Turbulent kinetic energy budget in a gravel-bed channel flow

The present experimental investigation focuses on the characteristics of near bed turbulence in a fully rough, uniform open-channel flow over a gravel-type bed. Due to bed topography small scale heterogeneity, the flow is not uniform locally in the near bed region and a double averaging methodology is applied over a length scale much larger than the gravel size. The double-averaged Turbulent Kinetic Energy (TKE) budget derived in the context of the present flow over a gravel bed differs from the TKE budget written for flow over a vegetation canopy. The non-constant shape of the roughness function measured in our gravel bed leads to an additional bed-induced production term which is null for vertical roughness elements, such as simplified vegetation elements. The experimental estimation of the terms of the TKE budget reveals that the maximum turbulent activity takes place away from the reference plane, near the roughness crests. However, within the interface sublayer the work of the bed induced velocity fluctuations against the Reynolds stress is of the same magnitude as the main turbulence production term. Consequently, the characteristics of the TKE budget have similarities with uniform flows over canopies and strongly differ from uniform flows over smooth and transitionally rough flows over sedimentlike beds.     

Chloride source delineation in an urban-agricultural watershed: Deicing agents versus agricultural contributions

Analyses (n = 525) of chloride (Cl⁻), bromide (Br⁻), nitrate as nitrogen (NO₃-N), sodium (Na⁺), calcium (Ca²⁺) and potassium (K⁺) in stream water, tile-drain water and groundwater were conducted in an urban-agricultural watershed (10% urban/impervious, 87% agriculture) to explore potential differences in the signature of Cl⁻ originating from an urban source as compared with an agricultural source. Only during winter recharge events did measured Cl⁻ concentrations exceed the 230 mg/L chronic threshold. At base flow, nearly all surface water and tile water samples had Cl⁻ concentrations above the calculated background threshold of 18 mg/L. Mann–Whitney U tests revealed ratios of Cl⁻ to Br⁻ (p = .045), to NO₃-N (p < .0001), to Ca²⁺ (p < .0001), and to Na⁺ (p < .0001) to be significantly different between urban and agricultural waters. While Cl⁻ ratios indicate that road salt was the dominant source of Cl⁻ in the watershed, potassium chloride fertilizer contributed as an important secondary source. Deicing in watersheds where urban land use is minimal had a profound impact on Cl⁻ dynamics; however, agricultural practices contributed Cl⁻ year-round, elevating stream base flow Cl⁻ concentrations above the background level.     

Microtopographic evolution of mineral surfaces as a tool to identify and date young fault scarps in bedrock

Faulting that results in surface ruptures through bedrock can be particularly difficult to date. For example, stratigraphic control on the age of faulting, based on the age of the bedrock, often leaves unacceptably large uncertainty on the age of the faulting. From a paleoseismological perspective, there is a clear need to determine if a bedrock fault scarp is actually a young feature. For young fault ruptures that create fresh mineral surfaces, analysis of microtopography developed by weathering of the mineral surface may provide a quantifiable method for determining the fault age. The direct quantitative measurement of mineral surface microtopography using Atomic Force Microscopy affords a novel method to study the rupture ages of active faults. The method for using microtopographic evolution of mineral surfaces depends on three conditions. The first condition is that freshly exposed mineral cleavage surfaces, which can be described geometrically as planes, are formed during a rupture event. The formation of these fresh surfaces is analogous to the initiation of a weathering ‘clock’ that defines time t=0. Following cleavage formation dissolution of the planar mineral surface occurs. The rate of dissolution for a mineral species under given climatic conditions, governs the rate of mineral surface alteration. Thus as dissolution proceeds, the roughness of the mineral surface increases. We suggest that the progression of microtopographic roughness over time, which can be estimated by computing quantitative statistics derived from digital mineral surface topography, will systematically vary until a steady state surface topography is reached. The fractal dimension, D_f, is one such measure of surface roughness where, D_f at time t=0 is 2. The dissolution of the mineral surface increases the fractal dimension as the removal of material proceeds. We posit that somewhere between D_f=2 and D_f=3, the microtopography reaches a steady state. Therefore, in the pre-steady state stage of surface roughness, the quantitative measure of roughness of the mineral may serve as a measure of time elapsed since faulting. The period of time this initial stage of surface roughening represents is dependent on the mineral and as a consequence, its dissolution rate, in a specific set of environmental conditions. The time elapsed since fault rupture and grain cleavage can also be estimated from the measurement of the volume of material removed through dissolution. If part of the original cleavage surface remains and can be identified then AFM measurements of the surface microtopography can be used to calculate the dissolved volume per unit area.     

