photosynthesis
Software:59592
CRANphotosynthesisMaRDI QIDQ59592
Tools for Plant Ecophysiology & Modeling
Demi Sargent, Chris Muir, Patrick Hudson, Bridget Murphy, Joseph R. Stinziano, Cassaundra Roback
Last update: 15 August 2023
Copyright license: MIT license, File License
Software version identifier: 2.1.2, 2.1.3, 1.0.0, 1.0.2, 2.0.0, 2.0.1, 2.0.3, 2.1.0, 2.1.1, 2.1.4
Contains modeling and analytical tools for plant ecophysiology. MODELING: Simulate C3 photosynthesis using the Farquhar, von Caemmerer, Berry (1980) <doi:10.1007/BF00386231> model as described in Buckley and Diaz-Espejo (2015) <doi:10.1111/pce.12459>. It uses units to ensure that parameters are properly specified and transformed before calculations. Temperature response functions get automatically "baked" into all parameters based on leaf temperature following Bernacchi et al. (2002) <doi:10.1104/pp.008250>. The package includes boundary layer, cuticular, stomatal, and mesophyll conductances to CO2, which each can vary on the upper and lower portions of the leaf. Use straightforward functions to simulate photosynthesis over environmental gradients such as Photosynthetic Photon Flux Density (PPFD) and leaf temperature, or over trait gradients such as CO2 conductance or photochemistry. ANALYTICAL TOOLS: Fit ACi (Farquhar et al. (1980) <doi:10.1007/BF00386231>) and AQ curves (Marshall & Biscoe (1980) <doi:10.1093/jxb/31.1.29>), temperature responses (Heskel et al. (2016) <doi:10.1073/pnas.1520282113>; Kruse et al. (2008) <doi:10.1111/j.1365-3040.2008.01809.x>, Medlyn et al. (2002) <doi:10.1046/j.1365-3040.2002.00891.x>, Hobbs et al. (2013) <doi:10.1021/cb4005029>), respiration in the light (Kok (1956) <doi:10.1016/0006-3002(56)90003-8>, Walker & Ort (2015) <doi:10.1111/pce.12562>, Yin et al. (2009) <doi:10.1111/j.1365-3040.2009.01934.x>, Yin et al. (2011) <doi:10.1093/jxb/err038>), mesophyll conductance (Harley et al. (1992) <doi:10.1104/pp.98.4.1429>), pressure-volume curves (Koide et al. (2000) <doi:10.1007/978-94-009-2221-1_9>, Sack et al. (2003) <doi:10.1046/j.0016-8025.2003.01058.x>, Tyree et al. (1972) <doi:10.1093/jxb/23.1.267>), hydraulic vulnerability curves (Ogle et al. (2009) <doi:10.1111/j.1469-8137.2008.02760.x>, Pammenter et al. (1998) <doi:10.1093/treephys/18.8-9.589>), and tools for running sensitivity analyses particularly for variables with uncertainty (e.g. g_mc(), gamma_star(), R_d()).
- A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species
- Partitioning changes in photosynthetic rate into contributions from different variables
- Temperature Response of Mesophyll Conductance. Implications for the Determination of Rubisco Enzyme Kinetics and for Limitations to Photosynthesis in Vivo
- A Model for C3Leaves Describing the Dependence of Net Photosynthesis on Irradiance
- Convergence in the temperature response of leaf respiration across biomes and plant functional types
- Three parameters comprehensively describe the temperature response of respiratory oxygen reduction
- Temperature response of parameters of a biochemically based model of photosynthesis. II. A review of experimental data
- Change in Heat Capacity for Enzyme Catalysis Determines Temperature Dependence of Enzyme Catalyzed Rates
- On the inhibition of photosynthesis by intense light
- Improved method for measuring the apparent CO2photocompensation point resolves the impact of multiple internal conductances to CO2to net gas exchange
- Using combined measurements of gas exchange and chlorophyll fluorescence to estimate parameters of a biochemical C3photosynthesis model: a critical appraisal and a new integrated approach applied to leaves in a wheat (Triticum aestivum) canopy
- Evaluating a new method to estimate the rate of leaf respiration in the light by analysis of combined gas exchange and chlorophyll fluorescence measurements
- Theoretical Considerations when Estimating the Mesophyll Conductance to CO2 Flux by Analysis of the Response of Photosynthesis to CO2
- Plant water status, hydraulic resistance and capacitance
- The ‘hydrology’ of leaves: co-ordination of structure and function in temperate woody species
- The Measurement of the Turgor Pressure and the Water Relations of Plants by the Pressure-bomb Technique
- Hierarchical statistical modeling of xylem vulnerability to cavitation
- A mathematical and statistical analysis of the curves illustrating vulnerability of xylem to cavitation
