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Highlights • A complex and sophisticated mathematical model at the pore scale has been developed for simulating biofilm growth, fluid flow, and the dissolution of immobile non-aqueous-phase-liquids (NAPLs). • A series of numerical simulations were conducted to investigate the mechanisms involved in the enhanced dissolution of the NAPLs due to microbial activity. • The model can be used to validate assumptions which are typically invoked to simplify upscaling of NAPL dissolution to larger scales. Abstract In this paper, we introduce a pore-scale model to study the interaction between biofilm growth and non-aqueous-phase-liquid (NAPL) dissolution. Liquid flow and dissolved NAPL transport are coupled with a biofilm growth model to correctly describe the complex dynamics of the processes including fluid flow, NAPL dissolution/biodegradation and biofilm growth. Fluid flow is simulated using an immersed boundary-lattice Boltzmann (IB-LB) model; while solute transport is solved by a cut-cell finite volume method (FVM). A uniform dissolution approach is also adopted to capture the temporal evolution of trapped blobs. Spatio-temporal distributions of the biomass are investigated using a cellular automaton algorithm combined with the immersed boundary method (IBM). Simulations focused on NAPL dissolution in both abiotic and biotic conditions are conducted to assess the capability of the model. In abiotic conditions, we analyze the effects of the hydrodynamic regimes and the spatial distribution of NAPL blobs on the dissolution rate under different assumptions (i.e., blob size and Péclet number). In biotic conditions, a series of impact factors are also investigated (i.e., spatial distribution, reaction kinetics and NAPL-induced toxicity). Finally, the current model is used to evaluate the pore scale relevance of a local equilibrium assumption between fluid phase and biofilm phase in the vicinity of the NAPL source. [ABSTRACT FROM AUTHOR]

• A coupling algorithm of flow at pore-scale and porous medium permeability at REV-scale. • Spatial and temporal characteristics of microbial growth at pore-scale. • The equivalent porosity change with time caused by microbial growth. • The linear relationship between clogging periods at REV-scale and pore-scale. In this study, a novel algorithm coupling the flow at the pore and representative elementary volume (REV) scales was developed to analyze the effect of microbial growth at the pore scale on the permeability decay of porous media at the REV scale. This provides a new method for investigating microbial clogging in porous media. At the pore scale, an immersed boundary-lattice Boltzmann model was used to simulate the flow field and solute transportation in porous media, and the cellular automata (CA) model was employed to investigate microbial growth. According to Ergun's empirical relationship, the equivalent porosity change at the pore scale caused by microbial growth was calculated and used in a generalised seepage model describing the fluid flow in the porous medium at the REV scale. First, the microbial growth experiments were conducted to validate the coupling algorithm. Second, the spatial and temporal characteristics of microbial growth at the pore scale were analyzed. Third, we investigated the effects of nutrient inlet concentrations and pH on microbial growth at the pore scale and the macroscopic permeability properties of porous media. The main results are as follows. (1) Microbial growth changes the local porosity and dominant flow path. Spatial non-uniformity in microbial growth depends on the availability of nutrients in the dominant flow path. (2) The discrepancy in microbial growth under different nutrient inlet concentrations was gradually amplified from the pore scale to the REV scale. (3) The microbial clogging period was the shortest at a pH of 6.7. When the pH was >6.7, the microbial clogging period slightly increased at a rate of 6.1 h/pH. When the pH was <6.7, the microbial clogging period increased significantly with decreasing pH at a rate of 20.0 h/pH. (4) A linear relationship was observed between the microbial clogging periods at the REV and pore scales, which enriches the theory about microbial clogging in porous medium. [ABSTRACT FROM AUTHOR]

In this paper, we present a two-dimensional pore-scale numerical model to investigate the main mechanisms governing biofilm growth in porous media. The fluid flow and solute transport equations are coupled with a biofilm evolution model. Fluid flow is simulated with an immersed boundary–lattice Boltzmann model while solute transport is described with a volume-of-fluid-type approach. A cellular automaton algorithm combined with immersed boundary methods was developed to describe the spreading and distribution of biomass. Bacterial attachment and detachment mechanisms are also taken into account. The capability of this model to describe correctly the couplings involved between fluid circulation, nutrient transport and bacterial growth is tested under different hydrostatic and hydrodynamic conditions (i) on a flat medium and (ii) for a complex porous medium. For the second case, different regimes of biofilm growth are identified and are found to be related to the dimensionless parameters of the model, Damköhler and Péclet numbers and dimensionless shear stress. Finally, the impact of biofilm growth on the macroscopic properties of the porous medium is investigated and we discuss the unicity of the relationships between hydraulic conductivity and biofilm volume fraction. [ABSTRACT FROM AUTHOR]

Abstract: The concentration of greenhouse gases – particularly carbon dioxide (CO2) – in the atmosphere has been on the rise in the past decades. One of the methods which have been proposed to help reduce anthropogenic CO2 emissions is the capture of CO2from large, stationary point sources and storage in deep geological formations. The caprock is an impermeable geological layer which prevents the leakage of stored CO2, and its integrity is of utmost importance for storage security. Due to the high pressure build-up during injection, the caprock in the vicinity of the well is particularly at risk of fracturing. Biofilms could be used as biobarriers which help prevent the leakage of CO2 through the caprock in injection well vicinity by blocking leakage pathways. The biofilm could also protect well cement from corrosion by CO2-rich brine. The goal of this paper is to develop and test a numerical model which is capable of simulating the development of a biofilm in a CO2 storage reservoir. This involves the description of the growth of the biofilm, flow and transport in the geological formation, and the interaction between the biofilm and the flow processes. Important processes which are accounted for in the model include the effect of biofilm growth on the permeability of the formation, the hazardous effect of supercritical CO2 on suspended and attached bacteria, attachment and detachment of biomass, and two-phase fluid flow processes. The model is tested by comparing simulation results to experimental data. [Copyright &y& Elsevier]

Abstract: A new simulator is developed for the prediction of the rate and pattern of growth of biofilms in granular porous media. The biofilm is considered as a heterogeneous porous material that exhibits a hierarchy of length scales. An effective-medium model is used to calculate the local hydraulic permeability and diffusion coefficient in the biofilm, as functions of the local geometric and physicochemical properties. The Navier–Stokes equations and the Brinkman equation are solved numerically to determine the velocity and pressure fields within the pore space and the biofilm, respectively. Biofilm fragments become detached if they are exposed to shear stress higher than a critical value. The detached fragments re-enter into the fluid stream and move within the pore space until they exit from the system or become reattached to downstream grain or biofilm surfaces. A Lagrangian-type simulation is used to determine the trajectories of detached fragments. The spatiotemporal distributions of a carbon source, an electron acceptor and a cell-to-cell signaling molecule are determined from the numerical solution of the governing convection–diffusion–reaction equations. The simulator incorporates growth and apoptosis kinetics for the bacterial cells and production and lysis kinetics for the EPS. The specific growth rate of active bacterial cells depends on the local concentrations of nutrients, mechanical stresses, and a quorum sensing mechanism. Growth-induced deformation of the biofilms is implemented with a cellular automaton approach. In this work, the spatiotemporal evolution of biofilms in the pore space of a 2D granular medium is simulated under high flow rate and nutrient-rich conditions. Transient changes in the pore geometry caused by biofilm growth lead to the formation of preferential flowpaths within the granular porous medium. The decrease of permeability caused by clogging of the porous medium is calculated and is found to be in qualitative agreement with published experimental results. [Copyright &y& Elsevier]