Pore‐scale simulation of biomass growth along the transverse mixing zone of a model two‐dimensional porous medium

Abstract

[1] The success of in situ bioremediation projects depends on the mixing of contaminants and nutrients in the presence of microbes. In this work, a pore-scale model is developed to simulate biomass growth that is controlled by the mixing of an electron donor and acceptor. A homogeneous packing of cylinders representing solid grains is used as the model two-dimensional porous medium. The system is initially seeded with microbes in computational cells located at grain-water interfaces. The solutes enter the system completely unmixed; each solute is input over one half of the inlet boundary. Solute mixing is controlled by molecular diffusion transverse to the flow direction, and solutes are biotransformed according to dual Monod kinetics only where biomass is present. Simulation of biomass growth requires calculation of the water flow field as well as transport and reaction of solutes. The lattice Boltzmann method is used to obtain the flow field. Transport and reaction of the solutes is modeled by a finite volume discretization of the advection-diffusion-reaction equation. Biomass is allowed to grow and spread by means of a cellular automata algorithm. Model parameters are systematically varied to understand their effects on biomass development. Base case parameter values are obtained from batch experiments reported in the literature and are modified to achieve agreement between simulation results and previously reported micromodel experimental results. The most significant mechanisms that control biomass development are shear strength of new biomass and solute degradation rates. The biomass growth model achieves good qualitative agreement with experimental results.

Three-dimensional distribution of water and air in soil pores: Comparison of two-phase two-relaxation-times lattice-Boltzmann and morphological model outputs with synchrotron X-ray computed tomography data

“…Among them, lattice-Boltzmann models (LBM) [29,20] are able to describe water, solute, and particulate transport in the interstitial space of soils, as well as the shape of air-water interfaces [13,53], without having to invoke the kind of simplifying assumptions about the geometry or topology of soil pores that were typical of earlier generations of models, based on traditional partial differential equations or capillary network idealizations. Similarly, agent-or individual-based models describe quantitatively the growth and metabolism of microorganisms much more realistically than traditional models, based on descriptions of population dynamics, and are able to account in great detail for the effects of the relative spatial distributions of fungi [13], bacteria [27,30,18,15], and the organic matter on which they feed. At the moment, the development of each of these different models is moving forward, in parallel with interdisciplinary efforts to combine them in order to describe various types of micro-scale scenarios and assess the nature of emergent properties of soil systems [13].…”

Variational inequality approach to enforcing the non-negative constraint for advection–diffusion equations

“…For several transport applications, it is highly desirable to possess element-wise mass balance property, as it is an important fundamental physical law [Turner et al, 2011]. This is particularly true when the transport is coupled with chemical reactions and biofilm growth [Werth and Valocchi, 2005;von der Schulenburg et al, 2009]. The GAL and SUPG formulations do not possess this property without any further modification or enrichment to their formulations.…”

Biomechanical Analysis of Infectious Biofilms

“…Quantifying biomass effluent from complex biofilms grown in a glass-bead reactor in terms of a spatially-averaged model has revealed design principles that could be exploited to control growth and detachment [18]. Spatially-extended models reveal a complex biomass distribution on the scale of reactor pores, with reduced nutrient availability and biofilm growth downstream from clogged pores [52,93]. A suite of techniques has been employed to measure velocity profiles and metabolic fluxes in terms of biofilm age and microbial composition [47], generating a range of data that could be used to validate highly sophisticated and predictive models.…”

“…Non-linear streamers often form in rapid flow [89], whose visually-determined deformation fields can be fitted to those of simple elastic bodies to estimate static moduli [6,90]. More recently, microfluidic devices have been employed to provide better environmental control and ensure laminar flow [52,80,86,101], and fitting of visually-identified streamers [50] or partitioning walls [43] permits parameter estimation.…”

“…In addition, the response to surface airflow and known airborne dispersal modes should be considered in the design of nosocomial ventilation systems [38,83]. Flow is also a key consideration for industrial biofilms as overgrowth can cause clogging in biofilm reactors [52,93], although here the goal is to maximise metabolic efficacy rather than microbial eradication.…”