Journal of Marine Science and Engineering

1638 KiB

Open AccessArticle

Uncovering Spatio-Temporal and Treatment-Derived Differences in the Molecular Physiology of a Model Coral-Dinoflagellate Mutualism with Multivariate Statistical Approaches

by Anderson B. Mayfield

J. Mar. Sci. Eng. 2016, 4(3), 63; https://doi.org/10.3390/jmse4030063 - 19 Sep 2016

Cited by 9 | Viewed by 4740

Abstract

In light of current global climate change forecasts, there is an urgent need to better understand how reef-building corals respond to changes in temperature. Multivariate statistical approaches (MSA), including principal components analysis and multidimensional scaling, were used herein to attempt to understand the [...] Read more.

In light of current global climate change forecasts, there is an urgent need to better understand how reef-building corals respond to changes in temperature. Multivariate statistical approaches (MSA), including principal components analysis and multidimensional scaling, were used herein to attempt to understand the response of the common, Indo-Pacific reef coral Seriatopora hystrix to temperature changes using data from laboratory-based temperature challenge studies performed in Southern Taiwan. S. hystrix and its dinoflagellate endosymbionts displayed physiological and molecular signatures that were characteristic of sampling time, site of colony origin, and/or temperature regime. Specifically, upon assessing a series of both host coral and Symbiodinium response variables, corals exposed to fluctuating temperatures were found to display greater variability in their physiological response than experimental controls incubated at stable temperatures. These findings further promote the utility of MSA for documenting biologically meaningful shifts in the physiological and/or sub-cellular response of marine invertebrates exposed to environmental change. Full article

(This article belongs to the Section Marine Biology)

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5532 KiB

Open AccessArticle

Influence of Wind Strength and Duration on Relative Hypoxia Reductions by Opposite Wind Directions in an Estuary with an Asymmetric Channel

by Ping Wang, Harry Wang, Lewis Linker and Kyle Hinson

J. Mar. Sci. Eng. 2016, 4(3), 62; https://doi.org/10.3390/jmse4030062 - 19 Sep 2016

Cited by 5 | Viewed by 5167

Abstract

Computer model experiments are applied to analyze hypoxia reductions for opposing wind directions under various speeds and durations in the north–south oriented, two-layer-circulated Chesapeake estuary. Wind’s role in destratification is the main mechanism in short-term reduction of hypoxia. Hypoxia can also be reduced [...] Read more.

Computer model experiments are applied to analyze hypoxia reductions for opposing wind directions under various speeds and durations in the north–south oriented, two-layer-circulated Chesapeake estuary. Wind’s role in destratification is the main mechanism in short-term reduction of hypoxia. Hypoxia can also be reduced by wind-enhanced estuarine circulation associated with winds that have down-estuary straining components that promote bottom-returned oxygen-rich seawater intrusion. The up-bay-ward along-channel component of straining by the southerly or easterly wind induces greater destratification than the down-bay-ward straining by the opposite wind direction, i.e., northerly or westerly winds. While under the modulation of the west-skewed asymmetric cross-channel bathymetry in the Bay’s hypoxic zone, the westward cross-channel straining by easterly or northerly winds causes greater destratification than its opposite wind direction. The wind-induced cross-channel circulation can be completed much more rapidly than the wind-induced along-channel circulation, and the former is usually more effective than the latter in destratification and hypoxia reduction in an early wind period. The relative importance of cross-channel versus along-channel circulation for a particular wind direction can change with wind speed and duration. The existence of month-long prevailing unidirectional winds in the Chesapeake is explored, and the relative hypoxia reductions among different prevailing directions are analyzed. Scenarios of wind with intermittent calm or reversing directions on an hourly scale are also simulated and compared. Full article

(This article belongs to the Special Issue Selected Papers from the 14th Estuarine and Coastal Modeling Conference)

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2684 KiB

Open AccessArticle

Perspectives on Geoacoustic Inversion of Ocean Bottom Reflectivity Data

by N. Ross Chapman

J. Mar. Sci. Eng. 2016, 4(3), 61; https://doi.org/10.3390/jmse4030061 - 14 Sep 2016

Cited by 11 | Viewed by 5097

Abstract

This paper focuses on acoustic reflectivity of the ocean bottom, and describes inversion of reflection data from an experiment designed to study the physical properties and structure of the ocean bottom. The formalism of Bayesian inference is reviewed briefly to establish an understanding [...] Read more.

This paper focuses on acoustic reflectivity of the ocean bottom, and describes inversion of reflection data from an experiment designed to study the physical properties and structure of the ocean bottom. The formalism of Bayesian inference is reviewed briefly to establish an understanding of the approach for inversion that is in widespread use. A Bayesian inversion of ocean bottom reflection coefficient versus angle data to estimate geoacoustic model parameters of young oceanic crust is presented. The data were obtained in an experiment to study the variation of sound speed in crustal basalt with age of the crust at deep water sites in the Pacific Ocean where the sediment deposits overlying the basalt are very thin. The inversion results show that sound speed of both compressional and shear waves is increasing with crustal age over the track of the experiment where age increased from 40 to 70 million years. Full article

(This article belongs to the Special Issue Underwater Acoustics and the Ocean Environment)

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289 KiB

Open AccessReview

Golden Tides: Problem or Golden Opportunity? The Valorisation of Sargassum from Beach Inundations

by John J. Milledge and Patricia J. Harvey

J. Mar. Sci. Eng. 2016, 4(3), 60; https://doi.org/10.3390/jmse4030060 - 13 Sep 2016

Cited by 160 | Viewed by 17567

Abstract

In recent years there have been massive inundations of pelagic Sargassum, known as golden tides, on the beaches of the Caribbean, Gulf of Mexico, and West Africa, causing considerable damage to the local economy and environment. Commercial exploration of this biomass for [...] Read more.

