Line vortices and the vacillation of Langmuir circulation

AbstractThree types of breakdown of Langmuir circulation (Lc) are observed, two of which are represented in large-eddy simulation (LES) models, but the third, vacillation, is not. The stability of Lc can be examined by representing the downwind-aligned vortices by line vortices that are subjected to perturbations. Earlier conclusions relating to stability in homogeneous water of infinite depth are found to be in error because no stationary unperturbed state exists. The motion of vortices is examined and shown to be consistent with an explanation of Lc devised by Csanady. Motion of line vortices in water of limited depth or bounded below by a thermocline is examined. The motion replicates some of the features of vacillation observed by Smith in deep water bounded by a thermocline, including its periodicity and fluctuations in the formation of bubble bands. Vortices describe closed orbits within the Langmuir cells. Particle motions in the vacillating Lc pattern exhibit trapping close to the line vortices or near the cell boundaries. Vacillation appears not to have been observed in water of limited depth. Here, the vacillation period is predicted to be longer than the deep-water equivalent and may be too long for vacillations to be detected.</jats:p

2DV modelling of sediment transport processes over full-scale ripples in regular asymmetric oscillatory flow

Wave-induced, steep vortex ripples are ubiquitous features in shallow coastal seas and it is therefore important to fully understand and model the sediment transport processes that occur over them. To this end, two two-dimensional vertical (2DV) models have been critically tested against detailed velocity and sediment concentration measurements above mobile ripples in regular asymmetric oscillatory flow. The two models are a k–ω turbulence-closure model and a discrete-vortex, particle-tracking (DVPT) model, while the data are obtained in the Aberdeen oscillatory flow tunnel (AOFT). The models and the data demonstrate that the time-dependent velocity and suspended sediment concentration above the ripple are dominated by the generation of lee-side vortices and their subsequent ejection at flow reversal. The DVPT model predicts the positions and strengths of the vortices reasonably well, but tends to overpredict the velocity close to the ripple surface. The k–ω model, on the other hand, underpredicts the height to which the vortices are lifted, but is better able to predict the velocity close to the bed. In terms of the cycle- and ripple-averaged horizontal velocity, both models are able to reproduce the observed offshore flow close to and below the ripple crest and the DVPT model is able to produce the onshore flow higher up. In the vicinity of the vortices, the DVPT model better represents the concentration (because of its better prediction of vorticity). The k–ω model, on the other hand, better represents the concentration close to the ripple surface and higher up in the flow (because of the better representation of the near-bed flow and background turbulence). The measured and predicted cycle- and ripple-averaged suspended sediment concentrations are in reasonable agreement and demonstrate the expected region of exponential decay. The models are able to reproduce the observed offshore cycle- and ripple-averaged suspended sediment flux from the ripple troughs upwards, and as a result, produce net offshore suspended sediment transport rates that are in reasonable agreement. The net measured offshore suspended transport rate, based on the integration of fluxes, was found to be consistent with the total net offshore transport measured in the tunnel as a whole once the onshore transport resulting from ripple migration was taken into account, as would be expected. This demonstrates the importance of models being able to predict ripple-migration rates. However, at present neither of the models is able to do so

The hiding-exposure effect revisited:A method to calculate the mobility of bimodal sediment mixtures

Predicting seabed mobility is hampered by the limited accuracy of sediment transport models when the bed is composed of mixed sediments. The hiding-exposure (HE) effect modifies the threshold of motion of individual grain classes in sediment mixtures and its strength is dependent on the grain size distribution. However, an appropriate method of predicting this effect for bimodal sediment mixtures remains to be developed. The prototypical example of a bimodal mixture is that consisting of a well-sorted sand and gravel for the fine and coarse fractions respectively. Through a comprehensive series of laboratory experiments, the HE effect has been quantified for a full range of sand-gravel mixtures from pure sand to pure gravel, the choice of which has been underpinned by an integrated study of offshore geophysical and sedimentological data found in coastal and shelf seas. In the sand–gravel mixtures used in the present study the critical shear stress needed to mobilise the sand and gravel fractions increased by up to 75% and decreased by up to 64%, respectively, compared to that needed to mobilise well-sorted sediment of similar size. The HE effect was found to be dependent on the percentage of gravel (coarse mode) present in the bimodal mixture, whereby the effect for the mixture is the weighted sum of the HE effect for the fine and coarse modes

Sticky stuff : redefining bedform prediction in modern and ancient environments

This work was funded by the UK Natural Environment Research Council (NERC) under the COHBED project (NE/1027223/1). Paterson was funded by the Marine Alliance for Science and Technology for Scotland (MASTS).The dimensions and dynamics of subaqueous bedforms are well known for cohesionless sediments. However, the effect of physical cohesion imparted by cohesive clay within mixed sand-mud substrates has not been examined, despite its recognized influence on sediment stability. Here we present a series of controlled laboratory experiments to establish the influence of substrate clay content on subaqueous bedform dynamics within mixtures of sand and clay exposed to unidirectional flow. The results show that bedform dimensions and steepness decrease linearly with clay content, and comparison with existing predictors of bedform dimensions, established within cohesionless sediments, reveals significant over-prediction of bedform size for all but the lowermost clay contents examined. The profound effect substrate clay content has on bedform dimensions has a number of important implications for interpretation in a range of modern and ancient environments, including reduced roughness and bedform heights in estuarine systems and the often cited lack of large dune cross-sets in turbidites. The results therefore offer a step change in our understanding of bedform formation and dynamics in these, and many other, sedimentary environments.Publisher PDFPeer reviewe

