[Epic] Bioreactor digital-twin demonstrator

[andres9403]

Goal

Deliver a bioreactor digital-twin demonstrator: a baseline mechanistic model,
an estimation workflow, and a reproducible case study.

Status: scope decision required before work begins

A full-time bioreactor developer is starting, and the scope of this deliverable
is not yet agreed. Without a decision, that capacity is spent undirected.

Decision deadline: end of Month 2.

Options

Option	Content	Estimate
Reduced (recommended default)	Baseline mechanistic model + estimation + case study. dFBA and hybrid/surrogate kinetics as stretch	12-20 FTE-wk
Full	Adds dynamic flux balance analysis and hybrid/surrogate kinetics hooks	12-20 FTE-wk, feasible only with prior dFBA expertise

If no decision is recorded by the deadline, the reduced scope applies by default
and that is recorded as a decision-by-default.

Why this is a good greenfield assignment

area:bioreactors is currently used on exactly one issue (#14, a scoping issue).
There is no bioreactor code in the package. That makes this the one workstream
with no conflict against the MultiPhaseVessel refactor (#148) and no
dependency on the correctness backlog - new files only. It is the only
demonstrator not queued behind existing defect work.

Acceptance criteria (reduced scope)

• Baseline dynamic bioreactor model: growth, substrate consumption, product formation, dissolved oxygen
• Fed-batch and continuous (chemostat) operating modes
• Kinetics interface that allows mechanistic, hybrid, or surrogate substitution
• Parameter-estimation workflow on public or openly shareable data
• Uncertainty reporting for estimated parameters
• Reproducible notebook and documentation page
• Unit tests; units annotated per AGENTS.md

Interim direction (useful under either option)

Refine #14 into a design spec with acceptance criteria, and build the greenfield
module skeleton with tests. Both survive whichever scope is chosen.

Dependencies

• Scope decision (this issue)
• Integration contract for parallel development workflows #150 integration contract, before the first commit