Analysis and mathematical modeling of wave-structure interaction

The aim of this thesis, included within the THESEUS project, is the development of a mathematical model 2DV two-phase, based on the existing code IH-2VOF developed by the University of Cantabria, able to represent together the overtopping phenomenon and the sediment transport. Several numerical simulations were carried out in order to analyze the flow characteristics on a dike crest. The results show that the seaward/landward slope does not affect the evolution of the flow depth and velocity over the dike crest whereas the most important parameter is the relative submergence. Wave heights decrease and flow velocities increase while waves travel over the crest. In particular, by increasing the submergence, the wave height decay and the increase of the velocity are less marked. Besides, an appropriate curve able to fit the variation of the wave height/velocity over the dike crest were found. Both for the wave height and for the wave velocity different fitting coefficients were determined on the basis of the submergence and of the significant wave height. An equation describing the trend of the dimensionless coefficient c_h for the wave height was derived. These conclusions could be taken into consideration for the design criteria and the upgrade of the structures. In the second part of the thesis, new equations for the representation of the sediment transport in the IH-2VOF model were introduced in order to represent beach erosion while waves run-up and overtop the sea banks during storms. The new model allows to calculate sediment fluxes in the water column together with the sediment concentration. Moreover it is possible to model the bed profile evolution. Different tests were performed under low-intensity regular waves with an homogeneous layer of sand on the bottom of a channel in order to analyze the erosion-deposition patterns and verify the model results.

Thermal structure and dynamical modeling of a Mediterranean tropical-like cyclone

In the present work, a detailed analysis of a Mediterranean TLC occurred in January 2014 has been conducted. The author is not aware of other studies regarding this particular event at the publication of this thesis. In order to outline the cyclone evolution, observational data, including weather-stations data, satellite data, radar data and photographic evidence, were collected at first. After having identified the cyclone path and its general features, the GLOBO, BOLAM and MOLOCH NWP models, developed at ISAC-CNR (Bologna), were used to simulate the phenomenon. Particular attention was paid on the Mediterranean phase as well as on the Atlantic phase, since the cyclone showed a well defined precursor up to 3 days before the minimum formation in the Alboran Sea. The Mediterranean phase has been studied using different combinations of GLOBO, BOLAM and MOLOCH models, so as to evaluate the best model chain to simulate this kind of phenomena. The BOLAM and MOLOCH models showed the best performance, by adjusting the path erroneously deviated in the National Centre for Environmental Prediction (NCEP) and ECMWF operational models. The analysis of the cyclone thermal phase shown the presence of a deep-warm core structure in many cases, thus confirming the tropical-like nature of the system. Furthermore, the results showed high sensitivity to initial conditions in the whole lifetime of the cyclone, while the Sea Surface Temperature (SST) modification leads only to small changes in the Adriatic phase. The Atlantic phase has been studied using GLOBO and BOLAM model and with the aid of the same methodology already developed. After tracing the precursor, in the form of a low-pressure system, from the American East Coast to Spain, the thermal phase analysis was conducted. The parameters obtained showed evidence of a deep-cold core asymmetric structure during the whole Atlantic phase, while the first contact with the Mediterranean Sea caused a sudden transition to a shallow-warm core structure. The examination of Potential Vorticity (PV) 3-dimensional structure revealed the presence of a PV streamer that individually formed over Greenland and eventually interacted with the low-pressure system over the Spanish coast, favouring the first phase of the cyclone baroclinic intensification. Finally, the development of an automated system that tracks and studies the thermal phase of Mediterranean cyclones has been encouraged. This could lead to the forecast of potential tropical transition, against with a minimum computational investment.

Conceptual and normative issues of memory enhancement

Our growing understanding of human mind and cognition and the development of neurotechnology has triggered debate around cognitive enhancement in neuroethics. The dissertation examines the normative issues of memory enhancement, and focuses on two issues: (1) the distinction between memory treatment and enhancement; and (2) how the issue of authenticity concerns memory interventions, including memory treatments and enhancements. rnThe first part consists of a conceptual analysis of the concepts required for normative considerations. First, the representational nature and the function of memory are discussed. Memory is regarded as a special form of self-representation resulting from a constructive processes. Next, the concepts of selfhood, personhood, and identity are examined and a conceptual tool—the autobiographical self-model (ASM)—is introduced. An ASM is a collection of mental representations of the system’s relations with its past and potential future states. Third, the debate between objectivist and constructivist views of health are considered. I argue for a phenomenological account of health, which is based on the primacy of illness and negative utilitarianism.rnThe second part presents a synthesis of the relevant normative issues based on the conceptual tools developed. I argue that memory enhancement can be distinguished from memory treatment using a demarcation regarding the existence of memory-related suffering. That is, memory enhancements are, under standard circumstances and without any unwilling suffering or potential suffering resulting from the alteration of memory functions, interventions that aim to manipulate memory function based on the self-interests of the individual. I then consider the issue of authenticity, namely whether memory intervention or enhancement endangers “one’s true self”. By analyzing two conceptions of authenticity—authenticity as self-discovery and authenticity as self-creation, I propose that authenticity should be understood in terms of the satisfaction of the functional constraints of an ASM—synchronic coherence, diachronic coherence, and global veridicality. This framework provides clearer criteria for considering the relevant concerns and allows us to examine the moral values of authenticity. rn

