Fig. 2. Barriers to CO₂ diffusion out of the pyrenoid matrix enable an effective PCCM driven only by intercompartmental pH differences.

a–i, A model with no barrier to CO₂ diffusion out of the pyrenoid matrix (a–c) is compared to a model with thylakoid stacks slowing inorganic carbon diffusion in the stroma (d–f) and a model with an impermeable starch sheath (g–i) under air-level CO₂ (10 µM cytosolic). a,d,g, Schematics of the modelled chloroplast. b,e,h, Heatmaps of normalized CO₂ fixation flux, defined as the ratio of the total Rubisco carboxylation flux to its maximum if Rubisco were saturated, at varying LCIA^C-mediated chloroplast membrane permeabilities to HCO₃⁻ and varying LCIB rates. The BST-mediated thylakoid membrane permeability to HCO₃⁻ is the same as in Fig. 1c,d. For e and h, dashed black curves indicate a normalized CO₂ fixation flux of 0.5. c,f,i, Overall fluxes of HCO₃⁻ (left) and CO₂ (middle) into the chloroplast, normalized by the maximum CO₂ fixation flux if Rubisco were saturated, at varying LCIA^C-mediated chloroplast membrane permeabilities to HCO₃⁻ and varying LCIB rates. Negative values denote efflux out of the chloroplast. The inorganic carbon (Ci) species with a positive influx is defined as the Ci source (right). Axes are the same as in b, e and h.