Topographic forcing of flow partition and flow structures at river bifurcations

This paper presents the predicted flow dynamics from the application of a Reynolds-averaged NavierStokes model to a series of bifurcation geometries with morphologies measured during previous flume experiments. The topography of the bifurcations consists of either plane or bedform-dominated beds which may or may not possess discordance between the two bifurcation distributaries. Numerical predictions are compared with experimental results to assess the ability of the numerical model to reproduce the division of flow into the bifurcation distributaries. The hydrodynamic model predicts: (1) diverting fluxes in the upstream channel which direct water into the distributaries; (2) super-elevation of the free surface induced at the bifurcation edge by pressure differences; and (3) counter-rotating secondary circulation cells which develop upstream of the apex of the bifurcation and move into the downstream channels, with water converging at the surface and diverging at the bed. When bedforms are not present, weak transversal fluxes characterize the upstream channel for almost its entire length, associated with clearly distinguishable secondary circulation cells, although these may be under-estimated by the turbulence model used in the solution. In the bedform dominated case, the same hydrodynamic conditions were not observed, with the bifurcation influence restricted and depth scale secondary circulation cells not forming. The results also demonstrate the dominant effect bed discordance has upon flow division between the two distributaries. Finally, results indicate that in bedform dominated rivers. Consequently, we suggest that sand-bed river bifurcations are more likely to have an influence that extends much further upstream and have a greater impact upon water distribution. This may contribute to observed morphological differences between sand-bedded and gravel-bedded braided river networks. Copyright (C) 2012 John Wiley & Sons, Ltd.

Three-dimensional aspects of fluid flows in channels. I. Meniscus and thin film regimes

We study the forced displacement of a fluid-fluid interface in a three-dimensional channel formed by two parallel solid plates. Using a lattice-Boltzmann method, we study situations in which a slip velocity arises from diffusion effects near the contact line. The difference between the slip and channel velocities determines whether the interface advances as a meniscus or a thin film of fluid is left adhered to the plates. We find that this effect is controlled by the capillary and Péclet numbers. We estimate the crossover from a meniscus to a thin film and find good agreement with numerical results. The penetration regime is examined in the steady state. We find that the occupation fraction of the advancing finger relative to the channel thickness is controlled by the capillary number and the viscosity contrast between the fluids. For high viscosity contrast, lattice-Boltzmann results agree with previous results. For zero viscosity contrast, we observe remarkably narrow fingers. The shape of the finger is found to be universal.

Perturbing Hele-Shaw flow with a small gap gradient

A controlled perturbation is introduced into the Saffman-Taylor flow problem by adding a gradient to the gap of a Hele-Shaw cell. The stability of the single-finger steady state was found to be strongly affected by such a perturbation. Compared with patterns in a standard Hele-Shaw cell, the single Saffman-Taylor finger was stabilized or destabilized according to the sign of the gap gradient. While a linear stability analysis shows that this perturbation should have a negligible effect on the early-stage pattern formation, the experimental data indicate that the characteristic length for the initial breakup of a flat interface has been changed by the perturbation.

Seismic attenuation due to wave-induced fluid flow at microscopic and macroscopic scales

Wave-induced fluid flow at microscopic and mesoscopic scales arguably constitutes the major cause of intrinsic seismic attenuation throughout the exploration seismic and sonic frequency ranges. The quantitative analysis of these phenomena is, however, complicated by the fact that the governing physical processes may be dependent. The reason for this is that the presence of microscopic heterogeneities, such as micro-cracks or broken grain contacts, causes the stiffness of the so-called modified dry frame to be complex-valued and frequency-dependent, which in turn may affect the viscoelastic behaviour in response to fluid flow at mesoscopic scales. In this work, we propose a simple but effective procedure to estimate the seismic attenuation and velocity dispersion behaviour associated with wave-induced fluid flow due to both microscopic and mesoscopic heterogeneities and discuss the results obtained for a range of pertinent scenarios.

Endocytic and secretory traffic in Arabidopsis merge in the trans-Golgi network/early endosome, an independent and highly dynamic organelle.

