| Literature DB >> 31844509 |
Abstract
Plants must regulate leaf temperature to optimize photosynthesis, control water loss and prevent damage caused by overheating or freezing. Physical models of leaf energy budgets calculate the energy fluxes and leaf temperatures for a given set leaf and environmental parameters. These models can provide deep insight into the variation in leaf form and function, but there are few computational tools available to use these models. Here I introduce a new R package called tealeaves to make complex leaf energy budget models accessible to a broader array of plant scientists. This package enables novice users to start modelling leaf energy budgets quickly while allowing experts to customize their parameter settings. The code is open source, freely available and readily integrates with other R tools for scientific computing. This paper describes the current functionality of tealeaves, but new features will be added in future releases. This software tool will advance new research on leaf thermal physiology to advance our understanding of basic and applied plant science.Entities:
Keywords: Boundary layer; R; energy balance; leaf size; leaf temperature; mathematical model; plant leaves; plant physiology
Year: 2019 PMID: 31844509 PMCID: PMC6899345 DOI: 10.1093/aobpla/plz054
Source DB: PubMed Journal: AoB Plants Impact factor: 3.276
Figure 1.The leaf energy budget model in tealeaves takes environmental and leaf parameters to find the equilibrium leaf temperature () at which incoming energy exactly matches outgoing energy. Under typical daytime conditions, this means thermal infrared radiation losses, sensible heat loss and latent heat loss must balance absorbed radiation. (A) The components of leaf energy budgets (thin orange lines) vary with leaf temperature (x-axis). is where the net energy flux (thick blue line) is 0 (blue point; see Equation 1). (B) 1) Radiation is emitted from sunlight and surrounding objects is absorbed by the leaf. 2) The leaf radiates some energy. 3) Heat is lost through convection when the leaf temperature is greater than air temperature. 4) Latent heat is lost through evaporation, which is driven by the vapor-pressure deficit between the air and leaf interior and the leaf conductance to water vapor. Calculations used the following leaf parameter values in this example: d = 0.1 m; ; ; ; ; . Calculations used the following environmental parameter values in this example: P = 101.3246 kPa; r = 0.2; ; W m−2; K; u = 2 m s−1. See Table 1 for symbol definitions.
Parameter inputs for tealeaves. Each parameter has a mathematical symbol used in the text, the R character string used in the tealeaves package, a brief description and the units. For physical constants, a value is provided where applicable, though users can modify these if desired.
| Symbol | R character | Description | Units |
|---|---|---|---|
| Leaf parameters: | |||
|
| leafsize | Leaf characteristic dimension | m |
|
| abs_l | Absorbtivity of long-wave radiation (4–80 µm) | None |
|
| abs_s | Absorbtivity of short-wave radiation (0.3–4 µm) | None |
|
| g_sw | Stomatal conductance to water vapour | µmol m−2 s−1 Pa−1† |
|
| g_uw | Cuticular conductance to water vapour | µmol m−2 s−1 Pa−1† |
| SR | Stomatal ratio (untransformed) | None | |
|
| logit_sr | Stomatal ratio (logit transformed) | None |
| Environmental parameters: | |||
|
| P | Atmospheric pressure | kPa |
|
| r | Reflectance for short-wave irradiance (albedo) | None |
| RH | RH | Relative humidity | None |
|
| S_sw | Incident short-wave (solar) radiation flux density | W m−2 |
|
| T_air | Air temperature | K |
|
| wind | Wind speed | m s−1 |
| Physical constants: | |||
|
| a, b, c, d | Coefficients for calculating Nu and Sh numbers | None |
|
| c_p | Heat capacity of air | 1.01 J g−1 K−1 |
|
| D_h0 | Diffusion coefficient for heat in air at 0 °C | 19.0 × 10−6 m2 s−1 |
|
| D_m0 | Diffusion coefficient for momentum in air at 0 °C | 13.3 × 10−6 m2 s−1 |
|
| D_w0 | Diffusion coefficient for water vapour in air at 0 °C | 21.2 × 10−6 m2 s−1 |
|
| epsilon | Ratio of water to air molar masses | 0.622 |
|
| eT | Exponent for temperature dependence of diffusion | 1.75 |
|
| G | Gravitational acceleration | 9.8 m s−2 |
|
| R | Ideal gas constant | 8.3144598 J mol−1 K−1 |
|
| R_air | Specific gas constant for dry air | 287.058 J kg−1 K−1 |
|
| s | Stefan–Boltzmann constant | 5.67 × 10−8 W m−2 K−4 |
†Conductances are presented in molar units for consistency with literature on photosynthesis but are converted to m s−1 using the ideal gas law (see text for details) to match conductance to heat transfer.