In recent years there have been massive inundations of pelagic Sargassum, known as golden tides, on the beaches of the Caribbean, Gulf of Mexico, and West Africa, causing considerable damage to the local economy and environment. Commercial exploration of this biomass for food, fuel, and pharmaceutical products could fund clean-up and offset the economic impact of these golden tides. This paper reviews the potential uses and obstacles for exploitation of pelagic Sargassum. Although Sargassum has considerable potential as a source of biochemicals, feed, food, fertiliser, and fuel, variable and undefined composition together with the possible presence of marine pollutants may make golden tides unsuitable for food, nutraceuticals, and pharmaceuticals and limit their use in feed and fertilisers. Discontinuous and unreliable supply of Sargassum also presents considerable challenges. Low-cost methods of preservation such as solar drying and ensiling may address the problem of discontinuity. The use of processes that can handle a variety of biological and waste feedstocks in addition to Sargassum is a solution to unreliable supply, and anaerobic digestion for the production of biogas is one such process. More research is needed to characterise golden tides and identify and develop commercial products and processes. Full article

(This article belongs to the Special Issue Algal Biofuels)

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Open AccessReview

An Exploration of Wind Stress Calculation Techniques in Hurricane Storm Surge Modeling

by Kyra M. Bryant and Muhammad Akbar

J. Mar. Sci. Eng. 2016, 4(3), 58; https://doi.org/10.3390/jmse4030058 - 13 Sep 2016

Cited by 52 | Viewed by 11514

Abstract

As hurricanes continue to threaten coastal communities, accurate storm surge forecasting remains a global priority. Achieving a reliable storm surge prediction necessitates accurate hurricane intensity and wind field information. The wind field must be converted to wind stress, which represents the air-sea momentum [...] Read more.

As hurricanes continue to threaten coastal communities, accurate storm surge forecasting remains a global priority. Achieving a reliable storm surge prediction necessitates accurate hurricane intensity and wind field information. The wind field must be converted to wind stress, which represents the air-sea momentum flux component required in storm surge and other oceanic models. This conversion requires a multiplicative drag coefficient for the air density and wind speed to represent the air-sea momentum exchange at a given location. Air density is a known parameter and wind speed is a forecasted variable, whereas the drag coefficient is calculated using an empirical correlation. The correlation’s accuracy has brewed a controversy of its own for more than half a century. This review paper examines the lineage of drag coefficient correlations and their acceptance among scientists. Full article

(This article belongs to the Special Issue Selected Papers from the 14th Estuarine and Coastal Modeling Conference)

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14319 KiB

Open AccessArticle

Dynamics of a Marine Turbine for Deep Ocean Currents

by Ling-Yuan Chang, Falin Chen and Kuo-Tung Tseng

J. Mar. Sci. Eng. 2016, 4(3), 59; https://doi.org/10.3390/jmse4030059 - 12 Sep 2016

Cited by 2 | Viewed by 5565

Abstract

For most of the ocean currents, such as the Kuroshio at east Taiwan, the Gulf Stream at east Florida and the Agulhas Current at southeast Africa, the depth of the seabed is generally deeper than one hundred meters, some waters of which can [...] Read more.

For most of the ocean currents, such as the Kuroshio at east Taiwan, the Gulf Stream at east Florida and the Agulhas Current at southeast Africa, the depth of the seabed is generally deeper than one hundred meters, some waters of which can even reach one thousand meters. In such deep waters, the design of the turbine, as well as the anchoring system shall have special features so that existing ocean engineering technologies can be applied and the engineering cost can be lowered. Thus, as regards design, in addition to the analysis of the interaction between turbine and current, priority shall also be given to the design of the anchoring system of the turbine. To address the concerns, the authors propose an ocean turbine featured as follows: (1) it can be anchored in deep waters with a single cable; (2) it can generate high power in a current of moderate flow speed while producing low drag; (3) it can be self-balanced against current disturbance; (4) it is shrouded to enhance power efficiency; (5) the dynamic variations due to the interaction between the turbine and current are small. All of these features are confirmed with the computational results, leading to a detailed design of the turbine structure. If the easy-to-install high-efficiency shrouded turbines, having the capability to self-balance and requiring minimum maintenance effort, are successfully developed, the power supply pressure in Taiwan can be greatly alleviated. The Kuroshio was chosen as the typical current for the present dynamic analysis because, firstly, the flow characteristics of Kuroshio are similar to those of other large-scale currents mentioned above, and secondly, the data of Kuroshio are highly available to us so that a thorough analysis can be done. Full article

(This article belongs to the Section Ocean Engineering)

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Open AccessArticle

Atmospheric Bulk Deposition of Polychlorinated Dibenzo-p-Dioxins, Dibenzofurans, and Polychlorinated Biphenyls in Finland

by Markku Korhonen, Matti Verta, Simo Salo, Jussi Vuorenmaa, Hannu Kiviranta and Päivi Ruokojärvi

J. Mar. Sci. Eng. 2016, 4(3), 56; https://doi.org/10.3390/jmse4030056 - 7 Sep 2016

Cited by 10 | Viewed by 4601

Abstract

The deposition of polychlorinated dibenzo-p-dioxins, dibenzofurans (PCDD/Fs), and polychlorinated biphenyls (PCBs) was studied during the period 2006–2008 in northern Finland (Pallas), 1998–2008 in southern Finland (Evo) and 2002–2004 in the Gulf of Finland archipelago (Utö). Retrospective snow samples were taken from [...] Read more.

