Numerical simulation of unsteady free-surface motions using a boundary integral formulation

A numerical time simulation method is described to solve fluid flow problems including unsteady free surface motion. The method is based on potential flow theory. At every time step, the problem is solved using a boundary integral formulation of the fluid domain. The linearized free surface conditions are integrated in time and the solution is marched forward. Computational results simulating the free surface motion for the cases of a linear progressive wave, wave propagating into a region of calm water and the wave maker motion are presented. Comparison with theoretical results demonstrate the feasibility of the proposed simulation scheme.     

Properties of structure and function of cadmium-binding proteins/peptides from Euglena gracilis

Euglena gracilis makes two small Cd-binding proteins/peptides (Cd-BP I and Cd-BP II) in response to exposure to Cd²⁺. These proteins migrate slower than mammalian Cd-metallothionein (Cd-Mt) through Sephadex G-75, but like Cd-Mt also contain Zn and are separated into two species when chromatographed over a DEAE column. Both BPs are much less stable than Cd-Mt under acidic conditions. One source of this instability is that at least Cd-BP II contains acid-labile sulfide co-ordinated to the metals. It has been quantitated in Cd-BP II and shown to have a value of 1·25 ± 0·10 S²⁻/Cd. The reactivity of the Cd-binding sites in ligand substitution and thioldisulfide exchange reactions has been assessed. The reactions of Cd-BP I and II with pyridylazoresorcinol (PAR) were slow and displayed complex kinetic behavior. Similarly, both Cd-BPs react slowly and with complicated kinetics with 5,5′-dithiobis-(2-nitrobenzoate).     

Holocene sedimentation of a wave-dominated barrierisland shoreline: Cape Lookout, North Carolina

The sedimentary record of 130 km of microtidal (0.9 m tidal range) high wave energy (1.5 m average wave height) barrier island shoreline of the Cape Lookout cuspate foreland has been evaluated through examination of 3136 m of subsurface samples from closely spaced drill holes. Holocene sedimentation and coastal evolution has been a function of five major depositional processes: (1) eustatic sea-level rise and barrier-shoreline transgression; (2) lateral tidal inlet migration and reworking of barrier island deposits; (3) shoreface sedimentation and local barrier progradation; (4) storm washover deposition with infilling of shallow lagoons; and (5) flood-tidal delta sedimentation in back-barrier environments.

Twenty-five radiocarbon dates of subsurface peat and shell material from the Cape Lookout area are the basis for a late Holocene sea-level curve. From 9000 to 4000 B.P. eustatic sea level rose rapidly, resulting in landward migration of both barrier limbs of the cuspate foreland. A decline in the rate of sea-level rise since 4000 B.P. resulted in relative shoreline stabilization and deposition of contrasting coastal sedimentary sequences. The higher energy, storm-dominated northeast barrier limb (Core and Portsmouth Banks) has migrated landward producing a transgressive sequence of coarse-grained, horizontally bedded washover sands overlying burrowed to laminated back-barrier and lagoonal silty sands. Locally, ephemeral tidal inlets have reworked the transgressive barrier sequence depositing fining-upward spit platform and channel-fill sequences of cross-bedded, pebble gravel to fine sand and shell. Shoreface sedimentation along a portion of the lower energy, northwest barrier limb (Bogue Banks) has resulted in shoreline progradation and deposition of a coarsening-up sequence of burrowed to cross-bedded and laminated, fine-grained shoreface and foreshore sands. In contrast, the adjacent barrier island (Shackleford Banks) consists almost totally of inlet-fill sediments deposited by lateral tidal inlet migration. Holocene sediments in the shallow lagoons behind the barriers are 5–8 m thick fining-up sequences of interbedded burrowed, rooted and laminated flood-tidal delta, salt marsh, and washover sands, silts and clays.

While barrier island sequences are generally 10 m in thickness, inlet-fill sequences may be as much as 25 m thick and comprise an average of 35% of the Holocene sedimentary deposits. Tidal inlet-fill, back-barrier (including flood-tidal delta) and shoreface deposits are the most highly preservable facies in the wave-dominated barrier-shoreline setting. In the Cape Lookout cuspate foreland, these three facies account for over 80% of the sedimentary deposits preserved beneath the barriers. Foreshore, spit platform and overwash facies account for the remaining 20%.     

