Confinement and activity regulate bacterial motion in porous media

Tapomoy Bhattacharjee; Sujit S. Datta

doi:10.1039/c9sm01735f

Comparison of Competing Invasion-Percolation Models for Simulation of Multiphase Flow in Porous Media

10.5194/egusphere-egu21-8826 ◽

2021 ◽

Author(s):

Ishani Banerjee ◽

Anneli Guthke ◽

Kevin Mumford ◽

Wolfgang Nowak

Keyword(s):

Porous Medium ◽

Porous Media ◽

Gas Flow ◽

Flow Regimes ◽

Flow In Porous Media ◽

Invasion Percolation ◽

Pore Scale ◽

Discontinuous Flow ◽

Model Version ◽

Water Saturated

Invasion-Percolation (IP) models are used to simulate multiphase flow in porous media across various scales (from pore-scale IP to Macro-IP). Numerous variations of IP models have emerged; here we are interested in simulating gas flow in a water-saturated porous medium. Gas flow in porous media occurs either as a continuous or as a discontinuous flow, depending on the rate of flow and the nature of the porous medium. A particular IP model version may be well suited for predictions in a specific gas flow regime, but not applicable to other regimes. Our research aims to compare various macro-scale versions of IP models existing in the literature and rank their performance in relevant gas flow regimes.We test the performance of Macro-IP models on a range of gas-injection rates in water-saturated sand experiments, including both continuous and discontinuous flow regimes. The experimental data is obtained as a time series of images using the light transmission technique. To represent pore-scale heterogeneities of sand, we let each model version run on several random realizations of the initial entry pressure field. As a metric for ranking the models, we introduce a diffused version of the so-called Jaccard index (adapted from image analysis and object recognition). We average this metric over time and over all realizations per model version to evaluate each model&#8217;s overall performance. This metric may also be used to calibrate model parameters such as gas saturation.&#160;Our proposed approach evaluates the performance of competing IP model versions in different gas-flow regimes objectively and quantitatively, and thus provides guidance on their applicability under specific conditions. Moreover, our comparison method is not limited to gas-water phase systems in porous media but generalizes to any modelling situation accompanied by spatially and temporally highly resolved data.

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Diffusion limited mixing in heterogeneous porous media

10.5194/egusphere-egu21-15721 ◽

2021 ◽

Author(s):

Mayumi Hamada ◽

Pietro de Anna

Keyword(s):

Porous Medium ◽

Porous Media ◽

Flow Field ◽

Fast Diffusion ◽

Pore Scale ◽

Mixing Processes ◽

Local Flow ◽

Gaussian Shape ◽

Diffusion Limited ◽

The Impact

A pore-scale description of the transport and mixing processes is particularly relevant when looking at biological and chemical reactions. For instance, a microbial population growth is controlled by local concentrations of nutrients and oxygen, and chemical reaction are driven by molecular-scale concentration gradients. The heterogeneous flow field typically found in porous media results from the contrast of velocities that deforms and elongates the mixing fronts between solutes that often evolves through a lamella-like topology. For continuous Darcy type flow field a novel framework that describes the statistical distribution of concentration being transported was recently developed (Le Borgne et al., JFM 2015). In this model, concentrations in each lamella are distributed as a Gaussian-like profile which experiences diffusion in the transverse direction while the lamella is elongated by advection along the local flow direction. The evolving concentration field is described as the superposition of each lamella. We hypothesize that this novel view, while perfectly predicting the distribution of concentration for Darcy scale mixing processes, will breakdown when the processes description is at the pore scale. Indeed the presence of solid and impermeable boundaries prevents lamella concentration to diffuse freely according to the a Gaussian shape, and therefore changes the mixing front profile, the lamella superposition and elongation rules. Previous work (Hamada et al, PRF, 2020) demonstrated that the presence of solid boundaries leads to an enhanced diffusion and thus fast homogenization of concentrations. In a purely diffusive process the local mixing time is reduced by a factor of ten with respect to the continuous case and concentration gradient are dissipated exponentially fast while a power law decrease is observed in continuous medium. To investigate the impact of these mechanisms on mixing we developed an experimental set-up to visualize and quantify the displacement of a conservative tracer in a synthetic porous medium. The designed apparatus allows to obtain high resolution concentration measurements at the pore scale. We show that the resulting mixing measures, computed in terms of concentration probability density function and dilution index values, diverge qualitatively and quantitatively from what happens in a continuous domain. These observations suggest that description of pore-scale diffusion-limited mixing requires model that takes into account the confined nature of porous medium, otherwise we will tend to overestimate concentration value and neglect the fast diffusion dynamic taking place at microscopic level.