The deposition of polychlorinated dibenzo-p-dioxins, dibenzofurans (PCDD/Fs), and polychlorinated biphenyls (PCBs) was studied during the period 2006–2008 in northern Finland (Pallas), 1998–2008 in southern Finland (Evo) and 2002–2004 in the Gulf of Finland archipelago (Utö). Retrospective snow samples were taken from the whole snowbank in Evo in 2003 and 2004, and recently fallen snow was collected in Evo in 2006–2008. The concentrations of PCDD/Fs in the depositions were usually small. The limit of quantification (LOQ) was often reached in Pallas and Utö. The analysis results of PCDD/F and PCB congeners from Evo were used to predict numerical results with linear regression for those congeners with results below LOQ. The deposition of PCDD/Fs in Pallas was mostly less than 0.4 pg·m⁻²·day⁻¹ WHO-TEQ and less than 1.0 pg·m⁻²·day⁻¹ WHO-TEQ and 0.5 pg·m⁻²·day⁻¹ WHO-TEQ in Evo and Utö, respectively. The deposition of co-planar PCBs (cPCBs) was between 0.01 and 0.1 pg·m⁻²·day⁻¹ WHO-TEQ. Annual PCDD/F deposition, calculated from the amount of collected rain and chemical analysis results, varied in Pallas between 0.04 and 0.15 ng·m⁻²·year⁻¹ WHO-TEQ, in Evo between 0.11 and 0.22 ng·m⁻²·year⁻¹ WHO-TEQ and in Utö between 50 and 145 pg·m⁻²·year⁻¹ WHO-TEQ. For cPCBs the annual deposition in Pallas was 2–11 pg·m⁻²·year⁻¹ WHO-TEQ, in Evo 6–17 pg·m⁻²·year⁻¹ WHO-TEQ and in Utö 4–8 pg·m⁻²·year⁻¹ WHO-TEQ. Wind directions are considered to be the main reason for the variation between seasons. Congener 1,2,3,7,8-PeCDD dominated in Pallas, Evo, and Utö, being 35%, 48%, and 47% of the overall WHO-TEQ, followed by 2,3,4,7,8-PeCDF (about 10%). The calculated pg/L concentrations of 1,2,3,7,8-PeCDD were about the same level as 2,3,4,7,8-PeCDF, but the TEF correlations being twice as big ensured that all WHO-TEQ contributions were bigger. PCB126 accounted for 30% of WHO-TEQ in Pallas, whereas in Evo and Utö the proportion was less than 5%. Of PCDD/F homology groups, the highest concentration was found in Pallas as OCDDs (55%), followed by Evo and Utö, at 42% and 38%, respectively. Decreasing temporal PCDD/F deposition trends were observed for highly chlorinated octa-, hepta-, and hexacongeners. The findings indicate that, regardless of the major importance of Kymijoki to the dioxins in the Gulf of Finland, deposition sources may contribute more to the PCDD/Fs’ intake of fish in the studied sea area. Full article

(This article belongs to the Special Issue Impacts of Climate Change on a Marginal Ecosystems—the Baltic Sea)

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143 KiB

Open AccessErratum

Erratum: Chen, C.Y.; Ward, D.M.; Williams, J.J.; Fisher, N.S. Metal Bioaccumulation by Estuarine Food Webs in New England, USA. J. Mar. Sci. Eng. 2016, 4, 41

by Celia Y. Chen, Darren M. Ward, Jason J. Williams and Nicholas S. Fisher

J. Mar. Sci. Eng. 2016, 4(3), 57; https://doi.org/10.3390/jmse4030057 - 5 Sep 2016

Cited by 1 | Viewed by 3233

Abstract

The authors wish to correct the NIH grant number in this paper [1] as follows:[...] Full article

24858 KiB

Open AccessArticle

Effects of Harbor Shape on the Induced Sedimentation; L-Type Basin

by Rozita Kian, Deniz Velioglu, Ahmet Cevdet Yalciner and Andrey Zaytsev

J. Mar. Sci. Eng. 2016, 4(3), 55; https://doi.org/10.3390/jmse4030055 - 2 Sep 2016

Cited by 11 | Viewed by 4542

Abstract

Tsunamis in shallow water zones lead to sea water level rise and fall, strong currents, forces (drag, impact, uplift, etc.), morphological changes (erosion, deposition), dynamic water pressure, as well as resonant oscillations. As a result, ground materials under the tsunami motion move, and [...] Read more.

