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  • Garnier, Patricia  (28)
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  • 1
    Language: English
    In: Journal of Hydrology, December 2017, Vol.555, pp.253-256
    Description: In the last decade, X-ray computed tomography (CT) has become widely used to characterize the geometry and topology of the pore space of soils and natural porous media. Regardless of the resolution of CT images, a fundamental problem associated with their use, for example as a starting point in simulation efforts, is that sub-resolution pores are not detected. Over the last few years, a particular type of modeling method, known as "Grey" or "Partial Bounce Back" Lattice-Boltzmann (LB), has been adopted by increasing numbers of researchers to try to account for sub-resolution pores in the modeling of water and solute transport in natural porous media. In this short paper, we assess the extent to which Grey LB methods indeed offer a workable solution to the problem at hand. We conclude that, in spite of significant computational advances, a major experimental hurdle related to the evaluation of the penetrability of sub-resolution pores, is blocking the way ahead. This hurdle will need to be cleared before Grey LB can become a credible option in the microscale modeling of soils and sediments. A necessarily interdisciplinary effort, involving both modelers and experimentalists, is needed to clear the path forward.
    Keywords: Computer Modeling ; Transport Processes ; Image Resolution ; Measurement ; Interdisciplinary Research ; Geography
    ISSN: 0022-1694
    E-ISSN: 1879-2707
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  • 2
    Language: English
    In: Ecological Modelling, 2018, Vol.383, pp.10-22
    Description: Soil respiration causes the second largest C flux between ecosystems and the atmosphere. Emerging soil carbon dynamics models consider the complex interplay of microscale interactions between the physical and biological drivers of soil organic...
    Keywords: Life Sciences ; Uncertainty Analysis ; Sensitivity Analysis ; Lattice–Boltzmann Model ; Soil Architecture ; Carbon ; Bacteria ; Environmental Sciences ; Ecology
    ISSN: 0304-3800
    E-ISSN: 1872-7026
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  • 3
    Language: English
    In: Soil Biology and Biochemistry, November 2014, Vol.78, pp.189-194
    Description: Modelling carbon mineralisation in natural soils is a major topic in soil and climate research. Current models need to be improved to include soil structure as an influencing factor to better predict C fluxes between pedosphere and atmosphere and to estimate carbon sequestration potentials. Geometry-based mechanistic modelling approaches have recently been developed to systematically study the effect of soil structure on carbon decomposition. Such models require spatially explicit input parameters describing the architecture of the pore space and the heterogeneous distribution of microbes and organic matter as decomposable substrate. The latter is very difficult to determine , resulting in increased uncertainty in the models. To obtain more realistic input data, we have developed a novel approach to locate soil organic matter (SOM) in undisturbed aggregates of soil using a combination of synchrotron-based X-ray microtomography and osmium as a staining agent for SOM. Here, we present the first results using 5 mm sized soil aggregate samples with contrasting C-contents in which we obtained maps of organic matter distributions in relation to the pore networks at the aggregate scale.
    Keywords: Soil Organic Matter ; Soil Structure ; Carbon Sequestration ; Synchrotron Microtomography ; Staining ; Agriculture ; Chemistry
    ISSN: 0038-0717
    E-ISSN: 1879-3428
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  • 4
    Language: English
    In: Ecological Modelling, 2008, Vol.216(3), pp.291-302
    Description: During the past 10 years, soil scientists have started to use 3D Computed Tomography in order to gain a clearer understanding of the geometry of soil structure and its relationships with soil properties. We propose a geometric model for the 3D representation of pore space and a practical method for its computation. Our basic idea consists in representing pore space using a minimal set of maximal balls (Delaunay spheres) recovering the shape skeleton. In this representation, each ball could be considered as a maximal local cavity corresponding to the “intuitive” notion of a pore as described in the literature. The space segmentation induced by the network of balls (pores) was then used to spatialize biological dynamics. Organic matter and microbial decomposers were distributed within the balls (pores). A valuated graph representing the pore network, organic matter and distribution of micro-organisms was then defined. Microbial soil organic matter decomposition was simulated by updating this valuated graph. The method was implemented and tested using real CT images. The model produced realistic simulated results when compared with data in the literature in terms of the water retention curve and carbon mineralization. A decrease in water pressure decreased carbon mineralization, which is also in accordance with findings in the literature. From our results we showed that the influence of water pressure on decomposition is a function of organic matter distribution in the pore space. As far as we know, this is the approach to have linked pore space geometry and biological dynamics in a formal way. Our next goal will be to compare the model with experimental data of decomposition using different soil structures, and to define geometric typologies of pore space shape that can be attached to specific biological and dynamic properties.
