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  • Prodinra, Archive Ouverte  (76)
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  • 1
    Language: English
    In: Transport in Porous Media, 2013, Vol.96(2), pp.271-294
    Description: The 3D description of the soil structure at the pore scale level can help to elucidate the biological functioning of soil. The water–air distribution in the 3D-pore space is of particular interest because it determines the diffusion pathways of nutrients and the localisation of active soil microorganisms. We used the Shan–Chen interparticle-potential approach to simulate spontaneous phase separation in complex academic and real 3D-porous media using the advanced TRT lattice Boltzmann scheme. The equation of state and phase diagram were calculated and the model was verified using hydrostatic laws. The 3D pattern of water/air interface in two complex academic pore geometries was accurately computed. Finally, 3D maps of static liquid–gas distribution were simulated in a real 3D X-ray computed tomography image obtained from an undisturbed soil column sampled in a silty clay loam soil. The simulated soil sample of 1.7 cm 3 was described at a voxel-resolution of 60 μm. The range of the simulated saturations (from 0.5 to 0.9) was in a good agreement with the expected saturations calculated from the phase diagram.
    Keywords: Lattice Boltzmann method ; Water meniscus ; TRT ; Shan–Chen ; Porous media
    ISSN: 0169-3913
    E-ISSN: 1573-1634
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  • 2
    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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  • 3
    Language: English
    In: Journal of Hydrology, 2011, Vol.403(1), pp.141-156
    Description: ► A surface-subsurface flow model with multi-objective global optimization is presented. ► The model performance was evaluated using bench-scale flow experiments. ► Inverse parameter estimation required observations at different spatial positions. ► The Pareto trade-off and model mismatch suggest lateral flow in soil layers. ► The model system is versatile for studying soil water and overland flow. A comprehensive description of water flow in environmental and agricultural systems requires an account of both surface and subsurface pathways. We present a new model which combines a 1D overland flow model and the 2D subsurface flow HYDRUS-2D model, and uses the multi-objective global search method AMALGAM for inverse parameter estimation. Furthermore, we present data from bench-scale flow experiments which were conducted with two 5-m long replicate soil channels. While rainfall was applied, surface runoff was recorded at the downstream end of the soil channel, subsurface drainage waters were sampled at three positions equally spaced along the channels, and pressure heads were recorded at five depths. The experimental observations were used to evaluate the performance of our modeling system. The complexity of the modeling approach was increased in three steps. First, only runoff and total drainage were simulated, then drainage flows from individual compartments were additionally evaluated, and finally a surface crust and immobile soil water were also considered. The results showed that a good match between measured and observed surface runoff and total drainage does not guarantee accurate representation of the flow process. An inspection of the Pareto results of different multiobjective calibration runs revealed a significant trade-off between individual objectives, showing that no single solution existed to match spatial variability in the flow. In spite of the observed crust formation, its consideration in the more complex model structure did not significantly improve the fit between the model and measurements. Accounting for immobile water regions only slightly improved the fit for one of the two replicate soil channels. Discrepancies between relatively complex model simulations and seemingly simple soil channel experiments suggest the presence of additional unknowns, such as heterogeneity of the soil hydraulic properties. Nevertheless, with its versatile subsurface options and powerful inverse method, the model system shows promise for studying hillslope flow problems involving both surface runoff and subsurface flow.
    Keywords: Overland Flow ; Surface Runoff ; Multi-Objective Global Parameter Optimization ; Mobile–Immobile Model ; Simulation ; Flow Channel Experiment ; Geography
    ISSN: 0022-1694
    E-ISSN: 1879-2707
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  • 4
    Language: English
    In: Science of the Total Environment, 15 November 2014, Vol.499, pp.560-573
    Description: Recycling composted organic residues in agriculture can reduce the need of mineral fertilizers and improve the physicochemical and biological properties of cultivated soils. However, some trace elements may accumulate in soils following repeated applications and impact other compartments of the agrosystems. This study aims at evaluating the long-term impact of such practices on the composition of soil leaching water, especially on trace metal concentrations. The field experiment QualiAgro started in 1998 on typical loess Luvisol of the Paris Basin, with a maize–wheat crop succession and five modalities: spreading of three different urban waste composts, farmyard manure (FYM), and no organic amendment (CTR). Inputs of trace metals have been close to regulatory limits, but supplies of organic matter and nitrogen overpassed common practices. Soil solutions were collected from wick lysimeters at 45 and 100 cm in one plot for each modality, during two drainage periods after the last spreading. Despite wide temporal variations, a significant effect of treatments on major solutes appears at 45 cm: DOC, Ca, K, Mg, Na, nitrate, sulphate and chloride concentrations were higher in most amended plots compared to CTR. Cu concentrations were also significantly higher in leachates of amended plots compared to CTR, whereas no clear effect emerged for Zn. The influence of amendments on solute concentrations appeared weaker at 1 m than at 45 cm, but still significant and positive for major anions and DOC. Average concentrations of Cu and Zn at 1 m depth lied in the ranges [2.5; 3.8] and [2.5; 10.5 μg/L], respectively, with values slightly higher for plots amended with sewage sludge compost or FYM than for CTR. However, leaching of both metals was less than 1% of their respective inputs through organic amendments. For Cd, most values were 〈 0.05 μg/L. So, metals added through spreading of compost or manure during 14 years may have increased metal concentrations in leachates of amended plots, in spite of increased soil organic matter, factor of metal retention. Indeed, DOC, also increased by amendments, favours the mobility of Cu; whereas pH variations, depending on treatments, influence negatively the solubility of Zn. Generic adsorption functions of these variables partly explain the variations of trace metal concentrations and helped to unravel the numerous processes induced by regular amendments with organic waste products.
