/calc_aci

Primary LanguageR

Calculate vcmax and vqmax from A/Ci curve

Vcmax is Rubisco-limited photosynthesis Vqmax is Cytochrome b6f-limited photosnthesis as descibed by Johnson & Berry 2022

Inputs

  • Dataframe including:
    • Photo = Photosynthesis, umol m-2 s-1
    • Ci = Intercellular CO2, umol mol-1
    • Rd = Dark respiration, umol m-2 s-1
    • PAR = Photosynthetically active radiation, umol m-2 s-1
    • Tleaf = Leaf temperature, C
  • ci_trans = Ci transition point, estimated from data
  • nl = ATP per e- in linear flow, ATP/e- (defaults to 0.75)
  • nc = ATP per e- in cyclic flow, ATP/e- (defaults to 1)
  • Abs = Total leaf absorptance to PAR, mol PPFD absorbed mol-1 PPFD incident (defaults to 0.85)
  • beta = PSII fraction of total leaf absorptance, mol PPFD absorbed by PSII mol-1 PPFD absorbed (defaults to 0.52)
  • Kf = Rate constant for fluoresence at PSII and PSI, s-1 (defaults to 0.05e09)
  • Kd = Rate constant for constitutive heat loss at PSII and PSI, s-1 (defaults to 0.55e09)
  • Kp1 = Rate constant for photochemistry at PSI, s-1 (defaults to 14.5e09)
  • start_vmax = a named list or named numeric vector of starting estimates (defaults to 30)
  • control_maxiter = positive integer, termination occurs when the number of iterations reaches maxiter (defaults to 500)
  • control_minFactor = positive numeric value specifying the minimum step-size factor allowed on any step in the iteration (defaults to 1/10000)

Citation

Johnson, J. E. and J. A. Berry. 2021. The role of Cytochrome b6f in the control of steady-state photosynthesis: a conceptual and quantitative model. Photosynthesis Research, DOI: 10.1007/s11120-021-00840-4