Imagerie quatitative non invasive et expérimentation pour l'intégration des phénomènes d'écoulement non uniforme dans les modèles de transfert de masse en milieux poreux hétérogènes : Application aux sols structurés

Predicting the evolution of groundwater resource due to future climate change requires a better knowledge of water flows in soils which are highly complex porous medium. A lot of research has been conducted about soil water flow complexity over the last decades but predicting water flow in soils whatever soil texture, soil structure and rainfall intensities still remains a challenge. The objective of this work is to improve the modeling of water flow in structured soils by accounting to water flow from macropores to the soil matrix. We follow three successive steps : (i) to perform infiltration – drainage experiments on decimetric undisturbed soils columns under a medical tomograph to better observe flow phenomena within the soil macroporosity, (ii) to extract structural indicators from tomographic images, and study the macroporous soil structure, and (iii) to integrate structural indicators into a Darcy-Richards – KDW dual compartment flow model. Undisturbed soils studied are sampled from three different plots: (i) a clay soil worked in a field crop, (ii) a clay soil not worked in an orchard and (iii) a silt – sandy soil not worked and not cultivated. Three infiltration – drainage experiment are performed in a medical tomograph with fast image acquisition (~15 sec), 30 mm of water is supplied with a rainfall simulator and an intensity of 20 mm.h-1. Infiltration duration was of 90 min followed by 30 min of drainage. In total, the tomographic follow-up takes 120 min. Each experiment is done at three initial moisture conditions: (1) field capacity, (2) matrix potential at – 4 m, and (3) matrix potential at – 8 m. The initial structure observed before each infiltration shows that the soil macroporosity increases from 2 to 5% with the decrease of the initial water content. This increase is higher for the two clay soils compared to the silty – sandy soil. The hypothesis is that soil texture influences the evolution of the soil structure according to the matric water content. Thus, clay soils have the most variable soil structure over time, unlike silt – sandy soils which seem more structurally stable. Rapid movements of the soil structure during the infiltration and drainage phases was observed thanks to the time lapse tomographic monitoring. During water flow, soil macroporosity decreases between 7 to 30 % and increases again during drainage. The decrease of soil macroporosity during infiltration is more pronounced for the most saturated initial condition. The increase is less marked for the driest conditions. The hypothesis is that water flow along the macropores’ walls destabilizes causes an ‘over-swelling’ of the walls, which reverses during drainage. The study of overall indicators show that temporal monitoring of macropores density and their volumes makes it possible to discriminate specific texture and tillage behaviors different for the three soils. Models performed with the addition of profiled data measured on tomographic image in water flow model show that these measurements allow to reconstruct experimental data. Although the gap between modelling and observation for the driest experiments seems to indicate that it is necessary to continue the study of macropores – matrix exchanges in unsaturated conditions. This requires further study of the movements of the structure during wetting – drying cycles but also during the fast water flux transit.Mieux comprendre les écoulements d’eau dans les milieux poreux hétérogènes tels que les sols est nécessaire. Aussi bien pour piloter l’irrigation des cultures, améliorer la prédiction des modèles climatiques et météorologiques ou gérer quantitativement et qualitativement les ressources en eaux et leurs évolutions sous l’effet des changements globaux, notamment en zone Méditerranéenne. Cependant, la complexité des écoulements dans les sols, découlant de la complexité de leur système poral, constitue un frein à la connaissance complète du système. Les objectifs de ce travail sont de progresser sur ce dernier point en : (i) réalisant des expériences d’infiltration – drainage sur des colonnes décimétriques de sols non remaniés en tomographie médicale et observer au mieux les écoulements au sein de la macroporosité du sol, (ii) en étudiant la structure macroporeuse des sols et déterminer des indicateurs structuraux sur les images tomographiques et (iii) en intégrant les indicateurs structuraux dans un modèle d’écoulement à double compartiment Darcy-Richards – KDW. Les sols étudiés sont prélevés dans trois parcelles différentes : (i) un sol argileux travaillé en grande culture, (ii) un sol argileux non travaillé utilisé en verger et (iii) un sol limono – sableux non travaillé non cultivé. Trois expériences d’infiltration – drainage ont été faites dans un scanner médical à acquisition d’images rapide (~15 sec). Elles sont réalisées à une intensité de 20 mm.h-1 pour 30 mm d’eau apporté, soit 90 min d’infiltration et une phase de drainage de 30 min. Les expériences sont faites à trois humidités initiales : (1) capacité au champ, (2) potentiel matriciel moyen – 4 m et (3) potentiel matriciel moyen – 8 m. La macroporosité des sols augmente de 2 à 5% avant chaque infiltration lorsque la teneur en eau initiale diminue. Cette augmentation est plus grande pour les deux sols argileux que pour le sol limono – sableux. L’hypothèse avancée est que la texture des sols influence ces différences de réponse. Les sols argileux présentent la structure la plus variable dans le temps au contraire des sols sableux qui semblent plus stables. Le suivi tomographique temporel a permis d’observer des phénomènes de mouvements très rapides de la structure durant l’infiltration et le drainage. Pendant le passage de l’eau, le volume de macroporosité diminue de 7 à 30%, et augmente rapidement durant la phase de ressuyage de 30 min. La diminution de macroporosité durant l’infiltration est plus marquée lorsque la teneur en eau initiale est la plus importante. L’augmentation de macroporosité durant la phase de ressuyage est moins marquée pour les conditions initiales les plus sèches. L’hypothèse avancée est que le passage de l’eau le long des parois des macropores les déstabilise et entraine un « sur – gonflement » des parois, qui s’inverse durant le drainage. L’étude des indicateurs structuraux globaux montre que le suivi temporel de la densité de macropores et de leur volume permet, pour ces trois sols, de discriminer des comportements selon la texture et le travail du sol. Les modélisations réalisées avec l’ajout de paramètres mesurés sur les images tomographiques dans le modèle d’écoulement montrent qu’elles permettent de reconstruire les données expérimentales. Ce travail montre que les écarts subsistant entre la modélisation et l’observation des expériences les plus sèches montrent que la dynamique des échanges entre macropores et matrice du sol doit être mieux comprise, surtout en condition insaturée. Cela nécessite de poursuivre l’étude des mouvements de la structure durant les cycles d’humectation – dessication mais aussi pendant le passage rapide d’un flux d’eau

