make_parameters {photosynthesis}R Documentation

Make lists of parameters for photosynthesis

Description

Make lists of parameters for photosynthesis

make_leafpar

make_enviropar

make_bakepar

make_constants

Usage

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().

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

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()

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
)

[Package photosynthesis version 2.1.4 Index]