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C-CoMP-STC / GEM-mit1002

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Fix false proton gradient generating cycles. #44

Closed hgscott closed 7 months ago

hgscott commented 8 months ago

I found a common type of erroneous energy generating cycle, a pair of transporters that move protons around for free, e.g. this one.

How do I fix these?

I know Devlin had a solution to this, it may have been his leakage reactions, but I don't remember for sure. The leakage reactions are for pairs of Metabolite objects that represent the same real-world compound in different subcellular compartments. Devlin's code created a new reversible reaction that reversibly interconverts them with a flux of up to +/- bound (which should be a relatively small non-negative non-zero number). This represents "leakage" of this metabolite across the boundary separating the two compartments.

I'll ask Devlin.

hgscott commented 8 months ago

Maybe a first step is to make a minimal model with this cycle, and show that is generates ATP. Then I can try to add the leakage flux to fix it.

hgscott commented 8 months ago

I removed reaction 05206, and then the MEMOTE function didn't find any cycles anymore.

hgscott commented 7 months ago

Daniel says the ion transporters shouldn't effect the kind of metabolism we care about anyways.