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• 11
Article
Language: English
In: Transport in Porous Media, Nov, 2014, Vol.105(2), p.391(20)
Description: Byline: Alain Genty (1), Valerie Pot (2) Keywords: Lattice Boltzmann method; Effective diffusion; TRT; Unsaturated; Porous media Abstract: Numerical models that solve transport of pollutants at the macroscopic scale in unsaturated porous media need the effective diffusion dependence on saturation as an input. We conducted numerical computations at the pore scale in order to obtain the effective diffusion curve as a function of saturation for an academic sphere packing porous medium and for a real porous medium where pore structure knowledge was obtained through X-ray tomography. The computations were performed using a combination of lattice Boltzmann models based on two relaxation time (TRT) scheme. The first stage of the calculations consisted in recovering the water spatial distribution into the pore structure for several fixed saturations using a phase separation TRT lattice Boltzmann model. Then, we performed diffusion computation of a non-reactive solute in the connected water structure using a diffusion TRT lattice Boltzmann model. Finally, the effective diffusion for each selected saturation value was estimated through inversion of a macroscopic classical analytical solution. Author Affiliation: (1) DEN DANS DM2S STMF, CEA-Saclay, Commissariat a l'Energie Atomique et aux Energies Alternatives, 91191, Gif sur Yvette Cedex, France (2) UMR 1091 EGC, AgroParisTech, INRA, 78850, Thiverval-Grignon, France Article History: Registration Date: 04/08/2014 Received Date: 20/03/2014 Accepted Date: 04/08/2014 Online Date: 15/08/2014
ISSN: 0169-3913
Source: Cengage Learning, Inc.
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• 12
Article
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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• 13
Article
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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• 14
Article
Language: English
In: Geoderma, 15 April 2016, Vol.268, pp.29-40
Description: Compost amendments and tillage practices can modify soil structure and create heterogeneities at the local scale. Tillage affects soil physical properties and consequently water and solute transport in soil, while compost addition to soil influences pesticide sorption and degradation processes. Based on the long-term field experiment QualiAgro (a INRA–Veolia partnership), a modeling study was carried out using HYDRUS-2D to evaluate how two different compost types combined with the presence of heterogeneities due to tillage affect water and isoproturon dynamics in soil compared to a control plot. A municipal solid waste compost (MSW) and a co-compost of sewage sludge and green wastes (SGW) have been applied to experimental plots. In each plot, wick lysimeters, TDR probes, and tensiometers were installed to monitor water and solute dynamics. In the plowed layer, four zones differing in their structure were identified: compacted clods, non-compacted soil, interfurrows, and the plow pan. From 2004 to 2010, the unamended control (CONT) plot had the largest cumulative water outflow (1388 mm) compared to the MSW plot (962 mm) and SGW plot (979 mm). After calibration, the model was able to describe cumulative water outflow for the whole 2004–2010 period with a model efficiency value of 0.99 for all three plots. The CONT plot had the largest isoproturon cumulated leaching (21.31 μg) while similar cumulated isoproturon leaching was measured in the SGW (0.663 μg) and MSW (0.245 μg) plots. The model was able to simulate isoproturon leaching patterns except for the large preferential flow events that were observed in the MSW and CONT plots. The timing of these preferential flow events could be reproduced by the model but not their magnitude. Modeling results indicate that spatial and temporal variations in pesticide degradation rate due to tillage and compost application play a major role in the dynamics of isoproturon leaching. Both types of compost were found to reduce isoproturon leaching on the 6 year duration of the experiment.
Keywords: Soil Heterogeneity ; Compost Amendments ; Conventional Tillage ; Water Flow ; Isoproturon ; Hydrus-2d ; Agriculture
ISSN: 0016-7061
E-ISSN: 1872-6259
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• 15
Article
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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• 16
Article
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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• 17
Article
Language: English
In: Transport in Porous Media, 2017, Vol.116(3), pp.975-1003
Description: Hydrogen gas migration modeling through water-saturated engineering barriers and the host rock of a deep geological repository for radioactive waste is of concern for safety assessment of such facilities. A two-phase two-relaxation-time lattice Boltzmann model using the Rothman and Keller approach was parallelized on graphic processing units to simulate hydrogen gas migration in a 3D image obtained by X-ray microtomography of Opalinus clay microfractures. A dimensional analysis combined with a grid refinement analysis was carried out to set the model parameters to reproduce the realistic viscous, capillary and inertial forces of the natural system. Relative permeabilities curves were first calculated in a simple regular fracture with different initial two-phase configurations. We observed that segmented gas flow configurations led to a drop in the relative gas permeability by two orders of magnitude as compared to parallel flow configuration. The model was then applied to 4 $$\times$$ × refined 3D images. For lower water saturation values ( $$0.5 \le S_\mathrm{w} 〈 0.7$$ 0.5 ≤ S w 〈 0.7 ), hydrogen gas migrated through continuous gas paths oriented in the flow direction. At high water saturation values ( $$S_\mathrm{w}\ge 0.7$$ S w ≥ 0.7 ), the relative gas permeability dropped to zero because the hydrogen phase segmented into gas pockets that were stuck in local narrow throats of the clay fracture. The study pointed out that the high capillary forces prevented the gas bubbles from distorting themselves to pass through these narrow paths.