    Keywords: Computational Geometry ; Soil Science ; Pore Space Modelling ; Microbial Decomposition Simulation ; 3d Computer Vision ; Environmental Sciences ; Ecology
    ISSN: 0304-3800
    E-ISSN: 1872-7026
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  • 5
    Language: English
    In: Frontiers in Microbiology, 2018, Vol.9, p.1583
    Description: There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly biodiverse as they are. The present article explores in silico the hypothesis that the heterogeneous distribution of soil organic...
    Keywords: Life Sciences ; Bacteria ; Resource Allocation ; Organic Matter ; Pore Scale ; Soil ; Biodiversity ; Agent-Based Modeling ; Biology
    ISSN: 1664-302X
    E-ISSN: 1664-302X
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  • 6
    Language: English
    In: Advances in Water Resources, September 2015, Vol.83, pp.123-136
    Description: Soil structure and interactions between biotic and abiotic processes are increasingly recognized as important for explaining the large uncertainties in the outputs of macroscopic SOM decomposition models. We present a numerical analysis to assess the role of meso- and macropore topology on the biodegradation of a soluble carbon substrate in variably water saturated and pure diffusion conditions . Our analysis was built as a complete factorial design and used a new 3D pore-scale model, LBioS, that couples a diffusion lattice-Boltzmann model and a compartmental biodegradation model. The scenarios combined contrasted modalities of four factors: meso- and macropore space geometry, water saturation, bacterial distribution and physiology. A global sensitivity analysis of these factors highlighted the role of physical factors in the biodegradation kinetics of our scenarios. Bacteria location explained 28% of the total variance in substrate concentration in all scenarios, while the interactions among location, saturation and geometry explained up to 51% of it.
    Keywords: Biodegradation ; Lattice-Boltzmann Method ; Pore-Scale Heterogeneity ; Spatial Distribution ; Substrate Diffusion ; Microbial Habitats ; Engineering
    ISSN: 0309-1708
    E-ISSN: 1872-9657
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  • 7
    In: Global Change Biology, July 2019, Vol.25(7), pp.2205-2208
    Description: The goal of this comment is to show that the “aggregate reactor” framework recently proposed in an article published in this journal is severely limited by two kinds of indeterminacy. The first is related to the size of aggregates, which is not defined precisely. The second issue is with the impossibility to replicate boundary conditions that are identical to what chunks of soils would have experienced in their natural state. We suggest that the study of GHG release in undisturbed soil samples is a better way to proceed forward.