Tsunamis in shallow water zones lead to sea water level rise and fall, strong currents, forces (drag, impact, uplift, etc.), morphological changes (erosion, deposition), dynamic water pressure, as well as resonant oscillations. As a result, ground materials under the tsunami motion move, and scour/erosion/deposition patterns can be observed in the region. Ports and harbors as enclosed basins are the main examples of coastal structures that usually encounter natural hazards with small or huge damaging scales. Morphological changes are one of the important phenomena in the basins under short and long wave attack. Tsunamis as long waves lead to sedimentation in the basins, and therefore, in this study, the relation to the current pattern is noticed to determine sedimentation modes. Accordingly, we present a methodology based on the computation of the instantaneous Rouse number to investigate the tsunami motion and to calculate the respective sedimentation. This study aims to investigate the effects of the incident wave period on an L-type harbor sedimentation with a flat bathymetry using a numerical tool, NAMI DANCE, which solves non-linear shallow water equations. The results showed that the corner points on the bending part of the basin are always the critical points where water surface elevation and current velocity amplify in the exterior and interior corners, respectively. Full article

(This article belongs to the Special Issue Selected Papers from the 14th Estuarine and Coastal Modeling Conference)

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1792 KiB

Open AccessArticle

Wave Energy Converter Annual Energy Production Uncertainty Using Simulations

by Clayton E. Hiles, Scott J. Beatty and Adrian De Andres

J. Mar. Sci. Eng. 2016, 4(3), 53; https://doi.org/10.3390/jmse4030053 - 2 Sep 2016

Cited by 24 | Viewed by 6062

Abstract

Critical to evaluating the economic viability of a wave energy project is: (1) a robust estimate of the electricity production throughout the project lifetime and (2) an understanding of the uncertainty associated with said estimate. Standardization efforts have established mean annual energy production [...] Read more.

Critical to evaluating the economic viability of a wave energy project is: (1) a robust estimate of the electricity production throughout the project lifetime and (2) an understanding of the uncertainty associated with said estimate. Standardization efforts have established mean annual energy production (MAEP) as the metric for quantification of wave energy converter (WEC) electricity production and the performance matrix approach as the appropriate method for calculation. General acceptance of a method for calculating the MAEP uncertainty has not yet been achieved. Several authors have proposed methods based on the standard engineering approach to error propagation, however, a lack of available WEC deployment data has restricted testing of these methods. In this work the magnitude and sensitivity of MAEP uncertainty is investigated. The analysis is driven by data from simulated deployments of 2 WECs of different operating principle at 4 different locations. A Monte Carlo simulation approach is proposed for calculating the variability of MAEP estimates and is used to explore the sensitivity of the calculation. The uncertainty of MAEP ranged from 2%–20% of the mean value. Of the contributing uncertainties studied, the variability in the wave climate was found responsible for most of the uncertainty in MAEP. Uncertainty in MAEP differs considerably between WEC types and between deployment locations and is sensitive to the length of the input data-sets. This implies that if a certain maximum level of uncertainty in MAEP is targeted, the minimum required lengths of the input data-sets will be different for every WEC-location combination. Full article

(This article belongs to the Special Issue Ocean Wave Energy Conversion)

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Open AccessArticle

Application of an Unstructured Grid-Based Water Quality Model to Chesapeake Bay and Its Adjacent Coastal Ocean

by Meng Xia and Long Jiang

J. Mar. Sci. Eng. 2016, 4(3), 52; https://doi.org/10.3390/jmse4030052 - 1 Sep 2016

Cited by 28 | Viewed by 7375

Abstract

To provide insightful information on water quality management, it is crucial to improve the understanding of the complex biogeochemical cycles of Chesapeake Bay (CB), so a three-dimensional unstructured grid-based water quality model (ICM based on the finite-volume coastal ocean model (FVCOM)) was configured [...] Read more.

To provide insightful information on water quality management, it is crucial to improve the understanding of the complex biogeochemical cycles of Chesapeake Bay (CB), so a three-dimensional unstructured grid-based water quality model (ICM based on the finite-volume coastal ocean model (FVCOM)) was configured for CB. To fully accommodate the CB study, the water quality simulations were evaluated by using different horizontal and vertical model resolutions, various wind sources and other hydrodynamic and boundary settings. It was found that sufficient horizontal and vertical resolution favored simulating material transport efficiently and that winds from North American Regional Reanalysis (NARR) generated stronger mixing and higher model skill for dissolved oxygen simulation relative to observed winds. Additionally, simulated turbulent mixing was more influential on water quality dynamics than that of bottom friction: the former considerably influenced the summer oxygen ventilation and new primary production, while the latter was found to have little effect on the vertical oxygen exchange. Finally, uncertainties in riverine loading led to larger deviation in nutrient and phytoplankton simulation than that of benthic flux, open boundary loading and predation. Considering these factors, the model showed reasonable skill in simulating water quality dynamics in a 10-year (2003–2012) period and captured the seasonal chlorophyll-a distribution patterns. Overall, this coupled modeling system could be utilized to analyze the spatiotemporal variation of water quality dynamics and to predict their key biophysical drivers in the future. Full article

(This article belongs to the Special Issue Selected Papers from the 14th Estuarine and Coastal Modeling Conference)

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31990 KiB

Open AccessArticle

STORMTOOLS: Coastal Environmental Risk Index (CERI)

by Malcolm L. Spaulding, Annette Grilli, Chris Damon, Teresa Crean, Grover Fugate, Bryan A. Oakley and Peter Stempel

J. Mar. Sci. Eng. 2016, 4(3), 54; https://doi.org/10.3390/jmse4030054 - 31 Aug 2016

Cited by 27 | Viewed by 8827

Abstract

One of the challenges facing coastal zone managers and municipal planners is the development of an objective, quantitative assessment of the risk to structures, infrastructure, and public safety that coastal communities face from storm surge in the presence of changing climatic conditions, particularly [...] Read more.

