Three-dimensional liquid sloshing in a tank with baffles

A numerical model has been developed to study three-dimensional (3D) liquid sloshing in a tank with baffles. The numerical model solves the spatially averaged Navier-Stokes equations, which are constructed on a non-inertial reference frame having six degree-of-freedom (DOF) of motions. The large-eddy-simulation (LES) approach is employed to model turbulence by using the Smagorinsky sub-grid scale (SGS) closure model. The two-step projection method is employed in the numerical solutions, aided by the Bi-CGSTAB technique to solve the pressure Poisson equation for the filtered pressure field. The second-order accurate volume-of-fluid (VOF) method is used to track the distorted and broken free surface. The baffles in the tank are modeled by the concept of virtual boundary force (VBF) method. The numerical model is first validated against the available analytical solution and experimental data for two-dimensional (2D) liquid sloshing in a tank without baffles. The 2D liquid sloshing in tanks with baffles is then investigated. The numerical results are compared with other results from available literatures. Good agreement is obtained. Finally, the model is used to study 3D liquid sloshing in a tank with vertical baffles. The effect of the baffle is investigated and discussed.     

The influence of light availability and predatory behavior of the decapod crustacean Nephrops norvegicus on the activity rhythms of continental margin prey decapods

The day–night cycle is one of the strongest geophysical cycles modulating species' behavioral rhythms. However, in deep-water continental margins, where light intensity decreases over depth, interspecific competition may alter behavioral responses to day–night cycles. The burrowing decapod crustacean Nephrops norvegicus is a large-size predator in benthic communities, exerting despotic territorial behavior. In this study, we analysed how the effect of light intensity cycles on decapod behavioral rhythms is reduced as one moves from shelves to slopes. In the Western Mediterranean, the predatory behavior and interspecific competition for substrate use of Nephrops increases moving from the shelf (100–110 m) to the slope (400–430 m). Vector fitting and generalized additive models were used to assess the effect of light intensity and behavioral rhythms of N. norvegicus on the temporal variation of prey decapods co-occurring in trawl tow catches carried out on the shelf and the slope during October 1999 and June 2000. The combination of diel variations in light intensity and N. norvegicus abundance influences the activity rhythms of prey decapods in a depth- and seasonal-dependent manner. Light modulation is stronger on the shelf and weaker on the slope, where Nephrops population size is greater. Although present regression analysis does not necessarily imply a direct cause–effect relationship between rhythms of predators and prey, we suggest that Nephrops alters the temporal patterning in the behavior of its prey on the slope, where light intensity is reduced. This alteration is stronger in endobenthic species than in benthopelagic species; the former rely on bottom substrate for the expression of behavioral rhythms, experiencing stronger interspecific competitions with Nephrops at time of activity.     

Tectonic evolution of the Cape and Karoo basins of South Africa

The Cape and Karoo basins formed within the continental interior of Gondwana. Subsidence resulted from the vertical motion of rigid basement blocks and intervening crustal faults. Each basin episode records a three-stage evolution consisting of crustal uplift, fault-controlled subsidence, and long periods of regional subsidence largely unaccompanied by faulting or erosional truncation. The large-scale episodes of subsidence were probably the result of lithospheric deflection due to subduction-driven mantle flow. The early Paleozoic Cape basin records the combined effects of a north-dipping intra-crustal décollement (a late Neoproterozoic suture) and a right-stepping offset between thick Rio de la Plata craton and Namaqua basement. Following the Saldanian orogeny, a suite of small rift basins and their post-rift drape formed at this releasing stepover. Great thicknesses of quartz sandstone (Ordovician–Silurian) and mudstone (Devonian) accumulation are attributed to subsidence by rheological weakening and mantle flow. In contrast, the Karoo basin is a cratonic cover that mimics the underlying basement blocks. The Permian Ecca and lower Beaufort groups were deposited in a southward-deepening ramp syncline by extensional decoupling on the intra-crustal décollement. Reflection seismic and deep-burial diagenetic studies indicate that the Cape orogeny started in the Early Triassic. Deformation was partitioned into basement-involved strike-slip faults and thin-skinned thrusting. Uplift of the Namaqua basement resulted in erosion of the Beaufort cover. East of the Cape fold belt, contemporaneous subsidence and tilting of the Natal basement created a late Karoo transtensional foreland basin, the Stormberg depocentre. Early Jurassic tectonic resetting and continental flood basalts terminated the Karoo basin.     

