Hierarchical hybrid simulation of biofilm growth dynamics in 3D porous media

Recently, we developed the first hierarchical, hybrid simulator for the prediction of the pattern of evolution and the rate of growth of heterogeneous biofilms within the pore space of porous media [Kapellos et al., Adv. Water Resour. (2007) 30:1648-1667]. A n improved version of our simulator is presented in this work. A continuum-based approach for fluid flow and solute transport is combined with individual-based approaches for biofilm growth, detachment, and migration in the pore space. The Navier-Stokes-Brinkman equations are solved numerically with a marker-and-cell finite difference scheme to determine the velocity and pressure fields in the pore space. Momentum transport in the biofilms is described in the context of biphasic poroelasticity and a Galerkin finite element method is used to determine the solid stress field. Shear-induced biofilm detachment is taken into account explicitly and a Lagrangian-type simulation is used to determine the trajectories of detached fragments. Nutrient transport in the pore space is described by the convectiondiffusion- reaction equation, which is solved numerically with an operator-splitting finite difference scheme. Further, a novel, physically-constrained cellular-automaton model is used for biofilm proliferation. As an example application, the simulator is used to investigate the impact of biofilm formation on the fate and transport of suspended particles in a network of three-dimensional pores

Computational study of the interaction between a newtonian fluid and a cellular biological medium in a straight vessel

In this work, we solve numerically the governing equations for quasi-steady Newtonian flow past and through a cellular biological medium, which is attached to the surface of a straight vessel. The flow past the cellular biological medium is described by the Navier-Stokes equations. For the modeling of momentum transfer within the cellular biological medium, we consider that the cellular biological medium constitutes a biphasic fluid-solid mixture with poroelastic behaviour. The system of governing equations is solved numerically with the mixed finite element method. The computational domain is discretized using an unstructured, variable density triangular element mesh. From the numerical solution we obtain the spatial distributions of: (i) the fluid velocity and pressure, and (ii) the displacement and stresses of the solid matrix within the cellular biological medium. Also, the components of the overall hydrodynamic force exerted by the flowing fluid on the cellular biological medium are calculated. A parametric analysis is performed with regard to the Reynolds and Darcy numbers that characterize the flow past and through the cellular biological medium

Theoretical Insight into the Biodegradation of Solitary Oil Microdroplets Moving through a Water Column

In the aftermath of oil spills in the sea, clouds of droplets drift into the seawater column and are carried away by sea currents. The fate of the drifting droplets is determined by natural attenuation processes, mainly dissolution into the seawater and biodegradation by oil-degrading microbial communities. Specifically, microbes have developed three fundamental strategies for accessing and assimilating oily substrates. Depending on their affinity for the oily phase and ability to proliferate in multicellular structures, microbes might either attach to the oil surface and directly uptake compounds from the oily phase, or grow suspended in the aqueous phase consuming solubilized oil, or form three-dimensional biofilms over the oil–water interface. In this work, a compound particle model that accounts for all three microbial strategies is developed for the biodegradation of solitary oil microdroplets moving through a water column. Under a set of educated hypotheses, the hydrodynamics and solute transport problems are amenable to analytical solutions and a closed-form correlation is established for the overall dissolution rate as a function of the Thiele modulus, the Biot number and other key parameters. Moreover, two coupled ordinary differential equations are formulated for the evolution of the particle size and used to investigate the impact of the dissolution and biodegradation processes on the droplet shrinking rate

Impact of Microbial Uptake on the Nutrient Plume around Marine Organic Particles: High-Resolution Numerical Analysis

The interactions between marine bacteria and particulate matter play a pivotal role in the biogeochemical cycles of carbon and associated inorganic elements in the oceans. Eutrophic plumes typically form around nutrient-releasing particles and host intense bacterial activities. However, the potential of bacteria to reshape the nutrient plumes remains largely unexplored. We present a high-resolution numerical analysis for the impacts of nutrient uptake by free-living bacteria on the pattern of dissolution around slow-moving particles. At the single-particle level, the nutrient field is parameterized by the Péclet and Damköhler numbers (0 < Pe < 1000, 0 < Da < 10) that quantify the relative contribution of advection, diffusion and uptake to nutrient transport. In spite of reducing the extent of the nutrient plume in the wake of the particle, bacterial uptake enhances the rates of particle dissolution and nutrient depletion. These effects are amplified when the uptake timescale is shorter than the plume lifetime (Pe/Da < 100, Da > 0.0001), while otherwise they are suppressed by advection or diffusion. Our analysis suggests that the quenching of eutrophic plumes is significant for individual phytoplankton cells, as well as marine aggregates with sizes ranging from 0.1 mm to 10 mm and sinking velocities up to 40 m per day. This microscale process has a large potential impact on microbial growth dynamics and nutrient cycling in marine ecosystems

Theoretical insight into the biodegradation of solitary oil microdroplets moving through a water column

Summarization: In the aftermath of oil spills in the sea, clouds of droplets drift into the seawater column and are carried away by sea currents. The fate of the drifting droplets is determined by natural attenuation processes, mainly dissolution into the seawater and biodegradation by oil-degrading microbial communities. Specifically, microbes have developed three fundamental strategies for accessing and assimilating oily substrates. Depending on their affinity for the oily phase and ability to proliferate in multicellular structures, microbes might either attach to the oil surface and directly uptake compounds from the oily phase, or grow suspended in the aqueous phase consuming solubilized oil, or form three-dimensional biofilms over the oil–water interface. In this work, a compound particle model that accounts for all three microbial strategies is developed for the biodegradation of solitary oil microdroplets moving through a water column. Under a set of educated hypotheses, the hydrodynamics and solute transport problems are amenable to analytical solutions and a closed-form correlation is established for the overall dissolution rate as a function of the Thiele modulus, the Biot number and other key parameters. Moreover, two coupled ordinary differential equations are formulated for the evolution of the particle size and used to investigate the impact of the dissolution and biodegradation processes on the droplet shrinking rate.Παρουσιάστηκε στο: Bioengineerin