On the use of combined compact scheme for numerical solution of the two-layer oceanic shallow water equations

Many types of oceanic physical phenomena have a wide range in both space and time. In general, simplified models, such as shallow water model, are used to describe these oceanic motions. The shallow water equations are widely applied in various oceanic and atmospheric extents. By using the two-layer shallow water equations, the stratification effects can be considered too. In this research, the sixth-order combined compact method is investigated and numerically implemented as a high-order method to solve the two-layer shallow water equations. The second-order centered, fourth-order compact and sixth-order super compact finite difference methods are also used to spatial differencing of the equations. The first part of the present work is devoted to accuracy assessment of the sixth-order super compact finite difference method (SCFDM) and the sixth-order combined compact finite difference method (CCFDM) for spatial differencing of the linearized two-layer shallow water equations on the Arakawa's A-E and Randall's Z numerical grids. Two general discrete dispersion relations on different numerical grids, for inertia-gravity and Rossby waves, are derived. These general relations can be used for evaluation of the performance of any desired numerical scheme. For both inertia-gravity and Rossby waves, minimum error generally occurs on Z grid using either the sixth-order SCFDM or CCFDM methods. For the Randall's Z grid, the sixth-order CCFDM exhibits a substantial improvement , for the frequency of the barotropic and baroclinic modes of the linear inertia-gravity waves of the two layer shallow water model, over the sixth-order SCFDM. For the Rossby waves, the sixth-order SCFDM shows improvement, for the barotropic and baroclinic modes, over the sixth-order CCFDM method except on Arakawa's C grid. In the second part of the present work, the sixth-order CCFDM method is used to solve the one-layer and two-layer shallow water equations in their nonlinear form. In one-layer model with periodic boundaries, the performance of the methods for mass conservation is compared. The results show high accuracy of the sixth-order CCFDM method to simulate a complex flow field. Furthermore, to evaluate the performance of the method in a non-periodic domain the sixth-order CCFDM is applied to spatial differencing of vorticity-divergence-mass representation of one-layer shallow water equations to solve a wind-driven current problem with no-slip boundary conditions. The results show good agreement with published works. Finally, the performance of different schemes for spatial differencing of two-layer shallow water equations on Z grid with periodic boundaries is investigated. Results illustrate the high accuracy of combined compact method.

Characterization of the benthos, marine debris and bottom fish at Gray’s Reef National Marine Sanctuary

