The effect of Schmidt number on gravity current flows: The formation of large-scale three-dimensional structures

The Schmidt number, defined as the ratio of scalar to momentum diffusivity, varies by multiple orders of magnitude in real-world flows, with large differences in scalar diffusivity between temperature, solute, and sediment driven flows. This is especially crucial in gravity currents, where the flow dynamics may be driven by differences in temperature, solute, or sediment, and yet the effect of Schmidt number on the structure and dynamics of gravity currents is poorly understood. Existing numerical work has typically assumed a Schmidt number near unity, despite the impact of Schmidt number on the development of fine-scale flow structure. The few numerical investigations considering high Schmidt number gravity currents have relied heavily on two-dimensional simulations when discussing Schmidt number effects, leaving the effect of high Schmidt number on three-dimensional flow features unknown. In this paper, three-dimensional direct numerical simulations of constant-influx solute-based gravity currents with Reynolds numbers 100 ≤ R e ≤ 3000 and Schmidt number 1 are presented, with the effect of Schmidt number considered in cases with (R e, S c) = (100, 10), (100, 100), and (500, 10). These data are used to establish the effect of Schmidt number on different properties of gravity currents, such as density distribution and interface stability. It is shown that increasing Schmidt number from 1 leads to substantial structural changes not seen with increased Reynolds number in the range considered here. Recommendations are made regarding lower Schmidt number assumptions, usually made to reduce computational cost

Effect of hydro-climate variation on biofilm dynamics and its impact in intertidal environments

Shallow tidal environments are very productive ecosystems but are sensitive to environmental changes and sea level rise. Bio-morphodynamic control of these environments is therefore a crucial consideration; however, the effect of small-scale biological activity on large-scale cohesive sediment dynamics like tidal basins and estuaries is still largely unquantified. This study advances our understanding by assessing the influence of biotic and abiotic factors on biologically cohesive sediment transport and morphology. An idealised benthic biofilm model is incorporated in a 1D morphodynamic model of tide-dominated channels. This study investigates the effect of a range of environmental and biological conditions on biofilm growth and their feedback on the morphological evolution of the entire intertidal channel. By carrying out a sensitivity analysis of the bio-morphodynamic model, parameters like (i) hydrodynamic disturbances, (ii) seasonality, (iii) biofilm growth rate, (iv) temperature variation and (v) bio-cohesivity of the sediment are systematically changed. Results reveal that key parameters such as growth rate and temperature strongly influence the development of biofilm and are key determinants of equilibrium biofilm configuration and development under a range of disturbance periodicities and intensities. Long-term simulations of intertidal channel development demonstrate that the hydrodynamic disturbances induced by tides play a key role in shaping the morphology of the bed and that the presence of surface biofilm increases the time to reach morphological equilibrium. In locations characterised by low hydrodynamic forces, the biofilm grows and stabilises the bed, inhibiting the transport of coarse sediment (medium and fine sand). These findings suggest biofilm presence in channel beds results in intertidal channels that have significantly different characteristics in terms of morphology and stratigraphy compared abiotic sediments. It is concluded that inclusion of bio-cohesion in morphodynamic models is essential to predict estuary development and mitigate coastal erosion.</p

Progressive and biased divergent evolution underpins the origin and diversification of peridinin dinoflagellate plastids

Dinoflagellates are algae of tremendous importance to ecosystems and to public health. The cell biology and genome organization of dinoflagellate species is highly unusual. For example, the plastid genomes of peridinin-containing dinoflagellates encode only a minimal number of genes arranged on small elements termed "minicircles". Previous studies of peridinin plastid genes have found evidence for divergent sequence evolution, including extensive substitutions, novel insertions and deletions, and use of alternative translation initiation codons. Understanding the extent of this divergent evolution has been hampered by the lack of characterized peridinin plastid sequences. We have identified over 300 previously unannotated peridinin plastid mRNAs from published transcriptome projects, vastly increasing the number of sequences available. Using these data, we have produced a well-resolved phylogeny of peridinin plastid lineages, which uncovers several novel relationships within the dinoflagellates. This enables us to define changes to plastid sequences that occurred early in dinoflagellate evolution, and that have contributed to the subsequent diversification of individual dinoflagellate clades. We find that the origin of the peridinin dinoflagellates was specifically accompanied by elevations both in the overall number of substitutions that occurred on plastid sequences, and in the Ka/Ks ratio associated with plastid sequences, consistent with changes in selective pressure. These substitutions, alongside other changes, have accumulated progressively in individual peridinin plastid lineages. Throughout our entire dataset, we identify a persistent bias toward non-synonymous substitutions occurring on sequences encoding photosystem I subunits and stromal regions of peridinin plastid proteins, which may have underpinned the evolution of this unusual organelle.Wellcome Trus

