaf_photosynthesis! (see page API for all supported methods). At leaf level, one can simply call the function, for example

using Photosynthesis

air    = ClimaCache.AirLayer{FT}();
g_mode = ClimaCache.GCO₂Mode();
p_mode = ClimaCache.PCO₂Mode();
Photosynthesis.leaf_photosynthesis!(leaf_c3, air, g_mode);
Photosynthesis.leaf_photosynthesis!(leaf_cy, air, p_mode);

Note here that (1) we need parameters from surrounding air to compute photosynthetic rates, such as oxygen concentration, (2) GCO₂Mode mode is used when leaf total diffusive conductance for CO₂ is known, and PCO₂Mode is used when leaf internal CO₂ partial pressure is known, and (3) leaf and air conditions must be synced before calling the leaf_photosynthesis! function. For example, to construct an A-Ci curve, one will need to change the field _p_CO₂_i to proceed:

leaf_c3.t = 300;
leaf_c3.ppar = 1000;
for _p in 5:5:100
    leaf_c3._p_CO₂_i = _p;
    Photosynthesis.leaf_photosynthesis!(leaf_c3, air, p_mode);
    @info "Photosynthetic rate at" leaf_c3._p_CO₂_i leaf_c3.a_net;
end

In the example above, we first defined leaf temperature is 300 K (note that we use Kelvin here, not Celcius), then prescribed a PPAR of 1000 μmol m⁻² s⁻¹. PPAR is the photosynthetically active radiation (PAR) that goes to photosystems; PPAR is different from APAR (PAR absorbed by leaf, some APAR does not go to photosystems). See our technical note for the difference between PAR, APAR, and PPAR. Similarly, we can try out how Anet responds to leaf temperature and PPAR by modifying the example above.

Photosynthesis model

Photosynthesis.leaf_photosynthesis! — Function

Per refactored Photosynthesis module, the only things one need to know is the public function leaf_photosynthesis! and some construtors from ClimaCache. See the examples in the methods below for details about how to use the function. The steps for computing photosynthetic rates are

Update temperature dependent variables using photosystem_temperature_dependence!
Calculate electron transport rate using photosystem_electron_transport!
Calculate RubisCO limited rate using rubisco_limited_rate!
Calculate light limited rate using light_limited_rate!
Calculate product limited rate using product_limited_rate!
Calculate gross and net rates using colimit_photosynthesis!
Update fluorescence related variables using photosystem_coefficients!