Executive Summary: Baseline characterization of resources is an essential part of marine protected area (MPA) management and is critical to inform adaptive management. Gray’s Reef National Marine Sanctuary (GRNMS) currently lacks adequate characterization of several key resources as identified in the 2006 Final Management Plan. The objectives of this characterization were to fulfill this need by characterizing the bottom fish, benthic features, marine debris, and the relationships among them for the different bottom types within the sanctuary: ledges, sparse live bottom, rippled sand, and flat sand. Particular attention was given to characterizing the different ledge types, their fish communities, and the marine debris associated with them given the importance of this bottom type to the sanctuary. The characterization has been divided into four sections. Section 1 provides a brief overview of the project, its relevance to sanctuary needs, methods of site selection, and general field procedures. Section 2 provides the survey methods, results, discussion, and recommendations for monitoring specific to the benthic characterization. Section 3 describes the characterization of marine debris. Section 4 is specific to the characterization of bottom fish. Field surveys were conducted during August 2004, May 2005, and August 2005. A total of 179 surveys were completed over ledge bottom (n=92), sparse live bottom (n=51), flat sand (n=20), and rippled sand (n=16). There were three components to each field survey: fish counting, benthic assessment, and quantification of marine debris. All components occurred within a 25 x 4 m belt transect. Two divers performed the transect at each survey site. One diver was responsible for identification of fish species, size, and abundance using a visual survey. The second diver was responsible for characterization of benthic features using five randomly placed 1 m2 quadrats, measuring ledge height and other benthic structures, and quantifying marine debris within the entire transect. GRNMS is composed of four main bottom types: flat sand, rippled sand, sparsely colonized live bottom, and densely colonized live bottom (ledges). Independent evaluation of the thematic accuracy of the GRNMS benthic map produced by Kendall et al. (2005) revealed high overall accuracy (93%). Most discrepancies between map and diver classification occurred during August 2004 and likely can be attributed to several factors, including actual map or diver errors, and changes in the bottom type due to physical forces. The four bottom types have distinct physical and biological characteristics. Flat and rippled sand bottom types were composed primarily of sand substrate and secondarily shell rubble. Flat sand and rippled sand bottom types were characterized by low percent cover (0-2%) of benthic organisms at all sites. Although the sand bottom types were largely devoid of epifauna, numerous burrows indicate the presence of infaunal organisms. Sparse live bottom and ledges were colonized by macroalgae and numerous invertebrates, including coral, gorgonians, sponges, and “other” benthic species (such as tunicates, anemones, and bryozoans). Ledges and sparse live bottom were similar in terms of diversity (H’) given the level of classification used here. However, percent cover of benthic species, with the exception of gorgonians, was significantly greater on ledge than on sparse live bottom. Percent biotic cover at sparse live bottom ranged from 0.7-26.3%, but was greater than 10% at only 7 out of 51 sites. Colonization on sparse live bottom is likely inhibited by shifting sands, as most sites were covered in a layer of sediment up to several centimeters thick. On ledge bottom type, percent cover ranged from 0.42-100%, with the highest percent cover at ledges in the central and south-central region of GRNMS. Biotic cover on ledges is influenced by local ledge characteristics. Cluster analysis of ledge dimensions (total height, undercut height, undercut width) resulted in three main categories of ledges, which were classified as short, medium, and tall. Median total percent cover was 97.6%, 75.1%, and 17.7% on tall, medium, and short ledges, respectively. Total percent cover and cover of macroalgae, sponges, and other organisms was significantly lower on short ledges compared to medium and tall ledges, but did not vary significantly between medium and tall ledges. Like sparse live bottom, short ledges may be susceptible to burial by sand, however the results indicate that ledge height may only be important to a certain threshold. There are likely other factors not considered here that also influence spatial distribution and community structure (e.g., small scale complexity, ocean currents, differential settlement patterns, and biological interactions). GRNMS is a popular site for recreational fishing and boating, and there has been increased concern about the accumulation of debris in the sanctuary and potential effects on sanctuary resources. Understanding the types, abundance, and distribution of debris is essential to improving debris removal and education efforts. Approximately two-thirds of all observed debris items found during the field surveys were fishing gear, and about half of the fishing related debris was monofilament fishing line. Other fishing related debris included leaders and spear gun parts, and non-gear debris included cans, bottles, and rope. The