Make lists of parameters for photosynthesis

Make lists of parameters for photosynthesis

make_leafpar

make_enviropar

make_bakepar

make_constants

make_leafpar(replace = NULL, use_tealeaves)

make_enviropar(replace = NULL, use_tealeaves)

make_bakepar(replace = NULL)

make_constants(replace = NULL, use_tealeaves)

Arguments

replace

A named list of parameters to replace defaults. If NULL, defaults will be used.

use_tealeaves

Logical. Should leaf energy balance be used to calculate leaf temperature (T_leaf)? If TRUE, tleaf() calculates T_leaf. If FALSE, user-defined T_leaf is used. Additional parameters and constants are required, see make_parameters().

Value

make_leafpar: An object inheriting from class leaf_par()

make_enviropar: An object inheriting from class enviro_par()

make_bakepar: An object inheriting from class bake_par()

make_constants: An object inheriting from class constants()

Details

Constants:

Symbol	R	Description	Units	Default
\(D_{\mathrm{c},0}\)	D_c0	diffusion coefficient for CO2 in air at 0 °C	m\(^2\) / s	\(1.29\times 10^{-5}\)
\(D_{\mathrm{h},0}\)	D_h0	diffusion coefficient for heat in air at 0 °C	m\(^2\) / s	\(1.90\times 10^{-5}\)
\(D_{\mathrm{m},0}\)	D_m0	diffusion coefficient for momentum in air at 0 °C	m\(^2\) / s	\(1.33\times 10^{-5}\)
\(D_{\mathrm{w},0}\)	D_w0	diffusion coefficient for water vapor in air at 0 °C	m\(^2\) / s	\(2.12\times 10^{-5}\)
\(\epsilon\)	epsilon	ratio of water to air molar masses	none	0.622
\(G\)	G	gravitational acceleration	m / s\(^2\)	9.8
\(eT\)	eT	exponent for temperature dependence of diffusion	none	1.75
\(R\)	R	ideal gas constant	J / mol / K	8.31
\(\sigma\)	sigma	Stephan-Boltzmann constant	W / m\(^2\) / K\(^4\)	\(5.67\times 10^{-8}\)
\(f_\mathrm{Sh}\)	f_sh	function to calculate constant(s) for Sherwood number	none	NA
\(f_\mathrm{Nu}\)	f_nu	function to calculate constant(s) for Nusselt number	none	NA

Baking (i.e. temperature response) parameters:

Symbol	R	Description	Units	Default
\(D_\mathrm{s,gmc}\)	Ds_gmc	empirical temperature response parameter	J / mol / K	487
\(D_\mathrm{s,Jmax}\)	Ds_Jmax	empirical temperature response parameter	J / mol / K	388
\(E_\mathrm{a,\Gamma *}\)	Ea_gammastar	empirical temperature response parameter	J / mol	24500
\(E_\mathrm{a,gmc}\)	Ea_gmc	empirical temperature response parameter	J / mol	68900
\(E_\mathrm{a,Jmax}\)	Ea_Jmax	empirical temperature response parameter	J / mol	56100
\(E_\mathrm{a,KC}\)	Ea_KC	empirical temperature response parameter	J / mol	81000
\(E_\mathrm{a,KO}\)	Ea_KO	empirical temperature response parameter	J / mol	23700
\(E_\mathrm{a,Rd}\)	Ea_Rd	empirical temperature response parameter	J / mol	40400
\(E_\mathrm{a,Vcmax}\)	Ea_Vcmax	empirical temperature response parameter	J / mol	52200
\(E_\mathrm{a,Vtpu}\)	Ea_Vtpu	empirical temperature response parameter	J / mol	52200
\(E_\mathrm{d,gmc}\)	Ed_gmc	empirical temperature response parameter	J / mol	149000
\(E_\mathrm{d,Jmax}\)	Ed_Jmax	empirical temperature response parameter	J / mol	121000

Environment parameters:

Symbol	R	Description	Units	Default
\(C_\mathrm{air}\)	C_air	atmospheric CO2 concentration	umol/mol	420
\(O\)	O	atmospheric O2 concentration	mol/mol	0.21
\(P\)	P	atmospheric pressure	kPa	101
\(\mathrm{PPFD}\)	PPFD	photosynthetic photon flux density	umol / m\(^2\) / s	1500
\(\mathrm{RH}\)	RH	relative humidity	none	0.5
\(u\)	wind	windspeed	m / s	2

Leaf parameters:

