Table 1.

Acronyms, definitions, and variables. Quantities with dimensions are consistent with assimilation (μmol m⁻² s⁻¹).

A	Net assimilation
ALA, ALA	Alanine, ALA diffusion rate
ASP, ASP	Aspartate, ASP diffusion rate
ATP, ATPTOT, ATPBS, ATPM	Adenosine triphosphate, rate of ATP demand: total, in the BS, or in the M respectively
BS	Bundle sheath
CCM	Carbon-concentrating mechanism
CEF	Cyclic electron flow
CS, CSTOT, CSBS, CSM	Carbohydrate synthesis, rate of carbohydrate synthesis: total, in the BS, or in the M, respectively
DHAP, DHAP	Dihydroxyacetone phosphate, DHAP diffusion rate, respectively
DHAP RPP, DHAPRPPM, DHAPRPPBS	Rate of DHAP entering the RPP, in the M, or in the BS respectively
F	Rate of photorespiratory CO2 release $F=0.5 V_{\text{O}}$
f C, fO, fRLIGHT, fPR, fCS, fPPDK	Input parameters defining, relative to total, the BS fraction of: Rubisco rate of carboxylation, Rubisco rate of oxygenation, Respiration in the light, PGA reduction, carbohydrate synthesis, and PPDK activity, respectively
GA	Gross assimilation (A + RLIGHT)
GDC, GDCTOT, GDCBS, GDCM	Glycine decarboxylase, GDC reaction rate: total, in the BS, or in the M, respectively
GLA	Glycolic acid
GLY, GLY	Glycine, GLY diffusion rate, respectively
L	Leak rate, i.e. magnitude of CO2 flux diffusing out of the BS, Eqn S19
LEF	Linear electron flow (flow of electrons derived from the photo-oxidation of water)
M	Mesophyll
MAL, MAL	Malate, MAL diffusion rate, respectively
MDH, MDHBS , MDHM	Malate dehydrogenase, MDH reaction rate in the BS or M, respectively
ME, ME	Malic enzyme, ME reaction rate, respectively
NADPH TOT , NADPH BS	NADPH demand: total or in the BS, respectively
OAA, OAA	Oxaloacetate, OAA diffusion rate, respectively
PCO	Photosynthetic carbon oxygenation (cycle), also known as photorespiratory cycle
PEP	Phosphoenolpyruvate
PEP, PEP	Phosphoenolpyruvate, PEP diffusion rate, respectively
PEPC	Phosphoenolpyruvate carboxylase
PEPCK, PEPCK	Phosphoenolpyruvate carboxykinase, PEPCK reaction rate, respectively
PGA, PGA	3-phosphoglyceric acid, PGA diffusion rate, respectively
PGLA	2-phosphoglycolic acid
PPDK, PPDK	Pyruvate phosphate dikinase, PPDK reaction rate, respectively
PR, PRTOT, PRBS, PRM	PGA reduction, reduction rate: total, in the BS, or in the M, respectively
PYR, PYR	Pyruvate, PYR diffusion rate, respectively
R	Rate of CO2 and NH3 release in the BS associated with the operation of the C2 shuttle, Eqn S16
R LIGHT , R LIGHT BS , R LIGHT M	Respiration in the light: total, in the BS, or in the M, respectively
r O/C	Input defining leaf-level Rubisco rate of oxygenation relative to carboxylation, also referred to as φ or VO/VC
r PEPCK	input parameter defining the activity of PECK relative to VP
RPP	Reductive pentose phosphate (cycle); also known as Calvin‒Benson‒Bassham cycle or photosynthetic carbon reduction cycle
Rubisco	RuBP carboxylase oxygenase
RuBP	Ribulose–1,5–bisphosphate
RuP	Ribulose–5–phosphate
RuP phosp, RuPphosp M, RuPphosp BS	Rate of RuP phosphorylation: total, in the M, or in the BS, respectively
SER, SER	Serine, SER diffusion rate, respectively
SMA	Stoichiometric model of assimilation
T, T	Transamination, Transamination rate
V C, VCM, VCBS	Rubisco rate of carboxylation: total, in the M, or in the BS, respectively
V O, VOM, VOBS	Rubisco rate of oxygenation: total, in the M, or in the BS, respectively
V P	PEPC rate of carboxylation
αKG	alpha–Ketoglutarate