Keywords: LBM ; Two-phase flow ; Relative permeability ; RK ; TRT ; GPU
ISSN: 0169-3913
E-ISSN: 1573-1634
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• 18
Article
Language: English
In: Geoderma, 2015, Vol.243-244, p.18(11)
Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.geoderma.2014.12.006 Byline: Lionel Alletto, Valerie Pot, Simon Giuliano, Mathieu Costes, Francois Perdrieux, Eric Justes Abstract: 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 (K.sub.s), bulk density ([rho].sub.b) 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, [rho].sub.b values ranged from 1.21 to 1.56gcm.sup.-3 and increased with time (by 15-25% of the initial value). K.sub.s values, ranging from 2.9 to 56.3mmh.sup.-1, significantly decreased with time (by a factor of 3 to 6) according to the soil compartment, and were negatively correlated with [rho].sub.b. 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 100cm 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 K.sub.s and [theta].sub.s, 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. Article History: Received 18 July 2014; Revised 5 December 2014; Accepted 14 December 2014
Keywords: Hydrogeology – Analysis ; Soil Moisture – Analysis
ISSN: 0016-7061
Source: Cengage Learning, Inc.
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• 19
Article
Language: English
In: European Journal of Soil Science, 2011, Vol.62(6), pp.797-810
Description: To authenticate to the full-text of this article, please visit this link: http://dx.doi.org/10.1111/j.1365-2389.2011.01402.x Byline: V. Pot (a), P. Benoit (a), V. Etievant (a), N. Bernet (a), C. Labat (a), Y. Coquet (a), S. Houot (a) Abstract: We quantified the effects of tillage practice and repeated compost (municipal solid waste compost, MSW, and co-compost of sewage sludge and green wastes, SGW, compared with a control plot without compost addition, CONT) application on bromide and isoproturon transport into the tilled horizon of a loamy Albeluvisol. To do this we conducted field measurements of near-saturated hydraulic conductivity (K), bromide and isoproturon leaching in column experiments and batch isoproturon sorption measurements. While the K measurements showed that tillage practice had the major effect compared with the different organic amendments, with greater conductivities measured after ploughing and smaller Kvalues measured after sowing, the column leaching experiments showed no statistically significant effect of either the tillage practice or the compost amendments. The batch sorption coefficient, K.sub.d, of isoproturon increased in the order CONT 〈 MSW 〈 SGW, while the leaching of isoproturon for the MSW and SGW was either equal, retarded or quicker compared with CONT. Rate-limited sorption of isoproturon in the CONT and SGW treatments columns was found, and the overall dissipation of isoproturon increased in the order CONT 〈 SGW 〈 MSW. It was suggested that irreversible sorption as well as degradation occured during isoproturon leaching. Author Affiliation: (a)INRA, AgroParisTech , UMR 1091 EGC, F-78850 Thiverval-Grignon, France Article History: Received 3 January 2011; revised version accepted 30 August 2011 Article note: V. Pot. E-mail: vpot@grignon.inra.fr
Keywords: Life Sciences ; Agricultural Sciences ; Sciences Du Sol  ; Tillage Practice ; Isoproturon Transport ; Soil Science ; Agriculture ; Agriculture
ISSN: 1351-0754
E-ISSN: 1365-2389
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• 20
Article
Language: English
In: Environmental Science and Pollution Research, 2016, Vol.23(7), pp.6907-6918
Description: Compost amendment on agricultural soil is a current practice to compensate the loss of organic matter. As a consequence, dissolved organic carbon concentration in soil leachates can be increased and potentially modify the transport of other solutes. This study aims to characterize the processes controlling the mobility of dissolved organic matter (DOM) in deep soil layers and their potential impacts on the leaching of organic contaminants (pesticides and pharmaceutical compounds) potentially present in cultivated soils receiving organic waste composts. We sampled undisturbed soil cores in the illuviated horizon (60–90 cm depth) of an Albeluvisol. Percolation experiments were made in presence and absence of DOM with two different pesticides, isoproturon and epoxiconazole, and two pharmaceutical compounds, ibuprofen and sulfamethoxazole. Two types of DOM were extracted from two different soil surface horizons: one sampled in a plot receiving a co-compost of green wastes and sewage sludge applied once every 2 years since 1998 and one sampled in an unamended plot. Results show that DOM behaved as a highly reactive solute, which was continuously generated within the soil columns during flow and increased after flow interruption. DOM significantly increased the mobility of bromide and all pollutants, but the effects differed according the hydrophobic and the ionic character of the molecules. However, no clear effects of the origin of DOM on the mobility of the different contaminants were observed.
Keywords: Dissolved organic matter ; Pesticides ; Pharmaceutical compounds ; Undisturbed soil columns ; Non-equilibrium transport
ISSN: 0944-1344
E-ISSN: 1614-7499
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