TURBULENT MIXING IN THE GULF OF TRIESTE UNDER CRITICAL CONDITIONS

2002/2003La tesi è parte integrante di un progetto di ricerca indirizzato allo studio delle caratteristiche del mescolamento turbolento nel Golfo di Trieste in condizioni critiche, ovvero quando le forzanti agenti sulla colonna d'acqua sono costituite da: corrente di marea, effetto della rotazione terrestre e presenza di una stratificazione stabile verticale dovuta a flussi di calore forniti alla superficie libera. Tali condizioni critiche si possono verificare sia in inverno, quando il flusso è forzato solamente dalla corrente di marea e dalla rotazione, sia durante l'estate, quando il contributo della stratificazione risulta essere determinante. Il caso invernale rappresenta l'oggetto della tesi. Poiché il numero di Reynolds oceanografico associato al problema è troppo elevato per poter essere affrontato dalle tecniche numeriche oggi disponibili, l'esperimento viene scalato ad un valore Re = 1.6 x 106 , un ordine di grandezza inferiore rispetto a quello reale. Il sistema viene tuttavia mantenuto in regime turbolento e vengono preservati i parametri fisici caratterizzanti il caso reale (il numero di Keulegan-Carpenter ed il numero di Rossby). Le equazioni filtrate che descrivono il flusso turbolento oscillante-rotante sono risolte mediante resolved large-eddy simulation (LES), parametrizzando le scale di sottogriglia con un modello di tipo dinamico misto. A causa degli elevati sforzi computazionali richiesti per tale studio, il codice adottato è stato totalmente riscritto mediante un paradigma di programmazione parallela. Il primo capitolo della tesi presenta un'introduzione generale che descrive il Golfo di Trieste e le forzanti agenti, il secondo capitolo è dedicato all'inquadramento del problema ed al modello matematico adottato, il terzo capitolo descrive l'implementazione in ambiente parallelo ed i test di validazione. Di seguito vengono discussi i risultati: nel quarto capitolo viene analizzato il flusso puramente oscillante, mentre nel quinto sono descritti gli effetti dovuti alla rotazione del sistema di riferimento. Il sesto capitolo presenta le conclusioni principali. Occorre sottolineare che la simulazione dello strato limite turbolento di Stokes qui descritta rappresenta il primo studio numerico che analizza in dettaglio il campo turbolento di un flusso puramente oscillante ad un numero di Reynolds per il quale la maggiorparte del ciclo di oscillazione è caratterizzata dalla presenza di turbolenza pienamente sviluppata. I risultati sono in buon accordo con le misure sperimentali ed ampliano quanto trovato a tal proposito negli studi presenti in letteratura. Il flusso oscillante-rotante turbolento, secondo caso studiato, per quanto ne sappiamo non è stato finora affrontato da un punto di vista numerico. La rotazione del sistema di riferimento induce un duplice effetto destabilizzante/stabilizzante sul flusso, dipendente dalla direzione della corrente forzante. Tale effetto è stato descritto sia da studi teorici che da lavori precedenti riguardanti lo strato di Ekman stazionario non stratificato. Inoltre, dall'analisi dei nostri risultati si evince come la turbolenza si sviluppi con un carattere fortemente anisotropico. I risultati della presente dissertazione mostrano che: i processi di mescolamento nel Golfo di Trieste in condizioni critiche durante la stagione invernale appaiono caratterizzati da un'intensa attività turbolenta durante le fasi centrali di entrambi i semiperiodi di oscillazione della componente di marea M2, ed interessano più della metà della colonna d'acqua. I livelli di turbolenza tipici del secondo semiperiodo (corrente mareale che fluisce da NE a SW) risultano essere considerevolmente più marcati rispetto al primo, e si osserva attività turbolenta fin quasi alla superficie libera. Il ruolo giocato dalla rotazione risulta essere di fondamentale importanza nell'incremento del mescolamento orizzontale e verticale lungo l'intero ciclo di oscillazione. A differenza del caso puramente oscillante, le tre componenti fluttuanti sono mutualmente correlate fra di loro, e le intensità turbolente contribuiscono ad intensificare il mescolamento anche vicino alla superficie libera. Dal punto di vista metodologico, il presente lavoro ha dimostrato come una resolved LES può fornire risultati accurati anche nello studio di strati limite non