Symbol	R	Description	Units	Default
\(d\)	leafsize	leaf characteristic dimension	m	0.1
\(\Gamma*\)	gamma_star	chloroplastic CO2 compensation point (T_leaf)	umol/mol	NA
\(\Gamma*_{25}\)	gamma_star25	chloroplastic CO2 compensation point (25 °C)	umol/mol	37.9
\(g_\mathrm{mc}\)	g_mc	mesophyll conductance to CO2 (T_leaf)	mol / m\(^2\) / s	NA
\(g_\mathrm{mc,25}\)	g_mc25	mesophyll conductance to CO2 (25 °C)	mol / m\(^2\) / s	0.4
\(g_\mathrm{sc}\)	g_sc	stomatal conductance to CO2	mol / m\(^2\) / s	0.4
\(g_\mathrm{uc}\)	g_uc	cuticular conductance to CO2	mol / m\(^2\) / s	0.01
\(J_\mathrm{max,25}\)	J_max25	potential electron transport (25 °C)	umol / m\(^2\) / s	200
\(J_\mathrm{max}\)	J_max	potential electron transport (T_leaf)	umol / m\(^2\) / s	NA
\(k_\mathrm{mc}\)	k_mc	partition of g_mc to lower mesophyll	none	1
\(k_\mathrm{sc}\)	k_sc	partition of g_sc to lower surface	none	1
\(k_\mathrm{uc}\)	k_uc	partition of g_uc to lower surface	none	1
\(K_\mathrm{C,25}\)	K_C25	Michaelis constant for carboxylation (25 °C)	umol / mol	268
\(K_\mathrm{C}\)	K_C	Michaelis constant for carboxylation (T_leaf)	umol / mol	NA
\(K_\mathrm{O,25}\)	K_O25	Michaelis constant for oxygenation (25 °C)	umol / mol	165000
\(K_\mathrm{O}\)	K_O	Michaelis constant for oxygenation (T_leaf)	umol / mol	NA
\(\phi_J\)	phi_J	initial slope of the response of J to PPFD	none	0.331
\(R_\mathrm{d,25}\)	R_d25	nonphotorespiratory CO2 release (25 °C)	umol / m\(^2\) / s	2
\(R_\mathrm{d}\)	R_d	nonphotorespiratory CO2 release (T_leaf)	umol / m\(^2\) / s	NA
\(\theta_J\)	theta_J	curvature factor for light-response curve	none	0.825
\(T_\mathrm{leaf}\)	T_leaf	leaf temperature	K	298
\(V_\mathrm{c,max,25}\)	V_cmax25	maximum rate of carboxylation (25 °C)	umol / m\(^2\) / s	150
\(V_\mathrm{c,max}\)	V_cmax	maximum rate of carboxylation (T_leaf)	umol / m\(^2\) / s	NA
\(V_\mathrm{tpu,25}\)	V_tpu25	rate of triose phosphate utilization (25 °C)	umol / m\(^2\) / s	200
\(V_\mathrm{tpu}\)	V_tpu	rate of triose phosphate utilisation (T_leaf)	umol / m\(^2\) / s	NA

If use_tealeaves = TRUE, additional parameters are:

Constants:

Symbol	R	Description	Units	Default
\(c_p\)	c_p	heat capacity of air	J / g / K	1.01
\(R_\mathrm{air}\)	R_air	specific gas constant for dry air	J / kg / K	287

Baking (i.e. temperature response) parameters:

Symbol

R

Description

Units

Default

Environment parameters:

Symbol	R	Description	Units	Default
\(E_q\)	E_q	energy per mole quanta	kJ / mol	220
\(f_\mathrm{PAR}\)	f_par	fraction of incoming shortwave radiation that is photosynthetically active radiation (PAR)	none	0.5
\(r\)	r	reflectance for shortwave irradiance (albedo)	none	0.2
\(T_\mathrm{air}\)	T_air	air temperature	K	298
\(T_\mathrm{sky}\)	T_sky	sky temperature	K	NA

Leaf parameters:

Symbol	R	Description	Units	Default
\(\alpha_\mathrm{l}\)	abs_l	absorbtivity of longwave radiation (4 - 80 um)	none	0.97
\(\alpha_\mathrm{s}\)	abs_s	absorbtivity of shortwave radiation (0.3 - 4 um)	none	0.5
\(g_\mathrm{sw}\)	g_sw	stomatal conductance to H2O	mol / m\(^2\) / s	NA
\(g_\mathrm{uw}\)	g_uw	cuticular conductance to H2O	mol / m\(^2\) / s	NA
\(\mathrm{logit}(sr)\)	logit_sr	stomatal ratio (logit transformed)	none	NA

Optional leaf parameters:

Symbol	R	Description	Units	Default
\(\delta_\mathrm{ias,lower}\)	delta_ias_lower	effective distance through lower internal airspace	um	NA
\(\delta_\mathrm{ias,upper}\)	delta_ias_upper	effective distance through upper internal airspace	um	NA
\(A_\mathrm{mes} / A\)	A_mes_A	mesophyll surface area per unit leaf area	none	NA
\(g_\mathrm{liq,c,25}\)	g_liqc25	liquid-phase conductance to CO2 (25 °C)	mol / m\(^2\) / s	NA
\(g_\mathrm{liq,c}\)	g_liqc	liquid-phase conductance to CO2 (T_leaf)	mol / m\(^2\) / s	NA
\(g_\mathrm{ias,c,lower}\)	g_iasc_lower	internal airspace conductance to CO2 in lower part of leaf (T_leaf)	mol / m\(^2\) / s	NA
\(g_\mathrm{ias,c,upper}\)	g_iasc_upper	internal airspace conductance to CO2 in upper part of leaf (T_leaf)	mol / m\(^2\) / s	NA

References

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

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 = make_leafpar(
  replace = list(
    g_sc = set_units(0.3, mol / m^2 / s),
    V_cmax25 = set_units(100, umol / m^2 / s)
  ), use_tealeaves = FALSE
)