Module Photosynthesis
CO2 assimilation and stomatal conductance
# Ecophys.Photosynthesis.C3
— Type.
C3(Sco25 = 2800.0, E_Sco = -24.46e3, Kmc25 = 270.0, E_Kmc = 80.99e3,
= 165.0e3, E_Kmo = 23.72e3, Vcmax25 = 120.0, E_Vcmax = 65.33e3,
Kmo25 = 0.7, Phi2 = 0.82, sigma2 = 0.5, beta = 0.85, fcyc = 0.1,
theta = 0.05, Jmax25 = 230.0, E_Jmax = 30.0e3, D_Jmax = 200.0e3,
fpseudo = 300.5, TPU25 = 12.0, E_TPU = 53.1e3, D_TPU = 20.18e3) Topt_Jmax
Data structure to store all the parameters for the C3 photosynthesis model.
Arguments
Sco25
: Sc/o parameter at 25 CE_Sco
: Apparent activation energy of Sc/o (J/mol)Kmc25
: Km for CO2 at 25 C (μmol/mol)E_Kmc
: Activation energy of Kmc (J/mol)Kmo25
: Km for O2 at 25 C (umol/mol)E_Kmo
: Activation energy of Kmo (J/mol)Vcmax25
: Maximum rate of carboxylation at 25 C (μmol/m2/s)E_Vcmax
: Activation energy of Vcmax (J/mol)theta
: Curvature parameterPhi2
: Low-light PSII quantum yieldsigma2
: Partitioning of excitation between PSII and PSIbeta
: Leaf absorptance of PARfcyc
: Fraction of electrons at PSI that follow cyclic transport around PSIfpseudo
: Fraction of electrons at PSI that are used by alternative electron sinksJmax25
: Maximum rate of electron transport (μmol/m2/s)E_Jmax
: Activation energy Jmax (J/mol)D_Jmax
: Deactivation energy of Jmax (J/mol)Topt_Jmax
: Optimal temperature for Jmax (K)TPU25
: Maximum rate of triose phosphate utilisation (μmol/m2/s)E_TPU
: Activation energy TPU (J/mol)D_TPU
: Deactivation energy of TPU (J/mol)
# Ecophys.Photosynthesis.C3Q
— Type.
C3Q(Sco25 = 2800.0, E_Sco = -24.46e3J/mol, Kmc25 = 270.0μmol/mol, E_Kmc = 80.99e3J/mol,
= 165.0e3μmol/mol, E_Kmo = 23.72e3J/mol, Vcmax25 = 120.0μmol/m^2/s, E_Vcmax = 65.33e3J/mol,
Kmo25 = 0.7, Phi2 = 0.82, sigma2 = 0.5, beta = 0.85, fcyc = 0.1, fpseudo = 0.05,
theta = 230.0μmol/m^2/s, E_Jmax = 30.0e3J/mol, D_Jmax = 200.0e3J/mol, Topt_Jmax = 300.5K,
Jmax25 = 12.0μmol/m^2/s, E_TPU = 53.1e3J/mol, D_TPU = 201.8e3J/mol, Topt_TPU = 306.5K,
TPU25 = 1.2μmol/m^2/s, E_Rd = 46.39e3J/mol, gm25 = 0.4mol/m^2/s, E_gm = 49.6e3J/mol,
Rd25 = 437.4e3J/mol, Topt_gm = 308.6K, gso = 0.01mol/m^2/s, a1 = 0.85, b1 = 0.14e-3/Pa) D_gm
Data structure to store all the parameters for the C3 photosynthesis model using Quantity
objects from Unitful.jl.