stazionari. Inoltre, grazie alla capacità del modello dinamico-misto scelto di adeguarsi alle caratteristiche locali ed istantanee del campo di flusso, esso si è dimostrato essere uno strumento adatto alla simulazione di strati limite di Stokes sia in sistemi di riferimento fissi che rotanti.The present dissertation is part of a research project aimed at investigate the characteristics of the turbulent mixing in the Gulf of Trieste under critical conditions, namely when the forcings acting on the water column are: the tidal current, the effect of the Earth rotation and the presence of a vertical stable stratification due to heat fluxes supplied at the free surface. Critical conditions can occur both in winter, when only tidal current and rotation influence the flow, and in summer, when also the effect of stratification plays a very important role. The former case is the object of the thesis. Since the Reynolds number of the oceanographic system is too high to be studied by means of the present numerical techniques, the numerical experiment is carried aut at Re = 1.6 x 106 , one arder of magnitude smaller than the effective one, still considering the flow in a turbulent regime and keeping constant the physical parameters characterizing the actual flow, i.e. the Keulegan-Carpenter and the Rossby numbers. The filtered governing equations describing the oscillating, rotating turbulent flow are solved by means of resolved large-eddy simulation (LES), modeling the subgrid-scale stresses through a dynamic-mixed model. Due to the burdensome computational efforts required far such study, the code adopted is implemented in a parallel framework. The work is organized as follows: the first chapter presents a general introduction describing the Gulf of Trieste and the forcings, chapter 2 is devoted to the formulation of the problem and the mathematical model adopted, chapter 3 describes the parallel implementation together with validation tests. The results are presented in two different chapters: the purely oscillating flow is given in chapter 4, whereas the rotating-oscillating one is discussed in chapter 5. Finally, conclusions are given in chapter 6. It has to be remarked that the present simulation of the Stokes boundary layer represents the first numerical study that investigates the details of the turbulent field in a purely oscillating flow at a Reynolds number such that most of the cycle of oscillation is characterized by the presence of fully developed turbulence. Our results are in good agreement with the experimental observations and corroborate the findings of the relevant experimental studies. Moreover, to the best of our knowledge, the turbulent rotating-oscillating flow has been never investigated. The rotation of the reference frame induces a destabilizing effect on the flow, depending on the forcing current direction, which agrees with theory an d precedent studi es regarding the turbulent neutral steady Ekman layer. Furthermore, a highly anisotropie character of turbulence can be drawn from our simulations. The results of the present dissertation show that: mixing processes in the Gulf of Trieste under critical conditions during the winter season are characterized by an intense turbulent activity during the central phases of both the half-periods of oscillation of the M2 tide, along more than half the water column. Levels of turbulence peculiar of the second half-period (tidal current flowing from NEto SW) appear remarkably stronger than those of the first, and the vertical extension where turbulent activity can be observed results increased. The role played by rotation is of fundamental importance in the enhancement of horizontal and vertical mixing throughout the whole tidal cycle of oscillation. Unlike the purely oscillating case, the three fluctuating components are mutually correlated, and turbulent intensities contribute to intensify mixing also near the surface. From the numerical point of view, the present dissertation has also shown t ha t a resolved LES gives accurate results in the case of unsteady boundary layers. Moreover, the dynamic-mixed model adopted appears to be a robust tool for simulating both the Stokes boundary layer, since it is able to adjust to the local and instantaneous characteristics of the flow field, and its rotating counterpart.XVI Ciclo1972Versione digitalizzata della tesi di dottorato cartacea

