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

Jung, Heewon; Song, Hyun-Seob; Meile, Christof

doi:10.5194/gmd-16-1683-2023

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

Journal Article · Mon Mar 27 00:00:00 EDT 2023 · Geoscientific Model Development (Online)

DOI:https://doi.org/10.5194/gmd-16-1683-2023· OSTI ID:1963515

Jung, Heewon; Song, Hyun-Seob;

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 analysis, 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 automaton 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.

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Research Organization:: California Institute of Technology (CalTech), Pasadena, CA (United States)

Sponsoring Organization:: USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0016469; SC0020373

OSTI ID:: 1963515

Alternate ID(s):: OSTI ID: 2420519

Journal Information:: Geoscientific Model Development (Online), Journal Name: Geoscientific Model Development (Online) Journal Issue: 6 Vol. 16; ISSN 1991-9603

Publisher:: Copernicus GmbHCopyright Statement

Country of Publication:: Germany

Language:: English

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