Lateral Sorting Research Articles

Computational fluid dynamics and the physical modelling of an upland urban river

This paper describes the application of a commercially available, three-dimensional computational fluid dynamic (CFD) model to simulate the flow structure in an upland river that is prone to flooding. Simulations use a rectangular channel geometry, smooth sidewalls and a bed topography obtained from the field site that contains a subdued pool–riffle sequence. The CFD model uses the RNG κ– ε turbulence closure scheme of Yakhot and Orszag (J. Sci. Comput. 1 (1986) 1), as implemented in FLUENT 4.4.4, with a free surface. Results are shown for numerical runs simulating a 1:100 year return interval flood. Output from the numerical model is compared to a physical model experiment that uses a 1:35 scale fibreglass mould of the field study reach and measures velocity using ultrasonic Doppler velocity profiling (UDVP). Results are presented from the numerical and flume models for the water surface and streamwise velocity pattern and for the secondary flows simulated in the numerical model. A good agreement is achieved between the CFD model output and the physical model results for the downstream velocities. Results suggest that the streamwise velocity is the main influence on the flow structure at the discharge and channel configuration studied. Secondary flows are, in general, very weak being below the resolution of measurement in the physical model and less than 10% of the streamwise velocity in the numerical model. Consequently, there is no evidence for a ‘velocity dip’. It is suggested that the subdued topography or inlet morphology may inhibit the development of secondary flows that have been recorded in previous flat-bed, rectangular open channel flows. A significant corollary of these results is that the morphological evolution of the pool–riffle sequence at high discharges may be controlled primarily by the downstream distribution of velocity and sediment transport with little role for lateral sorting and sediment routing by secondary flows. This paper also raises a number of issues that may be of use in future CFD modelling of three-dimensional flow in open channels within the geomorphological community.

Lipid Rafts Exist as Stable Cholesterol-independent Microdomains in the Brush Border Membrane of Enterocytes

Glycosphingolipid/cholesterol-rich membranes ("rafts")can be isolated from many types of cells, but their existence as stable microdomains in the cell membrane has been elusive. Addressing this problem, we studied the distribution of galectin-4, a raft marker, and lactase, a protein excluded from rafts, on microvillar vesicles from the enterocyte brush border membrane. Magnetic beads coated with either anti-galectin-4 or anti-lactase antibodies were used for immunoisolation of vesicles followed by double immunogold labeling of the two proteins. A morphometric analysis revealed subpopulations of raft-rich and raft-poor vesicles by the following criteria: 1) the lactase/galectin-4 labeling ratio/vesicle captured by the anti-lactase beads was significantly higher (p < or = 0.01) than that of vesicles captured by anti-galectin-4 beads, 2) subpopulations of vesicles labeled by only one of the two antibodies were preferentially captured by beads coated with the respective antibody (p < or = 0.01), 3) the average diameter of "galectin-4 positive only" vesicles was smaller than that of vesicles labeled for lactase. Surprisingly, pretreatment with methyl-beta-cyclodextrin, which removed >70% of microvillar cholesterol, did not affect the microdomain localization of galectin-4. We conclude that stable, cholesterol-independent raft microdomains exist in the enterocyte brush border.

Autophagic tubes: vacuolar invaginations involved in lateral membrane sorting and inverse vesicle budding.

Many intracellular compartments of eukaryotic cells do not adopt a spherical shape, which would be expected in the absence of mechanisms organizing their structure. However, little is known about the principles determining the shape of organelles. We have observed very defined structural changes of vacuoles, the lysosome equivalents of yeast. The vacuolar membrane can form a large tubular invagination from which vesicles bud off into the lumen of the organelle. Formation of the tube is regulated via the Apg/Aut pathway. Its lumen is continuous with the cytosol, making this inverse budding reaction equivalent to microautophagocytosis. The tube is highly dynamic, often branched, and defined by a sharp kink of the vacuolar membrane at the site of invagination. The tube is formed by vacuoles in an autonomous fashion. It persists after vacuole isolation and, therefore, is independent of surrounding cytoskeleton. There is a striking lateral heterogeneity along the tube, with a high density of transmembrane particles at the base and a smooth zone devoid of transmembrane particles at the tip where budding occurs. We postulate a lateral sorting mechanism along the tube that mediates a depletion of large transmembrane proteins at the tip and results in the inverse budding of lipid-rich vesicles into the lumen of the organelle.