Arguments
Sco25
: Sc/o parameter at 25 CE_Sco
: Apparent activation energy of Sc/o (J/mol)Kmc25
: Km for CO2 at 25 C (μmol/mol)E_Kmc
: Activation energy of Kmc (J/mol)Kmo25
: Km for O2 at 25 C (umol/mol)E_Kmo
: Activation energy of Kmo (J/mol)Vcmax25
: Maximum rate of carboxylation at 25 C (μmol/m2/s)E_Vcmax
: Activation energy of Vcmax (J/mol)theta
: Curvature parameterPhi2
: Low-light PSII quantum yieldsigma2
: Partitioning of excitation between PSII and PSIbeta
: Leaf absorptance of PARfcyc
: Fraction of electrons at PSI that follow cyclic transport around PSIfpseudo
: Fraction of electrons at PSI that are used by alternative electron sinksJmax25
: Maximum rate of electron transport (μmol/m2/s)E_Jmax
: Activation energy Jmax (J/mol)D_Jmax
: Deactivation energy of Jmax (J/mol)Topt_Jmax
: Optimal temperature for Jmax (K)TPU25
: Maximum rate of triose phosphate utilisation (μmol/m2/s)E_TPU
: Activation energy TPU (J/mol)D_TPU
: Deactivation energy of TPU (J/mol)
# Ecophys.Photosynthesis.C4
— Type.
C4(Sco25 = 2590.0, E_Sco = -24.46e3, Kmc25 = 650.0, E_Kmc = 79.43e3, Kmo25 = 450e3,
= 36380.0, Vcmax25 = 120.0, E_Vcmax = 65.33, theta = 0.7, Phi2 = 0.83, sigma2 = 0.5,
E_Kmo = 0.85, fQ = 1.0, fpseudo = 0.1, h = 4.0, Jmax25 = 230.0, E_Jmax = 48e3, D_Jmax = 200e3,
beta = 300.5, x = 0.4, alpha = 0.1, kp25 = 0.7, E_kp = 46.39e3, gbs = 0.003, Rd25 = 1.2,
Topt_Jmax = 46.39e3, gso = 0.01, a1 = 0.9, b1 = 0.15e-3) E_Rd
Data structure to store all the parameters for the C3 photosynthesis model.
Arguments
Sco25
: Sc/o parameter at 25 CE_Sco
: Apparent activation energy of Sc/o (J/mol)Kmc25
: Km for CO2 at 25 C (μmol/mol)E_Kmc3
: Activation energy of Kmc (J/mol)Kmo25
: Km for O2 at 25 C (umol/mol)E_Kmo
: Activation energy of Kmo (J/mol)Vcmax25
: Maximum rate of carboxylation at 25 C (μmol/m2/s)E_Vcmax
: Activation energy of Vcmax (J/mol)theta
: Curvature parameterPhi2
: Low-light PSII quantum yieldsigma2
: Partitioning of excitation between PSII and PSIbeta
: Leaf absorptance of PARfQ
: Fraction of electrons at reduced plastoquinone that follow the Q-cyclefpseudo
: Fraction of electrons at PSI that follow cyclic transport around PSIh
: Number of protons required to produce one ATPJmax25
: Maximum rate of electron transport (μmol/m2/s)E_Jmax
: Activation energy Jmax (J/mol)D_Jmax
: Deactivation energy of Jmax (J/mol)Topt_Jmax
: Entropy coefficient of Jmax (J/mol/K)x
: Fraction of electron transport partitioned to mesophyll cellsalpha
: Fraction of O2 evolution occuring in the bundle sheathkp25
: Initial carboxylation efficiency of the PEP carboxylase (mol/m2/s)E_kp
: Activation energy of kp (J/mol)gbs
: Bundle sheath conductance (mol/m^2/s)Rd25:
: Respiration rate at 25 C (μmol/m2/s)E_Rd
: Activation energy of Rd (J/mol)gso
: Minimum stomatal conductance to fluxes of CO2 in darkness (mol/m2/s)a1
: Empirical parameter in gs formulab1
: Empirical parameter in gs formula (1/kPa)
# Ecophys.Photosynthesis.C4Q
— Type.