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Driving factors for bioclogging of pores and porous media

10.5194/biofilms9-23 ◽

2020 ◽

Author(s):

Dorothee Kurz ◽

Eleonora Secchi ◽

Roman Stocker ◽

Joaquin Jimenez-Martinez

Keyword(s):

Porous Medium ◽

Porous Media ◽

Biofilm Formation ◽

Driving Factors ◽

High Temporal Resolution ◽

Pore Scale ◽

Biofilm Growth ◽

Medium Scale ◽

Biofilm Development ◽

Biofilm Structure

Understanding the interplay between hydrodynamics and biogeochemical processes is of growing importance in environmental applications and studies, especially in the fields of bioremediation and ecology. The majority of the microbial communities living in soil have a surface-attached lifestyle, allowing them to form biofilms. The biofilm growth influences pore geometries by clogging them and thus redirecting the flow, which in return affects biofilm development and local mass transport. After initially clogging single pores, the biofilm structure expands to larger clusters before eventually clogging the porous medium entirely. We study these processes with a soil-born microorganism, Bacillus subtilis, in microfluidic devices mimicking porous media to get a mechanistic understanding of the driving factors of bioclogging of porous media on different scales. Carefully designed porous geometries were used for the experiments to study biofilm growth under different flow conditions. After being seeded with bacteria, devices were exposed to a continuous nutrient flow during several days. Continuously monitoring the pressure evaluation and imaging the biofilm growth using Brightfield microscopy allowed a high temporal resolution of biofilm growth processes. An interplay of hydraulic parameters and geometric features of the porous medium as well as the mass flow rate of nutrients drive the speed of pore clogging. Besides the pore scale clogging, the initiation of biofilm formation as well as the speed of clogging of the entire medium are influenced by the before mentioned parameters. Furthermore, the size and number of the biofilm clusters formed seem to drive the medium scale clogging. This leads to inverting trends concerning the clogging rate in one pore when compared to the porous medium scale for different pore sizes. These results shed light on the pore-scale mechanism as well as driving parameters of biofilm formation and bioclogging and their transferability to the next larger scale, e.g. a porous medium.

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Effect of Microscopic Vortices Caused by Flow Interaction With Solid Obstacles on Heat Transfer in Turbulent Porous Media Flows

Volume 2: Computational Fluid Dynamics ◽

10.1115/ajkfluids2019-4617 ◽

2019 ◽

Author(s):

Ching-Wei Huang ◽

Vishal Srikanth ◽

Haodong Li ◽

Andrey V. Kuznetsov

Keyword(s):

Heat Transfer ◽

Reynolds Number ◽

Porous Medium ◽

Porous Media ◽

Heat Transfer Rate ◽

Contact Area ◽

Transfer Rate ◽

Porous Media Flow ◽

Pore Scale ◽

Solid Obstacles

Abstract Turbulent flow in a homogeneous porous medium was investigated through the use of numerical methods by employing the Reynolds Averaged Navier-Stokes (RANS) modeling technique. The focus of our research was to study how microscopic vortices in porous media flow influence the heat transfer from the solid obstacles comprising the porous medium to the fluid. A Representative Elementary Volume (REV) with 4 × 4 cylindrical obstacles and periodic boundary conditions was used to represent the infinite porous medium structure. Our hypothesis is that the rate of heat transfer between the obstacle surface and the fluid (qavg) is strongly influenced by the size of the contact area between the vortices and the solid obstacles in the porous medium (Avc). This is because vortices are regions with low velocity that form an insulating layer on the surface of the obstacles. Factors such as the porosity (φ), Pore Scale Reynolds number (Rep), and obstacle shape of the porous medium were investigated. All three of these factors have different influences on the contact area Avc, and, by extension, the overall heat transfer rate qavg. Under the same Pore Scale Reynolds number (Rep), our results suggest that a higher overall heat transfer rate is exhibited for smaller contact areas between the vortices and the obstacle surface. Although the size of the contact area, Avc, is affected by Rep, the direct influence of Rep on the overall heat transfer rate qavg is much stronger, and exceeds the effect of Avc on qavg. The Pore Scale Reynolds number, Rep, and the mean Nusselt number, Num, have a seemingly logarithmic relationship.

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A “lab-on-a-chip” experiment for assessing mineral precipitation processes in fractured porous media

10.5194/egusphere-egu2020-13613 ◽

2020 ◽

Author(s):

Jenna Poonoosamy ◽

Sophie Roman ◽

Cyprien Soulaine ◽

Hang Deng ◽

Sergi Molins ◽

...