Plants constantly adjust their repertoire of plasma membrane proteins that mediates transduction of environmental and developmental signals as well as transport of ions, nutrients, and hormones. The importance of regulated secretory and endocytic trafficking is becoming increasingly clear; however, our knowledge of the compartments and molecular machinery involved is still fragmentary. We used immunogold electron microscopy and confocal laser scanning microscopy to trace the route of cargo molecules, including the BRASSINOSTEROID INSENSITIVE1 receptor and the REQUIRES HIGH BORON1 boron exporter, throughout the plant endomembrane system. Our results provide evidence that both endocytic and secretory cargo pass through the trans-Golgi network/early endosome (TGN/EE) and demonstrate that cargo in late endosomes/multivesicular bodies is destined for vacuolar degradation. Moreover, using spinning disc microscopy, we show that TGN/EEs move independently and are only transiently associated with an individual Golgi stack.

Effects of traffic control on the soil physical quality and the cultivation of sugarcane

The cultivation of sugarcane with intensive use of machinery, especially for harvest, induces soil compaction, affecting the crop development. The control of agricultural traffic is an alternative of management in the sector, with a view to preserve the soil physical quality, resulting in increased sugarcane root growth, productivity and technological quality. The objective of this study was to evaluate the physical quality of an Oxisol with and without control traffic and the resulting effects on sugarcane root development, productivity and technological quality. The following managements were tested: no traffic control (NTC), traffic control consisting of an adjustment of the track width of the tractor and sugarcane trailer (TC1) and traffic control consisting of an adjustment of the track width of the tractor and trailer and use of an autopilot (TC2). Soil samples were collected (layers 0.00-0.10; 0.10-0.20 and 0.20-0.30 m) in the plant rows, inter-row center and seedbed region, 0.30 m away from the plant row. The productivity was measured with a specific weighing scale. The technological variables of sugarcane were measured in each plot. Soil cores were collected to analyze the root system. In TC2, the soil bulk density and compaction degree were lowest and total porosity and macroporosity highest in the plant row. Soil penetration resistance in the plant row, was less than 2 MPa in TC1 and TC2. Soil aggregation and total organic carbon did not differ between the management systems. The root surface and volume were increased in TC1 and TC2, with higher productivity and sugar yield than under NTC. The sugarcane variables did not differ between the managements. The soil physical quality in the plant row was preserved under management TC1 and TC2, with an improved root development and increases of 18.72 and 20.29 % in productivity and sugar yield, respectively.

Accurate and efficient simulation of multiphase flow in a heterogeneous reservoir by using error estimate and control in the multiscale finite-volume framework

The multiscale finite-volume (MSFV) method is designed to reduce the computational cost of elliptic and parabolic problems with highly heterogeneous anisotropic coefficients. The reduction is achieved by splitting the original global problem into a set of local problems (with approximate local boundary conditions) coupled by a coarse global problem. It has been shown recently that the numerical errors in MSFV results can be reduced systematically with an iterative procedure that provides a conservative velocity field after any iteration step. The iterative MSFV (i-MSFV) method can be obtained with an improved (smoothed) multiscale solution to enhance the localization conditions, with a Krylov subspace method [e.g., the generalized-minimal-residual (GMRES) algorithm] preconditioned by the MSFV system, or with a combination of both. In a multiphase-flow system, a balance between accuracy and computational efficiency should be achieved by finding a minimum number of i-MSFV iterations (on pressure), which is necessary to achieve the desired accuracy in the saturation solution. In this work, we extend the i-MSFV method to sequential implicit simulation of time-dependent problems. To control the error of the coupled saturation/pressure system, we analyze the transport error caused by an approximate velocity field. We then propose an error-control strategy on the basis of the residual of the pressure equation. At the beginning of simulation, the pressure solution is iterated until a specified accuracy is achieved. To minimize the number of iterations in a multiphase-flow problem, the solution at the previous timestep is used to improve the localization assumption at the current timestep. Additional iterations are used only when the residual becomes larger than a specified threshold value. Numerical results show that only a few iterations on average are necessary to improve the MSFV results significantly, even for very challenging problems. Therefore, the proposed adaptive strategy yields efficient and accurate simulation of multiphase flow in heterogeneous porous media.

Roles of multiple acyl-CoA oxidases in the routing of carbon flow towards β-oxidation and polyhydroxyalkanoate biosynthesis in Yarrowia lipolytica.