Calculated parameters and outputs for tealeaves. Some parameters are intermediate calculations (see Methods) but are not included in the tealeaves output (see R documentation accompanying package for further detail). Each parameter has a mathematical symbol used in the text, the R character string used in the tealeaves package, a brief description and the units.
| Symbol | R character | Description | Units |
|---|---|---|---|
| Leaf parameters: | |||
|
| E | Transpiration rate | mol m−2 s−1 |
|
| g_h | Boundary layer conductance to heat | m s−1 |
|
| g_bw | Boundary layer conductance to water vapour | m s−1 |
|
| g_tw | Total conductance to water vapour | m s−1 |
| Gr | Gr | Grashof number | None |
|
| H | Sensible heat flux | W m−2 |
|
| L | Latend heat flux | W m−2 |
| Nu | Nu | Nusselt number | None |
|
| R_abs | Absorbed radiation | W m−2 |
| Re | Re | Reynolds number | None |
|
| S_r | Thermal infrared radiation losses | W m−2 |
| Sh | Sh | Sherwood number | None |
|
| T_leaf | Leaf temperature | K |
| Environmental parameters: | |||
|
| d_wv | Water vapour pressure differential | mol m−3 |
|
| h_vap | Latent heat of vapourization | J mol−1 |
|
| P_a | Density of dry air | g m−3 |
|
| p_air | Water vapour pressure of the air | kPa |
|
| p_sat | Saturating water vapour pressure | kPa |
|
| S_lw | Incident long-wave (thermal infrared) radiation flux density | W m−2 |
|
| T_sky | Clear sky temperature | K |
| Physical constants: | |||
|
| D_h | Diffusion coefficient for heat in air at a given temperature | m2 s−1 |
|
| D_m | Diffusion coefficient for momentum in air at a given temperature | m2 s−1 |
|
| D_w | Diffusion coefficient for water vapour in air at a given temperature | m2 s−1 |
| Convergence diagnostics: | |||
| value | Energy balance at equilibrium | W m−2 | |
| convergence | 0 = converged; 1 = failed | none |
Figure 2.Extended examples of tealeaves. Code to generate these examples is provided in the . (A) The temperature of smaller leaves is more closely coupled to air temperature. Each line represents a different leaf size (small, dashed line; medium, dotted line; large, solid line) and the leaf-to-air temperature differential (y-axis) over an air temperature gradient (x-axis). (B) Greater stomatal conductance cools leaves. Each line represents a different stomatal conductance (low, dashed line, 1 µmol m−2 s−1 Pa−1; medium, dotted line, 3 µmol m−2 s−1 Pa−1; high, solid line, 5 µmol m−2 s−1 Pa−1) and the leaf-to-air temperature differential (y-axis) over a gradient of incident solar radiation (x-axis). (C) Forced convection dominates in small leaves; free convection dominates in very large leaves. Leaf size is indicated by line type as in Panel (A). Vertical lines indicate approximate shifts from forced convection (), mixed convection () and free convection (). Small leaves always experience forced convection, leading to lower leaf temperature compared to large leaves experiencing free convection. (D) Amphistomatous leaves (stomatal ratio ~ 0.5) evaporate more than hypo- or hyperstomatous leaves (stomatal ratio ~ 0 or 1, respectively), especially under free convection (low wind speed, u).