Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model
Rubisco-limited assimilation rate
RuBP regeneration-limited assimilation rate
TPU-limited assimilation rate
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)Chloroplastic CO2 concentration in Pa of class units
Concatenated parameters (leaf_par, enviro_par, and constants)
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.
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
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) | \(\mu\)mol CO2 / (m\(^2\) s) | calculated |
| \(K_\mathrm{C}\) | K_C | Michaelis constant for carboxylation (T_leaf) | \(\mu\)mol / mol | calculated |
| \(K_\mathrm{O}\) | K_O | Michaelis constant for oxygenation (T_leaf) | \(\mu\)mol / 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) | \(\mu\)mol 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) | \(\mu\)mol CO2 / (m\(^2\) s) | calculated |
| \(V_\mathrm{tpu}\) | V_tpu | rate of triose phosphate utilization (T_leaf) | \(\mu\)mol CO2 / (m\(^2\) s) | calculated |
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.
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)
#> $W_carbox
#> 43.12971 [umol/m^2/s]
#>
#> $W_regen
#> 34.71203 [umol/m^2/s]
#>
#> $W_tpu
#> 709.3539 [umol/m^2/s]
#>
#> $A
#> 34.71203 [umol/m^2/s]
#>