Loading [MathJax]/jax/output/HTML-CSS/fonts/TeX/fontdata.js
Preprints
https://doi.org/10.5194/egusphere-2022-1016
https://doi.org/10.5194/egusphere-2022-1016
04 Oct 2022
 | 04 Oct 2022

CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics

Heewon Jung, Hyun-Seob Song, and Christof Meile

Abstract. Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes, and that can integrate genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions. The model couples a Lattice-Boltzmann implementation of Navier-Stokes (flow) and advection-diffusion-reaction (mass conservation) equations. Reaction formulations can include both kinetic rate expressions and flux balance analyses, thereby integrating reactive transport modeling and systems biology. We also show that the use of surrogate models such as neural network representations of in silico cell models can speed up computations significantly, facilitating applications to complex environmental systems. Parallelization enables simulations that resolve heterogeneity at multiple scales, and a cellular automata module provides additional capabilities to simulate biofilm dynamics. The code thus constitutes a platform suitable for a range of environmental, engineering and – potentially – medical applications, in particular ones that involve the simulation of microbial dynamics.

Publisher's note: Copernicus Publications remains neutral with regard to jurisdictional claims made in the text, published maps, institutional affiliations, or any other geographical representation in this preprint. The responsibility to include appropriate place names lies with the authors.
Share

Journal article(s) based on this preprint

27 Mar 2023
CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics
Heewon Jung, Hyun-Seob Song, and Christof Meile
Geosci. Model Dev., 16, 1683–1696, https://doi.org/10.5194/gmd-16-1683-2023,https://doi.org/10.5194/gmd-16-1683-2023, 2023
Short summary
Download

The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.

Short summary
Microbial activity responsible for many chemical transformations depends on environmental...
Share