photo: Photosynthesis submodel functions

In medfate: Mediterranean Forest Simulation

Photosynthesis submodel functions

Description

Set of functions used in the calculation of photosynthesis

Usage

photo_GammaTemp(Tleaf)

photo_KmTemp(Tleaf, Oi = 209)

photo_VmaxTemp(Vmax298, Tleaf)

photo_JmaxTemp(Jmax298, Tleaf)

photo_electronLimitedPhotosynthesis(Q, Ci, GT, Jmax)

photo_rubiscoLimitedPhotosynthesis(Ci, GT, Km, Vmax)

photo_photosynthesis(Q, Catm, Gc, Tleaf, Vmax298, Jmax298, verbose = FALSE)

photo_photosynthesisBaldocchi(
  Q,
  Catm,
  Tleaf,
  u,
  Vmax298,
  Jmax298,
  leafWidth,
  Gsw_AC_slope,
  Gsw_AC_intercept
)

photo_leafPhotosynthesisFunction(
  E,
  psiLeaf,
  Catm,
  Patm,
  Tair,
  vpa,
  u,
  absRad,
  Q,
  Vmax298,
  Jmax298,
  leafWidth = 1,
  refLeafArea = 1,
  verbose = FALSE
)

photo_leafPhotosynthesisFunction2(
  E,
  psiLeaf,
  Catm,
  Patm,
  Tair,
  vpa,
  u,
  SWRabs,
  LWRnet,
  Q,
  Vmax298,
  Jmax298,
  leafWidth = 1,
  refLeafArea = 1,
  verbose = FALSE
)

photo_sunshadePhotosynthesisFunction(
  E,
  psiLeaf,
  Catm,
  Patm,
  Tair,
  vpa,
  SLarea,
  SHarea,
  u,
  absRadSL,
  absRadSH,
  QSL,
  QSH,
  Vmax298SL,
  Vmax298SH,
  Jmax298SL,
  Jmax298SH,
  leafWidth = 1,
  verbose = FALSE
)

photo_multilayerPhotosynthesisFunction(
  E,
  psiLeaf,
  Catm,
  Patm,
  Tair,
  vpa,
  SLarea,
  SHarea,
  u,
  absRadSL,
  absRadSH,
  QSL,
  QSH,
  Vmax298,
  Jmax298,
  leafWidth = 1,
  verbose = FALSE
)

Arguments

Tleaf	Leaf temperature (in ºC).
Oi	Oxigen concentration (mmol*mol-1).
Vmax298, Vmax298SL, Vmax298SH	Maximum Rubisco carboxylation rate per leaf area at 298ºK (i.e. 25 ºC) (micromol*s-1*m-2) (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction). 'SH' stands for shade leaves, whereas 'SL' stands for sunlit leaves.
Jmax298, Jmax298SL, Jmax298SH	Maximum electron transport rate per leaf area at 298ºK (i.e. 25 ºC) (micromol*s-1*m-2) (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction). 'SH' stands for shade leaves, whereas 'SL' stands for sunlit leaves.
Q	Active photon flux density (micromol * s-1 * m-2).
Ci	CO2 internal concentration (micromol * mol-1).
GT	CO2 saturation point corrected by temperature (micromol * mol-1).
Jmax	Maximum electron transport rate per leaf area (micromol*s-1*m-2).
Km	Km = Kc*(1.0+(Oi/Ko)) - Michaelis-Menten term corrected by temperature (in micromol * mol-1).
Vmax	Maximum Rubisco carboxylation rate per leaf area (micromol*s-1*m-2).
Catm	CO2 air concentration (micromol * mol-1).
Gc	CO2 leaf (stomatal) conductance (mol * s-1 * m-2).
verbose	Boolean flag to indicate console output.
u	Wind speed above the leaf boundary (in m/s) (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).
leafWidth	Leaf width (in cm).
Gsw_AC_slope	Slope of the An/C vs Gsw relationship
Gsw_AC_intercept	Intercept of the An/C vs Gsw relationship
E	Transpiration flow rate per leaf area (mmol*s-1*m-2).
psiLeaf	Leaf water potential (MPa).
Patm	Atmospheric air pressure (in kPa).
Tair	Air temperature (in ºC).
vpa	Vapour pressure deficit (in kPa).
absRad	Absorbed long- and short-wave radiation (in W*m^-2).
refLeafArea	Leaf reference area.
SWRabs	Absorbed short-wave radiation (in W·m-2).
LWRnet	Net long-wave radiation balance (in W·m-2).
SLarea, SHarea	Leaf area index of sunlit/shade leaves (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).
absRadSL, absRadSH	Instantaneous absorbed radiation (W·m-2) per unit of sunlit/shade leaf area (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).
QSL, QSH	Active photon flux density (micromol * s-1 * m-2) per unit of sunlit/shade leaf area (for each canopy layer in the case of photo_multilayerPhotosynthesisFunction).