Imaging techniques and infiltration experiments for the integration of non-uniform flow phenomena in mass transfer models applied to heterogeneous porous media : the case of structured soil

Mieux comprendre les écoulements d’eau dans les milieux poreux hétérogènes tels que les sols est nécessaire. Aussi bien pour piloter l’irrigation des cultures, améliorer la prédiction des modèles climatiques et météorologiques ou gérer quantitativement et qualitativement les ressources en eaux et leurs évolutions sous l’effet des changements globaux, notamment en zone Méditerranéenne. Cependant, la complexité des écoulements dans les sols, découlant de la complexité de leur système poral, constitue un frein à la connaissance complète du système. Les objectifs de ce travail sont de progresser sur ce dernier point en : (i) réalisant des expériences d’infiltration – drainage sur des colonnes décimétriques de sols non remaniés en tomographie médicale et observer au mieux les écoulements au sein de la macroporosité du sol, (ii) en étudiant la structure macroporeuse des sols et déterminer des indicateurs structuraux sur les images tomographiques et (iii) en intégrant les indicateurs structuraux dans un modèle d’écoulement à double compartiment Darcy-Richards – KDW. Les sols étudiés sont prélevés dans trois parcelles différentes : (i) un sol argileux travaillé en grande culture, (ii) un sol argileux non travaillé utilisé en verger et (iii) un sol limono – sableux non travaillé non cultivé. Trois expériences d’infiltration – drainage ont été faites dans un scanner médical à acquisition d’images rapide (~15 sec). Elles sont réalisées à une intensité de 20 mm.h-1 pour 30 mm d’eau apporté, soit 90 min d’infiltration et une phase de drainage de 30 min. Les expériences sont faites à trois humidités initiales : (1) capacité au champ, (2) potentiel matriciel moyen – 4 m et (3) potentiel matriciel moyen – 8 m. La macroporosité des sols augmente de 2 à 5% avant chaque infiltration lorsque la teneur en eau initiale diminue. Cette augmentation est plus grande pour les deux sols argileux que pour le sol limono – sableux. L’hypothèse avancée est que la texture des sols influence ces différences de réponse. Les sols argileux présentent la structure la plus variable dans le temps au contraire des sols sableux qui semblent plus stables. Le suivi tomographique temporel a permis d’observer des phénomènes de mouvements très rapides de la structure durant l’infiltration et le drainage. Pendant le passage de l’eau, le volume de macroporosité diminue de 7 à 30%, et augmente rapidement durant la phase de ressuyage de 30 min. La diminution de macroporosité durant l’infiltration est plus marquée lorsque la teneur en eau initiale est la plus importante. L’augmentation de macroporosité durant la phase de ressuyage est moins marquée pour les conditions initiales les plus sèches. L’hypothèse avancée est que le passage de l’eau le long des parois des macropores les déstabilise et entraine un « sur – gonflement » des parois, qui s’inverse durant le drainage. L’étude des indicateurs structuraux globaux montre que le suivi temporel de la densité de macropores et de leur volume permet, pour ces trois sols, de discriminer des comportements selon la texture et le travail du sol. Les modélisations réalisées avec l’ajout de paramètres mesurés sur les images tomographiques dans le modèle d’écoulement montrent qu’elles permettent de reconstruire les données expérimentales. Ce travail montre que les écarts subsistant entre la modélisation et l’observation des expériences les plus sèches montrent que la dynamique des échanges entre macropores et matrice du sol doit être mieux comprise, surtout en condition insaturée. Cela nécessite de poursuivre l’étude des mouvements de la structure durant les cycles d’humectation – dessication mais aussi pendant le passage rapide d’un flux d’eau.Predicting the evolution of groundwater resource due to future climate change requires a better knowledge of water flows in soils which are highly complex porous medium. A lot of research has been conducted about soil water flow complexity over the last decades but predicting water flow in soils whatever soil texture, soil structure and rainfall intensities still remains a challenge. The objective of this work is to improve the modeling of water flow in structured soils by accounting to water flow from macropores to the soil matrix. We follow three successive steps : (i) to perform infiltration – drainage experiments on decimetric undisturbed soils columns under a medical tomograph to better observe flow phenomena within the soil macroporosity, (ii) to extract structural indicators from tomographic images, and study the macroporous soil structure, and (iii) to integrate structural indicators into a Darcy-Richards – KDW dual compartment flow model. Undisturbed soils studied are sampled from three different plots: (i) a clay soil worked in a field crop, (ii) a clay soil not worked in an orchard and (iii) a silt – sandy soil not worked and not cultivated. Three infiltration – drainage experiment are performed in a medical tomograph with fast image acquisition (~15 sec), 30 mm of water is supplied with a rainfall simulator and an intensity of 20 mm.h-1. Infiltration duration was of 90 min followed by 30 min of drainage. In total, the tomographic follow-up takes 120 min. Each experiment is done at three initial moisture conditions: (1) field capacity, (2) matrix potential at – 4 m, and (3) matrix potential at – 8 m. The initial structure observed before each infiltration shows that the soil macroporosity increases from 2 to 5% with the decrease of the initial water content. This increase is higher for the two clay soils compared to the silty – sandy soil. The hypothesis is that soil texture influences the evolution of the soil structure according to the matric water content. Thus, clay soils have the most variable soil structure over time, unlike silt – sandy soils which seem more structurally stable. Rapid movements of the soil structure during the infiltration and drainage phases was observed thanks to the time lapse tomographic monitoring. During water flow, soil macroporosity decreases between 7 to 30 % and increases again during drainage. The decrease of soil macroporosity during infiltration is more pronounced for the most saturated initial condition. The increase is less marked for the driest conditions. The hypothesis is that water flow along the macropores’ walls destabilizes causes an ‘over-swelling’ of the walls, which reverses during drainage. The study of overall indicators show that temporal monitoring of macropores density and their volumes makes it possible to discriminate specific texture and tillage behaviors different for the three soils. Models performed with the addition of profiled data measured on tomographic image in water flow model show that these measurements allow to reconstruct experimental data. Although the gap between modelling and observation for the driest experiments seems to indicate that it is necessary to continue the study of macropores – matrix exchanges in unsaturated conditions. This requires further study of the movements of the structure during wetting – drying cycles but also during the fast water flux transit