Keyword(s):

Porous Medium ◽

Porous Media ◽

Reactive Transport ◽

Surface Passivation ◽

Pore Scale ◽

Mineral Precipitation ◽

Transport Models ◽

Mineral Transformation ◽

Fractured Porous Medium ◽

Fractured Medium

The understanding of dissolution and precipitation of minerals and its impact on the transport of fluids in fractured media is essential for various subsurface applications including shale gas production using hydraulic fracturing (&#8220;fracking&#8221;), CO2 sequestration, or geothermal energy extraction. The implementation of such coupled processes into numerical reactive transport codes requires a mechanistic process understanding and model validation with quantitative experiments. In this context, we developed a microfluidic &#8220;lab-on-chip&#8221; of a reactive fractured porous medium of 800 &#181;m &#215; 900 &#181;m size with 10 &#181;m depth. The fractured medium consisted of compacted celestine grains (grain size 4 &#8211; 9 &#181;m). A BaCl2 solution was injected into the microreactor at a flow rate of 500 nl&#160;min-1, leading to the dissolution of celestine and an epitaxial growth of barite on its surface (Poonoosamy et al., 2016). Our investigations including confocal Raman spectroscopic techniques allowed for monitoring the temporal mineral transformation at the pore scale in 2D and 3D geometries. The fractured porous medium causes a heterogeneous flow field in the microreactor that leads to spatially different mineral transformation rates. In these experiments, the dynamic evolution of surface passivation processes depends on two intertwined processes: i) the dissolution of the primary mineral that is needed for the subsequent precipitation, and ii) the suppression of the dissolution reaction as a result of secondary mineral precipitation. However, the description of evolving reactive surface areas to account for mineral passivation mechanisms in reactive transport models following Daval et al. (2009) showed several limitations, and prompt for an improved description of passivation processes that includes the diffusive properties of secondary phases (Poonoosamy et al., 2020). The results of the ongoing microfluidic experiments in combination with advanced pore-scale modelling will provide new insights regarding application and extension of the description of surface passivation processes to be included in (continuum-scale) reactive transport models.Daval D., Martinez I., Corvisier J., Findling N., Goff&#233; B. and Guyotac F. (2009) Carbonation of Ca-bearing silicates, the case of wollastonite: Experimental investigations and kinetic modelling. Chem. Geol. 265(1&#8211;2), 63-78.Poonoosamy J., Curti E., Kosakowski G., Van Loon L. R., Grolimund D. and M&#228;der U. (2016) Barite precipitation following celestite dissolution in a porous medium: a SEM/BSE and micro XRF/XRD study. Geochim. Cosmochim. Acta 182, 131-144.Poonoosamy J., Klinkenberg M., Deissmann G., Brandt F., Bosbach D., M&#228;der U. and Kosakowski G. (2020) Effects of solution supersaturation on barite precipitation in porous media and consequences on permeability: experiments and modelling. Geochim. Cosmochim. Acta 270, 43-60.

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Numerical investigation of the possibility of macroscopic turbulence in porous media: a direct numerical simulation study

Journal of Fluid Mechanics ◽

10.1017/jfm.2015.9 ◽

2015 ◽

Vol 766 ◽

pp. 76-103 ◽

Cited By ~ 43

Author(s):

Y. Jin ◽

M.-F. Uth ◽

A. V. Kuznetsov ◽

H. Herwig

Keyword(s):

Numerical Simulation ◽

Porous Medium ◽

Porous Media ◽

Direct Numerical Simulation ◽

Turbulent Flow ◽

Flow In Porous Media ◽

Minimum Size ◽

Solid Matrix ◽

Pore Scale ◽

Turbulent Structures

AbstractWhen a turbulent flow in a porous medium is determined numerically, the crucial question is whether turbulence models should account only for turbulent structures restricted in size to the pore scale or whether the size of turbulent structures could exceed the pore scale. The latter would mean the existence of macroscopic turbulence in porous media, when turbulent eddies exceed the pore size. In order to determine the real size of turbulent structures in a porous medium, we simulated the turbulent flow by direct numerical simulation (DNS) calculations, thus avoiding turbulence modelling of any kind. With this study, which for the first time uses DNS calculations, we provide benchmark data for turbulent flow in porous media. Since perfect DNS calculations require the resolution of scales down to the Kolmogorov scale, often only approximate DNS solutions can be obtained, especially for high Reynolds numbers. This is accounted for by using and comparing two different DNS approaches, a finite volume method (FVM) with grid refinement towards the wall and a lattice Boltzmann method (LBM) with equal grid distribution. The solid matrix was simulated by a large number of rectangular bars arranged periodically. The number of bars in the solution domain with periodic boundary conditions was reduced systematically until a minimum size was found that does not suppress any large-scale turbulent structures. Two-point correlations, integral length scales and energy spectra were determined in order to answer the question of whether or not macroscopic turbulence can be found in porous media.