Definition of distinct compartments in polarized Madin-Darby canine kidney (MDCK) cells for membrane-volume sorting, polarized sorting and apical recycling.

Previous studies of fibroblasts have demonstrated that recycling of endocytic receptors occurs through a default mechanism of membrane-volume sorting. Epithelial cells require an additional level of polar membrane sorting, but there are conflicting models of polar sorting, some suggesting that it occurs in early endosomes, others suggesting it occurs in a specialized apical recycling endosome (ARE). The relationship between endocytic sorting to the lysosomal, recycling and transcytotic pathways in polarized cells was addressed by characterizing the endocytic itineraries of LDL, transferrin (Tf) and IgA, respectively, in polarized Madin-Darby canine kidney (MDCK) cells. Quantitative analyses of 3-dimensional images of living and fixed polarized cells demonstrate that endocytic sorting occurs sequentially. Initially internalized into lateral sorting endosomes, Tf and IgA are jointly sorted from LDL into apical and medical recycling endosomes, in a manner consistent with default sorting of membrane from volume. While Tf is recycled to the basolateral membrane from recycling endosomes, IgA is sorted to the ARE prior to apical delivery. Quantifications of the efficiency of sorting of IgA from Tf between the recycling endosomes and the ARE match biochemical measurements of transepithelial protein transport, indicating that all polar sorting occurs in this step. Unlike fibroblasts, rab11 is not associated with Tf recycling compartments in either polarized or glass-grown MDCK cells, rather it is associated with the compartments to which IgA is directed after sorting from Tf. These results complicate a suggested homology between the ARE and the fibroblast perinuclear recycling compartment and provide a framework that justifies previous conflicting models of polarized sorting.

Sphingolipid organization in biomembranes: what physical studies of model membranes reveal.

Recent cell biological studies suggest that sphingolipids and cholesterol may cluster in biomembranes to form raft-like microdomains. Such lipid domains are postulated to function as platforms involved in the lateral sorting of certain proteins during their trafficking within cells as well as during signal transduction events. Here, the physical interactions that occur between cholesterol and sphingolipids in model membrane systems are discussed within the context of microdomain formation. A model is presented in which the role of cholesterol is refined compared to earlier models.

Cryptogamic soil buds in the equatorial Andes of Venezuela

Soil buds, formed by particle heaving and sorting by needle ice, were studied in a high Andean paramo. Soils were finer in buds than in adjacent trough areas, where pebbles had been concentrated by lateral sorting. Some buds were composed only of mineral grains, others were covered by a cryptogamic crust of liverworts (Marsupella spp.) or mosses (Grimmia longirostris). Particle sorting was studied by comparing the grain-size distributions of buds and troughs, and by using a numerical sorting index. Degree of sorting varied widely among bare bud sites, where it was dependent on the presence of gravel in the substrate. Sorting was pronounced in sites with cryptogamic plants, where fines (<0.05 mm) were concentrated within buds, which also contained higher amounts of organic matter than the adjacent troughs. Microscopic examination showed that cryptogamic buds were layered in three concentric bands. This resulted in a gradual increase of fines and organic matter toward the bud top, as well as in a lower pH and darker colour. The pronounced rise in silt and clay near bud surfaces is due to interception of aeolian material by plants, which can trap fines and then grow above the deposited dust, thus forming a cumulic sequence of thin crustal laminae. Vughs and vesicles formed by frost activity were common in buds, particularly in their basal layer. Field experiments showed that cryptogamic crusts increase the infiltration rates and compressive strength of soil buds. This results in a lower chance of runoff generation and in an increased resistance to detachment by various geomorphic agents. An idealized developmental sequence of cryptogamic soil buds is discussed in detail.