The oleaginous yeast Yarrowia lipolytica possesses six acyl-CoA oxidase (Aox) isoenzymes encoded by genes POX1-POX6. The respective roles of these multiple Aox isoenzymes were studied in recombinant Y. lipolytica strains that express heterologous polyhydroxyalkanoate (PHA) synthase (phaC) of Pseudomonas aeruginosa in varying POX genetic backgrounds, thus allowing assessment of the impact of specific Aox enzymes on the routing of carbon flow to β-oxidation or to PHA biosynthesis. Analysis of PHA production yields during growth on fatty acids with different chain lengths has revealed that the POX genotype significantly affects the PHA levels, but not the monomer composition of PHA. Aox3p function was found to be responsible for 90% and 75% of the total PHA produced from either C9:0 or C13:0 fatty acid, respectively, whereas Aox5p encodes the main Aox involved in the biosynthesis of 70% of PHA from C9:0 fatty acid. Other Aoxs, such as Aox1p, Aox2p, Aox4p and Aox6p, were not found to play a significant role in PHA biosynthesis, independent of the chain length of the fatty acid used. Finally, three known models of β-oxidation are discussed and it is shown that a 'leaky-hose pipe model' of the cycle can be applied to Y. lipolytica.

Properties of debris flow deposits and source materials compared: implications for debris flow characterization

In the Alps, debris flow deposits generally contain < 5% clay-size particles, and the role of the surface-charged < 2 mu m particles is often neglected, although these particles may have a significant impact on the rheological properties of the interstitial fluid. The objective of this study was to compare debris flow deposits and parent materials from two neighbouring catchments of the Swiss Alps, with special emphasis on the colloidal constituents. The catchments are small in area (4 km(2)), 2.5 km long, similar in morphology, but different in geology. The average slopes are 35-40%. The catchments were monitored for debris flow events and mapped for surface aspect and erosion activity. Debris flow deposits and parent materials were sampled, the clay and silt fractions extracted and the bulk density, < 2 mm fraction bulk density, particle size distribution, chemical composition, cation exchange capacity (CEC) and mineralogy analysed. The results show that the deposits are similar to the parent screes in terms of chemical composition, but differ in terms of: (i) particle size distribution; and (ii) mineralogy, reactivity and density of the < 2 mm fraction. In this fraction, compared with the parent materials the deposits show dense materials enriched in coarse monocrystalline particles, of which the smallest and more reactive particles were leached. The results suggest that deposit samples should not be considered as representative of source or flow materials, particularly with respect to their physical properties.