spatial distribution of debris was concentrated in the center of the sanctuary and was most frequently associated with ledges rather than at other bottom types. Several factors may contribute to this observation. Ledges are often targeted by fishermen due to the association of recreationally important fish species with this bottom type. In addition, ledges are structurally complex and are often densely colonized by biota, providing numerous places for debris to become stuck or entangled. Analysis of observed boat locations indicated that higher boat activity, which is an indication of fishing, occurs in the center of the sanctuary. On ledges, the presence and abundance of debris was significantly related to observed boat density and physiographic features including ledge height, ledge area, and percent cover. While it is likely that most fishing related debris originates from boats inside the sanctuary, preliminary investigation of ocean current data indicate that currents may influence the distribution and local retention of more mobile items. Fish communities at GRNMS are closely linked to benthic habitats. A list of species encountered, probability of occurrence, abundance, and biomass by habitat is provided. Species richness, diversity, composition, abundance, and biomass of fish all showed striking differences depending on bottom type with ledges showing the highest values of nearly all metrics. Species membership was distinctly separated by bottom type as well, although very short, sparsely colonized ledges often had a similar community composition to that of sparse live bottom. Analysis of fish communities at ledges alone indicated that species richness and total abundance of fish were positively related to total percent cover of sessile invertebrates and ledge height. Either ledge attribute was sufficient to result in high abundance or species richness of fish. Fish diversity (H`) was negatively correlated with undercut height due to schools of fish species that utilize ledge undercuts such as Pareques species. Concurrent analysis of ledge types and fish communities indicated that there are five distinct combinations of ledge type and species assemblage. These include, 1) short ledges with little or no undercut that lacked many of the undercut associated species except Urophycis earlii ; 2) tall, heavily colonized, deeply undercut ledges typically with Archosargus probatocephalus, Mycteroperca sp., and Pareques sp.; 3) tall, heavily colonized but less undercut with high occurrence of Lagodon rhomboides and Balistes capriscus; 4) short, heavily colonized ledges typically with Centropristis ocyurus, Halichoeres caudalis, and Stenotomus sp.; and 5) tall, heavily colonized, less undercut typically with Archosargus probatocephalus, Caranx crysos and Seriola sp.. Higher levels of boating activity and presumably fishing pressure did not appear to influence species composition or abundance at the community level although individual species appeared affected. These results indicate that merely knowing the basic characteristics of a ledge such as total height, undercut width, and percent cover of sessile invertebrates would allow good prediction of not only species richness and abundance of fish but also which particular fish species assemblages are likely to occur there. Comparisons with prior studies indicate some major changes in the fish community at GRNMS over the last two decades although the causes of the changes are unknown. Species of interest to recreational fishermen including Centropristis striata, Mycteroperca microlepis, and Mycteroperca phenax were examined in relation to bottom features, areas of assumed high versus low fishing pressure, and spatial dispersion. Both Mycteroperca species were found more frequently when undercut height of ledges was taller. They often were found together in small mixed species groups at ledges in the north central and southwest central regions of the sanctuary. Both had lower mode size and proportion of fish above the fishery size limit in heavily fished areas of the sanctuary (i.e. high boat density) despite the presence of better habitat in that region. Black sea bass, C. striata, occurred at 98% of the ledges surveyed and appeared to be evenly distributed throughout the sanctuary. Abundance was best explained by a positive relationship with percent cover of sessile biota but was also negatively related to presence of either Mycteroperca species. This may be due to predation by the Mycteroperca species or avoidance of sites where they are present by C. striata. Suggestions for monitoring bottom features, marine debris, and bottom fish at GRNMS are provided at the end of each chapter. The present assessment has established quantitative baseline characteristics of many of the key resources and use issues at GRNMS. The methods can be used as a model for future assessments to track the trajectory of GRNMS resources. Belt transects are ideally suited to providing efficient and quantitative assessment of bottom features, debris, and fish at GRNMS. The limited visibility, sensitivity of sessile biota, and linear nature of ledge habitats greatly diminish the utility of other sampling techniques. Ledges should receive the bulk of future characterization effort due to their importance to the sanctuary and high variability in physical structure, benthic composition, and fish assemblages. (PDF contains 107 pages.)

