Continuation checkpoint: effective reaction models and finite numerical evidence

9 October 2026. Previous turn: random-SAT research and software progress, pushed/deployed at 29d33e8547f555e6be59af062d3c4b7f67906bba. This turn: progress through two selected family-149 manuscripts, a bounded model audit, independent graph/algebra controls and conventional numerical comparisons. The full perpetual goal stays active; no completion or blocked audit applies.

Findings that change the opportunity

The newer mass-action paper asserts one eventual compact convex absorber per fixed positive stoichiometric class and positive fixed rates; entry time can depend on initial state. Selected formal scope covers older initial-state-dependent all-time bounds. The affine construction uses finite slopes and compactness-based thresholds; no practical numerical absorber, entry time or full source proof was obtained. Parts of the affine induction/gluing remain unread; precise extents are recorded.

The prototype normalizes explicit rate conventions, zero-rate reactions, self-loops and parallel reactions before checking the effective complex graph. Supplied nonnegative conservation vectors can give exact coordinate upper bounds. Exact face inequalities can certify supplied positive invariant rectangles; an initial state outside a valid rectangle receives no all-time or entry-time claim. No SBML/Catalyst import, unit bridge, physical process or stochastic extension is verified.

The A<->2A fixture shows identical nominal rates produce equilibria one versus two under different factorial conventions. Setting the reverse rate to zero leaves two drawn arrows but yields the unbounded equation A'=A. A coarse explicit Euler step can produce a negative value even when the continuous model has an independently verified positive invariant interval. These distinct errors must not be conflated with source-theorem validity.

Evidence and current editions

• Report, comparison figure, fixture summary.
• 702 finite controls: all 64 directed edge subsets on three complexes, sixty stored generated models, eleven named fixtures and parser/output preservation. NetworkX 3.4.2 and SymPy 1.13.1 provide independent graph/algebra comparisons.
• Eleven numerical controls: SciPy 1.18.1 DOP853 matches eight logistic analytic cases with maximum observed error below 6.29e-11; sampled dimer mass drift is below 3.56e-15. These are floating diagnostics, not validated enclosures. Total new controls: 713, all passing.
• A transcribed public Catalyst tutorial graph has eight species, seven complexes, rank five and two linkage classes. It fails weak reversibility yet admits a checked positive conservation vector giving finite coordinate upper bounds. Rates/initial states were chosen for the experiment; it is not a customer model. Julia and libSBML were absent; no package installation or live Catalyst execution occurred.
• Manifest: 34 files, including five inert tooling copies, and eleven source hashes. Ledger v19: 53 selected-section manuscripts, 158 source hashes and 666 pending/earlier-not-imported. Four PDF pages visually inspected.
• Dossier 013 v2, catalog v31, directory v26, coverage v31.
• 42 utilities v28, priorities v28, feasibility v26: 32,820 controls in 67 reports. Facility planning remains first; reaction assurance stays low confidence until a useful real import path and recurring buyer problem are validated.

Publication and continuation

Integrity v31 passed with zero issues: 32,820 controls, 162 current Python syntax checks, 1,553 local links, 158 reading-source hashes and all 34 new artifact/eleven source hashes. The subsequent build checks all rendered routes.

Check rendered routes, then push normally to strykesg/mathideas and verify Dokploy application 6yFD3JCmfp0uZcCuJGex2 serves the new report, figure, exact certificate and manifest bytes. No deletion, force push, outreach, purchases or paid compute occurred.

The 02:56:08 UTC upstream check still governs cadence: no repeat before 03:56:08 UTC without a signal. Source remains at fd4aeeb2ee4fc729c18d98444fed42fd0529eeeb. The existing hourly heartbeat stays active while the app/host are available.

Continue substantive manuscript reviews, such as tensor-network representation/compute feasibility or inverse-problem identifiability, and practical first-product gaps. Stronger independently checked facility-capacity bounds and standard-browser export completion remain open. Real buyer studies require permissioned data; no customer validation is inferred from these technical fixtures.