Evidence from heterologous expression of glutathione S-transferases A and A1 of the plaice (Pleuronectes platessa) that their endogenous role is in detoxification of lipid peroxidation products

cDNA clones for glutathione S-transferases A (GST-A) and A1 (GST-A1) from plaice (Pleuronectes platessa) were expressed as N-terminally 6XHis tagged proteins in Escherichia coli and purified to homogeneity from Ni-NTA silica. GST-A was an efficient catalyst for conjugation of unsaturated alkenals derived from peroxidation of polyunsaturated fatty acids with the highest activity observed with trans-non-2-enal (8 micromol min(-1) mg(-1)). GST-A1 was a very efficient Se-independent glutathione peroxidase with an activity towards cumene hydroperoxide of 25 micromol min(-1) mg(-1). Although the enzymes exhibited moderately high activities towards the model substrate 1-chloro-2,4-dinitrobenzene (CDNB) they exhibited little or no activity towards other common prototypical xenobiotic substrates. Together with data for ontogeny, tissue distribution and inducibility of these enzymes, we contend that a primary function of these enzymes is protection from the harmful effects of lipid peroxidation products generated naturally or exacerbated by xenobiotic exposure.     

Evaluation of toxicity in tributaries of the Mersey estuary using the isopod Asellus aquaticus (L.)

Increasing numbers of industrial, agricultural and natural chemicals are present in sewage effluent and are known to elicit toxic effects in laboratory exposures, but little is known of their combined sub-lethal effect in the field. In this study, a combination of esterase activity and ventilation rate assays was performed to determine the neurological and physiological function of the freshwater crustacean Asellus aquaticus (L.) at sites above and below a sewage treatment works (STW). Cholinesterase and carboxylesterase activities were significantly inhibited (n=8, P<0.05) and ventilation rates increased (n=8, P=0.0001) in A. aquaticus at STW sites compared to those from reference sites, indicating a decrease in neurological and physiological function. The ecological relevance of these findings for the population dynamics of the organisms in the field is discussed.     

Burial and scour around short cylinder under progressive shoaling waves

The results of a laboratory experimental program aimed at better understanding the scour around and burial of heavy cylindrical objects under oscillating flow on a sandy bed are described. This study was motivated by its application to the dynamics of isolated cobbles/mines on a sandy floor under nonlinear progressive waves, such as that occur in shallow coastal waters beyond the wave-breaking region. In the experiments, nonlinear progressive waves were generated in a long wave tank of rectangular cross-section with a bottom slope. Model mines (short cylinders) were placed on the sandy bottom and the temporal evolution of the bed profile and the velocity field in the near field of the object were observed. Experiments were conducted at relatively high Reynolds numbers for a range of flow conditions, which can be characterized by the Keulegan–Carpenter number and Shields parameter. Depending on the values of these parameters, four different scour regimes around the cylinder including periodical burial of cylinder under migrating sand ripples were observed; they were classified as: (i) no scour/burial, (ii) initial scour, (iii) expanded scour, and (iv) periodic burial cases. A scour regime diagram was developed and the demarcation criteria between different regimes were deduced. Semi-empirical formulae that permit estimation of the scour depth with time, the equilibrium maximum scour depth and length, and conditions necessary for the burial of the cylinder as a function of main external parameters are also proposed.     

Upstream dams and downstream clams: growth rates of bivalve mollusks unveil impact of river management on estuarine ecosystems (Colorado River Delta, Mexico)

We studied how the extensive diversion of Colorado River water, induced by dams and agricultural activities of the last 70 years, affected the growth rates of two abundant bivalve mollusk species (Chione cortezi and Chione fluctifraga) in the northern Gulf of California. Shells alive on the delta today (‘Post-dam’ shells) grow 5.8–27.9% faster than shells alive prior to the construction of dams (‘Pre-dam’ shells). This increase in annual shell production is linked to the currently sharply reduced freshwater influx to the Colorado River estuary. Before the upstream river management, lower salinity retarded growth rates in these bivalves. Intra-annual growth rates were 50% lower during spring and early summer, when river flow was at its maximum. Growth rates in Chione today are largely controlled by temperature and nutrients; prior to the construction of dams and the diversion of the Colorado River flow, seasonal changes in salinity played an important role in regulating calcification rates.Our study employs sclerochronological (growth increment analysis) and geochemical techniques to assess the impact of reduced freshwater influx on bivalve growth rates in the Colorado River estuary. A combination of both techniques provides an excellent tool to evaluate the impact of river management in areas where no pre-impact studies were made.     