Les travaux d'étude des sols réalisés au scanner médical : bilan et perspectives de la plateforme PIXANIM

National audienc

Comparing dynamics recording of infiltration by X-ray tomography to the results of a dual porosity model for structured soils.

With climate change, preferential flow phenomenon in soil could be predominant in Mediterranean zone. Under- standing this phenomenon becomes a fundamental issue for preserving the water resource in quantity (drinking water) and quality (pesticide content). Non-invasive imaging technics, as X-ray tomography, allow studying water infiltration in laboratory with time-lapse imaging to visualize preferential flow path in soil columns (Sammartino et al. 2012). The modeling of water flow with a dual porosity model (matrix and macropores) integrates these fast flow phenomena (Ilhem 2014). These models, however needs more explicit links with the soil structure. The comparison of experimental results of infiltration (dynamics images and mass data) and modeling could improve our comprehension of preferential flow phenomenon and allow a better integration of the functional macroporosity (i.e. which drains water infiltration during a rain event) in such mass transfer models (Sammartino et al. 2015). Soil columns (Ø 12 cm – hauteur 13 cm, clay-loamy & medium sandy loam) have been sampled in the field to preserve their structure (field plowed or not). Several rains have been simulated in the laboratory and the last one was performed in an X-ray medical scanner (Siemens Somatom® 128 slices) at the CIRE platform (INRA, Centre – Val de Loire). Total and functional macro porosities were identified from time lapse tridimensional images. Water dynamics in the porosities was characterized from the identification and analysis of voxels filled by water. With an image resolution of 350µm only water in the largest macropores can be identified.The modeling of these experiments was carried out via the VirtualSoil platform (UMR Emmah, Avignon; www6.inra.fr/vsoil) using a water flow model coupling Darcy-Richards and KDW equations (Di Pietro et al.,2003). The simulated water flux drained by macropores is similar to the experimental hydrograph obtained for rainfalls on soils close to the saturation.The model reproduced well the flow dynamics: (1) breakthrough time (arrival time of the first drop at the bottom of the column) and (2) the total drained water quantity. A sensitivity analysis of this model is in progress in order to determine the influence of each KDW parameters (two kinematic parameters and one dispersion parameter) and to probe where the functional soil structure could be accounted for in the model structure or in the model parameters. First results show that the kinematic parameters modify the breakthrough time and the slope of the drainage curve