C4(Sco25 = 2590.0, E_Sco = -24.46e3J/mol, Kmc25 = 650.0μmol/mol, E_Kmc = 79.43e3J/mol,
= 450e3μmol/mol, E_Kmo = 36380.0J/mol, Vcmax25 = 120.0μmol/m^2/s, E_Vcmax = 65.33J/mol,
Kmo25 = 0.7, Phi2 = 0.83, sigma2 = 0.5, beta = 0.85, fQ = 1.0, fpseudo = 0.1, h = 4.0,
theta = 230.0μmol/m^2/s, E_Jmax = 48e3J/mol, D_Jmax = 200e3J/mol, Topt_Jmax = 300.5K,
Jmax25 = 0.4, alpha = 0.1, kp25 = 0.7mol/m^2/s, E_kp = 46.39e3J/mol, gbs = 0.003mol/m^2/s,
x = 1.2μmol/m^2/s, E_Rd = 46.39e3J/mol, gso = 0.01mol/m^2/s, a1 = 0.9, b1 = 0.15e-3/Pa) Rd25
Data structure to store all the parameters for the C4 photosynthesis model using Quantity
objects from Unitful.jl.
Arguments
Sco25
: Sc/o parameter at 25 CE_Sco
: Apparent activation energy of Sc/o (J/mol)Kmc25
: Km for CO2 at 25 C (μmol/mol)E_Kmc3
: Activation energy of Kmc (J/mol)Kmo25
: Km for O2 at 25 C (umol/mol)E_Kmo
: Activation energy of Kmo (J/mol)Vcmax25
: Maximum rate of carboxylation at 25 C (μmol/m2/s)E_Vcmax
: Activation energy of Vcmax (J/mol)theta
: Curvature parameterPhi2
: Low-light PSII quantum yieldsigma2
: Partitioning of excitation between PSII and PSIbeta
: Leaf absorptance of PARfQ
: Fraction of electrons at reduced plastoquinone that follow the Q-cyclefpseudo
: Fraction of electrons at PSI that follow cyclic transport around PSIh
: Number of protons required to produce one ATPJmax25
: Maximum rate of electron transport (μmol/m2/s)E_Jmax
: Activation energy Jmax (J/mol)D_Jmax
: Deactivation energy of Jmax (J/mol)Topt_Jmax
: Entropy coefficient of Jmax (J/mol/K)x
: Fraction of electron transport partitioned to mesophyll cellsalpha
: Fraction of O2 evolution occuring in the bundle sheathkp25
: Initial carboxylation efficiency of the PEP carboxylase (mol/m2/s)E_kp
: Activation energy of kp (J/mol)gbs
: Bundle sheath conductance (mol/m^2/s)Rd25:
: Respiration rate at 25 C (μmol/m2/s)E_Rd
: Activation energy of Rd (J/mol)gso
: Minimum stomatal conductance to fluxes of CO2 in darkness (mol/m2/s)a1
: Empirical parameter in gs formulab1
: Empirical parameter in gs formula (1/kPa)
# Ecophys.Photosynthesis.photosynthesis
— Function.
photosynthesis(par::C3, PAR = 1000.0, RH = 0.75, Tleaf = 298.0, Ca = 400.0, O2 = 210e3, gb = 0.5)
photosynthesis(par::C4, PAR = 1000.0, RH = 0.75, Tleaf = 298.0, Ca = 400.0, O2 = 210e3, gb = 0.5)
photosynthesis(par::C3Q, PAR = 1000.0μmol/m^2/s, RH = 0.75, Tleaf = 298.0K, Ca = 400.0μmol/mol, O2 = 210e3μmol/mol, gb = 0.5mol/m^2/s)
photosynthesis(par::C4Q, PAR = 1000.0μmol/m^2/s, RH = 0.75, Tleaf = 298.0K, Ca = 400.0μmol/mol, O2 = 210e3μmol/mol, gb = 0.5mol/m^2/s)
Calculate net CO2 assimilation (umol/m2/s), transpiration (mmol/m2/s) and stomatal condutance to fluxes of CO2 (mol/m2/s) as a function of photosynthetically active radiation (PAR, umol/m2/s), relative humidity (RH), leaf temperature (Tleaf, K), air CO2 partial pressure (Ca, μmol/mol), oxygen (O2, μmol/mol) and boundary layer conductance to CO2 (gb, mol/m2/s). Environmental inputs must be scalar.
Boundary layer conductance
# Ecophys.Photosynthesis.gb
— Function.
gb(p::gbType, ws, Tleaf, Tair, P)
Compute boundary layer conductance for heat, water vapor and CO2.