2D magnetic resonance tomography applied to karstic conduit imaging

Karstic conduits play a crucial role for water supply in many parts of the world. However, the imaging of such targets is generally a difficult task for most geophysical methods. Magnetic Resonance Sounding (MRS) is a geophysical method designed for imaging of water bearing structures. Initially, MRS was developed for characterizing horizontally stratified aquifers. However, when applying a 1D MRS measuring setup to the imaging of 2D–3D targets, the size of which may be much smaller than the loop, the accuracy and the lateral resolution may not be sufficient. We have studied the possibility of simultaneously processing several MRS aligned along a profile to perform a Magnetic Resonance Tomography (MRT). This work emphasizes the gain of resolution for 2D–3D imagery of MRT versus the interpolation of 1D inversion results of MRS along the same profile. Numerical modelling results show that the MRT response is sensitive to the size and location of the 2D target in the subsurface. Sensitivity studies reveal that by using the coincident transmitting/receiving (TX/RX) setup and shifting the loop around the anomaly area, the depth, section and position of a single karstic conduit with a size smaller than the MRS loop size can be resolved. The accuracy of the results depends on the noise level and signal level, the latter parameter being linked to the depth and volume of the karstic conduit and the water content in the limestone matrix. It was shown that when applying MRT to the localization of 2D anomalies such as karstic conduits, the inclination of the geomagnetic field, the orientation of the MRT profile and the angle of crossover of the conduit by the MRT profile must be taken into account. Otherwise additional errors in interpretation should be expected. A 2D inversion scheme was developed and tested. Both numerical and experimental results confirm the efficiency of the developed approach.     

A discontinuous finite element baroclinic marine model on unstructured prismatic meshes

We describe the time discretization of a three-dimensional baroclinic finite element model for the hydrostatic Boussinesq equations based upon a discontinuous Galerkin finite element method. On one hand, the time marching algorithm is based on an efficient mode splitting. To ensure compatibility between the barotropic and baroclinic modes in the splitting algorithm, we introduce Lagrange multipliers in the discrete formulation. On the other hand, the use of implicit–explicit Runge–Kutta methods enables us to treat stiff linear operators implicitly, while the rest of the nonlinear dynamics is treated explicitly. By way of illustration, the time evolution of the flow over a tall isolated seamount on the sphere is simulated. The seamount height is 90% of the mean sea depth. Vortex shedding and Taylor caps are observed. The simulation compares well with results published by other authors.     

Capturing the residence time boundary layer—application to the Scheldt Estuary

At high Peclet number, the residence time exhibits a boundary layer adjacent to incoming open boundaries. In a Eulerian model, not resolving this boundary layer can generate spurious oscillations that can propagate into the area of interest. However, resolving this boundary layer would require an unacceptably high spatial resolution. Therefore, alternative methods are needed in which no grid refinement is required to capture the key aspects of the physics of the residence time boundary layer. An extended finite element method representation and a boundary layer parameterisation are presented and tested herein. It is also explained how to preserve local consistency in reversed time simulations so as to avoid the generation of spurious residence time extrema. Finally, the boundary layer parameterisation is applied to the computation of the residence time in the Scheldt Estuary (Belgium/The Netherlands). This timescale is simulated by means of a depth-integrated, finite element, unstructured mesh model, with a high space–time resolution. It is seen that the residence time temporal variations are mainly affected by the semi-diurnal tides. However, the spring–neap variability also impacts the residence time, particularly in the sandbank and shallow areas. Seasonal variability is also observed, which is induced by the fluctuations over the year of the upstream flows. In general, the residence time is an increasing function of the distance to the mouth of the estuary. However, smaller-scale fluctuations are also present: they are caused by local bathymetric features and their impact on the hydrodynamics.     

Isolation of 12 microsatellite markers following a pyrosequencing procedure and cross-priming in two invasive cryptic species, Alexandrium catenella (group IV) and A. tamarense (group III) (Dinophyceae)

Alexandrium catenella (group IV) and Alexandrium tamarense (group III) (Dinophyceae) are two cryptic invasive phytoplankton species belonging to the A. tamarense species complex. Their worldwide spread is favored by the human activities, transportation and climate change. In order to describe their diversity in the Mediterranean Sea and understand their settlements and maintenances in this area, new microsatellite markers were developed based on Thau lagoon (France) samples of A. catenella and A. tamarense strains. In this study twelve new microsatellite markers are proposed. Five of these microsatellite markers show amplifications on A. tamarense and ten on A. catenella. Three of these 12 microsatellite markers allowed amplifications on both cryptic species. Finally, the haplotypic diversity ranged from 0.000 to 0.791 and 0.000 to 0.942 for A. catenella and A. tamarense respectively.     

