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Biology — Calvin Cycle (Petri Net)

Carbon fixation regenerating RuBP.

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Calvin cycle (carbon fixation)CO2≤3RuBP≤39ATP≤96NADPH≤6Glycerate-3-P≤3Triose phosphate≤3Rubisco fixes CO2enabledReduce GP to TPRegenerate RuBPReachable markings206 places · 3 transitionsTerminatesyes1 final markingLive transitions3/3every one firesSafe places0/6bound ≤ 1 tokenConservation laws13 places in none20 reachable markings, 6 places, 3 transitions — bounded, deadlock-free, and every transition fires: it stops at 1 final marking, each of them a net that used up what it was give…This net runs to completion and stops at RuBP 3 · ATP 6 · NADPH 3. Nothing is enabled there, and it is not a deadlock: every transition still short of an input is short of one that NOTHING in this net pro…Conservation law: RuBP + Glycerate-3-P + Triose phosphate = 3, at every reachable marking, for ever. No firing of any transition can change it — that is proved from the incidence matrix, not observed over…3 places are weighted by no conservation law — `CO2`, `ATP`, `NADPH`. Nothing in the structure of this net holds what they hold constant, so their token count is free to drift with the firing sequence. Th…

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title Calvin cycle (carbon fixation)

place CO2 tokens 3 "CO2"
place RuBP tokens 3 "RuBP"
place ATP tokens 9 "ATP"
place NADPH tokens 6 "NADPH"
place GP tokens 0 "Glycerate-3-P"
place TP tokens 0 "Triose phosphate"
transition fix "Rubisco fixes CO2"
transition reduce "Reduce GP to TP"
transition regen "Regenerate RuBP"

CO2 -> fix
RuBP -> fix
fix -> GP
GP -> reduce
ATP -> reduce
NADPH -> reduce
reduce -> TP
TP -> regen
regen -> RuBP