Cryptogamic soil buds in the equatorial Andes of Venezuela

Soil buds, formed by particle heaving and sorting by needle ice, were studied in a high Andean paramo. Soils were finer in buds than in adjacent trough areas, where pebbles had been concentrated by lateral sorting. Some buds were composed only of mineral grains, others were covered by a cryptogamic crust of liverworts (Marsupella spp.) or mosses (Grimmia longirostris). Particle sorting was studied by comparing the grain-size distributions of buds and troughs, and by using a numerical sorting index. Degree of sorting varied widely among bare bud sites, where it was dependent on the presence of gravel in the substrate. Sorting was pronounced in sites with cryptogamic plants, where fines (<0.05 mm) were concentrated within buds, which also contained higher amounts of organic matter than the adjacent troughs. Microscopic examination showed that cryptogamic buds were layered in three concentric bands. This resulted in a gradual increase of fines and organic matter toward the bud top, as well as in a lower pH and darker colour. The pronounced rise in silt and clay near bud surfaces is due to interception of aeolian material by plants, which can trap fines and then grow above the deposited dust, thus forming a cumulic sequence of thin crustal laminae. Vughs and vesicles formed by frost activity were common in buds, particularly in their basal layer. Field experiments showed that cryptogamic crusts increase the infiltration rates and compressive strength of soil buds. This results in a lower chance of runoff generation and in an increased resistance to detachment by various geomorphic agents. An idealized developmental sequence of cryptogamic soil buds is discussed in detail.

Absence of frost sorting at an experimental site, green lakes valley, colorado front range, usa

A field experiment at 3,350 m.a.s.l. in the Colorado Alpine was initiated in 1959, to investigate frost sorting. Four plots, of varying grain-size composition, were used to test whether sorting by freeze-thaw activity could be related to the percentage of soil particles finer than 0.074 mm and whether there was a characteristic grain size at which lateral and/or vertical sorting could be expected. Re-examination of the site in 1984 indicated that macrofabrics, microfabrics, soil physical properties and surface clast distributions showed no evidence of large-scale sorting. Critical conditions for the onset of pore water convection, as a mechanism for the initiation of sorting, could occur in only two of the test soils (A and B), and permeability in the third (C) was too low to allow instability. Soil convection is also unlikely, owing to the coarse, freely drained nature of the test soils. Des conditions favorables au declenchement de phenomenes de convection contreles par l'eau des pores comme mecanisme responsable du triage pourraient seulement survenir dans deux des sols testes (A et B); la permeabilite du troisieme (C) etait trop faible pour permettre une instabilite. Une convection du sol est aussi improbable etant donne la nature grossiere et librement drainee des sols etudies.

Precambrian storm wave-base deposits of Early Proterozoic age (1.9 Ga), preserved in andalusite-cordierite-rich granofels and quartzite (Rämsberg area, Värmland, Sweden)

Well preserved laminites, wave ripples and thin hummocky cross-stratified beds arranged in several, thickening- and thinning-upward sequences have been interpreted as lobe-like storm wave-base deposits. Delicate features in thin sections confirm the importance of wave activity over current activity. These features include thinning- and fining-upwards sequences on a centimetre-scale with a great variety of laminae (graded, inversely graded, non-graded); with diffuse or sharp tops due to winnowing; micro-flaser bedding on millimetre-scale with 2 cm wavelength; lateral sorting and grain-size differences; and silty streaks of single grain thickness of approximately 0.5–1 cm in length. These structures are exceptionally well preserved in the medium-grade metamorphics, due to the lack of burrowing in Early Proterozoic sediments and to the non-deformational character of the thermal metamorphism. The Proterozoic sequence is compared with existing depositional models of storm-influenced shelves from the recent and fossil record.

Formation of Longitudinal Stripes Due to Lateral Sorting by Cellular Secondary Currents

In a stream composed of sand and gravel, we often observe longitudinal stripes of alternate lateral sorting and cellular secondary currents. They are promoted or suppressed each other. In this paper the interaction between them is investigated mainly from the view point of mechanics of bed-load transport of heterogeneous size material affected by a secondary current.A secondary current brings about a lateral bed-load transport from a “rough” part to a “smooth” part, and alternate sorting develops when the finer material is predominantly transported laterally. A transport model constituted by pick-up rate and step length for each grain size is prepared and the mechanics of lateral sorting is described. Based on it, a criterion of occurrence of longitudinal stripes of sorting is clarified. Considering the decrease of the exposed fine material in the “rough” stripes with the progress of sorting, the equilibrium stripes of sorting are also investigated.