Arguments
p
: Model of boundary layer conductancews
: Wind speed (m/s)Tleaf
: Leaf temperature (K)Tair
: Air temperature (K)P
: Air pressure (Pa)
Returns
gbh
: Boundary layer conductance for heat (W/m²/K)gbw
: Boundary layer conductance for water vapor (mol/m²/s)gbc
: Boundary layer conductance for CO2 (mol/m²/s)
# Ecophys.Photosynthesis.simplegb
— Type.
simplegb(; d = 0.01)
Simple model of boundary layer conductance.
Arguments
d
: Characteristic leaf length (m)
# Ecophys.Photosynthesis.simplegbQ
— Type.
simplegbQ(; d = 0.01m)
Simple model of boundary layer conductance using Quantity
from Unitful.jl.
Arguments
d
: Characteristic leaf length (m)
# Ecophys.Photosynthesis.gbAngle
— Type.
gbAngle(; d = 0.01, ang = 0.0, ar = 1.0, fangm = 1.381, fangk = 0.034,
= 2.738, b0_0 = 0.455, d_b0 = 2.625, b0_n = 0.373, b0_KAR = 28.125, db_0 = 0.085,
α = 0.437, db_n = 5.175, db_KAR = 0.884, β_0 = 3.362, d_β = 17.664, β_n = 4.727,
d_db = 0.677) β_KAR
Model of boundary layer conductance that accounts for inclination angle and leaf aspect ratio (see documentation for details).
Arguments
d
: Characteristic leaf length (m)ang
: Leaf inclination angle (°)ar
: Leaf aspect ratio (length/width)fangm
: Maximum enhancement factor due to inclination anglefangk
: Exponent in response to inclination angleα
: Effect on back boundary layer conductance due to leaf inclination angle and aspect ratiob0_0
: Parameter in the effect of aspect ratio (see documentation)d_b0
: Parameter in the effect of aspect ratio (see documentation)b0_n
: Parameter in the effect of aspect ratio (see documentation)b0_KAR
: Parameter in the effect of aspect ratio (see documentation)db_0
: Parameter in the effect of aspect ratio (see documentation)d_db
: Parameter in the effect of aspect ratio (see documentation)db_n
: Parameter in the effect of aspect ratio (see documentation)db_KAR
: Parameter in the effect of aspect ratio (see documentation)β_0
: Parameter in the effect of aspect ratio (see documentation)d_β
: Parameter in the effect of aspect ratio (see documentation)β_n
: Parameter in the effect of aspect ratio (see documentation)β_KAR
: Parameter in the effect of aspect ratio (see documentation)
# Ecophys.Photosynthesis.gbAngleQ
— Type.
gbAngleQ(; d = 0.01m, ang = 0.0, ar = 1.0, fangm = 1.381, fangk = 0.034,
= 2.738, b0_0 = 0.455, d_b0 = 2.625, b0_n = 0.373, b0_KAR = 28.125, db_0 = 0.085,
α = 0.437, db_n = 5.175, db_KAR = 0.884, β_0 = 3.362, d_β = 17.664, β_n = 4.727,
d_db = 0.677) β_KAR
Model of boundary layer conductance that accounts for inclination angle and leaf aspect ratio (see documentation for details) using Quantity
for Unitful.jl.
Arguments
d
: Characteristic leaf length (m)ang
: Leaf inclination angle (°)ar
: Leaf aspect ratio (length/width)fangm
: Maximum enhancement factor due to inclination anglefangk
: Exponent in response to inclination angleα
: Effect on back boundary layer conductance due to leaf inclination angle and aspect ratiob0_0
: Parameter in the effect of aspect ratio (see documentation)d_b0
: Parameter in the effect of aspect ratio (see documentation)b0_n
: Parameter in the effect of aspect ratio (see documentation)b0_KAR
: Parameter in the effect of aspect ratio (see documentation)db_0
: Parameter in the effect of aspect ratio (see documentation)d_db
: Parameter in the effect of aspect ratio (see documentation)db_n
: Parameter in the effect of aspect ratio (see documentation)db_KAR
: Parameter in the effect of aspect ratio (see documentation)β_0
: Parameter in the effect of aspect ratio (see documentation)d_β
: Parameter in the effect of aspect ratio (see documentation)β_n
: Parameter in the effect of aspect ratio (see documentation)β_KAR
: Parameter in the effect of aspect ratio (see documentation)
Energy balance
# Ecophys.Photosynthesis.SimpleOptical
— Type.