Bathymetry of the Tonga Trench and Forearc: a map series

Four new bathymetric maps of the Tonga Trench and forearc between 14 °S and 27 °S display the important morphologic and structural features of this dynamic convergent margin. The maps document a number of important geologic features of the margin. Major normal faults and fault lineaments on the Tonga platform can be traced along and across the upper trench slope. Numerous submarine canyons incised in the landward slope of the trench mark the pathways of sediment transport from the platform to mid- and lower-slope basins. Discontinuities in the trench axis and changes in the morphology of the landward slope can be clearly documented and may be associated with the passage and subduction of the Louisville Ridge and other structures on the subducting Pacific Plate. Changes in the morphology of the forearc as convergence changes from normal in the south to highly-oblique in the north are clearly documented. The bathymetric compilations, gridded at 500- and 200-m resolutions and extending along 500 km of the landward trench slope and axis, provide complete coverage of the outer forearc from the latitude of the Louisville Ridge-Tonga Trench collision to the northern terminus of the Tonga Ridge. These maps should serve as a valuable reference for other sea-going programs in the region, particularly the Ocean Drilling Program (ODP) and the National Science Foundation MARGINS initiative.     

Comparisons between the influences of habitat, body size and season on the dietary composition of the sparid Acanthopagrus latus in a large marine embayment

Seasonal samples from Shark Bay on the west coast of Australia were used to determine (1) the habitats occupied by the juveniles and adults of Acanthopagrus latus in this large subtropical marine embayment and (2) the extent to which the dietary composition of this sparid is influenced by habitat type, body length and season. Sampling was undertaken in two habitat types in which A. latus was known to be abundant, namely mangrove (Avicennia marina) creeks and nearby rocky areas, the latter comprising sandstone boulders and/or limestone reefs. The mean total length ±95% CLs of A. latus was far lower in mangrove creeks, 126 ± 6.1 mm, than in rocky areas, 313 ± 4.7 mm. As A. latus attains maturity at ca. 245 mm, the juveniles of this species typically occupy mangrove areas and then, with increasing body size, move to nearshore rocky areas, where they become adults. The species composition of the food ingested by juvenile A. latus in mangrove creeks differed markedly from that of large juveniles and adults in rocky areas. Based on analyses of data for both habitat types combined, this difference was far greater than that between size classes and season, which was negligible. There were indications, however, that, overall within each habitat, the dietary composition did change seasonally, although not with body size. Acanthopagrus latus fed predominantly on mangrove material, sesarmid crabs and small gastropods in mangrove habitats, and mainly on Brachidontes ustulatus in rocky areas, where this mytilid bivalve is very abundant. The mangrove material, which contributed nearly 40% of its overall dietary volume in mangrove creeks, consisted mainly of lateral root primordia. This apparently unique food source for a teleost is presumably ingested through subsurface nipping, which would be facilitated by the mouth and dentitional characteristics of sparids. The almost total lack of correspondence in the dietary compositions of fish in the length class that was well represented in both mangrove and rocky areas illustrates the extent to which this sparid is capable of opportunistic feeding behaviour.     

Short-term and interannual variability of redox-sensitive chemical parameters in hypoxic/anoxic bottom waters of the Chesapeake Bay

A combination of CTD casts, discrete bottle sampling and in situ voltammetric microelectrode profiling was used to examine changing redox conditions in the water column at a single station south of the Bay Bridge in the upper Chesapeake Bay in late July/early August, 2002–2005. Short-term (2–4 h) fluctuations in the oxic/suboxic/anoxic interface were documented using in situ voltammetric solid-state electrodes. Profiles of dissolved oxygen and sulfide revealed tidally-driven vertical fluctuations of several meters in the depth and thickness of the suboxic zone. Bottom water concentrations of sulfide, Mn²⁺ and Fe²⁺ also varied over the tidal cycle by approximately an order of magnitude. These data indicate that redox species concentrations at this site varied more due to physical processes than biogeochemical processes. Based on analysis of ADCP data, tidal currents at this station were strongly polarized, with the principal axis of tidal currents aligned with the mainstem channel. Together with the chemical data, the ADCP analysis suggests tidal flushing of anoxic bottom waters with suboxic water from north of the site. The present study is thus unique because while most previous studies have focused on processes across relatively stable redox interfaces, our data clearly demonstrate the influence of rapidly changing physical mixing processes on water column redox chemistry.Also noted during the study were interannual differences in maximum bottom water concentrations of sulfide, Mn²⁺ and Fe²⁺. In 2003, for example, heavy spring rains resulted in severe hypoxia/anoxia in June and early July. While reported storm-induced mixing in late July/early August 2003 partially alleviated the low-oxygen conditions, bottom water concentrations of sulfide, Mn²⁺ and Fe²⁺ were still much higher than in the previous year. The latter implies that the response time of the microbial community inhabiting the suboxic/anoxic bottom waters to changing redox conditions is slow compared to the time scale of episodic mixing events. Bottom water concentrations of the redox-sensitive chemical species should thus be useful as a tracer to infer prior hypoxic/anoxic conditions not apparent from ambient oxygen levels at the time of sampling.