One of the challenges facing coastal zone managers and municipal planners is the development of an objective, quantitative assessment of the risk to structures, infrastructure, and public safety that coastal communities face from storm surge in the presence of changing climatic conditions, particularly sea level rise and coastal erosion. Here we use state of the art modeling tool (ADCIRC and STWAVE) to predict storm surge and wave, combined with shoreline change maps (erosion), and damage functions to construct a Coastal Environmental Risk Index (CERI). Access to the state emergency data base (E-911) provides information on structure characteristics and the ability to perform analyses for individual structures. CERI has been designed as an on line Geographic Information System (GIS) based tool, and hence is fully compatible with current flooding maps, including those from FEMA. The basic framework and associated GIS methods can be readily applied to any coastal area. The approach can be used by local and state planners to objectively evaluate different policy options for effectiveness and cost/benefit. In this study, CERI is applied to RI two communities; Charlestown representing a typical coastal barrier system directly exposed to ocean waves and high erosion rates, with predominantly low density single family residences and Warwick located within Narragansett Bay, with more limited wave exposure, lower erosion rates, and higher residential housing density. Results of these applications are highlighted herein. Full article

(This article belongs to the Section Ocean Engineering)

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Open AccessArticle

On the Analysis of a Wave Energy Farm with Focus on Maintenance Operations

by Giovanni Rinaldi, Philipp R. Thies, Richard Walker and Lars Johanning

J. Mar. Sci. Eng. 2016, 4(3), 51; https://doi.org/10.3390/jmse4030051 - 23 Aug 2016

Cited by 24 | Viewed by 6863

Abstract

Wave energy has a promising technical potential that could contribute to the future energy mix. However, costs related to the deployment of wave energy converters (WECs) are still high compared to other technologies. In order to reduce these costs, two principle options are [...] Read more.

Wave energy has a promising technical potential that could contribute to the future energy mix. However, costs related to the deployment of wave energy converters (WECs) are still high compared to other technologies. In order to reduce these costs, two principle options are available, a reduction in cost and an increase in productivity. This paper presents a reliability-based computational tool to identify typical decision problems and to shed light on the complexity of optimising a wave power farm. The proposed tool is used to investigate productivity and availability of a wave energy farm during 10 years of operational life. A number of optimization possibilities to improve productivity, namely vessel choice, maintenance regime, failure rate and component redundancy, are then explored in order to assess their effectiveness. The paper quantifies the yield increase and provides a practical approach to evaluate the effectiveness of strategic and operational decision options. Results, in terms of the variations in productivity and availability of the farm, are analysed and discussed. Conclusions highlight the importance of reliability-centred simulations that consider the specific decision parameters throughout the operational life to find suitable solutions that increase the productivity and reduce the running cost for offshore farms. Full article

(This article belongs to the Special Issue Ocean Wave Energy Conversion)

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1146 KiB

Open AccessArticle

Metal Ions and Hydroperoxide Content: Main Drivers of Coastal Lipid Autoxidation in Riverine Suspended Particulate Matter and Higher Plant Debris

by Marie-Aimée Galeron, Olivier Radakovitch, Bruno Charrière and Jean-François Rontani

J. Mar. Sci. Eng. 2016, 4(3), 50; https://doi.org/10.3390/jmse4030050 - 23 Aug 2016

Cited by 3 | Viewed by 4450

Abstract

Autoxidation is a complex abiotic degradation process, and while it has long been known and well studied in biological compounds, it has been widely overlooked in environmental samples and as a part of environmental processes. With recent observations showing the magnitude of the [...] Read more.

Autoxidation is a complex abiotic degradation process, and while it has long been known and well studied in biological compounds, it has been widely overlooked in environmental samples and as a part of environmental processes. With recent observations showing the magnitude of the involvement of autoxidation in coastal environments, it has become critical to better understand how and why this degradative process takes place. At the riverine/marine interface, recent findings evidenced a spike in autoxidation rates upon the arrival of suspended particulate matter in seawater. In this study, we aimed at identifying autoxidation-favoring factors in vitro by analyzing suspended particulate matter incubated under different conditions. If metal ions have long been known to induce autoxidation in biological systems, we show that they indeed induce autoxidation in particulate matter incubated in water, but also that the content in photochemically-produced hydroperoxides in suspended particulate matter is crucial to the induction of its autoxidation in water. Full article

(This article belongs to the Section Chemical Oceanography)

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Open AccessArticle

Performance Assessment of NAMI DANCE in Tsunami Evolution and Currents Using a Benchmark Problem

by Deniz Velioglu, Rozita Kian, Ahmet Cevdet Yalciner and Andrey Zaytsev

J. Mar. Sci. Eng. 2016, 4(3), 49; https://doi.org/10.3390/jmse4030049 - 18 Aug 2016

Cited by 13 | Viewed by 5706

Abstract

Numerical modeling of tsunami evolution, propagation, and inundation is complicated due to numerous parameters involved in the phenomenon. It is important to assess the performance of numerical codes that solve tsunami motion, as well as flow and velocity patterns. NAMI DANCE is a [...] Read more.