Mutagenesis and computer modeling studies of a GPCR conserved residue W5.43(194) in ligand recognition and signal transduction for CB2 receptor

W5.43(194), a conserved tryptophan residue among G-protein coupled receptors (GPCRs) and cannabinoid receptors (CB), was examined in the present report for its significance in CB2 receptor ligand binding and adenylyl cyclase (AC) activity. Computer modeling postulates that this site in CB2 may be involved in the affinity of WIN55212-2 and SR144528 through aromatic contacts. In the present study, we reported that a CB2 receptor mutant, W5.43(194)Y, which had a tyrosine (Y) substitution for tryptophan (W), retained the binding affinity for CB agonist CP55940, but reduced binding affinity for CB2 agonist WIN55212-2 and inverse agonist SR144528 by 8-fold and 5-fold, respectively; the CB2 W5.43(194)F and W5.43(194)A mutations significantly affect the binding activities of CP55940, WIN55212-2 and SR144528. Furthermore, we found that agonist-mediated inhibition of the forskolin-induced cAMP production was dramatically diminished in the CB2 mutant W5.43(194)Y, whereas W5.43(194)F and W5.43(194)A mutants resulted in complete elimination of downstream signaling, suggesting that W5.43(194) was essential for the full activation of CB2. These results indicate that both aromatic interaction and hydrogen bonding are involved in ligand binding for the residue W5.43(194), and the mutations of this tryptophan site may affect the conformation of the ligand binding pocket and therefore control the active conformation of the wild type CB2 receptor. W5.43(194)Y/F/A mutations also displayed noticeable enhancement of the constitutive activation probably attributed to the receptor conformational changes resulted from the mutations.

Imaging emotional brain functions: conceptual and methodological issues

This article reviews the psychophysiological and brain imaging literature on emotional brain function from a methodological point of view. The difficulties in defining, operationalising and measuring emotional activation and, in particular, aversive learning will be considered. Emotion is a response of the organism during an episode of major significance and involves physiological activation, motivational, perceptual, evaluative and learning processes, motor expression, action tendencies and monitoring/subjective feelings. Despite the advances in assessing the physiological correlates of emotional perception and learning processes, a critical appraisal shows that functional neuroimaging approaches encounter methodological difficulties regarding measurement precision (e.g., response scaling and reproducibility) and validity (e.g., response specificity, generalisation to other paradigms, subjects or settings). Since emotional processes are not only the result of localised but also of widely distributed activation, a more representative model of assessment is needed that systematically relates the hierarchy of high- and low-level emotion constructs with the corresponding patterns of activity and functional connectivity of the brain.

RF-sputter fabrication of magnetic garnet thin films and simulation modeling for 1-D magnetic photonic crystal waveguide devices

