Poolman 2000, Exp. Botany

The Poolman 2000 model describes the Calvin-Benson-Bassham (CBB) cycle, covering the fixation of CO2 by rubisco through to the regeneration of RuBP and the export of triose phosphates, glycerate-3-phosphate and hexose phosphate from the chloroplast stroma.

This implementation is a variant of the classical Pettersson & Ryde-Petersson CBB cycle model. That original model was formulated as a differential-algebraic system (DAE): several near-equilibrium reactions (e.g. triose phosphate isomerase, the aldolase and transketolase steps, the pentose phosphate isomerase/epimerase, and phosphoglucomutase/PGI) were treated as instantaneous equilibria and enforced via algebraic constraints rather than rate equations. Here, each of those equilibrium constraints is instead replaced by a reversible mass-action rate law with a very fast rate constant (kre_*), driving the corresponding pool ratios to the same equilibrium constant (keq_*) dynamically rather than algebraically. This turns the DAE into a plain ODE system, at the cost of introducing stiffness from the disparate time scales of the fast quasi-equilibrium reactions and the slower, kinetically-limited steps (rubisco carboxylase, FBPase, SBPase, phosphoribulokinase, and the stromal export reactions).

This CBB cycle formulation is, in turn, the basis for the Calvin cycle in several later, more comprehensive photosynthesis models, including Matuszynska 2019 (10.1111/ppl.12962) and Saadat 2021 (10.3389/fpls.2021.750580).

Model definition