A predictive numerical model for potential mapping of the gas hydrate stability zone in the Gulf of Cadiz

This paper presents a computational model for mapping the regional 3D distribution in which seafloor gas hydrates would be stable, that is carried out in a Geographical Information System (GIS) environment. The construction of the model is comprised of three primary steps, namely: (1) the construction of surfaces for the various variables based on available 3D data (seafloor temperature, geothermal gradient and depth-pressure); (2) the calculation of the gas function equilibrium functions for the various hydrocarbon compositions reported from hydrate and sediment samples; and (3) the calculation of the thickness of the hydrate stability zone. The solution is based on a transcendental function, which is solved iteratively in a GIS environment.The model has been applied in the northernmost continental slope of the Gulf of Cadiz, an area where an abundant supply for hydrate formation, such as extensive hydrocarbon seeps, diapirs and fault structures, is combined with deep undercurrents and a complex seafloor morphology. In the Gulf of Cadiz, the model depicts the distribution of the base of the gas hydrate stability zone for both biogenic and thermogenic gas compositions, and explains the geometry and distribution of geological structures derived from gas venting in the Tasyo Field (Gulf of Cadiz) and the generation of BSR levels on the upper continental slope.     

A control-volume finite-element method for three-dimensional multiphase basin modeling

In this paper we describe a 3D control-volume finite-element method to solve numerically the coupled partial differential equations (PDEs) governing geological processes involved in the evolution of sedimentary basins. These processes include sediment deposition and deformation, hydrocarbon generation, multiphase fluid flow, and heat transfer in deforming porous media.     

Methylmercury production in sediments of Chesapeake Bay and the mid-Atlantic continental margin

Methylmercury (MeHg) concentration and production rates were studied in bottom sediments along the mainstem of Chesapeake Bay and on the adjoining continental shelf and slope. Our objectives were to 1) observe spatial and temporal changes in total mercury (HgT) and MeHg concentrations in the mid-Atlantic coastal region, 2) investigate biogeochemical factors that affect MeHg production, and 3) examine the potential of these sediments as sources of MeHg to coastal and open waters. Estuarine, shelf and slope sediments contained on average 0.5 to 1.5% Hg as MeHg (% MeHg), which increased significantly with salinity across our study site, with weak seasonal trends. Methylation rate constants (k_meth), estimated using enriched stable mercury isotope spikes to intact cores, showed a similar, but weaker, salinity trend, but strong seasonality, and was highly correlated with % MeHg. Together, these patterns suggest that some fraction of MeHg is preserved thru seasons, as found by others [Orihel, D.M., Paterson, M.J., Blanchfield, P.J., Bodaly, R.A., Gilmour, C.C., Hintelmann, H., 2008. Temporal changes in the distribution, methylation, and bioaccumulation of newly deposited mercury in an aquatic ecosystem. Environmental Pollution 154, 77] Similar to other ecosystems, methylation was most favored in sediment depth horizons where sulfate was available, but sulfide concentrations were low (between 0.1 and 10 μM). MeHg production was maximal at the sediment surface in the organic sediments of the upper and mid Bay where oxygen penetration was small, but was found at increasingly deeper depths, and across a wider vertical range, as salinity increased, where oxygen penetration was deeper. Vertical trends in MeHg production mirrored the deeper, vertically expanded redox boundary layers in these offshore sediments. The organic content of the sediments had a strong impact on the sediment:water partitioning of Hg, and therefore, on methylation rates. However, the HgT distribution coefficient (K_D) normalized to organic matter varied by more than an order of magnitude across the study area, suggesting an important role of organic matter quality in Hg sequestration. We hypothesize that the lower sulfur content organic matter of shelf and slope sediments has a lower binding capacity for Hg resulting in higher MeHg production, relative to sediments in the estuary. Substantially higher MeHg concentrations in pore water relative to the water column indicate all sites are sources of MeHg to the water column throughout the seasons studied. Calculated diffusional fluxes for MeHg averaged  1 pmol m^− 2 day^− 1. It is likely that the total MeHg flux in sediments of the lower Bay and continental margin are significantly higher than their estimated diffusive fluxes due to enhanced MeHg mobilization by biological and/or physical processes. Our flux estimates across the full salinity gradient of Chesapeake Bay and its adjacent slope and shelf strongly suggest that the flux from coastal sediments is of the same order as other sources and contributes substantially to the coastal MeHg budget.     