Multiscale descriptions of density-driven flow instabilities in porous media

Les instabilités engendrées par des gradients de densité interviennent dans une variété d'écoulements. Un exemple est celui de la séquestration géologique du dioxyde de carbone en milieux poreux. Ce gaz est injecté à haute pression dans des aquifères salines et profondes. La différence de densité entre la saumure saturée en CO2 dissous et la saumure environnante induit des courants favorables qui le transportent vers les couches géologiques profondes. Les gradients de densité peuvent aussi être la cause du transport indésirable de matières toxiques, ce qui peut éventuellement conduire à la pollution des sols et des eaux. La gamme d'échelles intervenant dans ce type de phénomènes est très large. Elle s'étend de l'échelle poreuse où les phénomènes de croissance des instabilités s'opèrent, jusqu'à l'échelle des aquifères à laquelle interviennent les phénomènes à temps long. Une reproduction fiable de la physique par la simulation numérique demeure donc un défi en raison du caractère multi-échelles aussi bien au niveau spatial et temporel de ces phénomènes. Il requiert donc le développement d'algorithmes performants et l'utilisation d'outils de calculs modernes. En conjugaison avec les méthodes de résolution itératives, les méthodes multi-échelles permettent de résoudre les grands systèmes d'équations algébriques de manière efficace. Ces méthodes ont été introduites comme méthodes d'upscaling et de downscaling pour la simulation d'écoulements en milieux poreux afin de traiter de fortes hétérogénéités du champ de perméabilité. Le principe repose sur l'utilisation parallèle de deux maillages, le premier est choisi en fonction de la résolution du champ de perméabilité (grille fine), alors que le second (grille grossière) est utilisé pour approximer le problème fin à moindre coût. La qualité de la solution multi-échelles peut être améliorée de manière itérative pour empêcher des erreurs trop importantes si le champ de perméabilité est complexe. Les méthodes adaptatives qui restreignent les procédures de mise à jour aux régions à forts gradients permettent de limiter les coûts de calculs additionnels. Dans le cas d'instabilités induites par des gradients de densité, l'échelle des phénomènes varie au cours du temps. En conséquence, des méthodes multi-échelles adaptatives sont requises pour tenir compte de cette dynamique. L'objectif de cette thèse est de développer des algorithmes multi-échelles adaptatifs et efficaces pour la simulation des instabilités induites par des gradients de densité. Pour cela, nous nous basons sur la méthode des volumes finis multi-échelles (MsFV) qui offre l'avantage de résoudre les phénomènes de transport tout en conservant la masse de manière exacte. Dans la première partie, nous pouvons démontrer que les approximations de la méthode MsFV engendrent des phénomènes de digitation non-physiques dont la suppression requiert des opérations de correction itératives. Les coûts de calculs additionnels de ces opérations peuvent toutefois être compensés par des méthodes adaptatives. Nous proposons aussi l'utilisation de la méthode MsFV comme méthode de downscaling: la grille grossière étant utilisée dans les zones où l'écoulement est relativement homogène alors que la grille plus fine est utilisée pour résoudre les forts gradients. Dans la seconde partie, la méthode multi-échelle est étendue à un nombre arbitraire de niveaux. Nous prouvons que la méthode généralisée est performante pour la résolution de grands systèmes d'équations algébriques. Dans la dernière partie, nous focalisons notre étude sur les échelles qui déterminent l'évolution des instabilités engendrées par des gradients de densité. L'identification de la structure locale ainsi que globale de l'écoulement permet de procéder à un upscaling des instabilités à temps long alors que les structures à petite échelle sont conservées lors du déclenchement de l'instabilité. Les résultats présentés dans ce travail permettent d'étendre les connaissances des méthodes MsFV et offrent des formulations multi-échelles efficaces pour la simulation des instabilités engendrées par des gradients de densité. - Density-driven instabilities in porous media are of interest for a wide range of applications, for instance, for geological sequestration of CO2, during which CO2 is injected at high pressure into deep saline aquifers. Due to the density difference between the C02-saturated brine and the surrounding brine, a downward migration of CO2 into deeper regions, where the risk of leakage is reduced, takes place. Similarly, undesired spontaneous mobilization of potentially hazardous substances that might endanger groundwater quality can be triggered by density differences. Over the last years, these effects have been investigated with the help of numerical groundwater models. Major challenges in simulating density-driven instabilities arise from the different scales of interest involved, i.e., the scale at which instabilities are triggered and the aquifer scale over which long-term processes take place. An accurate numerical reproduction is possible, only if the finest scale is captured. For large aquifers, this leads to problems with a large number of unknowns. Advanced numerical methods are required to efficiently solve these problems with today's available computational resources. Beside efficient iterative solvers, multiscale methods are available to solve large numerical