Identifying the Functional Macropore Network Related to Preferential Flow in Structured Soils

International audienceUnderstanding the processes and mechanisms that control preferential flow in soils in relation to the properties of their structures is still challenging since fast flow and transport occur in a small fraction of the porosity, that is, the functional macropore network, making it difficult to image and characterize these processes at decimeter scales. The aim of the paper was therefore to propose a new image acquisition and analysis methodology to characterize preferential flow at the core scale and identify the resulting active macropore network. Water infiltration was monitored by a sequence of three-dimensional images (taken at 5-, 10-, or 15-min intervals) with an X-ray scanner that allows very fast acquisitions (10 s for a 135-mm diameter). A simultaneous dye tracer experiment was also conducted. Water infiltration was then imaged at each acquisition time by the voxels impacted by water during infiltration, named the water voxels. The number of times a voxel was impacted by water during the experiment was converted into data reflecting the water detection frequency at the given position in the soil column, named the local detection frequency. Compared with dye staining, the active macropore network was defined by macropores in which water voxels were the most frequently detected during the experiment (local detection frequency above 65%). The geometric properties of this active network, such as the connectivity, were significantly different from those of the total structure. This image processing methodology coupled to dynamic acquisitions can be used to improve the analysis of preferential flow processes related to soil structures at the core scale

Confrontation du suivi dynamique de l'infiltration par tomographie RX et modèle à double porosité des sols structurés

Confrontation du suivi dynamique de l'infiltration par tomographie RX et modèle à double porosité des sols structurés. GFHN – 41. Journées Scientifiques, 23 – 25 Janvier 2017, Saint-Michel l’Observatoir

Precision medicine in monogenic inflammatory bowel disease:proposed mIBD REPORT standards

Owing to advances in genomics that enable differentiation of molecular aetiologies, patients with monogenic inflammatory bowel disease (mIBD) potentially have access to genotype-guided precision medicine. In this Expert Recommendation, we review the therapeutic research landscape of mIBD, the reported response to therapies, the medication-related risks and systematic bias in reporting. The mIBD field is characterized by the absence of randomized controlled trials and is dominated by retrospective observational data based on case series and case reports. More than 25 off-label therapeutics (including small-molecule inhibitors and biologics) as well as cellular therapies (including haematopoietic stem cell transplantation and gene therapy) have been reported. Heterogeneous reporting of outcomes impedes the generation of robust therapeutic evidence as the basis for clinical decision making in mIBD. We discuss therapeutic goals in mIBD and recommend standardized reporting (mIBD REPORT (monogenic Inflammatory Bowel Disease Report Extended Phenotype and Outcome of Treatments) standards) to stratify patients according to a genetic diagnosis and phenotype, to assess treatment effects and to record safety signals. Implementation of these pragmatic standards should help clinicians to assess the therapy responses of individual patients in clinical practice and improve comparability between observational retrospective studies and controlled prospective trials, supporting future meta-analysis.</p

Precision medicine in monogenic inflammatory bowel disease:proposed mIBD REPORT standards

Owing to advances in genomics that enable differentiation of molecular aetiologies, patients with monogenic inflammatory bowel disease (mIBD) potentially have access to genotype-guided precision medicine. In this Expert Recommendation, we review the therapeutic research landscape of mIBD, the reported response to therapies, the medication-related risks and systematic bias in reporting. The mIBD field is characterized by the absence of randomized controlled trials and is dominated by retrospective observational data based on case series and case reports. More than 25 off-label therapeutics (including small-molecule inhibitors and biologics) as well as cellular therapies (including haematopoietic stem cell transplantation and gene therapy) have been reported. Heterogeneous reporting of outcomes impedes the generation of robust therapeutic evidence as the basis for clinical decision making in mIBD. We discuss therapeutic goals in mIBD and recommend standardized reporting (mIBD REPORT (monogenic Inflammatory Bowel Disease Report Extended Phenotype and Outcome of Treatments) standards) to stratify patients according to a genetic diagnosis and phenotype, to assess treatment effects and to record safety signals. Implementation of these pragmatic standards should help clinicians to assess the therapy responses of individual patients in clinical practice and improve comparability between observational retrospective studies and controlled prospective trials, supporting future meta-analysis.</p