An inter-comparison of tidal solutions computed with a range of unstructured grid models of the Irish and Celtic Sea Regions

Three finite element codes, namely TELEMAC, ADCIRC and QUODDY, are used to compute the spatial distributions of the M₂, M₄ and M₆ components of the tide in the sea region off the west coast of Britain. This region is chosen because there is an accurate topographic dataset in the area and detailed open boundary M₂ tidal forcing for driving the model. In addition, accurate solutions (based upon comparisons with extensive observations) using uniform grid finite difference models forced with these open boundary data exist for comparison purposes. By using boundary forcing, bottom topography and bottom drag coefficients identical to those used in an earlier finite difference model, there is no danger of comparing finite element solutions for “untuned unoptimised solutions” with those from a “tuned optimised solution”. In addition, by placing the open boundary in all finite element calculations at the same location as that used in a previous finite difference model and using the same M₂ tidal boundary forcing and water depths, a like with like comparison of solutions derived with the various finite element models was possible. In addition, this open boundary was well removed from the shallow water region, namely the eastern Irish Sea where the higher harmonics were generated. Since these are not included in the open boundary, forcing their generation was determined by physical processes within the models. Consequently, an inter-comparison of these higher harmonics generated by the various finite element codes gives some indication of the degree of variability in the solution particularly in coastal regions from one finite element model to another. Initial calculations using high-resolution near-shore topography in the eastern Irish Sea and including “wetting and drying” showed that M₂ tidal amplitudes and phases in the region computed with TELEMAC were in good agreement with observations. The ADCIRC code gave amplitudes about 30 cm lower and phases about 8° higher. For the M₄ tide, in the eastern Irish Sea amplitudes computed with TELEMAC were about 4 cm higher than ADCIRC on average, with phase differences of order 5°. For the M₆ component, amplitudes and phases showed significant small-scale variability in the eastern Irish Sea, and no clear bias between the models could be found. Although setting a minimum water depth of 5 m in the near-shore region, hence removing wetting and drying, reduced the small-scale variability in the models, the differences in M₂ and M₄ tide between models remained. For M₆, a significant reduction in variability occurred in the eastern Irish Sea when a minimum 5-m water depth was specified. In this case, TELEMAC gave amplitudes that were 1 cm higher and phases 30° lower than ADCIRC on average. For QUODDY in the eastern Irish Sea, average M₂ tidal amplitudes were about 10 cm higher and phase 8° higher than those computed with TELEMAC. For M₄, amplitudes were approximately 2 cm higher with phases of order 15° higher in the northern part of the region and 15° lower in the southern part. For M₆ in the north of the region, amplitudes were 2 cm higher and about 2 cm lower in the south. Very rapid M₆ tidal-phase changes occurred in the near-shore regions. The lessons learned from this model inter-comparison study are summarised in the final section of the paper. In addition, the problems of performing a detailed model–model inter-comparison are discussed, as are the enormous difficulties of conducting a true model skill assessment that would require detailed measurements of tidal boundary forcing, near-shore topography and precise knowledge of bed types and bed forms. Such data are at present not available.     

Contrasting origins of Cenozoic silicic volcanic rocks from the western Cordillera of the United States

Two fundamentally different types of silicic volcanic rocks formed during the Cenozoic of the western Cordillera of the United States. Large volumes of dacite and rhyolite, mostly ignimbrites, erupted in the Oligocene in what is now the Great Basin and contrast with rhyolites erupted along the Snake River Plain during the Late Cenozoic. The Great Basin dacites and rhyolites are generally calc-alkaline, magnesian, oxidized, wet, cool (<850°C), Sr-and Al-rich, and Fe-poor. These silicic rocks are interpreted to have been derived from mafic parent magmas generated by dehydration of oceanic lithosphere and melting in the mantle wedge above a subduction zone. Plagioclase fractionation was minimized by the high water fugacity and oxide precipitation was enhanced by high oxygen fugacity. This resulted in the formation of Si-, Al-, and Sr-rich differentiates with low Fe/Mg ratios, relatively low temperatures, and declining densities. Magma mixing, large proportions of crustal assimilation, and polybaric crystal fractionation were all important processes in generating this Oligocene suite. In contrast, most of the rhyolites of the Snake River Plain are alkaline to calc-alkaline, ferroan, reduced, dry, hot (830–1,050°C), Sr-and Al-poor, and Nb-and Fe-rich. They are part of a distinctly bimodal sequence with tholeiitic basalt. These characteristics were largely imposed by their derivation from parental basalt (with low fH₂O and low fO₂) which formed by partial melting in or above a mantle plume. The differences in intensive parameters caused early precipitation of plagioclase and retarded crystallization of Fe–Ti oxides. Fractionation led to higher density magmas and mid-crustal entrapment. Renewed intrusion of mafic magma caused partial melting of the intrusive complex. Varying degrees of partial melting, fractionation, and minor assimilation of older crust led to the array of rhyolite compositions. Only very small volumes of distinctive rhyolite were derived by fractional crystallization of Fe-rich intermediate magmas like those of the Craters of the Moon-Cedar Butte trend. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.