Pulse propagation in gravity currents

Real world gravity current flows rarely exist as a single discrete event, but are instead made up of multiple surges. This paper examines the propagation of surges as pulses in gravity currents. Using theoretical shallow-water modeling, we analyze the structure of pulsed flows created by the sequential release of two lock-boxes. The first release creates a gravity current, while the second creates a pulse that eventually propagates to the head of the first current. Two parameters determine the flow structure: the densimetric Froude number at the head of the current, Fr, and a dimensionless time between releases, tre. The shallow-water model enables the flow behavior to be mapped in (Fr, tre) space. Pulse speed depends on three critical characteristic curves: two that derive from the first release and correspond to a wavelike disturbance which reflects between the head of the current and the back of the lock-box and a third that originates from the second release and represents the region of the flow affected by the finite supply of source material. Pulses have non-negative acceleration until they intersect the third characteristic, after which they decelerate. Variations in pulse speed affect energy transfer and dissipation. Critically for lahars, landslides, and avalanches, pulsed flows may change from erosional to depositional, further affecting their dynamics. Gravity current hazard prediction models for such surge-prone flows may underpredict risk if they neglect internal flow dynamics

Mixing in density- and viscosity-stratified flows

The lock-exchange problem is used extensively to study the flow dynamics of density-driven flows, such as gravity currents, and as a canonical problem to mixing in stratified flows. Opposite halves of a domain are filled with two fluids of different densities and held in place by a lock-gate. Upon release, the density difference drives the flow causing the fluids to slosh back and forth. In many scenarios, density stratification will also impose a viscosity stratification (e.g., if there are suspended sediments or the two fluids are distinct). However, numerical models often neglect variable viscosity. This paper characterizes the effect of both density and viscosity stratification in the lock-exchange configuration. The governing Navier-Stokes equations are solved using direct numerical simulation. Three regimes are identified in terms of the viscosity ratio μ 2 / μ 1 = (1 + γ) between the dense and less dense fluids: when γ ≪ 1, the flow dynamics are similar to the equal-viscosity case; for intermediate values (γ ∼ 1), viscosity inhibits interface-scale mixing leading to a global reduction in mixing and enhanced transfer between potential and kinetic energy. Increasing the excess viscosity ratio further (γ ≫ 1) results in significant viscous dissipation. Although many gravity or turbidity current models assume constant viscosity, our results demonstrate that viscosity stratification can only be neglected when γ ≪ 1. The initial turbidity current composition could enhance its ability to become self-sustaining or accelerating at intermediate excess viscosity ratios. Currents with initially high excess viscosity ratio may be unable to dilute and propagate long distances because of the decreased mixing rates and increased dissipation

Streamwise turbulence modulation in non-uniform open-channel clay suspension flows

Cohesive sediment particles are ubiquitous in environmental flows. The cohesive properties of clay promote the formation of clay flocs and gels and relatively small suspended clay concentrations can enhance or suppress turbulence in a flow. Furthermore, flows are naturally non-uniform, varying in space and time, yet the dynamics of non-uniform open-channel clay suspension flows is poorly understood. For the first time, the adaptation time and length scales of non-uniform clay suspension flows were quantified using novel experiments with spatially varying but temporally uniform flow. Different levels of turbulence enhancement and attenuation were identified as the flow decelerates or accelerates. Results highlight that decelerating clay suspension flows crucially have a longer adaptation time than accelerating clay suspension flows. This is explained by the longer timescale required for the formation of bonds between cohesive particles in turbulence attenuated flows after deceleration than the rapid breakdown of bonds in turbulent flows after acceleration of clay suspension flows. This hysteresis is more pronounced for higher concentration decelerating flows that pass through a larger variety of clay flow types of turbulence enhancement and attenuation. These different adaptation time scales and associated clay flow type transitions are likely to affect clay flow dynamics in a variety of fluvial and submarine settings

Hydrodynamic studies of floating structures: Comparison of wave-structure interaction modelling