Details

Details of the photosynthesis submodel are given in the medfate book

Value

Values returned for each function are:

• photo_GammaTemp: CO2 compensation concentration (micromol * mol-1).

• photo_KmTemp: Michaelis-Menten coefficients of Rubisco for Carbon (micromol * mol-1) and Oxigen (mmol * mol-1).

• photo_VmaxTemp: Temperature correction of Vmax298.

• photo_JmaxTemp: Temperature correction of Jmax298.

• photo_electronLimitedPhotosynthesis: Electron-limited photosynthesis (micromol*s-1*m-2) following Farquhar et al. (1980).

• photo_rubiscoLimitedPhotosynthesis: Rubisco-limited photosynthesis (micromol*s-1*m-2) following Farquhar et al. (1980).

• photo_photosynthesis: Calculates gross photosynthesis (micromol*s-1*m-2) following (Farquhar et al. (1980) and Collatz et al (1991).

• photo_leafPhotosynthesisFunction: Returns a data frame with the following columns:

  • LeafTemperature: Leaf temperature (ºC).

  • LeafVPD: Leaf vapor pressure deficit (kPa).

  • LeafCi: Internal CO2 concentration (micromol * mol-1).

  • Gsw: Leaf stomatal conductance to water vapor (mol * s-1 * m-2).

  • GrossPhotosynthesis: Gross photosynthesis (micromol*s-1*m-2).

  • NetPhotosynthesis: Net photosynthesis, after discounting autotrophic respiration (micromol*s-1*m-2).

• photo_sunshadePhotosynthesisFunction: Returns a data frame with the following columns:

  • GrossPhotosynthesis: Gross photosynthesis (micromol*s-1*m-2).

  • NetPhotosynthesis: Net photosynthesis, after discounting autotrophic respiration (micromol*s-1*m-2).

  • LeafCiSL: Sunlit leaf internal CO2 concentration (micromol * mol-1).

  • LeafCiSH: Shade leaf internal CO2 concentration (micromol * mol-1).

  • LeafTempSL: Sunlit leaf temperature (ºC).

  • LeafTempSH: Shade leaf temperature (ºC).

  • LeafVPDSL: Sunlit leaf vapor pressure deficit (kPa).

  • LeafVPDSH: Shade leaf vapor pressure deficit (kPa).

• photo_multilayerPhotosynthesisFunction: Return a data frame with the following columns:

  • GrossPhotosynthesis: Gross photosynthesis (micromol*s-1*m-2).

  • NetPhotosynthesis: Net photosynthesis, after discounting autotrophic respiration (micromol*s-1*m-2).

Author(s)

Miquel De Cáceres Ainsa, CREAF

References

Bernacchi, C. J., E. L. Singsaas, C. Pimentel, A. R. Portis, and S. P. Long. 2001. Improved temperature response functions for models of Rubisco-limited photosynthesis. Plant, Cell and Environment 24:253–259.

Collatz, G. J., J. T. Ball, C. Grivet, and J. A. Berry. 1991. Physiological and environmental regulation of stomatal conductance, photosynthesis and transpiration: a model that includes a laminar boundary layer. Agricultural and Forest Meteorology 54:107–136.

Farquhar, G. D., S. von Caemmerer, and J. A. Berry. 1980. A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149:78–90.

Leuning, R. 2002. Temperature dependence of two parameters in a photosynthesis model. Plant, Cell and Environment 25:1205–1210.

Sperry, J. S., M. D. Venturas, W. R. L. Anderegg, M. Mencuccini, D. S. Mackay, Y. Wang, and D. M. Love. 2016. Predicting stomatal responses to the environment from the optimization of photosynthetic gain and hydraulic cost. Plant Cell and Environment.

See Also

hydraulics_supplyFunctionNetwork, biophysics_leafTemperature, spwb

medfate documentation built on Sept. 11, 2024, 7:32 p.m.