systems. Originally, multiscale methods have been developed as upscaling-downscaling techniques to resolve strong permeability contrasts. In this case, two static grids are used: one is chosen with respect to the resolution of the permeability field (fine grid); the other (coarse grid) is used to approximate the fine-scale problem at low computational costs. The quality of the multiscale solution can be iteratively improved to avoid large errors in case of complex permeability structures. Adaptive formulations, which restrict the iterative update to domains with large gradients, enable limiting the additional computational costs of the iterations. In case of density-driven instabilities, additional spatial scales appear which change with time. Flexible adaptive methods are required to account for these emerging dynamic scales. The objective of this work is to develop an adaptive multiscale formulation for the efficient and accurate simulation of density-driven instabilities. We consider the Multiscale Finite-Volume (MsFV) method, which is well suited for simulations including the solution of transport problems as it guarantees a conservative velocity field. In the first part of this thesis, we investigate the applicability of the standard MsFV method to density- driven flow problems. We demonstrate that approximations in MsFV may trigger unphysical fingers and iterative corrections are necessary. Adaptive formulations (e.g., limiting a refined solution to domains with large concentration gradients where fingers form) can be used to balance the extra costs. We also propose to use the MsFV method as downscaling technique: the coarse discretization is used in areas without significant change in the flow field whereas the problem is refined in the zones of interest. This enables accounting for the dynamic change in scales of density-driven instabilities. In the second part of the thesis the MsFV algorithm, which originally employs one coarse level, is extended to an arbitrary number of coarse levels. We prove that this keeps the MsFV method efficient for problems with a large number of unknowns. In the last part of this thesis, we focus on the scales that control the evolution of density fingers. The identification of local and global flow patterns allows a coarse description at late times while conserving fine-scale details during onset stage. Results presented in this work advance the understanding of the Multiscale Finite-Volume method and offer efficient dynamic multiscale formulations to simulate density-driven instabilities. - Les nappes phréatiques caractérisées par des structures poreuses et des fractures très perméables représentent un intérêt particulier pour les hydrogéologues et ingénieurs environnementaux. Dans ces milieux, une large variété d'écoulements peut être observée. Les plus communs sont le transport de contaminants par les eaux souterraines, le transport réactif ou l'écoulement simultané de plusieurs phases non miscibles, comme le pétrole et l'eau. L'échelle qui caractérise ces écoulements est définie par l'interaction de l'hétérogénéité géologique et des processus physiques. Un fluide au repos dans l'espace interstitiel d'un milieu poreux peut être déstabilisé par des gradients de densité. Ils peuvent être induits par des changements locaux de température ou par dissolution d'un composé chimique. Les instabilités engendrées par des gradients de densité revêtent un intérêt particulier puisque qu'elles peuvent éventuellement compromettre la qualité des eaux. Un exemple frappant est la salinisation de l'eau douce dans les nappes phréatiques par pénétration d'eau salée plus dense dans les régions profondes. Dans le cas des écoulements gouvernés par les gradients de densité, les échelles caractéristiques de l'écoulement s'étendent de l'échelle poreuse où les phénomènes de croissance des instabilités s'opèrent, jusqu'à l'échelle des aquifères sur laquelle interviennent les phénomènes à temps long. Etant donné que les investigations in-situ sont pratiquement impossibles, les modèles numériques sont utilisés pour prédire et évaluer les risques liés aux instabilités engendrées par les gradients de densité. Une description correcte de ces phénomènes repose sur la description de toutes les échelles de l'écoulement dont la gamme peut s'étendre sur huit à dix ordres de grandeur dans le cas de grands aquifères. Il en résulte des problèmes numériques de grande taille qui sont très couteux à résoudre. Des schémas numériques sophistiqués sont donc nécessaires pour effectuer des simulations précises d'instabilités hydro-dynamiques à grande échelle. Dans ce travail, nous présentons différentes méthodes numériques qui permettent de simuler efficacement et avec précision les instabilités dues aux gradients de densité. Ces nouvelles méthodes sont basées sur les volumes finis multi-échelles. L'idée est de projeter le problème original à une échelle plus grande où il est moins coûteux à résoudre puis de relever la solution grossière vers l'échelle de départ. Cette technique est particulièrement adaptée pour résoudre des problèmes où une large gamme d'échelle intervient et évolue de manière spatio-temporelle. Ceci permet de réduire les coûts de calculs en limitant la description détaillée du problème aux régions qui contiennent un front de concentration mobile. Les aboutissements sont illustrés par la simulation de phénomènes tels que l'intrusion d'eau salée ou la séquestration de dioxyde de carbone.