Ocean Sound Propagation in a Changing Climate: Global Sound Speed Changes and Identification of Acoustic Hotspots

Climate change is a relevant threat on a global scale, leading to impacts on ecosystems and ocean biodiversity. A considerable fraction of marine life depends on sound. Marine mammals, in particular, exploit sound in all aspects of their life, including feeding and mating. This work explores the impact of climate change in sound propagation by computing the three-dimensional global field of underwater sound speed. The computation was performed based on present conditions (2006–2016) and a “business-as-usual” future climate scenario (Representative Concentration Pathway 8.5), identifying two “acoustic hotspots” where larger sound speed variations are expected. Our results indicate that the identified acoustic hotspots will present substantial climate-change-induced sound speed variations toward the end of the century, potentially affecting the vital activities of species in the areas. Evidence is provided of the impact of such variation on underwater sound transmission. As an example of a species impacted by underwater transmission, we considered one marine mammal endangered species, the North Atlantic right whale (Eubalaena glacialis), in the northwestern Atlantic Ocean. To the best of our knowledge, this is the first global-scale data set of climate-induced sound speed changes expected under a future scenario. This study provides a starting point for policies oriented research to promote the conservation of marine ecosystems and, in particular, endangered marine mammal

Climate Change in Mediterranean and Caribbean Seas: Research Experiences and New Scientific Challenges

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Merging bio-optical data from Biogeochemical-Argo floats and models in marine biogeochemistry

In numerical models for marine biogeochemistry, bio-optical data, such as measurements of the light field, may be important descriptors of the dynamics of primary producers and ultimately of oceanic carbon fluxes. However, the paucity of field observations has limited the integration of bio-optical data in such models so far. New autonomous robotic platforms for observing the ocean, i.e., Biogeochemical-Argo floats, have drastically increased the number of vertical profiles of irradiance, photosynthetically available radiation (PAR) and algal chlorophyll concentrations around the globe independently of the season. Such data may be therefore a fruitful resource to improve performances of numerical models for marine biogeochemistry. Here we present a work that integrates into a 1-dimensional model 1314 vertical profiles of PAR acquired by 31 BGC-Argo floats operated in the Mediterranean Sea between 2012 and 2016 to simulate the vertical and temporal variability of algal chlorophyll concentrations. In addition to PAR as input, alternative light and vertical mixing models were considered. We evaluated the models\u2019 skill to reproduce the spatial and temporal variability of deep chlorophyll maxima as observed by BGC-Argo floats. The assumptions used to set up the 1-D model are validated by the high number of co-located in-situ measurements. Our results illustrate the key role of PAR and vertical mixing in shaping the vertical dynamics of primary produces in the Mediterranean Sea. Moreover, we demonstrate the importance of modeling the diel cycle to simulate chlorophyll concentrations in stratified waters at the surface

Future projections of Mediterranean cyclone characteristics using the Med-CORDEX ensemble of coupled regional climate system models

Here, we analyze future projections of cyclone activity in the Mediterranean region at the end of the twenty-first century based on an ensemble of state-of-the-art fully-coupled Regional Climate System Models (RCSMs) from the Med-CORDEX initiative under the Representative Concentration Pathway (RCP) 8.5. Despite some noticeable biases, all the RCSMs capture spatial patterns and cyclone activity key characteristics in the region and thus all of them can be considered as plausible representations of the future evolution of Mediterranean cyclones. In general, the RCSMs show at the end of the twenty-first century a decrease in the number and an overall weakening of cyclones moving across the Mediterranean. Five out of seven RCSMs simulate also a decrease of the mean size of the systems. Moreover, in agreement with what already observed in CMIP5 projections for the area, the models suggest an increase in the Central part of the Mediterranean region and a decrease in the South-eastern part of the region in the cyclone-related wind speed and precipitation rate. These rather two opposite tendencies observed in the precipitation should compensate and amplify, respectively, the effect of the overall reduction of the frequency of cyclones on the water budget over the Central and South-eastern part of the region. A pronounced inter-model spread among the RCSMs emerges for the projected changes in the cyclone adjusted deepening rate, seasonal cycle occurrence and associated precipitation and wind patterns over some areas of the basin such as Ionian Sea and Iberian Peninsula. The differences observed appear to be determined by the driving Global Circulation Model (GCM) and influenced by the RCSM physics and internal variability. These results point to the importance of (1) better characterizing the range of plausible futures by relying on ensembles of models that explore well the existing diversity of GCMs and RCSMs as well as the climate natural variability and (2) better understanding the driving mechanisms of the future evolution of Mediterranean cyclones properties

