Bioreactor Simulation for Cultivated Meat Production

This repository contains the driver code for the two-phase flow simulation of a rocking bioreactor, implemented in the Basilisk open-source CFD platform. This collaborative work is conducted at the intersection between the Scientific Computing Group at the University of Warwick led by Dr. Radu Cimpeanu and the Harris Lab at Brown University led by Prof. Daniel Harris, with Dr. Minki Kim (Brown University) as lead developer. The open-access publication is available at doi: 10.1016/j.ijmultiphaseflow.2025.105375, while the associated preprint for this work is available on arXiv: 2504.05421.

📌 Features:

✅ Liquid-gas dynamics with embedded solid boundaries inside a two-dimensional rocking bioreactor
✅ Tracer advection/diffusion for evaluating mixing efficiency
✅ Oxygen transport, including advection, diffusion and gas-to-liquid interfacial transfer
✅ Body acceleration in a non-inertial frame of reference, accounting for gravity, Coriolis, and centrifugal effects

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🛠️ Installation

1. Requirements

• Basilisk (compiled with qcc)
• C compiler
• Gnuplot / ffmpeg (for visualizing results)

sudo apt install gnuplot imagemagick ffmpeg graphviz valgrind gifsicle pstoedit

2. Clone the repo

git clone https://github.com/rcsc-group/BioReactor
cd DriverCodes

3. Installing Basilisk

The code relies on Basilisk to solve the Navier–Stokes equations. Please refer to the Basilisk installation page for detailed setup instructions.

4. Copy and paste the header files and compile the main code

• Copy the four header files (draw3.h, henry_oxy2.h, utils2.h, and view3.h) into the src folder of the Basilisk source directory.
• Run the shell script using: sh BioReactor.sh
• The shell script runs the executable file: ./Bioreactor L_bio ANGLE RPM
  • L_bio: Reference length scale in meters (e.g., 0.25)
  • ANGLE: Rocking angle in degrees (e.g., 7)
  • RPM: Rocking frequency in RPM (e.g., 32.5)

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⚙️ Key Simulations Configuration Options

Modify flags at the top of main.c to enable features:

• EMBED: Enable embedded boundary for solid geometry
• OXYGEN: Enable oxygen concentration simulation
  • OXYGEN_CIRCLE: Initial distribution (circle) of oxygen (if OXYGEN == 1)
  • OXYGEN_AIR: Initial distribution (air side) of oxygen (if OXYGEN == 1)
• TRACER: Enable passive tracer simulation
  • HORIZONTAL_MIXL: Initial distribution (left side) of tracer: Horizontal mixing (if TRACER == 1)
  • HORIZONTAL_MIXR: Initial distribution (right side) of tracer: Horizontal mixing (if TRACER == 1)
  • VERTICAL_MIXUP: Initial distribution (top side) of tracer: Vertical mixing (if TRACER == 1)
  • VERTICAL_MIXDOWN: Initial distribution (bottom side) of tracer: Vertical mixing (if TRACER == 1)
• ACCELERATION: Enable acceleration (rocking motion)
• NORMCAL: Calculate statistics (norms)
• FIGURES: Save figures
• VIDEOS: Save videos
• OUT_FILES: Output full fields
• OUT_SPECIFIC_TIME: Output data at specific time ranges
• OUT_INTERFACE: Save interface geometry

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📁 Folder Structure

.                        
├── main.c                 # Main bioreactor simulation code
├── henry_oxy2.h           # Header for oxygen transport functionality
├── view3.h, utils2.h      # Visualization and utility functions (customized)
├── Data_all/              # Simulation output (velocity, tracer, oxygen, etc.)
├── Fig_vol/, Fig_tr/, ... # Saved PNG images for different fields
├── logstats.dat           # Performance and runtime log
├── normf.dat              # Velocity/vorticity/volume fraction norms over time
├── vol_frac_interf.dat    # Interface volume fraction statistics
├── tr_oxy.dat             # Integrated tracer and oxygen values

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📊 Outputs

Generates:

• Data_all/*.txt: all field variables and interface geometries for the chosen simulation times
• .dat files of statistics (e.g., vorticity, velocity, volume fraction, etc.) and performance logs
• *.mp4 videos (vorticity, tracer, oxygen, volume fraction)
• *.png figures (vorticity, tracer, oxygen, volume fraction)

Video generation is quite resource-intensive, and may be switched on and off depending on the stage of the development cycle. Beyond production runs purposes, we occasionally found these useful for debugging as well, however the frame rate can be adapted accordingly via the dt_video variable specification.

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📌 References

If you use this code for research or teaching, please cite Basilisk and include a reference to this repository.

• GitHub Repo: https://github.com/yourusername/bioreactor-basilisk
• Authors: Minki Kim, Dan M. Harris, Radu Cimpeanu
• License: MIT License

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🧑 Contributing

Please feel free to:

• Fork this repo
• Open issues
• Submit pull requests