Strontium isotope systematics of experimentally produced melts: understanding magma-carbonate interaction at Merapi volcano, Indonesia

There is considerable evidence for ongoing, late-stage interaction between the magmatic system at Merapi volcano, Indonesia, and local crustal carbonate. In order to resolve the interaction processes in detail, we have performed a series of time-variable carbonate dissolution experiments in silicate melt using Merapi basaltic-andesite and local limestone as starting materials, at magmatic pressure and temperature. Major element profiling of the experimental products has identified strongly contrasting compositional domains of glass: a Ca-enriched zone containing up to 36 wt% CaO, and an unaffected, Ca-normal zone containing 8 to 10 wt% CaO. To investigate the systematics of strontium isotopes and trace elements (TE) during carbonate assimilation, we have used micro-sampling and high-precision analytical techniques to measure 87Sr/86Sr ratios and TE concentrations over the magma-carbonate and intra-melt interfaces in two of our experimental products. The isotope variation between the different glass compositions is distinct, with 87Sr/86Sr ranging from 0.705641 in the Ca-normal glass to 0.706532 in the Ca-enriched glass. The upper end of this range is considerably more radiogenic than the range reported for Merapi whole rock volcanic products (0.70501 to 0.70583, Gertisser & Keller, 2003 J Pet, 44, 457-489). Our data hence support a model of assimilation of crustal carbonate with highly radiogenic 87Sr/86Sr (0.708799) at Merapi volcano. Given that the starting materials used in the experiments have markedly distinct 87Sr/86Sr values we here present new and detailed insights about the behaviour of Sr isotopes during carbonate assimilation, with a focus on the processes that operate across the carbonate-melt interface and the intra-melt transitions. Strontium is a reliable tracer of magma-crust interaction and so we anticipate that our results will significantly help to quantify our comprehension of magma-carbonate interaction processes occurring at Merapi volcano

Interactions between sediment microbial ecology and physical dynamics drive heterogeneity in contextually similar depositional systems

This study focuses on the interactions between sediment stability and biological and physical variables that influence the erodibility across different habitats. Sampling at short‐term temporal scales illustrated the persistence of the microphytobenthos (MPB) biomass even during periods of frequent, high physical disturbance. The role of MPB in biological stabilization along the changing sedimentary habitat was also assessed. Key biological and physical properties, such as the MPB biomass, composition, and extracellular polymeric substances, were used to predict the sediment stability (erosion threshold) of muddy and sandy habitats within close proximity to one another over multiple days, and within emersion periods. The effects of dewatering, MPB growth, and productivity were examined as well as the resilience and recovery of the MPB community after disturbance from tidal currents and waves. Canonical analysis of principal components (CAP) ordinations were used to visualize and assess the trends observed in biophysical properties between the sites, and marginal and sequential distance‐based linear models were used to identify the key properties influencing erodibility. While the particle size of the bed was important for differences between sites in the CAP analysis, it contributed less to the variability in sediment erodibility than key biological parameters. Among the biological predictors, MPB diversity explained very little variation in marginal tests but was a significant predictor in sequential tests when MPB biomass was also considered. MPB diversity and biomass were both key predictors of sediment stability, contributing 9% and 10%, respectively, to the final model compared to 2% explained by grain size

An inducible CiliaGFP mouse model for in vivo visualization and analysis of cilia in live tissue

BACKGROUND: Cilia are found on nearly every cell type in the mammalian body, and have been historically classified as either motile or immotile. Motile cilia are important for fluid and cellular movement; however, the roles of non-motile or primary cilia in most tissues remain unknown. Several genetic syndromes, called the ciliopathies, are associated with defects in cilia structure or function and have a wide range of clinical presentations. Much of what we know about the formation and maintenance of cilia comes from model systems like C. elegans and Chalmydomonas. Studies of mammalian cilia in live tissues have been hampered by difficulty visualizing them. RESULTS: To facilitate analyses of mammalian cilia function we generated an inducible Cilia(GFP) mouse by targeting mouse cDNA encoding a cilia-localized protein somatostatin receptor 3 fused to GFP (Sstr3::GFP) into the ROSA26 locus. In this system, Sstr3::GFP is expressed from the ubiquitous ROSA26 promoter after Cre mediated deletion of an upstream Neo cassette flanked by lox P sites. Fluorescent cilia labeling was observed in a variety of live tissues and after fixation. Both cell-type specific and temporally regulated cilia labeling were obtained using multiple Cre lines. The analysis of renal cilia in anesthetized live mice demonstrates that cilia commonly lay nearly parallel to the apical surface of the tubule. In contrast, in more deeply anesthetized mice the cilia display a synchronized, repetitive oscillation that ceases upon death, suggesting a relationship to heart beat, blood pressure or glomerular filtration. CONCLUSIONS: The ability to visualize cilia in live samples within the Cilia(GFP) mouse will greatly aid studies of ciliary function. This mouse will be useful for in vivo genetic and pharmacological screens to assess pathways regulating cilia motility, signaling, assembly, trafficking, resorption and length control and to study cilia regulated physiology in relation to ciliopathy phenotypes

