Modeling biofilm morphology along a transverse mixing zone in porous media at the pore scale

This work describes the development and application of a model to simulate substrate transport, biodegradation, and biofilm growth at the pore scale. Since field observations indicate that bioactive zones are located along plume boundaries where the contaminant mixes with nutrients in the ambient groundwater, we simulate a 2D porous medium in which biofilm growth is controlled by transverse mixing between the electron acceptor and donor.In the model, biofilms are initialized as thin films located on surfaces of cylinders that are arranged in a staggered packing. The lattice Boltzmann method is used to solve for the steady flow field, employing bounce-back boundary conditions to enforce no-slip and zero flux conditions at solid-fluid interfaces. The substrates enter the system completely unmixed and are degraded only in the presence of microbes. Transport and reaction of the solutes is modeled by a finite volume discretization of the advection-diffusion-reaction equation. The Newton-Raphson method is used to linearize the coupled equations. Biofilms are allowed to evolve by means of a cellular automata algorithm.Characteristics of simulated biofilms are qualitatively compared to biofilms from a micromodel experiment. The effects of reaction rate parameters and biofilm shear strength on biofilm length within a pore, thickness, and location of growth within the porous media are explored.