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Biology — Petri Net: Calvin Cycle

Carbon fixation regenerating RuBP (a source-fed cycle).

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Calvin cycle (carbon fixation)CO2≤3RuBP≤3RuBisCO fixationenabled3-PGA≤3Reduction (ATP, NADPH)G3P≤3RegenerationReachable markings204 places · 3 transitionsTerminatesyes1 final markingLive transitions3/3every one firesSafe places0/4bound ≤ 1 tokenConservation laws11 place in none20 reachable markings, 4 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 wa…This net runs to completion and stops at RuBP 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 produces, so t…Conservation law: RuBP + 3-PGA + G3P = 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 a search.1 place is weighted by no conservation law — `CO2`. Nothing in the structure of this net holds what it holds constant, so its token count is free to drift with the firing sequence. That is where an…

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title Calvin cycle (carbon fixation)

place CO2 tokens 3 "CO2"
place RuBP tokens 3 "RuBP"
transition fix "RuBisCO fixation"
place PGA tokens 0 "3-PGA"
transition reduce "Reduction (ATP, NADPH)"
place G3P tokens 0 "G3P"
transition regen "Regeneration"

CO2 -> fix
RuBP -> fix
fix -> PGA
PGA -> reduce
reduce -> G3P
G3P -> regen
regen -> RuBP