photosynthesis (version 1.0.2)

FvCB: 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.

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

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<U+2013>90.

Examples

# NOT RUN {
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, bake_par, constants)

pars <- c(leaf_par, enviro_par, constants)
C_chl <- set_units(24.28, "Pa")
FvCB(C_chl, pars)

# }