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  • 11
    Publication Date: 2022-10-27
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kalra, T. S., Li, X., Warner, J. C., Geyer, W. R., & Wu, H. Comparison of physical to numerical mixing with different tracer advection schemes in estuarine environments. Journal of Marine Science and Engineering, 7(10), (2019): 338, doi: 10.3390/jmse7100338.
    Description: The numerical simulation of estuarine dynamics requires accurate prediction for the transport of tracers, such as temperature and salinity. During the simulation of these processes, all the numerical models introduce two kinds of tracer mixing: (1) by parameterizing the tracer eddy diffusivity through turbulence models leading to a source of physical mixing and (2) discretization of the tracer advection term that leads to numerical mixing. Physical and numerical mixing both vary with the choice of horizontal advection schemes, grid resolution, and time step. By simulating four idealized cases, this study compares the physical and numerical mixing for three different tracer advection schemes. Idealized domains only involving physical and numerical mixing are used to verify the implementation of mixing terms by equating them to total tracer variance. Among the three horizontal advection schemes, the scheme that causes the least numerical mixing while maintaining a sharp front also results in larger physical mixing. Instantaneous spatial comparison of mixing components shows that physical mixing is dominant in regions of large vertical gradients, while numerical mixing dominates at sharp fronts that contain large horizontal tracer gradients. In the case of estuaries, numerical mixing might locally dominate over physical mixing; however, the amount of volume integrated numerical mixing through the domain compared to integrated physical mixing remains relatively small for this particular modeling system.
    Description: This study was funded through the Coastal Model Applications and Field Measurements Project and the Cross-shore and Inlets Project, US Geological Survey Coastal Marine Hazards and Resources Program.
    Keywords: Physical mixing ; Numerical mixing ; Advection schemes ; Estuarine mixing
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 12
    Publication Date: 2023-04-11
    Description: Understanding the dominant climate forcings in the Pliocene is crucial to assessing the usefulness of the Pliocene as an analogue for our warmer future. Here, we implement a novel yet simple linear factorisation method to assess the relative influence of CO2 forcing in seven models of the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2) ensemble. Outputs are termed “FCO2” and show the fraction of Pliocene climate change driven by CO2. The accuracy of the FCO2 method is first assessed through comparison to an energy balance analysis previously used to assess drivers of surface air temperature in the PlioMIP1 ensemble. After this assessment, the FCO2 method is applied to achieve an understanding of the drivers of Pliocene sea surface temperature and precipitation for the first time. CO2 is found to be the most important forcing in the ensemble for Pliocene surface air temperature (global mean FCO2=0.56), sea surface temperature (global mean FCO2=0.56), and precipitation (global mean FCO2=0.51). The range between individual models is found to be consistent between these three climate variables, and the models generally show good agreement on the sign of the most important forcing. Our results provide the most spatially complete view of the drivers of Pliocene climate to date and have implications for both data–model comparison and the use of the Pliocene as an analogue for the future. That CO2 is found to be the most important forcing reinforces the Pliocene as a good palaeoclimate analogue, but the significant effect of non-CO2 forcing at a regional scale (e.g. orography and ice sheet forcing at high latitudes) reminds us that it is not perfect, and these additional influencing factors must not be overlooked. This comparison is further complicated when considering the Pliocene as a state in quasi-equilibrium with CO2 forcing compared to the transient warming being experienced at present.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
    Format: application/pdf
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  • 13
    Publication Date: 2024-05-03