Bed Topography and Sorting in Bends

A mathematical model for defining the bed topography and the bed material size distribution in uniformly curved bends of alluvial rivers is developed, in which the coarsening of sediment size toward the outside bank is predicted and the bed topography is calculated coupling with the lateral sorting. The major agency for the sorting is that coarser grains feel a larger ratio of transverse gravitational force to fluid force than finer grains. It is revealed that the sorting reduces the depth of scour considerably in the outer area of bends. The model is tested with a laboratory test, and it is applied to an actual river, both of which support the current theory.

STABLE BED TOPOGRAPHY AND SORTING IN UNIFORMLY-CURVED CHANNELS WITH HETEROGENEOUS BED MATERIALS

A mathematical model for defining the bed topography and the bed material size distribution in uniformly-curved bends is developed, in which the coarsening of sediment size toward the outside is predicted and the bed topography is calculated coupling with the lateral sorting. The major agency for sorting is that coarser grains feel a larger ratio of transverse gravitational force to fluid force than finer grains. It is revealed that the sorting reduces the depth of scour considerably in the outer area of bends. The model is tested with a laboratory test, and it is applied to an actual river, both of which support the present theory.

Measurements of the Reynolds stress components close to a marine sand bank

Observations of turbulence have been made at a height of 65 cm above the sea bed in water 42 m deep on the edge of the Skerries sand bank off southwest England. The observations extended over a 4-h period from the time of maximum flood velocity to slack water. Electromagnetic current meters were used to measure the streamwise (μ), cross-stream (υ), and vertical (ω) velocity components, while simultaneously a conventional current meter measured the speed and direction 5 m below the water surface. Ratios of ( μ 2 ) 1 2 , ( υ 2 ) 1 2 , and ( ω 2 ) 1 2 to shear velocity agreed with accepted values for laboratory and atmospheric flows. Near to the surface the current was found to flow across the bank while near the bed it ran nearly parallel to the isobaths. Consequently the bottom current was directed 48° clockwise of the surface current. The azimuth of the Reynolds stress (ϱ μω , ϱ υω ) near the bed lay between these directions, and was directed about 6° anticlockwise of the near-bed current. This balanced the cross-stream as well as the streamwise shear. A lateral shear stress ϱ μυ associated with the bank was observed. Taken together with previous measurements of the velocity distribution over the bank, this yielded a value for lateral eddy viscosity of 1.2·10 5 cm 2 s −1. The scale over which this acts is of the order 1 km and the value is appreciably smaller than reported values deduced for larger scales. The veering of the current acts to lessen the bottom current convergence associated with Coriolis and curvature effects, and may contribute to lateral sorting by preferentially carrying finer sediment toward the crest of the bank. The lateral eddy viscosity coefficient may be useful in assessing the diffusion of sediment on or off the bank.

A physical model for the transport and sorting of fine‐grained sediment by turbidity currents

ABSTRACTTurbidite muds in cores from the outer Scotian continental margin, off eastern Canada, contain abundant thin silt laminae. Graded laminated units are recognized in parts of this sequence. These represent single depositional events, and show a regular decrease in modal grain size and thickness of the silt laminae through the unit. A similar fining trend is shown by both silt and mud layers over hundreds of kilometres downslope. Textural analysis of individual laminae allows the construction of a dynamically consistent physical model for transport and sorting in muddy turbidity currents. Hydraulic sorting aggregates finer material to the top and tail regions of a large turbidity flow which then overspills its channel banks. Downslope lateral sorting occurs with preferential deposition of coarser silt grains and larger mud flocs. Depositional sorting by increased shear in the boundary layer separates clay flocs from silt grains and results in a regular mud/silt lamination. Estimates can be made of the physical parameters of the turbidity flows involved. They are a minimum of several hundreds of metres thick, have low concentrations (of the order of 10−3 or 2500 mg 1−1), and move downslope at velocities of 10‐20 cm s−1. A 5 mm thick, coarse silt lamina takes about 10 h to deposit, and the subsequent mud layer ‘blankets’ very rapidly over this. A complete unit is deposited in 2‐6 days which is the time it takes for the turbidity flow to pass a particular point. These thick, dilute, low‐velocity flows are significantly different from the ‘classical’ turbidity current. However, there is mounting evidence in support of the new concept from laboratory observations and direct field measurements.