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TST: Add test for transition/cycle/operational flux relations #67

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nawtrey opened this issue Dec 16, 2022 · 3 comments
Open

TST: Add test for transition/cycle/operational flux relations #67

nawtrey opened this issue Dec 16, 2022 · 3 comments
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testing Testing/verification related improvements/bugs

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@nawtrey
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nawtrey commented Dec 16, 2022

In T.L. Hill's book, "Free Energy Transduction and Biochemical Cycle Kinetics", he discusses simple relationships between transition fluxes, net cycle fluxes, and operational fluxes. Specifically, equations 3.3 and 3.4 show flux identities for a simple model. A test should be added that verifies these identities to further ensure consistency between various flux calculation types.

Test should be written to compare the output expressions, which can be compared with the normalization factor Sigma.

@nawtrey nawtrey added the testing Testing/verification related improvements/bugs label Dec 16, 2022
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nawtrey commented Dec 16, 2022

Additionally equations 3.5 and 3.6 show several relationships that should all hold if everything is internally consistent.

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nawtrey commented Mar 1, 2024

See the kda-examples PR #18 for example code comparing operational fluxes generated using both net cycle fluxes and net transition fluxes.

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nawtrey commented Aug 10, 2024

With GH-83 merged this is already more tractable, but I think we will wait until the net cycle fluxes are added (issue #57) to complete this.

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