Current panel methods for wave-structure interactions employ the potential flow theory, which provide fast, reliable and relatively accurate predictions for the marine structures, and now some open source packages, NEMOH and HAMS, are available. In this research, the relative utility and performance of NEMOH and HAMS is compared with the well-known, state-of-art software, WAMIT. To bring focus to these comparisons, this research is based on three different floating structures: the truncated cylinder; the truncated cylinder with heave plate; and a novel multi-axis TALOS wave energy converter. To make the comparison more useful, this research investigates the incomplete and overlapped panels for the simple cylinder, to examine whether the respective code can handle these and still provide a meaningful solution. The comparisons may help us to understand whether the incomplete and/or overlapped panels can be used for simplifying the numerical modelling of those very complicated marine structures. From the comparisons, it can be seen the open source software, NEMOH and HAMS, both could produce very good results for the simple single marine structure, but also exhibit different capacities in dealing with more complicated marine structures. Specifically, HAMS could handle the thin structures and the overlapped panels effectively as WAMIT

Inorganic carbon concentrating mechanisms in free-living and symbiotic dinoflagellates and chromerids

Photosynthetic dinoflagellates are ecologically and biogeochemically important in marine and freshwater environments. However, surprisingly little is known of how this group acquires inorganic carbon or how these diverse processes evolved. Consequently, how CO2 availability ultimately influences the success of dinoflagellates over space and time remains poorly resolved compared to other microalgal groups. Here we review the evidence. Photosynthetic core dinoflagellates have a Form II RuBisCO (replaced by Form IB or Form ID in derived dinoflagellates). The in vitro kinetics of the Form II RuBisCO from dinoflagellates are largely unknown, but dinoflagellates with Form II (and other) RuBisCOs have inorganic carbon concentrating mechanisms (CCMs), as indicated by in vivo internal inorganic C accumulation and affinity for external inorganic C. However, the location of the membrane(s) at which the essential active transport component(s) of the CCM occur(s) is (are) unresolved; isolation and characterization of functionally competent chloroplasts would help in this respect. Endosymbiotic Symbiodiniaceae (in Foraminifera, Acantharia, Radiolaria, Ciliata, Porifera, Acoela, Cnidaria, and Mollusca) obtain inorganic C by transport from seawater through host tissue. In corals this transport apparently provides an inorganic C concentration around the photobiont that obviates the need for photobiont CCM. This is not the case for tridacnid bivalves, medusae, or, possibly, Foraminifera. Overcoming these long-standing knowledge gaps relies on technical advances (e.g., the in vitro kinetics of Form II RuBisCO) that can functionally track the fate of inorganic C forms

Evaluation of the national clinical sentinel surveillance system for sexually transmitted infections in South Africa: Analysis of provincial and district-level data

Background. Globally, >1 million new cases of curable sexually transmitted infections (STIs) are estimated to occur daily, an alarming rate that has prevailed for over a decade. Modelled STI prevalence estimates for South Africa (SA) are among the highest globally. Robust STI surveillance systems have implications for policy and planning, antimicrobial stewardship and prevention strategies, and are critical in stemming the tide of STIs. Objectives. To evaluate the STI clinical sentinel surveillance system (STI CSSS) in SA, to describe the population incidence of four designated STI syndromes in males and females ≥15 years, and to provide recommendations for strengthening the STI CSSS. Methods. This was a retrospective analysis of the STI CSSS in SA. Distribution of the primary healthcare facilities designated as STI CSSS sites was described, taking into account provincial population distribution and headcount coverage of STI CSSS facilities. Reporting compliance was evaluated to determine completion of data reporting. Further analysis was undertaken for those provinces that had good reporting compliance over a 12-month period. Population-level and demographic STI syndrome incidence were estimated from CSSS data using case reports of male urethritis syndrome (MUS) as a proxy for data extrapolation. Results. Reporting compliance exceeded 70% for seven of the nine provinces. STI syndromes with the highest incidence were MUS and vaginal discharge syndrome (VDS). The 20 - 24 years age group had the highest STI incidence, at least double the incidence estimated in the other two age groups. Overall STI incidence in females was higher than among males in all provinces, except Limpopo and Western Cape. The 15 - 19 years age group had the most prominent gender disparity, with the national STI incidence in females 70% higher than in males. District-level analysis revealed high regional STI incidence even in provinces with lower overall incidence. Conclusion. The STI CSSS is pivotal to epidemiological monitoring and proactive management of STIs, especially in view of the high HIV prevalence in SA. CSSS processes and facility selection should be reviewed and revised to be representative and responsive to the current STI needs of the country, with biennial analysis and reporting to support evidence-based policy development and targeted implementation