Numerical modeling of tsunami evolution, propagation, and inundation is complicated due to numerous parameters involved in the phenomenon. It is important to assess the performance of numerical codes that solve tsunami motion, as well as flow and velocity patterns. NAMI DANCE is a computational tool developed for the modeling of long waves. It provides numerical modeling and efficient visualization of tsunami generation, propagation, and inundation mechanisms and computes the tsunami parameters. In the theory of long waves, the vertical motion of water particles has no effect on the pressure distribution. Based upon this approximation and neglecting vertical acceleration, the equations of mass conservation and momentum are reduced to two-dimensional depth-averaged equations. NAMI DANCE uses finite difference computational method to solve linear and nonlinear forms of depth-averaged shallow water equations in long wave problems. In this study, NAMI DANCE is applied to a benchmark problem which was discussed in the 2015 National Tsunami Hazard Mitigation Program (NTHMP) annual meeting in Portland, USA. The benchmark problem features a series of experiments in which a single solitary wave propagates up a triangular shaped shelf which has an offshore island feature. The problem provides detailed free surface elevation and velocity time series in the vicinity of the island. The comparison of the results showed that NAMI DANCE is able to satisfactorily predict long wave evolution, propagation, amplification, and tsunami currents. Full article

(This article belongs to the Special Issue Selected Papers from the 14th Estuarine and Coastal Modeling Conference)

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Open AccessArticle

An Open-Access, Multi-Decadal, Three-Dimensional, Hydrodynamic Hindcast Dataset for the Long Island Sound and New York/New Jersey Harbor Estuaries

by Nickitas Georgas, Lun Yin, Yu Jiang, Yifan Wang, Penelope Howell, Vincent Saba, Justin Schulte, Philip Orton and Bin Wen

J. Mar. Sci. Eng. 2016, 4(3), 48; https://doi.org/10.3390/jmse4030048 - 16 Aug 2016

Cited by 24 | Viewed by 11243

Abstract

This article presents the results and validation of a comprehensive, multi-decadal, hindcast simulation performed using the New York Harbor Observing and Prediction System´s (NYHOPS) three-dimensional hydrodynamic model. Meteorological forcing was based on three-hourly gridded data from the North American Regional Reanalysis of the [...] Read more.

This article presents the results and validation of a comprehensive, multi-decadal, hindcast simulation performed using the New York Harbor Observing and Prediction System´s (NYHOPS) three-dimensional hydrodynamic model. Meteorological forcing was based on three-hourly gridded data from the North American Regional Reanalysis of the US National Centers for Environmental Prediction. Distributed hydrologic forcing was based on daily United States Geologic Survey records. Offshore boundary conditions for NYHOPS at the Mid-Atlantic Bight shelf break included hourly subtidal water levels from a larger-scale model ran for the same period, tides, and temperature and salinity profiles based on the Simple Ocean Data Assimilation datasets. The NYHOPS model’s application to hindcast total water level and 3D water temperature and salinity conditions in its region over three decades was validated against observations from multiple agencies. Average indices of agreement were: 0.93 for storm surge (9 cm RMSE, 90% of errors less than 15 cm), 0.99 for water temperature (1.1 °C RMSE, 99% of errors less than 3 °C), and 0.86 for salinity (1.8 psu RMSE, 96% of errors less than 3.5 psu). The model’s skill in simulating bottom water temperature, validated against historic data from the Long Island Sound bottom trawl survey, did not drift over the years, a significant and encouraging finding for multi-decadal model applications used to identify climatic trends, such as the warming presented here. However, the validation reveals residual biases in some areas such as small tributaries that receive urban discharges from the NYC drainage network. With regard to the validation of storm surge at coastal stations, both the considerable strengths and remaining limitations of the use of North American Regional Reanalysis (NARR) to force such a model application are discussed. Full article

(This article belongs to the Special Issue Selected Papers from the 14th Estuarine and Coastal Modeling Conference)

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Open AccessArticle

Modeling Water Motion near Seismic Waves Propagating across a Graded Seabed, as Generated by Man-Made Impacts

by Richard A. Hazelwood and Patrick C. Macey

J. Mar. Sci. Eng. 2016, 4(3), 47; https://doi.org/10.3390/jmse4030047 - 13 Aug 2016

Cited by 23 | Viewed by 6307

Abstract

Seismic interface waves generated by seabed impacts are believed to have biological importance. Various wave types are of interest to seismologists, who can minimize the unwanted, but often dominant, ground roll waves with suitable instrumentation. Waves made by dredging and piling have been [...] Read more.

