FvCB: Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model

View source: R/FvCB.R

FvCBR Documentation

Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model

Description

Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model

Rubisco-limited assimilation rate

RuBP regeneration-limited assimilation rate

TPU-limited assimilation rate

Usage

FvCB(C_chl, pars, unitless = FALSE)

W_carbox(C_chl, pars, unitless = FALSE)

W_regen(C_chl, pars, unitless = FALSE)

W_tpu(C_chl, pars, unitless = FALSE)

Arguments

C_chl

Chloroplastic CO2 concentration in Pa of class units

pars

Concatenated parameters (leaf_par, enviro_par, and constants)

unitless

Logical. Should units be set? The function is faster when FALSE, but input must be in correct units or else results will be incorrect without any warning.

Details

Equations following Buckley and Diaz-Espejo (2015):

Rubisco-limited assimilation rate:

W_\mathrm{carbox} = V_\mathrm{c,max} C_\mathrm{chl} / (C_\mathrm{chl} + K_\mathrm{m})

where:

K_\mathrm{m} = K_\mathrm{C} (1 + O / K_\mathrm{O})

RuBP regeneration-limited assimilation rate:

W_\mathrm{regen} = J C_\mathrm{chl} / (4 C_\mathrm{chl} + 8 \Gamma*)

where J is a function of PPFD, obtained by solving the equation:

0 = \theta_J J ^ 2 - J (J_\mathrm{max} + \phi_J PPFD) + J_\mathrm{max} \phi_J PPFD

TPU-limited assimilation rate:

W_\mathrm{tpu} = 3 V_\mathrm{tpu} C_\mathrm{chl} / (C_\mathrm{chl} - \Gamma*)


Symbol R Description Units Default
C_\mathrm{chl} C_chl chloroplastic CO2 concentration Pa input
\Gamma* gamma_star chloroplastic CO2 compensation point (T_leaf) Pa calculated
J_\mathrm{max} J_max potential electron transport (T_leaf) \mumol CO2 / (m^2 s) calculated
K_\mathrm{C} K_C Michaelis constant for carboxylation (T_leaf) \mumol / mol calculated
K_\mathrm{O} K_O Michaelis constant for oxygenation (T_leaf) \mumol / mol calculated
O O atmospheric O2 concentration kPa 21.27565
\phi_J phi_J initial slope of the response of J to PPFD none 0.331
PPFD PPFD photosynthetic photon flux density umol quanta / (m^2 s) 1500
R_\mathrm{d} R_d nonphotorespiratory CO2 release (T_leaf) \mumol CO2 / (m^2 s) calculated
\theta_J theta_J curvature factor for light-response curve none 0.825
V_\mathrm{c,max} V_cmax maximum rate of carboxylation (T_leaf) \mumol CO2 / (m^2 s) calculated
V_\mathrm{tpu} V_tpu rate of triose phosphate utilization (T_leaf) \mumol CO2 / (m^2 s) calculated

Value

A list of four values with units umol CO2 / (m^2 s) of class units:

  • W_carbox: Rubisco-limited assimilation rate

  • W_regen: RuBP regeneration-limited assimilation rate

  • W_tpu: TPU-limited assimilation rate

  • A: minimum of W_carbox, W_regen, and W_tpu

References

Buckley TN and Diaz-Espejo A. 2015. Partitioning changes in photosynthetic rate into contributions from different variables. Plant, Cell & Environment 38: 1200-11.

Farquhar GD, Caemmerer S, Berry JA. 1980. A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species. Planta 149: 78–90.

Examples

bake_par = make_bakepar()
constants = make_constants(use_tealeaves = FALSE)
enviro_par = make_enviropar(use_tealeaves = FALSE)
leaf_par = make_leafpar(use_tealeaves = FALSE)
leaf_par = bake(leaf_par, enviro_par, bake_par, constants)

pars = c(leaf_par, enviro_par, constants)
C_chl = set_units(246.0161, umol / mol)
FvCB(C_chl, pars)

photosynthesis documentation built on Aug. 15, 2023, 9:08 a.m.