Application of the characteristic CIP method to a shallow water model on the sphere

Semi-implicit algorithms are popularly used to deal with the gravitational term in numerical models. In this paper, we adopt the method of characteristics to compute the solutions for gravity waves on a sphere directly using a semi-Lagrangian advection scheme instead of the semi-implicit method in a shallow water model, to avoid expensive matrix inversions. Adoption of the semi-Lagrangian scheme renders the numerical model always stable for any Courant number, and which saves CPU time. To illustrate the efficiency of the characteristic constrained interpolation profile (CIP) method, some numerical results are shown for idealized test cases on a sphere in the Yin-Yang grid system.

A multi-moment finite volume formulation for shallow water equations on unstructured mesh

A novel and accurate finite volume method has been presented to solve the shallow water equations on unstructured grid in plane geometry. In addition to the volume integrated average (VIA moment) for each mesh cell, the point values (PV moment) defined on cell boundary are also treated as the model variables. The volume integrated average is updated via a finite volume formulation, and thus is numerically conserved, while the point value is computed by a point-wise Riemann solver. The cell-wise local interpolation reconstruction is built based on both the VIA and the PV moments, which results in a scheme of almost third order accuracy. Efforts have also been made to formulate the source term of the bottom topography in a way to balance the numerical flux function to satisfy the so-called C-property. The proposed numerical model is validated by numerical tests in comparison with other methods reported in the literature. (C) 2010 Elsevier Inc. All rights reserved.

A global shallow water model using high order multi-moment constrained finite volume method and icosahedral grid

A novel accurate numerical model for shallow water equations on sphere have been developed by implementing the high order multi-moment constrained finite volume (MCV) method on the icosahedral geodesic grid. High order reconstructions are conducted cell-wisely by making use of the point values as the unknowns distributed within each triangular cell element. The time evolution equations to update the unknowns are derived from a set of constrained conditions for two types of moments, i.e. the point values on the cell boundary edges and the cell-integrated average. The numerical conservation is rigorously guaranteed. in the present model, all unknowns or computational variables are point values and no numerical quadrature is involved, which particularly benefits the computational accuracy and efficiency in handling the spherical geometry, such as coordinate transformation and curved surface. Numerical formulations of third and fourth order accuracy are presented in detail. The proposed numerical model has been validated by widely used benchmark tests and competitive results are obtained. The present numerical framework provides a promising and practical base for further development of atmospheric and oceanic general circulation models. (C) 2009 Elsevier Inc. All rights reserved.

Heavy-ion conformal irradiation in the shallow-seated tumor therapy terminal at HIRFL

Basic research related to heavy-ion cancer therapy has been done at the Institute of Modern Physics (IMP), Chinese Academy of Sciences since 1995. Now a plan of clinical trial with heavy ions has been launched at IMP. First, superficially placed tumor treatment with heavy ions is expected in the therapy terminal at the Heavy Ion Research Facility in Lanzhou (HIRFL), where carbon ion beams with energy up to 100 MeV/u can be supplied. The shallow-seated tumor therapy terminal at HIRFL is equipped with a passive beam delivery system including two orthogonal dipole magnets, which continuously scan pencil beams laterally and generate a broad and uniform irradiation field, a motor-driven energy degrader and a multi-leaf collimator. Two different types of range modulator, ripple filter and ridge filter with which Guassian-shaped physical dose and uniform biological effective dose Bragg peaks can be shaped for therapeutic ion beams respectively, have been designed and manufactured. Therefore, two-dimensional and three-dimensional conformal irradiations to tumors can be performed with the passive beam delivery system at the earlier therapy terminal. Both the conformal irradiation methods have been verified experimentally and carbon-ion conformal irradiations to patients with superficially placed tumors have been carried out at HIRFL since November 2006.