Seismic interface waves generated by seabed impacts are believed to have biological importance. Various wave types are of interest to seismologists, who can minimize the unwanted, but often dominant, ground roll waves with suitable instrumentation. Waves made by dredging and piling have been measured using geophones and found to be of this interface type, which propagate much more slowly than the pressure waves in the water column above. Short interface wavelets of a few cycles were modeled using transient finite element analysis (FEA). Wavelets with low losses have been modeled using graded sediment data from the literature. They do not radiate energy away from the interface because the evanescent acoustic pressures they generate decay rapidly with distance from the seabed. Associated water particle velocities are much greater than would be expected from similar acoustic pressure measurements in a free field. This motion is significant to aquatic life which is dependent on inertial sensors (otoliths, etc.) to respond to the environment. Additional amplification of the horizontal seabed motion of the adjacent water is predicted for a short seismic wavelet modeled in a graded solid seabed. Further recent analysis studied the distribution of the energy flux within the sediment layers. Full article

(This article belongs to the Special Issue Underwater Acoustics and the Ocean Environment)

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5443 KiB

Open AccessArticle

Application of a Spectral Wave Model to Assess Breakwater Configurations at a Small Craft Harbour on Lake Ontario

by Amelia H. Cooper and Ryan P. Mulligan

J. Mar. Sci. Eng. 2016, 4(3), 46; https://doi.org/10.3390/jmse4030046 - 8 Aug 2016

Cited by 12 | Viewed by 5664

Abstract

A surface wave model using three nested grids is applied to the eastern end of Lake Ontario to investigate wave propagation from an open lake environment to a small craft harbour protected by a breakwater. The Simulating WAves Nearshore (SWAN) spectral wave model, [...] Read more.

A surface wave model using three nested grids is applied to the eastern end of Lake Ontario to investigate wave propagation from an open lake environment to a small craft harbour protected by a breakwater. The Simulating WAves Nearshore (SWAN) spectral wave model, coupled with the Delft3D hydrodynamic model, is applied to simulate a series of storms in November, 2013. The model results are compared to observations from two pressure sensors, and used to quantify wave properties around existing and future breakwaters to evaluate the bulk changes to the harbour configuration. Overall, the results indicate that the rubblemound breakwater reduces wave heights in the existing harbour by 63% compared to no breakwater, and that the addition of a surface breakwater extension could reduce wave heights by an additional 54%. Wave height attenuation was found to be highly dependent on the incident wave direction relative to breakwater orientation. The spectral wave model is useful for simulating wave transformation for broad directional spectra in wind-sea conditions over large scales to semi-protected areas such as small craft harbours. Full article

(This article belongs to the Section Ocean Engineering)

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4401 KiB

Open AccessArticle

Structure-Borne Wave Radiation by Impact and Vibratory Piling in Offshore Installations: From Sound Prediction to Auditory Damage

by Apostolos Tsouvalas and Andrei V. Metrikine

J. Mar. Sci. Eng. 2016, 4(3), 44; https://doi.org/10.3390/jmse4030044 - 1 Aug 2016

Cited by 23 | Viewed by 6809

Abstract

Anthropogenic noise emission in the marine environment is a key issue nowadays and has drawn the attention of regulatory bodies in various nations. In particular, the noise generated during the installation of foundation piles for the offshore wind industry is considered to be [...] Read more.

Anthropogenic noise emission in the marine environment is a key issue nowadays and has drawn the attention of regulatory bodies in various nations. In particular, the noise generated during the installation of foundation piles for the offshore wind industry is considered to be harmful for aquatic species. A reliable prediction of the underwater noise during the installation of a foundation pile is thus essential for the proper assessment of the ecological impact. In this paper, the structure-borne wave radiation is investigated with the help of a semi-analytical model for two cases. The first case considers a pile that is installed with the help of an impact hammer, whereas the second one deals with a pile that is driven into the seabed with the help of a vibratory device. The spatial distribution and the frequency content of the radiated sound are analyzed, and the differences are highlighted between the two cases. The model is validated with data available in the literature that were collected during several measurement campaigns. Subsequently, the predicted noise levels are converted into an equivalent index that reflects the auditory damage to certain marine species, and a method is presented for the derivation of zones of impact around the pile that are based on the noise predictions by the models and the chosen method of installation. This approach can be used to define critical zones within which a predefined level of auditory damage is to be expected based on a specific installation scenario. Full article

(This article belongs to the Special Issue Underwater Acoustics and the Ocean Environment)

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11069 KiB

Open AccessArticle

Storm Surge Modeling in Large Estuaries: Sensitivity Analyses to Parameters and Physical Processes in the Chesapeake Bay

by Juan L. Garzon and Celso M. Ferreira

J. Mar. Sci. Eng. 2016, 4(3), 45; https://doi.org/10.3390/jmse4030045 - 30 Jul 2016

Cited by 51 | Viewed by 9571

Abstract

Large estuaries are especially vulnerable to coastal flooding due to the potential of combined storm surges and riverine flows. Numerical models can support flood prevention and planning for coastal communities. However, while recent advancements in the development of numerical models for storm surge [...] Read more.