    Keywords: Reactors ; Soils ; Greenhouse Effect ; Greenhouse Gases ; Boundary Conditions ; Aggregates ; Boundary Conditions ; Boundary Conditions ; Soil Aggregates ; Greenhouse Gases ; Soils ; Aggregates ; Gases ; Aggregates ; Greenhouse Gases ; Greenhouse Effect ; Biogeochemistry ; Greenhouse Effect;
    ISSN: 1354-1013
    E-ISSN: 1365-2486
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  • 8
    Language: English
    In: Computers and Geosciences, 2009, Vol.35(9), pp.1789-1801
    Description: This study is the follow-up to a previous one devoted to soil pore space modelling. In the previous study, we proposed algorithms to represent soil pore space by means of optimal piecewise approximation using simple 3D geometrical primitives: balls, cylinders, cones, etc. In the present study, we use the ball-based piecewise approximation to simulate biological activity. The basic idea for modelling pore space consists in representing pore space using a minimal set of maximal balls (Delaunay spheres) recovering the shape skeleton. In this representation, each ball is considered as a maximal local cavity corresponding to the “intuitive” notion of a pore as described in the literature. The space segmentation induced by the network of balls (pores) is then used to spatialise biological dynamics. Organic matter and microbial decomposers are distributed within the balls (pores). A valuated graph representing the pore network, organic matter and microorganism distribution is then defined. Microbial soil organic matter decomposition is simulated by updating this valuated graph. The method has been implemented and tested on real data. As far as we know, this approach is the first one to formally link pore space geometry and biological dynamics. The long-term goal is to define geometrical typologies of pore space shape that can be attached to specific biological dynamic properties. This paper is a first attempt to achieve this goal.
    Keywords: 3d Computer Vision ; Biological Dynamics Simulation ; Computed Tomography ; Computational Geometry ; Microbial Decomposition ; Pore Space Modelling ; Geology
    ISSN: 0098-3004
    E-ISSN: 1873-7803
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  • 9
    Language: English
    In: Frontiers in Microbiology, 2018, Vol.9, p.1929
    Description: Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the usual bulk, macroscopic parameters used to characterize soils (e.g., granulometry, pH, soil organic matter and biomass contents) provide insufficient information to describe quantitatively...
    Keywords: Life Sciences ; X-Ray Computed ; Upscaling ; Biodiversity ; Soil Microbiology ; Tomography ; Single-Cell Genomics ; Nanosims Imaging ; Biology
    ISSN: 1664-302X
    E-ISSN: 1664-302X
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  • 10
    Language: English
    In: Computers and Geosciences, February 2019, Vol.123, pp.20-37
    Description: In recent years, technological advances have stimulated researchers to try to unravel the extremely complex microscale processes that control the activity of microorganisms in soils. In particular, significant work has been carried out on the development of models able to accurately predict the microscale distribution of water, and the location of air–water interfaces in pores. A comparison, by Pot et al. (2015), of two different modeling approaches with actual synchrotron-based tomography data, shows that a two-phase lattice Boltzmann model (LBM) is able to predict remarkably well the location of air–water interfaces but is extremely slow, whereas a morphological model (MOSAIC), representing the pore space as a collection of spherical balls, provides a reasonable approximation of the observed air–water interfaces when each ball is allowed to drain independently, but does so blazingly fast. Interfaces predicted by MOSAIC, however, tend to have nonphysical shapes. In that general context, the key objective of the research described in the present article, based on the same tomography data as Pot et al. (2015), was to find out to what extent the use of ellipsoids instead of spherical balls in MOSAIC could not appreciably speed up computations, or at least, at equal computational time, provide a quantitatively better approximation of water-air interfaces. As far as we know, this is the first time an ellipsoids-based approximation of the soil pore space is proposed. A secondary objective was to assess whether ellipsoids might yield smoother, more physical, interfaces. Simulation results indicate that the use of ellipsoids provides a sizeable increase in accuracy in the prediction of air-water interfaces, an approximately 6-fold drop in computation time, and much more realistic-looking interfaces, compared to what is obtained with spherical balls. These observations are encouraging for the use of models based on geometric primitives to describe a range of microscale processes, and to address the still daunting issue of upscaling to the macroscopic scale.
    Keywords: Pore Scale ; Synchroton X-Ray Micro Computed Tomography ; Soil Air-Water Interfaces ; Computational Geometry ; 3d Volume Segmentation ; Morphological Modeling ; Geology
    ISSN: 0098-3004
    E-ISSN: 1873-7803
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