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Biology — Krebs Cycle (Petri Net)

Oxaloacetate is regenerated as CO2 is released.

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Krebs cycle (simplified)w=2Acetyl-CoA≤2Oxaloacetate≤1Citrate≤1CO2 released≤4Acetyl-CoA + OAA -> c…enabledCitrate -> OAA + 2 CO2Reachable markings54 places · 2 transitionsTerminatesyes1 final markingLive transitions2/2every one firesSafe places2/4bound ≤ 1 tokenConservation laws2every place covered5 reachable markings, 4 places, 2 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…`oxidise -> CO2` is written 2 times. The weights ADD, so the pair moves 2 tokens per firing — which is exactly what a Petri net means by repeated arcs, and how a stoichiometric coefficient is writt…Place `CO2 released` has no outgoing arc: every token that reaches it stays there. A counter of completed work is exactly this, and so is a token leak — the two are the same drawing, and only the t…This net runs to completion and stops at Oxaloacetate 1 · CO2 released 4. Nothing is enabled there, and it is not a deadlock: every transition still short of an input is short of one that NOTHING i…Conservation law: 2·Acetyl-CoA + 2·Citrate + CO2 released = 4, at every reachable marking, for ever. No firing of any transition can change it — that is proved from the incidence matrix, not observ…Conservation law: Oxaloacetate + Citrate = 1, 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.

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title Krebs cycle (simplified)

place AcetylCoA tokens 2 "Acetyl-CoA"
place OAA tokens 1 "Oxaloacetate"
place Citrate tokens 0 "Citrate"
place CO2 tokens 0 "CO2 released"
transition condense "Acetyl-CoA + OAA -> citrate"
transition oxidise "Citrate -> OAA + 2 CO2"

AcetylCoA -> condense
OAA -> condense
condense -> Citrate
Citrate -> oxidise
oxidise -> OAA
oxidise -> CO2
oxidise -> CO2