Physical property measurement of therapeutic carbon ion beam in the shallow-seated tumor therapy terminal at HIRFL

For the first time the physical properties of therapeutic carbon-ion beam supplied by, the shallow-seated tumor therapy terminal at the Heavy Ion Research Facility in Lanzhou (HIRFL) are measured. For a 80.55MeV/u C-12 ion beam delivered to the therapy terminal, the homogeneity of irradiation fields is 73.48%, when the beam intensity varied in the range of 0.001-0.1nA (i.e. 1 X 10(6) - 1 X 10(8) particles per second). The stability of the beam intensity within a few minutes is estimated to be 80.87%. The depth-dose distribution of the beam at the isocenter of the therapy facility is measured, and the position of the high-dose Bragg peak is found to be located at the water-equivalent depth of 13.866mm. Based on the relationship between beam energy and Bragg peak position, the corresponding beam energy at the isocenter of the therapy terminal is evaluated to be 71.71MeV/u for the original 80.55MeV/u C-12 ion beam, which consisted basically with calculation. The readout of the previously-used air-free ionization chamber regarding absorbed dose is calibrated as well in this experiment. The results indicate that the performance of the therapy facility should be optimized further to meet the requirements of clinical trial.

A Global Crisis for Seagrass Ecosystems

Seagrasses, marine flowering plants, have a long evolutionary history but are now challenged with rapid environmental changes as a result of coastal human population pressures. Seagrasses provide key ecological services, including organic carbon production and export, nutrient cycling, sediment stabilization, enhanced biodiversity, and trophic transfers to adjacent habitats in tropical and temperate regions. They also serve as “coastal canaries,” global biological sentinels of increasing anthropogenic influences in coastal ecosystems, with large-scale losses reported worldwide. Multiple stressors, including sediment and nutrient runoff, physical disturbance, invasive species, disease, commercial fishing practices, aquaculture, overgrazing, algal blooms, and global warming, cause seagrass declines at scales of square meters to hundreds of square kilometers. Reported seagrass losses have led to increased awareness of the need for seagrass protection, monitoring, management, and restoration. However, seagrass science, which has rapidly grown, is disconnected from public awareness of seagrasses, which has lagged behind awareness of other coastal ecosystems. There is a critical need for a targeted global conservation effort that includes a reduction of watershed nutrient and sediment inputs to seagrass habitats and a targeted educational program informing regulators and the public of the value of seagrass meadows.

Shallow gas in the muddy sediments of Eckernförde Bay, Germany

The seafloor of central Eckernförde Bay is characterised by soft muddy sediments that contain free methane gas. Bubbles of free gas cause acoustic turbidity which is observed with acoustic remote sensing systems. Repeated surveys with subbottom profiler and side scan sonar revealed an annual period both of depth of the acoustic turbidity and backscatter strength. The effects are delayed by 3–4 months relative to the atmospheric temperature cycle. In addition, prominent pockmarks, partly related to gas seepage, were detected with the acoustic systems. In a direct approach gas concentrations were measured from cores using the gas chromatography technique. From different tests it is concluded that subsampling of a core should start at its base and should be completed as soon as possible, at least within 35 min after core recovery. Comparison of methane concentrations of summer and winter cores revealed no significant seasonal variation. Thus, it is concluded that the temperature and pressure influences upon solubility control the depth variability of acoustic turbidity which is observed with acoustic remote sensing systems. The delay relative to the atmospheric temperature cycle is caused by slow heat transfer through the water column. The atmospheric temperature cycle as ‘exiting function’ for variable gas solubility offers an opportunity for modelling and predicting the depth of the acoustic turbidity. In practice, however, small-scale variations of, e.g., salinity, or gas concentration profile in the sediment impose limits to predictions. In addition, oceanographic influences as mixing in the water column, variable water inflow, etc. are further complications that reduce the reliability of predictions.

Fruit anatomy,seed germination and seedling development in the Japanese seagrass phyllospadix

Phyllospadix iwatensis Makino and phyllospadix japonicus Makino have similar frunt morphology and anatomy.The rhomboid fruit of Japanese phyllospadix is dark brown in colour and is characterized by two arms bearing stiff inflected bristles which can act as an anchoring system. The fruit covering consists of a thin cuticular seed coat and pericarp remains mainly fibrous endocarp. In the groove region of the fruit.the cuticular seed coat and endocarp are replaced by nucellus cells with wall in growths and crushed pigment strands with lignified walls.these tissues appera to control the transfer of nutrients to developing seed.the seed is oval with a small embryo and a large hypocotyl. the embryo is straight and simple,with the plumule containing three leaf primordia and a pair of root primordia surrounded by a cotyledon.the hypocotyl has large vontral lobe containing central provascular tissue and two small dorsal lobes.the hypocotyl contains starch.lipid and protein.and acts as a nutrient store.the seed of P.iwatensis has a dormancy period of 2-6 weeks and germination eventually reaches-65%.but is not synchronized.during germination the leaves emerge first.and then after at least three young leaves have formed and abseised.the roots emerge,usually?6 months after the commencement of germination.Utilizaton of the nutrient reserves is initially from the perihpery of the hypocotyl and then progressively towards its centre.