    Description: During the mid-Pliocene warm period (mPWP; 3.264–3.025 Ma), atmospheric CO2 concentrations were approximately 400 ppm, and the Antarctic Ice Sheet was substantially reduced compared to today. Antarctica is surrounded by the Southern Ocean, which plays a crucial role in the global oceanic circulation and climate regulation. Using results from the Pliocene Model Intercomparison Project (PlioMIP2), we investigate Southern Ocean conditions during the mPWP with respect to the pre-industrial period. We find that the mean sea surface temperature (SST) warming in the Southern Ocean is 2.8 °C, while global mean SST warming is 2.4 °C. The enhanced warming is strongly tied to a dramatic decrease in sea ice cover over the mPWP Southern Ocean. We also see a freshening of the ocean (sub)surface, driven by an increase in precipitation over the Southern Ocean and Antarctica. The warmer and fresher surface leads to a highly stratified Southern Ocean that can be related to weakening of the deep abyssal overturning circulation. Sensitivity simulations show that the decrease in sea ice cover and enhanced warming is largely a consequence of the reduction in the Antarctic Ice Sheet. In addition, the mPWP geographic boundary conditions are responsible for approximately half of the increase in mPWP SST warming, sea ice loss, precipitation, and stratification increase over the Southern Ocean. From these results, we conclude that a strongly reduced Antarctic Ice Sheet during the mPWP has a substantial influence on the state of the Southern Ocean and exacerbates the changes that are induced by a higher CO2 concentration alone. This is relevant for the long-term future of the Southern Ocean, as we expect melting of the western Antarctic Ice Sheet in the future, an effect that is not currently taken into account in future projections by Coupled Model Intercomparison Project (CMIP) ensembles.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 14
    Publication Date: 2024-06-13
    Description: The Maritime Continent (MC) forms the western boundary of the tropical Pacific Ocean, and relatively small changes in this region can impact the climate locally and remotely. In the mid-Piacenzian warm period of the Pliocene (mPWP; 3.264 to 3.025 Ma) atmospheric CO2 concentrations were ∼ 400 ppm, and the subaerial Sunda and Sahul shelves made the land–sea distribution of the MC different to today. Topographic changes and elevated levels of CO2, combined with other forcings, are therefore expected to have driven a substantial climate signal in the MC region at this time. By using the results from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2), we study the mean climatic features of the MC in the mPWP and changes in Indonesian Throughflow (ITF) with respect to the preindustrial. Results show a warmer and wetter mPWP climate of the MC and lower sea surface salinity in the surrounding ocean compared with the preindustrial. Furthermore, we quantify the volume transfer through the ITF; although the ITF may be expected to be hindered by the subaerial shelves, 10 out of 15 models show an increased volume transport compared with the preindustrial. In order to avoid undue influence from closely related models that are present in the PlioMIP2 ensemble, we introduce a new metric, the multi-cluster mean (MCM), which is based on cluster analysis of the individual models. We study the effect that the choice of MCM versus the more traditional analysis of multi-model mean (MMM) and individual models has on the discrepancy between model results and data. We find that models, which reproduce modern MC climate well, are not always good at simulating the mPWP climate anomaly of the MC. By comparing with individual models, the MMM and MCM reproduce the preindustrial sea surface temperature (SST) of the reanalysis better than most individual models and produce less discrepancy with reconstructed sea surface temperature anomalies (SSTA) than most individual models in the MC. In addition, the clusters reveal spatial signals that are not captured by the MMM, so that the MCM provides us with a new way to explore the results from model ensembles that include similar models.
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 15
    Publication Date: 2015-12-19
    Description: Journal of Chemical & Engineering Data DOI: 10.1021/acs.jced.5b00458
    Print ISSN: 0021-9568
    Electronic ISSN: 1520-5134
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
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  • 16
    Publication Date: 2016-08-30
    Description: The present study demonstrated that the extracellular biosynthesis of gold nanoparticles (GNPs) using B. niabensis 45 may be mediated by a cyclic peptide (P2). The molecular weight of P2 was determined to be about 1122 Da by MALDI-TOF-MS and ESI-MS. A novel protocol for rapid biosynthesis of GNPs using P2 was developed. The results showed that GNP synthesis could be completed in a wide range of temperatures (40–100°C) and pH (6.0–10.0) within few minutes when 9 mL of P2 (2 mg/mL) and 1 mL of HAuCl4 solution (2 mM) were mixed together. The synthesized GNPs were further characterized. Energy dispersive spectroscopy (EDS) and X-ray diffraction (XRD) analysis confirmed the presence of elemental gold and crystalline structure of the GNPs, respectively. Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) revealed the formation of spherical metallic GNPs. The size distribution of GNPs calculated using ImageJ software was found to be 10–20 nm. And these GNPs showed excellent antibiofilm activity against Pseudomonas aeruginosa PAO1 and Staphylococcus aureus ATCC25923. The results revealed microbial cyclic peptides could be used as synthesis of GNPs which had potent antibiofilm potential.