Current- and wave- generated bedforms on mixed sand-clay intertidal flats : a new bedform phase diagram and implications for bed roughness and preservation potential

Funding: This work was supported by the United Kingdom’s Natural Environment Research Council (NERC) under Grant NE/I027223/1 (COHBED). JM, Julie Hope, and Daniel Parsons were partially funded by a Horizon 2020 European Research Council Consolidator Award (GEOSTICK, Grant 725955). The GEOSTICK project also kindly contributed the article processing fees. Andrew Manning’s contribution toward this research was partly supported by the National Science Foundation grants OCE-1924532 and OCE-1736668, TKI-MUSA project 11204950-000-ZKS-0002, and the HR Wallingford company research project FineScale (Grant Nos. ACK3013_62). DP received funding from the MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland) and their support is gratefully acknowledged. MASTS is funded by the Scottish Funding Council (Grant reference HR09011) and contributing institutions.The effect of bedforms on frictional roughness felt by the overlying flow is crucial to the regional modelling of estuaries and coastal seas. Bedforms are also a key marker of palaeoenvironments. Experiments have shown that even modest biotic and abiotic cohesion in sand inhibits bedform formation, modifies bedform size, and slows bedform development, but this has rarely been tested in nature. The present study used a comprehensive dataset recorded over a complete spring–neap cycle on an intertidal flat to investigate bedform dynamics controlled by a wide range of wave and current conditions, including the effects of wave–current angle and bed cohesion. A detailed picture of different bedform types and their relationship to the flow, be they equilibrium, non-equilibrium, or relict, was produced, and captured in a phase diagram that integrates wave-dominated, current-dominated, and combined wave–current bedforms. This bedform phase diagram incorporates a substantially wider range of flow conditions than previous phase diagrams, including bedforms related to near-orthogonal wave–current angles, such as ladderback ripples. Comparison with laboratory-derived bedform phase diagrams indicates that washed-out ripples, lunate interference ripples and upper-stage plane beds replace the subaqueous dune field; such bedform distributions may be a key characteristic of intertidal flats. The field data also provide a means of predicting the dimensions of these bedforms, which can be transferred to other areas and grain sizes. We show that an equation for the prediction of equilibrium bedform size is sufficient to predict the roughness, even though the bedforms are highly variable in character and only in equilibrium with the flow for approximately half the time. Whilst the effect of cohesive clay is limited under more active spring conditions, clay does play a role in reducing the bedform dimensions under more quiescent neap conditions. We also investigated which combinations of waves, currents, and bed clay contents in the intertidal zone have the highest potential for bedform preservation in the geological record. This shows that combined wave–current bedforms have the lowest preservation potential and equilibrium current ripples have the highest preservation potential, even in the presence of moderate and storm waves. Hence, the absence of wave ripples and combined-flow bedforms and their primary stratification in sedimentary successions cannot be taken as evidence that waves were absent at the time of deposition.Publisher PDFPeer reviewe

Chronic stress and age-related increases in the proinflammatory cytokine IL-6

Overproduction of IL-6, a proinflammatory cytokine, is associated with a spectrum of age-related conditions including cardiovascular disease, osteoporosis, arthritis, type 2 diabetes, certain cancers, periodontal disease, frailty, and functional decline. To describe the pattern of change in IL-6 over 6 years among older adults undergoing a chronic stressor, this longitudinal community study assessed the relationship between chronic stress and IL-6 production in 119 men and women who were caregiving for a spouse with dementia and 106 noncaregivers, with a mean age at study entry of 70.58 (SD = 8.03) for the full sample. On entry into this portion of the longitudinal study, 28 of the caregivers' spouses had already died, and an additional 50 of the 119 spouses died during the 6 years of this study. Levels of IL-6 and health behaviors associated with IL-6 were measured across 6 years. Caregivers' average rate of increase in IL-6 was about four times as large as that of noncaregivers. Moreover, the mean annual changes in IL-6 among former caregivers did not differ from that of current caregivers even several years after the death of the impaired spouse. There were no systematic group differences in chronic health problems, medications, or health-relevant behaviors that might have accounted for caregivers' steeper IL-6 slope. These data provide evidence of a key mechanism through which chronic stressors may accelerate risk of a host of age-related diseases by prematurely aging the immune response

Observations of velocities, sand concentrations, and fluxes under velocity-asymmetric oscillatory flows

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