The Copernicus Marine Service ocean forecasting system for the Mediterranean Sea

The Mediterranean Monitoring and Forecasting Center (MED-MFC) is part of the Copernicus Marine Environment and Monitoring Service (CMEMS) and provides regular and systematic information on the time-evolving Mediterranean Sea physical (including waves) and biogeochemical state. The systems consist of 3 components: 1) Med-Physics, a numerical ocean prediction systems, based on NEMO model, that operationally produces analyses, reanalysis and short term forecasts of the main physical parameters; 2) Med-Biogeochemistry, a biogeochemical analysis, reanalysis and forecasting system based on the Biogeochemical Flux Model (BFM) which provides information on chlorophyll, phosphate, nitrate, primary productivity, oxygen, phytoplankton biomass, pH and pCO2; 3) Med-Waves based on WAM model and providing analysis, forecast and reanalysis products for waves. The systems have been recently upgraded at a resolution of 1/24 degree in the horizontal and 141 vertical levels. The Med-Physics analysis and forecasting system is composed by the hydrodynamic model NEMO 2-way coupled with the third-generation wave model WaveWatchIII and forced by ECMWF atmospheric fields. The model solutions are corrected by the 3DVAR data assimilation system (3D variational scheme adapted to the oceanic assimilation problem) with a daily assimilation cycle of sea level anomaly and vertical profiles of temperature and salinity. The model has a non-linear explicit free surface and it is forced by surface pressure, interactive heat, momentum and water fluxes at the air-sea interface. The biogeochemical analysis and forecasts are produced by means of the MedBFM v2.1 modeling system (i.e. the physical-biogeochemical OGSTM-BFM model coupled with the 3DVARBIO assimilation scheme) forced by the outputs of the Med-Physics product. Seven days of analysis/hindcast and ten days of forecast are bi-weekly produced on Wednesday and on Saturday, with the assimilation of surface chlorophyll concentration from satellite observations. In-situ data are mainly used to estimate model uncertainty at different spatial scales. The Med-Waves modelling system is based on the WAM Cycle 4.5.4 wave model code. It consists of a wave model grid covering the Mediterranean Sea at a 1/24° horizontal resolution, nested to a North Atlantic grid at a 1/6° resolution. The system is forced by ECMWF winds at 1/8°. Refraction due to surface currents is accounted by the system which assimilates altimeter along-track significant wave height observations. On a daily basis, it provides 1-day analysis and 5-day forecast hourly wave parameters. Currently, wave buoy observations of significant wave height and mean wave period along with satellite observations are used to calibrate and validate the Med-waves modelling system.PublishedHalifax, Nova Scotia, Canada4A. Oceanografia e clim

Mediterranean monitoring and forecasting operational system for Copernicus Marine Service