Hydrodynamic induced deformation of and orientation of a microscopic elastic filament

We describe simulations of an elastic filament immersed in a fluid and subjected to a body force. The coupling between the fluid flow and the friction that the filament experiences induces bending and alignment perpendicular to the force. With increasing force there are four shape regimes, ranging from slight distortion to an unsteady tumbling motion. We also find marginally stable structures. The instability of these shapes and the alignment are explained by induced bending and nonlocal hydrodynamic interactions. These effects are experimentally relevant for stiff microfilaments.

Using flow cytometry for in situ monitoring of antimicrobial compound production in the biocontrol bacterium Pseudomonas fluorescens CHA0

Pseudomonas fluorescens strain CHA0 is able to protect plants against a variety of pathogens, notably by producing the two antimicrobial compounds 2,4-diacetylphloroglucinol (DAPG) and pyoluteorin (PLT). The regulation of the expression of these compounds is affected by many biotic factors, such as fungal pathogens, rhizosphere bacteria as well as plant species. Therefore, the influence of some plant phenolic compounds on the expression of DAPG and PLT biosynthetic genes has been tested using GFP-based reporter, monitored by standard fluometry and flow cytometry. In situ experiments were also performed with cucumber plants. We found that several plant metabolites such as IAA and umbelliferone are able to modify significantly the expression of DAPG and PLT. The use of flow cytometry with autofluorescents proteins seems to be a promising method to study rhizobacteria-plant interactions.

EFFECTS OF COMPACTION DUE TO MACHINERY TRAFFIC ON SOIL PORE CONFIGURATION

Soil compaction has been recognized as a severe problem in mechanized agriculture and has an influence on many soil properties and processes. Yet, there are few studies on the long-term effects of soil compaction, and the development of soil compaction has been shown through a limited number of soil parameters. The objectives of this study were to evaluate the persistence of soil compaction effects (three traffic treatments: T0, without traffic; T3, three tractor passes; and T5, five tractor passes) on pore system configuration, through static and dynamic determinations; and to determine changes in soil pore orientation due to soil compaction through measurement of hydraulic conductivity of saturated soil in samples taken vertically and horizontally. Traffic led to persistent changes in all the dynamic indicators studied (saturated hydraulic conductivity, K0; effective macro- and mesoporosity, εma and εme), with significantly lower values of K0, εma, and εme in the T5 treatment. The static indicators of bulk density (BD), derived total porosity (TP), and total macroporosity (θma) did not vary significantly among the treatments. This means that machine traffic did not produce persistent changes on these variables after two years. However, the orientation of the soil pore system was modified by traffic. Even in T0, there were greater changes in K0 measured in the samples taken vertically than horizontally, which was more related to the presence of vertical biopores, and to isotropy of K0 in the treatments with machine traffic. Overall, the results showed that dynamic indicators are more sensitive to the effects of compaction and that, in the future, static indicators should not be used as compaction indicators without being complemented by dynamic indicators.

Flow structures at an idealized bifurcation : a numerical experiment

River bifurcations are key nodes within braided river systems controlling the flow and sediment partitioning and therefore the dynamics of the river braiding process. Recent research has shown that certain geometrical configurations induce instabilities that lead to downstream mid-channel bar formation and the formation of bifurcations. However, we currently have a poor understanding of the flow division process within bifurcations and the flow dynamics in the downstream bifurcates, both of which are needed to understand bifurcation stability. This paper presents results of a numerical sensitivity experiment undertaken using computational fluid dynamics (CFD) with the purpose of understanding the flow dynamics of a series of idealized bifurcations. A geometric sensitivity analysis is undertaken for a range of channel slopes (0.005 to 0.03), bifurcation angles (22 degrees to 42 degrees) and a restricted set of inflow conditions based upon simulating flow through meander bends with different curvature on the flow field dynamics through the bifurcation. The results demonstrate that the overall slope of the bifurcation affects the velocity of flow through the bifurcation and when slope asymmetry is introduced, the flow structures in the bifurcation are modified. In terms of bifurcation evolution the most important observation appears to be that once slope asymmetry is greater than 0.2 the flow within the steep bifurcate shows potential instability and the potential for alternate channel bar formation. Bifurcation angle also defines the flow structures within the bifurcation with an increase in bifurcation angle increasing the flow velocity down both bifurcates. However, redistributive effects of secondary circulation caused by upstream curvature can very easily counter the effects of local bifurcation characteristics. Copyright (C) 2011 John Wiley & Sons, Ltd.

Stochastic resonance in a suspension of magnetic dipoles under shear flow

We show that a magnetic dipole in a shear flow under the action of an oscillating magnetic field displays stochastic resonance in the linear response regime. To this end, we compute the classical quantifiers of stochastic resonance, i.e., the signal to noise ratio, the escape time distribution, and the mean first passage time. We also discuss the limitations and role of the linear response theory in its applications to the theory of stochastic resonance.