    Keywords: Heavy Metal ; Trace Element ; Organic Waste ; Organic Amendment ; Cultivated Soil ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 5
    Language: English
    In: Science of the Total Environment, 01 July 2018, Vol.628-629, pp.1508-1517
    Description: Conservation tillage practices mainly based on cover crops and no-tillage with accumulation of crop residues at the soil surface (mulch) modify the environmental fate of pesticides. However, only few pesticide fate models are able to consider mulch of crop residues as well as the effect of intermediate cover crops. Thus, the objective was to develop an approach to model the effects of crop residues left at the soil surface and cover crops on the fate of pesticides. This approach consisted in (1) considering the crop residues as a soil layer with specific physical, hydrodynamic and pesticide-reactivity properties close to that of a high organic content soil layer, and (2) introducing a correction factor of the potential evapotranspiration, estimated through a calibration step, to take into account the reduction of soil evaporation by the presence of a mulch. This approach was developed using MACRO as support pesticide model. To assess the model performances, we used the data from a field experiment designed in an irrigated maize monoculture under conservation tillage. Soil water content, water percolates, soil temperature and S-metolachlor herbicide concentrations in the leachate at 1 m depth were measured during two years. The approach chosen to simulate the mulch effects allowed MACRO to make acceptable predictions of the observed water percolation, soil temperature and to a less extent herbicide leaching. However, it showed a poor performance to simulate the soil water content. Results are discussed in terms of further modelling options to better assess the environmental risks of pesticides under conservation tillage. This approach remains to be tested against various soils, crops, pesticides and types of mulch.
    Keywords: Pesticide Fate Model ; Macro ; Crop Residue ; Cover Crop ; Field Experiment ; Pesticide ; Environmental Sciences ; Biology ; Public Health
    ISSN: 0048-9697
    E-ISSN: 1879-1026
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  • 6
    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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  • 7
    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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  • 8
    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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  • 9
    Language: English
    In: Geoderma, April 2015, Vol.243-244, pp.18-28
    Description: Temporal variations in soil physical properties are rarely recorded in field experiments or considered when modeling water and solute dynamics in agricultural soils. This study aimed at (a) quantifying the temporal variations in soil physical properties, such as the saturated hydraulic conductivity ( ), bulk density ( ) and soil water retention during the growing season of an irrigated maize crop conventionally tilled with a moldboard plow, and (b) modeling the observed water dynamics. For modeling, the effect of temporal variations of soil properties was explored and compared to results with constant values of soil properties during the simulation period and with results after an optimization of soil parameters by inverse modeling. Field and laboratory experiments were performed to measure the soil physical properties of five soil compartments (defined according to the position relative to crop row and the depth) at three dates during the maize season (sowing, flowering and just before harvest). During the maize season, values ranged from 1.21 to 1.56 g cm and increased with time (by 15–25% of the initial value). values, ranging from 2.9 to 56.3 mm h , significantly decreased with time (by a factor of 3 to 6) according to the soil compartment, and were negatively correlated with . In the first step to model water dynamics, the initial values of soil physical properties (measured at maize sowing) were used as constant input parameters for the model HYDRUS-2D during the maize season. This simulation led to a poor description of soil water potentials and water content dynamics, without any drainage at 100 cm depth during the maize season. After an optimization of soil physical parameters, the description of the water dynamics was significantly improved, but optimized parameters, especially and , were not within the range of field measurements. In a last modeling step, the simulation period was divided into three periods with a specific parameterization of soil physical properties for each period. The description of the water dynamics was improved compared to the simulation with constant values for soil physical properties. Such results argue for taking into account time-variable soil physical properties in modeling to correctly assess the water and solute dynamics in soils.
    Keywords: Hydraulic Potential ; Volumetric Water Content ; Hydrus-2d ; Drainage ; Saturated Hydraulic Conductivity ; Agriculture
    ISSN: 0016-7061
    E-ISSN: 1872-6259
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  • 10
    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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