Large estuaries are especially vulnerable to coastal flooding due to the potential of combined storm surges and riverine flows. Numerical models can support flood prevention and planning for coastal communities. However, while recent advancements in the development of numerical models for storm surge prediction have led to robust and accurate models; an increasing number of parameters and physical processes’ representations are available to modelers and engineers. This study investigates uncertainties associated with the selection of physical parameters or processes involved in storm surge modeling in large estuaries. Specifically, we explored the sensitivity of a hydrodynamic model (ADCIRC) and a coupled wind-wave and circulation model system (ADCIRC + SWAN) to Manning’s n coefficient, wind waves and circulation interaction (wave setup), minimum depth (H₀) in the wetting and drying algorithm, and spatially constant horizontal eddy viscosity (ESLM) forced by tides and hurricane winds. Furthermore, sensitivity analysis to Manning’s n coefficient and the interaction of waves and circulation were analyzed by using three different numerical meshes. Manning’s coefficient analysis was divided into waterway (rivers, bay and shore, and open ocean) and overland. Overall, the rivers exhibited a larger sensitivity, and M₂ amplitude and maximum water elevations were reduced by 0.20 m and 0.56 m, respectively, by using a high friction value; similarly, high friction reduced maximum water levels up to 0.30 m in overland areas; the wave setup depended on the offshore wave height, angle of breaking, the profile morphology, and the mesh resolution, accounting for up to 0.19 m setup inside the bay; minimum depth analysis showed that H₀ = 0.01 added an artificial mass of water in marshes and channels, meanwhile H = 0.1 partially solved this problem; and the eddy viscosity study demonstrated that the ESLM = 40 values reduced up to 0.40 m the peak of the maximum water levels in the upper side of narrow rivers. Full article

(This article belongs to the Special Issue Modelling Waves in Coasts and Estuaries)

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311 KiB

Open AccessArticle

Power-Budget Equations and Calibration Factors for Fish Abundance Estimation Using Scientific Echo Sounder and Sonar Systems

by Per Lunde and Rolf J. Korneliussen

J. Mar. Sci. Eng. 2016, 4(3), 43; https://doi.org/10.3390/jmse4030043 - 9 Jul 2016

Cited by 8 | Viewed by 4572

Abstract

Acoustic methods used in fish abundance estimation constitute a key part of the analytic assessment that makes the basis for abundance estimation of marine resources. The methods rely on power-budget equations and calibrated systems. Different formulations of power-budget equations and calibration factors have [...] Read more.

Acoustic methods used in fish abundance estimation constitute a key part of the analytic assessment that makes the basis for abundance estimation of marine resources. The methods rely on power-budget equations and calibrated systems. Different formulations of power-budget equations and calibration factors have been proposed for use in scientific echo sounder and sonar systems. There are unresolved questions and apparent inconsistencies in prior literature related to this field. A generic (instrument independent) and unifying theory is presented that attempts to explain the different power-budget and calibration factor formulations proposed and used in prior literature, and how these are mutually related. Deviations and apparent inconsistencies in this literature appear to be explained and corrected. This also includes different (instrument specific) formulations employed in important modern scientific echo sounder systems, and their relationship to the generic theory of abundance estimation. Prior literature is extended to provide more complete power-budget equations for fish abundance estimation and species identification, by accounting for echo integration, electrical termination, and the full range of electrical and acoustical echo sounder parameters. The expressions provide a consistent theoretical basis for improved understanding of conventional methods and instruments used today, also enabling improved sensitivity and error analyses, and correction possibilities. Full article

(This article belongs to the Special Issue Underwater Acoustics and the Ocean Environment)

1499 KiB

Open AccessArticle

Growth-Prediction Model for Blue Mussels (Mytilus edulis) on Future Optimally Thinned Farm-Ropes in Great Belt (Denmark)

by Poul S. Larsen and Hans Ulrik Riisgård

J. Mar. Sci. Eng. 2016, 4(3), 42; https://doi.org/10.3390/jmse4030042 - 8 Jul 2016

Cited by 10 | Viewed by 5396

Abstract

A recently developed BioEnergetic Growth (BEG) model for blue mussels (Mytilus edulis), valid for juvenile mussels, has been further developed to an ‘extended model’ and an alternative ‘ad hoc BEG model’ valid for post-metamorphic mussels, where the latter accounts for changing [...] Read more.

A recently developed BioEnergetic Growth (BEG) model for blue mussels (Mytilus edulis), valid for juvenile mussels, has been further developed to an ‘extended model’ and an alternative ‘ad hoc BEG model’ valid for post-metamorphic mussels, where the latter accounts for changing ambient chl a concentration. It was used to predict the growth of M. edulis on optimally thinned farm-ropes in Great Belt (Denmark), from newly settled post-metamorphic mussels of an initial shell size of 0.8 mm to marketable juvenile 30–35 mm ‘mini-mussels’. Such mussels will presumably in the near future be introduced as a new Danish, smaller-sized consumer product. Field data for actual growth (from Day 0 = 14 June 2011) showed that size of ‘mini-mussel’ was reached on Day 109 (Oct 1) and length 38 mm on Day 178 (Dec 9) while the corresponding predictions using the extended model were Day 121 (Oct 13) and Day 159 (Nov 20). Similar results were obtained by use of the ad hoc BEG model which also demonstrated the sensitivity of growth prediction to levels of chl a concentration, but less to temperature. The results suggest that it is possible (when the conditions are optimal, i.e., no intraspecific competition ensured by sufficient thinning) to produce ‘mini-mussels’ in Great Belt during one season, but not the usual marketable 45-mm mussels. We suggest that the prediction model may be used as a practical instrument to evaluate to what degree the actual growth of mussels on farm ropes due to intraspecific competition may deviate from the potential (optimal) growth under specified chl a and temperature conditions, and this implies that the effect of thinning to optimize the individual growth by eliminating intraspecific competition can be rationally evaluated. Full article

(This article belongs to the Section Marine Biology)

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J. Mar. Sci. Eng., Volume 4, Issue 3 (September 2016) – 22 articles

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