The MEDiterranean Monitoring and Forecasting Center (Med-MFC) is part of the Copernicus Marine Environment Monitoring Service (CMEMS, http://marine.copernicus.eu/), provided on an operational mode by Mercator Ocean in agreement with the European Commission. Specifically, Med MFC system provides regular and systematic information about the physical state of the ocean and marine ecosystems for the Mediterranean Sea. The Med-MFC service started in May 2015 from the pre-operational system developed during the MyOcean projects, consolidating the understanding of regional Mediterranean Sea dynamics, from currents to biogeochemistry to waves, interfacing with local data collection networks and guaranteeing an efficient link with other Centers in Copernicus network. The Med-MFC products include analyses, 10 days forecasts and reanalysis, describing currents, temperature, salinity, sea level and pelagic biogeochemistry. Waves products will be available in MED-MFC version in 2017. The consortium, composed of INGV (Italy), HCMR (Greece) and OGS (Italy) and coordinated by the Euro-Mediterranean Centre on Climate Change (CMCC, Italy), performs advanced R&D activities and manages the service delivery. The Med-MFC infrastructure consists of 3 Production Units (PU), for Physics, Biogechemistry and Waves, a unique Dissemination Unit (DU) and Archiving Unit (AU) and Backup Units (BU) for all principal components, guaranteeing a resilient configuration of the service and providing and efficient and robust solution for the maintenance of the service and delivery. The Med-MFC includes also an evolution plan, both in terms of research and operational activities, oriented to increase the spatial resolution of products, to start wave products dissemination, to increase temporal extent of the reanalysis products and improving ocean physical modeling for delivering new products. The scientific activities carried out in 2015 concerned some improvements in the physical, biogeochemical and wave components of the system. Regarding the currents, new grid-point EOFs have been implemented in the Med-MFC assimilation system; the climatological CMAP precipitation was replaced by the ECMWF daily precipitation; reanalysis time-series have been increased by one year. Regarding the biogeochemistry, the main scientific achievement is related to the implementation of the carbon system in the Med-MFC biogeochemistry model system already available. The new model is able to reproduce the principal spatial patterns of the carbonate system variables in the Mediterranean Sea. Further, a key result consists of the calibration of the new variables (DIC and alkalinity), which serves to the estimation of the accuracy of the new products to be released in the next version of the system (i.e. pH and pCO2 at surface). Regarding the waves, the system has been validated against in-situ and satellite observations. For example, a very good agreement between model output and in-situ observations has been obtained at offshore and/or well-exposed wave buoys in the Mediterranean Sea.PublishedVienna3SR. AMBIENTE - Servizi e ricerca per la Societ

Proteomics identifies neddylation as a potential therapy target in small intestinal neuroendocrine tumors.

Patients with small intestinal neuroendocrine tumors (SI-NETs) frequently develop spread disease; however, the underlying molecular mechanisms of disease progression are not known and effective preventive treatment strategies are lacking. Here, protein expression profiling was performed by HiRIEF-LC-MS in 14 primary SI-NETs from patients with and without liver metastases detected at the time of surgery and initial treatment. Among differentially expressed proteins, overexpression of the ubiquitin-like protein NEDD8 was identified in samples from patients with liver metastasis. Further, NEDD8 correlation analysis indicated co-expression with RBX1, a key component in cullin-RING ubiquitin ligases (CRLs). In vitro inhibition of neddylation with the therapeutic agent pevonedistat (MLN4924) resulted in a dramatic decrease of proliferation in SI-NET cell lines. Subsequent mass spectrometry-based proteomics analysis of pevonedistat effects and effects of the proteasome inhibitor bortezomib revealed stabilization of multiple targets of CRLs including p27, an established tumor suppressor in SI-NET. Silencing of NEDD8 and RBX1 using siRNA resulted in a stabilization of p27, suggesting that the cellular levels of NEDD8 and RBX1 affect CRL activity. Inhibition of CRL activity, by either NEDD8/RBX1 silencing or pevonedistat treatment of cells resulted in induction of apoptosis that could be partially rescued by siRNA-based silencing of p27. Differential expression of both p27 and NEDD8 was confirmed in a second cohort of SI-NET using immunohistochemistry. Collectively, these findings suggest a role for CRLs and the ubiquitin proteasome system in suppression of p27 in SI-NET, and inhibition of neddylation as a putative therapeutic strategy in SI-NET