One dimensional magnetic photonic crystals (1D-MPC) are promising structures for integrated optical isolator applications. Rare earth substituted garnet thin films with proper Faraday rotation are required to fabricate planar 1D-MPCs. In this thesis, flat-top response 1D-MPC was proposed and spectral responses and Faraday rotation were modeled. Bismuth substituted iron garnet films were fabricated by RF magnetron sputtering and structures, compositions, birefringence and magnetooptical properties were studied. Double layer structures for single mode propagation were also fabricated by sputtering for the first time. Multilayer stacks with multiple defects (phase shift) composed of Ce-YIG and GGG quarter-wave plates were simulated by the transfer matrix method. The transmission and Faraday rotation characteristics were theoretically studied. It is found that flat-top response, with 100% transmission and near 45o rotation is achievable by adjusting the inter-defect spacing, for film structures as thin as 30 to 35 μm. This is better than 3-fold reduction in length compared to the best Ce-YIG films for comparable rotations, thus allows a considerable reduction in size in manufactured optical isolators. Transmission bands as wide as 7nm were predicted, which is considerable improvement over 2 defects structure. Effect of repetition number and ratio factor on transmission and Faraday rotation ripple factors for the case of 3 and 4 defects structure has been discussed. Diffraction across the structure corresponds to a longer optical path length. Thus the use of guided optics is required to minimize the insertion losses in integrated devices. This part is discussed in chapter 2 in this thesis. Bismuth substituted iron garnet thin films were prepared by RF magnetron sputtering. We investigated or measured the deposition parameters optimization, crystallinity, surface morphologies, composition, magnetic and magnetooptical properties. A very high crystalline quality garnet film with smooth surface has been heteroepitaxially grown on (111) GGG substrate for films less than 1μm. Dual layer structures with two distinct XRD peaks (within a single sputtered film) start to develop when films exceed this thickness. The development of dual layer structure was explained by compositional gradient across film thickness, rather than strain gradient proposed by other authors. Lower DC self bias or higher substrate temperature is found to help to delay the appearance of the 2nd layer. The deposited films show in-plane magnetization, which is advantageous for waveguide devices application. Propagation losses of fabricated waveguides can be decreased by annealing in an oxygen atmosphere from 25dB/cm to 10dB/cm. The Faraday rotation at λ=1.55μm were also measured for the waveguides. FR is small (10° for a 3mm long waveguide), due to the presence of linear birefringence. This part is covered in chapter 4. We also investigated the elimination of linear birefringence by thickness tuning method for our sputtered films. We examined the compressively and tensilely strained films and analyze the photoelastic response of the sputter deposited garnet films. It has been found that the net birefringence can be eliminated under planar compressive strain conditions by sputtering. Bi-layer GGG on garnet thin film yields a reduced birefringence. Temperature control during the sputter deposition of GGG cover layer is critical and strongly influences the magnetization and birefringence level in the waveguide. High temperature deposition lowers the magnetization and increases the linear birefringence in the garnet films. Double layer single mode structures fabricated by sputtering were also studied. The double layer, which shows an in-plane magnetization, has an increased RMS roughness upon upper layer deposition. The single mode characteristic was confirmed by prism coupler measurement. This part is discussed in chapter 5.

STATE-AND-TRANSITION MODELING AND ADAPTIVE MANAGEMENT: TOOLS FOR FUTURE CO-DEVELOPMENT OF MADAGASCAR’S NATURAL RESOURCES AND PEOPLE

Madagascar’s terrestrial and aquatic ecosystems have long supported a unique set of ecological communities, many of whom are endemic to the tropical island. Those same ecosystems have been a source of valuable natural resources to some of the poorest people in the world. Nevertheless, with pride, ingenuity and resourcefulness, the Malagasy people of the southwest coast, being of Vezo identity, subsist with low development fishing techniques aimed at an increasingly threatened host of aquatic seascapes. Mangroves, sea grass bed, and coral reefs of the region are under increased pressure from the general populace for both food provisions and support of economic opportunity. Besides purveyors and extractors, the coastal waters are also subject to a number of natural stressors, including cyclones and invasive, predator species of both flora and fauna. In addition, the aquatic ecosystems of the region are undergoing increased nutrient and sediment runoff due, in part, to Madagascar’s heavy reliance on land for agricultural purposes (Scales, 2011). Moreover, its coastal waters, like so many throughout the world, have been proven to be warming at an alarming rate over the past few decades. In recognizing the intimate interconnectedness of the both the social and ecological systems, conservation organizations have invoked a host of complimentary conservation and social development efforts with the dual aim of preserving or restoring the health of both the coastal ecosystems and the people of the region. This paper provides a way of thinking more holistically about the social-ecological system within a resiliency frame of understanding. Secondly, it applies a platform known as state-and-transition modeling to give form to the process. State-and-transition modeling is an iterative investigation into the physical makeup of a system of study as well as the boundaries and influences on that state, and has been used in restorative ecology for more than a decade. Lastly, that model is sited within an adaptive management scheme that provides a structured, cyclical, objective-oriented process for testing stakeholders cognitive understanding of the ecosystem through a pragmatic implementation and monitoring a host of small-scale interventions developed as part of the adaptive management process. Throughout, evidence of the application of the theories and frameworks are offered, with every effort made to retool conservation-minded development practitioners with a comprehensive strategy for addressing the increasingly fragile social-ecological systems of southwest Madagascar. It is offered, in conclusion, that the seascapes of the region would be an excellent case study worthy of future application of state-and-transition modeling and adaptive management as frameworks for conservation-minded development practitioners whose multiple projects, each with its own objective, have been implemented with a single goal in mind: preserve and protect the state of the supporting environment while providing for the basic needs of the local Malagasy people.