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.

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

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)	$\mu$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

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)
#> $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]
#>