Seed germination and seedling morphology of the seagrass, Halophila engelmannii (Hydrocharitaceae)

Seeds of Halophila engelmannii Aschers., that were collected in Redfish Bay, Texas, at weekly intervals from mid-May to mid-June 1986, began to germinate 3–4 weeks after collection. Most of the collections subsequently showed an increase in the rate of germination under increased light intensity and all had a stoppage of germination after transfer to darkness, indicating a light requirement to break endogenous seed dormancy. During the 5 weeks after seeds germinated, seedlings in soil culture produced a rosette of six leaves before the appearance of a rhizome bud in the axil of the third leaf. The first node of the rhizome produced a root and an upright shoot with a pseudowhorl of three to five leaves.

Seed-bank development, germination and early seedling survival of two seagrass species from The Netherlands: Zostera marina L. and Zostera noltii hornem

Flowering and seed-bank development of annual Zostera marina L. and perennial Z. noltii hornem. were studied in the Zandkreek (S.W. Netherlands). Flowering of Z. noltii started at the end of June and continued until the end of September. A maximum of ca. 1000 flowering shoots (11% of the total amount of shoots per square metre) occurred in early August. Flowering of Z. marina started at the end of July and continued throughout October. Seed banks of both species appeared to be annual. Actual seed densities of Z. noltii were much lower than predicted on the basis of the amount of inflorescences.Germination was studied in the laboratory in relation to temperature (10, 20 and 30°C), salinity (1.0, 10.0, 20.0, 30.0 and 40.0‰) and stratification (at 4°C). Both species showed a maximal germination at 30°C and 1.0‰ salinity, decreasing with higher salinities and lower temperatures. Stratification stimulated germination only at salinities 20.0‰. Desiccation and anaerobia were lethal to Z. marina seeds. Seedlings of Z. marina survived best at 10°C and 10.0–20.0‰ salinity and those of Z. noltii survived best at 10°C and 1.0‰ salinity. Overall, seedlings of Z. marina survived better than those of Z. noltii.

Antifeedant, antibacterial, and antilarval compounds from the South China Sea seagrass Enhalus acoroides

We investigated chemical constituents and the antifeedant, antibacterial, and antilarval activities of EtOH (ethanol) extracts of the South China Sea seagrass Enhalus acoroides. Eleven pure compounds including four flavonoids and five steroids were obtained. Among these compounds, three flavonoids were antifeedant against second-instar larvae of Spodoptera litura, two flavonoids had antibacterial activity towards several marine bacteria, and one flavonoid showed strong antilarval activity against Bugula neritina larvae. This is the first description of isolation and bioactivity of secondary metabolites from E. acoroides.

Characteristics of shallow gas hydrate in Okhotsk Sea

Multidisciplinary field investigations were carried out in Okhotsk Sea by R/V Akademik M.A. Lavrentyev (LV) of the Russian Academy of Sciences (RAS) in May 2006, supported by funding agencies from Korea, Russia, Japan and China. Geophysical data including echo-sounder, bottom profile, side-scan-sonar, and gravity core sample were obtained aimed to understand the characteristics and formation mechanism of shallow gas hydrates. Based on the geophysical data, we found that the methane flare detected by echo-sounder was the evidence of free gas in the sediment, while the dome structure detected by side-scan sonar and bottom profile was the root of gas venting. Gas hydrate retrieved from core on top of the dome structure which was interbedded as thin lamination or lenses with thickness varying from a few millimeters to 3 cm. Gas hydrate content in hydrate-bearing intervals visually amounted to 5%-30% of the sediment volume. This paper argued that gases in the sediment core were not all from gas hydrate decomposition during the gravity core lifting process, free gases must existed in the gas hydrate stability zone, and tectonic structure like dome structure in this paper was free gas central, gas hydrate formed only when gases over-saturated in this gas central, away from these structures, gas hydrate could not form due to low gas concentration.