https://github.com/upc-ghs/bioreactpy

Open-source tool for bio-reactive flow in porous media
https://github.com/upc-ghs/bioreactpy

Last synced: 18 days ago
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Open-source tool for bio-reactive flow in porous media

• Host: GitHub
• URL: https://github.com/upc-ghs/bioreactpy
• Owner: upc-ghs
• License: mit
• Created: 2023-07-24T15:18:06.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2024-11-26T10:00:50.000Z (27 days ago)
• Last Synced: 2024-11-26T11:00:52.898Z (27 days ago)
• Language: Python
• Size: 98.6 KB
• Stars: 2
• Watchers: 1
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# bioReactPy

A simulation tool for bio-reactive flow in porous media.

BioReactPy currently has the following features:

- Discretization of the Stokes equations of flow;

- Coupled flow and reactive transport, based on the microcontinuum approach;

- Fully coupled reactive transport and biomass-nutrient growth treated with Monod equation.

For more information, see the provided benchmarks and application tests.

BioReactPy is developed by Michele Starnoni, Hydrogeology Group (GHS) at the Universitat Politecnica de Catalunya (UPC), Barcelona, Spain. The software is developed under the Marie Sklodowska-Curie grant agreement No. 101063414 – CO2FOREARM Fundamental study of CO2 storage through microbially enhanced carbon mineralization.

## CITING

If you use BioReactPy in your research, we ask you to cite the following publication

Starnoni M., Dawi M. A., Sanchez-Vila X. (2024). BioReactPy: An open-source software for simulation of microbial-mediated reactive processes in porous media, Applied Computing and Geosciences, [doi: 10.1016/j.acags.2024.100166](https://doi.org/10.1016/j.acags.2024.100166).

## RELATED PUBLICATIONS

Starnoni, M., Dawi, M. A., & Sanchez-Vila, X. (2024). BioReactPy: An open-source software for simulation of microbial-mediated reactive processes in porous media. Applied Computing and Geosciences, 22, 100166. [doi: 10.1016/j.acags.2024.100166](https://doi.org/10.1016/j.acags.2024.100166)

Starnoni, M., & Sanchez-Vila, X. (2024). Pore-scale modelling of subsurface biomineralization for carbon mineral storage. Advances in Water Resources, 185, 104641. [doi: 10.1016/j.advwatres.2024.104641](https://doi.org/10.1016/j.advwatres.2024.104641)

Starnoni, M., Sanchez‐Vila, X., Recalcati, C., Riva, M., & Guadagnini, A. (2024). Process modeling of mineral dissolution from nano‐Scale surface topography observations. Geophysical Research Letters, 51(16), e2024GL110030. [doi: 10.1029/2024GL110030](https://doi.org/10.1029/2024GL110030)

Dawi, M. A., Starnoni, M., Porta, G., & Sanchez-Vila, X. (2024). Pore-scale coupling of flow, biofilm growth, and nutrient transport: A microcontinuum approach. Water Resources Research, 60, e2024WR038393 [doi:10.1029/2024WR038393](https://doi.org/10.1029/2024WR038393)

Runscripts for all simulations presented in these papers can be found in the associated Data Availability Statements.

## INSTALLATION

Installation of BioReactPy is straightforward: simply download from github.

## GETTING STARTED

Confer to the examples and application tests.