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Impact of Synthetic Porous Medium Geometric Properties on Solute Transport Using Direct 3D Pore-Scale Simulations

Geofluids ◽

10.1155/2019/6810467 ◽

2019 ◽

Vol 2019 ◽

pp. 1-13

Author(s):

Paolo Roberto Di Palma ◽

Nicolas Guyennon ◽

Andrea Parmigiani ◽

Christian Huber ◽

Falk Heβe ◽

...

Keyword(s):

Porous Medium ◽

Porous Media ◽

Effective Diffusion ◽

Volume Averaging ◽

Transport Processes ◽

Hydrodynamic Dispersion ◽

Pore Scale ◽

Geometric Properties ◽

Advection Diffusion ◽

The Impact

Transport processes in porous media have been traditionally studied through the parameterization of macroscale properties, by means of volume-averaging or upscaling methods over a representative elementary volume. The possibility of upscaling results from pore-scale simulations, to obtain volume-averaging properties useful for practical purpose, can enhance the understanding of transport effects that manifest at larger scales. Several studies have been carried out to investigate the impact of the geometric properties of porous media on transport processes for solute species. However, the range of pore-scale geometric properties, which can be investigated, is usually limited to the number of samples acquired from microcomputed tomography images of real porous media. The present study takes advantage of synthetic porous medium generation to propose a systematic analysis of the relationships between geometric features of the porous media and transport processes through direct simulations of fluid flow and advection-diffusion of a non-reactive solute. Numerical simulations are performed with the lattice Boltzmann method on synthetic media generated with a geostatistically based approach. Our findings suggest that the advective transport is primarily affected by the specific surface area and the mean curvature of the porous medium, while the effective diffusion coefficient scales as the inverse of the tortuosity squared. Finally, the possibility of estimating the hydrodynamic dispersion coefficient knowing only the geometric properties of porous media and the applied pressure gradient has been tested, within the range of tested porous media, against advection-diffusion simulations at low Reynolds (<10-1) and Peclet numbers ranging from 101 to 10-2.

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Pore-Scale Experimental Study of Boiling in Porous Media

Proceedings of the 15th International Heat Transfer Conference ◽

10.1615/ihtc15.pbl.009914 ◽

2014 ◽

Cited By ~ 3

Author(s):

Paul SAPIN ◽

Paul Duru ◽

Florian Fichot ◽

Marc Prat ◽

Michel Quintard

Keyword(s):

Experimental Study ◽

Porous Media ◽

Pore Scale

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PORE-SCALE SIMULATION OF ICE MELTING PROCESS IN POROUS MEDIA

10.1615/tfec2017.prm.017991 ◽

2017 ◽

Author(s):

Pu He ◽

Li Chen ◽

Yu-Tong Mu ◽

Wen-Quan Tao

Keyword(s):

Porous Media ◽

Melting Process ◽

Pore Scale ◽

Ice Melting

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Conservative solute transport with periodic velocity and sinusoidal source concentration in semi-infinite porous media: An analytical solution

JOURNAL OF ADVANCES IN PHYSICS ◽

10.24297/jap.v6i1.1818 ◽

2014 ◽

Vol 6 (1) ◽

pp. 1024-1031

Author(s):

R R Yadav ◽

Gulrana Gulrana ◽

Dilip Kumar Jaiswal

Keyword(s):

Porous Medium ◽

Porous Media ◽

Laplace Transformation ◽

Seepage Velocity ◽

Transformation Technique ◽

Numerical Examples ◽

One Dimensional ◽

Porous Domain ◽

Conservative Solute Transport ◽

Source Concentration

The present paper has been focused mainly towards understanding of the various parameters affecting the transport of conservative solutes in horizontally semi-infinite porous media. A model is presented for simulating one-dimensional transport of solute considering the porous medium to be homogeneous, isotropic and adsorbing nature under the influence of periodic seepage velocity. Initially the porous domain is not solute free. The solute is initially introduced from a sinusoidal point source. The transport equation is solved analytically by using Laplace Transformation Technique. Alternate as an illustration; solutions for the present problem are illustrated by numerical examples and graphs.

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