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

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