Fishing gear and methods of the river Brahmaputra in Assam

Potentially the inland fishery resources of the country are of very high order. But the present level of their exploitation is far from optimum, mainly because of the inadequacies of the existing fishing gear and methods. There is vast scope for increasing the fish production from inland waters by improving the existing gear and methods. This would require a thorough study of the fishing gear and methods in vogue, of which very little is known at present. In the present communication the authors discuss the fishing gear and methods of the river Brahmaputra, in Assam, based on a survey carried out by them during January-February 1964. The survey covers a 640 km stretch of the Brahmaputra River, its important tributaries and connected bheels, from Dhubri to Dibrugarh. As a result of the survey about 19 types of fishing nets, which could be grouped into eight classes, were identified. The salient technological features of the gears and their methods of operation are discussed class-wise. The characteristics of the individual types are shown in tables. The materials used for gear and gear accessories, are briefly discussed. The classification and relative importance of different types of gear are examined. Besides, the influence of the ecological and topographical features of the river on the development of different types of fishing gears, is also discussed.

Studies on phenolase enzymes in prawns. Pt. 1. The distribution and physical properties of phenolases in Penaeid prawns

The distribution of phenolases in certain species of Penaeid prawns has been studied. Attempts were made to locate the regions of maximum enzyme activity in the prawns. The relative dopase activity has been examined in extracts from head, tail, shell with cuticles and muscle. The head juice and tail extracts were found to register very high order of enzyme activity. Metapenaeus affinis, Metapenaeus monoceros and Penaeus indicus record comparatively higher enzyme activity than Parapenaeopsis stylifera and Metapenaeus dobsoni, no definite relationship has been found between the relative activity of the enzyme and size grade at least in one species examined. Experiments were done to determine the pH optima of the enzyme and the influence of pH on its deactivation. Exposure to higher temperatures up to 55°c was shown to activate the crude enzyme considerably. The possible implications of the observations have been discussed.

Wind wave prediction in the Caspian Sea

In this thesis, wind wave prediction and analysis in the Southern Caspian Sea are surveyed. Because of very much importance and application of this matter in reducing vital and financial damages or marine activities, such as monitoring marine pollution, designing marine structure, shipping, fishing, offshore industry, tourism and etc, gave attention by some marine activities. In this study are used the Caspian Sea topography data that are extracted from the Caspian Sea Hydrography map of Iran Armed Forces Geographical Organization and the I 0 meter wind field data that are extracted from the transmitted GTS synoptic data of regional centers to Forecasting Center of Iran Meteorological Organization for wave prediction and is used the 20012 wave are recorded by the oil company's buoy that was located at distance 28 Kilometers from Neka shore for wave analysis. The results of this research are as follows: - Because of disagreement between the prediction results of SMB method in the Caspian sea and wave data of the Anzali and Neka buoys. The SMB method isn't able to Predict wave characteristics in the Southern Caspian Sea. - Because of good relativity agreement between the WAM model output in the Caspian Sea and wave data of the Anzali buoy. The WAM model is able to predict wave characteristics in the southern Caspian Sea with high relativity accuracy. The extreme wave height distribution function for fitting to the Southern Caspian Sea wave data is obtained by determining free parameters of Poisson-Gumbel function through moment method. These parameters are as below: A=2.41, B=0.33. The maximum relative error between the estimated 4-year return value of the Southern Caspian Sea significant wave height by above function with the wave data of Neka buoy is about %35. The 100-year return value of the Southern Caspian Sea significant height wave is about 4.97 meter. The maximum relative error between the estimated 4-year return value of the Southern Caspian Sea significant wave height by statistical model of peak over threshold with the wave data of Neka buoy is about %2.28. The parametric relation for fitting to the Southern Caspian Sea frequency spectra is obtained by determining free parameters of the Strekalov, Massel and Krylov etal_ multipeak spectra through mathematical method. These parameters are as below: A = 2.9 B=26.26, C=0.0016 m=0.19 and n=3.69. The maximum relative error between calculated free parameters of the Southern Caspian Sea multipeak spectrum with the proposed free parameters of double-peaked spectrum by Massel and Strekalov on the experimental data from the Caspian Sea is about 36.1 % in spectrum energetic part and is about 74M% in spectrum high frequency part. The peak over threshold waverose of the Southern Caspian Sea shows that maximum occurrence probability of wave height is relevant to waves with 2-2.5 meters wave fhe error sources in the statistical analysis are mainly due to: l) the missing wave data in 2 years duration through battery discharge of Neka buoy. 2) the deportation %15 of significant height annual mean in single year than long period average value that is caused by lack of adequate measurement on oceanic waves, and the error sources in the spectral analysis are mainly due to above- mentioned items and low accurate of the proposed free parameters of double-peaked spectrum on the experimental data from the Caspian Sea.