Rocking Bioreactor 2D
📖 Documentation: rcsc-group.github.io/multi-fidelity-bioreactor
Fidelity-10 simulation of the rocking bioreactor (θ=7°, 32.5rpm, lab frame — tank rocks, water finds its level), colored by |u|.
Two-phase CFD solver for a rocking bioreactor, implemented in Basilisk and
forked from Kim, Harris, and Cimpeanu's original driver code
(rcsc-group/BioReactor). This is not the code behind
the paper cited below — it has since diverged with checkpoint-restart chaining, multi-harmonic
and horizontal forcing, and a multi-fidelity Bayesian optimization suite, and matching the
paper's own published numbers is a separate, ongoing effort (see
validating against Kim et al.).
The solver resolves two-phase (VOF) hydrodynamics and dissolved-oxygen transport
(Henry's law), producing kLa (volumetric oxygen mass-transfer coefficient) and
shear-stress KPIs as optimization objectives. A multi-fidelity Bayesian
optimization suite sits on top — a KRR-LR-GPR surrogate trained on cheap
low-fidelity screening runs plus a smaller number of expensive high-fidelity
corrections, with an Expected Improvement acquisition function choosing where
to sample next.
Quickstart
pip install uv && uv sync # Python dependencies
make build # compiles build/BioReactor (needs Basilisk's qcc on PATH)
uv run python -m pytest tests/ # fast unit suite, ~20s, no binary or SLURM needed
Documentation
Full setup, workflow tutorials, and reference material live on the
documentation site
(source in docs_site/, built with MkDocs;
run uv run --group docs mkdocs serve for a live local preview — auto-deployed
to Pages on every push to main):
References