Velocity potential formulations of highly accurate Boussinesq-type models

The highly accurate Boussinesq-type equations of Madsen et al. (Madsen, P.A., Bingham, H.B., Schäffer, H.A., 2003. Boussinesq-type formulations for fully nonlinear and extremely dispersive water waves: Derivation and analysis. Proc. R. Soc. Lond. A 459, 1075–1104; Madsen, P.A., Fuhrman, D.R., Wang, B., 2006. A Boussinesq-type method for fully nonlinear waves interacting with a rapidly varying bathymetry. Coast. Eng. 53, 487–504); Jamois et al. (Jamois, E., Fuhrman, D.R., Bingham, H.B., Molin, B., 2006. Wave-structure interactions and nonlinear wave processes on the weather side of reflective structures. Coast. Eng. 53, 929–945) are re-derived in a more general framework which establishes the correct relationship between the model in a velocity formulation and a velocity potential formulation. Although most work with this model has used the velocity formulation, the potential formulation is of interest because it reduces the computational effort by approximately a factor of two and facilitates a coupling to other potential flow solvers. A new shoaling enhancement operator is introduced to derive new models (in both formulations) with a velocity profile which is always consistent with the kinematic bottom boundary condition. The true behaviour of the velocity potential formulation with respect to linear shoaling is given for the first time, correcting errors made by Jamois et al. (Jamois, E., Fuhrman, D.R., Bingham, H.B., Molin, B., 2006. Wave-structure interactions and nonlinear wave processes on the weather side of reflective structures. Coast. Eng. 53, 929–945). An exact infinite series solution for the potential is obtained via a Taylor expansion about an arbitrary vertical position z = zˆ. For practical implementation however, the solution is expanded based on a slow variation of zˆ and terms are retained to first-order. With shoaling enhancement, the new models obtain a comparable accuracy in linear shoaling to the original velocity formulation. General consistency relations are also derived which are convenient for verifying that the differential operators satisfy a potential flow and/or conserve mass up to the order of truncation of the model. The performance of the new formulation is validated using computations of linear and nonlinear shoaling problems. The behaviour on a rapidly varying bathymetry is also checked using linear wave reflection from a shelf and Bragg scattering from an undulating bottom. Although the new models perform equally well for Bragg scattering they fail earlier than the existing model for reflection/transmission problems in very deep water.     

Fundamental study for morphodynamic modelling: Sand mounds in oscillatory flows

Experiments on sand mounds in oscillatory flow, undertaken in controlled, large-scale laboratory conditions, have produced well-defined data sets for model comparison. Three bathymetries with different levels of submergence, including a surface-piercing case, were tested. The maximum slope was about 1:5.5. Sediment transport is due to bed load with ripple formation. The principal time-dependent bulk parameters are the vertical distance of the centre of gravity above the base and the volume of the mound. A semi-implicit finite-volume depth-averaged hydrodynamic model is used to drive morphodynamics, using van Rijn's sediment flux model generalized to take account of bed slope, and some justification is given for depth-averaged modeling in these conditions. Starting the model runs with the conditions at the end of the first cycle avoided initial atypical physical behaviour. In general good predictions were obtained with an angle of repose reduced from the standard value of about 30° for stationary beds to 15°. For these situations, morphodynamics was largely unaffected by a hydrodynamic roughness height in the range 2.5D₅₀ to 51D₅₀, with larger values accounting for ripple roughness. The reduced angle of repose may be physically expected with mobile beds but this specific value is only expected to be suited to this form of bed motion. In one case an exaggerated ripple formed near the top of the mound reducing agreement with experiment. For the submerged case with normal ripple structure excellent predictions were obtained. For the initially surface-piercing mound, the time of submergence was better predicted with a 30° angle of repose, presumably due to the prominent influence of the near stationary bed near the wet/dry interface, although long term predictions were better predicted with 15°. The occurrence of vortex shedding in the first cycle modeled was in agreement with experimental observation.     

Two-dimensional,two-phase granular sediment transport model with applications to scouring downstream of an apron

We present a two-dimensional, two-phase model for non-cohesive sediment transport. This model solves concentration-weighted averaged equations of motion for both fluid and sediment phases. The model accounts for the interphase momentum transfer by considering drag forces. A collisional theory is used to compute the sediment stresses, while a two-equation (k–ε) fluid turbulence closure is implemented. A benchmark sediment transport problem concerning the scouring downstream of an apron is carried out as an example and numerical results agree with existing experimental data.     

Molecular ecological study of <Emphasis Type="Italic">Siganus spinus</Emphasis> and <Emphasis Type="Italic">S. guttatus</Emphasis> from Okinawan waters based on mitochondrial DNA control region sequences

The mitochondrial DNA (mtDNA) control region was sequenced to examine the genetic variability and gene flow of juvenile Siganus spinus and S. guttatus. In total, 461 nucleotide sequences were obtained from 69 specimens of juvenile S. spinus from Okinawa Island and Ishigaki Island, in which 17 variable sites and 22 haplotypes were identified. Haplotype diversity (h) was high (0.9244 in Okinawa and 0.8984 in Ishigaki), whereas nucleotide diversity (π) was low (0.0063 in Okinawa and 0.0059 in Ishigaki). The two populations were not genetically distinct. Siganus guttatus, which do not form large schools at recruitment, in contrast S. spinus, were also analyzed by studying 152 individuals collected off Okinawa Island, Miyako Island, and Ishigaki Island. Of 476 nucleotide sequences, 50 were variable, and 42 haplotypes were identified. Genetic variability values were high (h = 0.8766 and π = 0.0151 in Okinawa; h = 0.9640 and π = 0.0192 in Miyako; h = 0.9161 and π = 0.0199 in Ishigaki). The Okinawa population was genetically isolated from the Miyako and Ishigaki populations. As a result, genetic diversity was high for each of these siganid populations despite their being target species for fisheries; however, the degree of inter-population gene flow was higher for S. spinus than S. guttatus, suggesting that these species exhibit different dispersal strategies.