    Print ISSN: 2090-9063
    Topics: Chemistry and Pharmacology
    Published by Hindawi
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  • 17
    Publication Date: 2017-10-17
    Description: Energies, Vol. 10, Pages 1619: Effect of Injection Site on Fault Activation and Seismicity during Hydraulic Fracturing Energies doi: 10.3390/en10101619 Authors: Zhaohui Chong Xuehua Li Xiangyu Chen Hydraulic fracturing is a key technology to stimulate oil and gas wells to increase production in shale reservoirs with low permeability. Generally, the stimulated reservoir volume is performed based on pre-existing natural fractures (NF). Hydraulic fracturing in shale reservoirs with large natural fractures (i.e., faults) often results in fault activation and seismicity. In this paper, a coupled hydro-mechanical model was employed to investigate the effects of injection site on fault activation and seismicity. A moment tensor method was used to evaluate the magnitude and affected areas of seismic events. The micro-parameters of the proposed model were calibrated through analytical solutions of the interaction between hydraulic fractures (HF) and the fault. The results indicated that the slip displacement and activation range of the fault first decreased, then remained stable with the increase in the distance between the injection hole and the fault (Lif). In the scenario of the shortest Lif (Lif = 10 m), the b-value—which represents the proportion of frequency of small events in comparison with large events—reached its maximum value, and the magnitude of concentrated seismic events were in the range of −3.5 to −1.5. The frequency of seismic events containing only one crack was the lowest, and that of seismic events containing more than ten cracks was the highest. The interaction between the injection-induced stress disturbance and fault slip was gentle when Lif was longer than the critical distance (Lif = 40–50 m). The results may help optimize the fracturing treatment designs during hydraulic fracturing.
    Electronic ISSN: 1996-1073
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI Publishing
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  • 18
    Publication Date: 2017-10-04
    Description: Journal of Chemical Information and Modeling DOI: 10.1021/acs.jcim.7b00001
    Topics: Chemistry and Pharmacology
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  • 19
    Publication Date: 2018-04-03
    Description: Atomic structures of FUS LC domain segments reveal bases for reversible amyloid fibril formation Atomic structures of FUS LC domain segments reveal bases for reversible amyloid fibril formation, Published online: 02 April 2018; doi:10.1038/s41594-018-0050-8 Two segments from FUS LC are shown to form reversible fibrils. The structural bases for this behavior and for its regulation by phosphorylation is revealed using X-ray and microelectron diffraction.
    Print ISSN: 1545-9993
    Electronic ISSN: 1545-9985
    Topics: Biology , Medicine
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  • 20
    Publication Date: 2018-05-15
    Description: The novel 19q13 KRAB zinc-finger tumour suppressor ZNF382 is frequently methylated in oesophageal squamous cell carcinoma and antagonises Wnt/β-catenin signalling The novel 19q13 KRAB zinc-finger tumour suppressor ZNF382 is frequently methylated in oesophageal squamous cell carcinoma and antagonises Wnt/β-catenin signalling, Published online: 14 May 2018; doi:10.1038/s41419-018-0604-z The novel 19q13 KRAB zinc-finger tumour suppressor ZNF382 is frequently methylated in oesophageal squamous cell carcinoma and antagonises Wnt/β-catenin signalling
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
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