SimpleOptical(; αPAR = 0.85, αNIR = 0.20, ϵ = 0.95)
Simple optical properties of a leaf.
Arguments
αPAR
: Absorption coefficient of PARαNIR
: Absorption coefficient of NIRϵ
: Emissivity for thermal radiation
# Ecophys.Photosynthesis.energybalance
— Function.
energybalance(pgb, pAgs, pEb, PAR, NIR, ws, RH, Tair, Ca, P, O2)
Calculate the energy balance of a leaf.
Arguments
pgb
: Boundary layer conductance modelpAgs
: Photosynthesis and stomatal conductance modelpEb
: Optical properties of the leafPAR
: Photosynthetically active radiation (umol/m2/s)NIR
: Near-infrared radiation (W/m2)ws
: Wind speed (m/s)RH
: Relative humidityTair
: Air temperature (K)Ca
: Atmospheric CO2 concentration (μmol/mol)P
: Air pressure (kPa)O2
: Atmospheric O2 concentration (μmol/mol)
Details
Inputs maybe be either Real
or Quantity
types (i.e., with physical units). If Quantity
types are used, the output will be a Quantity
type.
# Ecophys.Photosynthesis.solve_energy_balance
— Function.
solve_energy_balance(Ags::Union{C3Q, C4Q}; gb = simplegbQ(),
= SimpleOptical(), PAR = 1000.0μmol/m^2/s,
opt = 250.0W/m^2, ws = 1.0m/s, RH = 0.75,
NIR = 298.0K, Ca = 400.0μmol/mol, P = 101.0kPa,
Tair = 210.0mmol/mol, order = Order2(), xatol = 0.01,
O2 = 100)
maxfnevals solve_energy_balance(Ags::Union{C3, C4}; gb = simplegb(),
= SimpleOptical(), PAR = 1000.0, NIR = 250.0,
opt = 1.0, RH = 0.75, Tair = 298.0, Ca = 400.0,
ws = 101.0e3, O2 = 210.0e3, order = Order2(), xatol = 0.01,
P = 100) maxfnevals
Solve the leaf energy balance coupled to photosynthesis and transpiration.
Arguments
Ags
: Photosynthesis and stomatal conductance modelgb
: Boundary layer conductance modelopt
: Optical properties of the leafPAR
: Photosynthetically active radiation (umol/m2/s)NIR
: Near-infrared radiation (W/m2)ws
: Wind speed (m/s)RH
: Relative humidityTair
: Air temperature (K)Ca
: Atmospheric CO2 concentration (μmol/mol)P
: Air pressure (Pa)O2
: Atmospheric O2 concentration (μmol/mol)order
: Order of the root solving algorithm that finds leaf temperature (see Roots.jl package for more information).xatol
: Absolute tolerance of the root solving algorithm (see Roots.jl package for more information),maxfnevals
: Maximum number of function evaluations of the root solving algorithm (see Roots.jl package for more information).
Details
Inputs maybe be either Real
or Quantity
types from Unitful.jl (i.e., with physical units). If Quantity
types are used, the output will be a Quantity
type.
Returns
A named tuple with net CO2 assimilation (A
, μmol/m^2/s), transpiration (Tr
, mol/m^2/s) and leaf temperature (Tleaf
, K).
# Ecophys.Photosynthesis.transpiration
— Function.
transpiration(;gsw = 0.1, gbw = 1.0, Tleaf = 300.0, Tair = 298.0, P = 101e3,
= 0.75) RH
Compute transpiration rate (mol/m^2/s) from conductance to water vapor and environmental variables.
Arguments
gsw
: Stomatal conductance to water vapor (mol/m^2/s)gbw
: Boundary layer conductance to water vapor (mol/m^2/s)Tleaf
: Leaf temperature (K)Tair
: Air temperature (K)P
: Air pressure (Pa)RH
: Relative humidity