A Trans-dimensional inversion algorithm to model deformation sources with unconstrained shape in finite element domains

Ground deformation provides valuable insights on subsurface processes with pattens reflecting the characteristics of the source at depth. In active volcanic sites displacements can be observed in unrest phases; therefore, a correct interpretation is essential to assess the hazard potential. Inverse modeling is employed to obtain quantitative estimates of parameters describing the source. However, despite the robustness of the available approaches, a realistic imaging of these reservoirs is still challenging. While analytical models return quick but simplistic results, assuming an isotropic and elastic crust, more sophisticated numerical models, accounting for the effects of topographic loads, crust inelasticity and structural discontinuities, require much higher computational effort and information about the crust rheology may be challenging to infer. All these approaches are based on a-priori source shape constraints, influencing the solution reliability. In this thesis, we present a new approach aimed at overcoming the aforementioned limitations, modeling sources free of a-priori shape constraints with the advantages of FEM simulations, but with a cost-efficient procedure. The source is represented as an assembly of elementary units, consisting in cubic elements of a regular FE mesh loaded with a unitary stress tensors. The surface response due to each of the six stress tensor components is computed and linearly combined to obtain the total displacement field. In this way, the source can assume potentially any shape. Our tests prove the equivalence of the deformation fields due to our assembly and that of corresponding cavities with uniform boundary pressure. Our ability to simulate pressurized cavities in a continuum domain permits to pre-compute surface responses, avoiding remeshing. A Bayesian trans-dimensional inversion algorithm implementing this strategy is developed. 3D Voronoi cells are used to sample the model domain, selecting the elementary units contributing to the source solution and those remaining inactive as part of the crust.

Identification of surface protein complexes of Streptococcus pyogenes through protein microarray technology

A systematic characterization of the composition and structure of the bacterial cell-surface proteome and its complexes can provide an invaluable tool for its comprehensive understanding. The knowledge of protein complexes composition and structure could offer new, more effective targets for a more specific and consequently effective immune response against a complex instead of a single protein. Large-scale protein-protein interaction screens are the first step towards the identification of complexes and their attribution to specific pathways. Currently, several methods exist for identifying protein interactions and protein microarrays provide the most appealing alternative to existing techniques for a high throughput screening of protein-protein interactions in vitro under reasonably straightforward conditions. In this study approximately 100 proteins of Group A Streptococcus (GAS) predicted to be secreted or surface exposed by genomic and proteomic approaches were purified in a His-tagged form and used to generate protein microarrays on nitrocellulose-coated slides. To identify protein-protein interactions each purified protein was then labeled with biotin, hybridized to the microarray and interactions were detected with Cy3-labelled streptavidin. Only reciprocal interactions, i. e. binding of the same two interactors irrespective of which of the two partners is in solid-phase or in solution, were taken as bona fide protein-protein interactions. Using this approach, we have identified 20 interactors of one of the potent toxins secreted by GAS and known as superantigens. Several of these interactors belong to the molecular chaperone or protein folding catalyst families and presumably are involved in the secretion and folding of the superantigen. In addition, a very interesting interaction was found between the superantigen and the substrate binding subunit of a well characterized ABC transporter. This finding opens a new perspective on the current understanding of how superantigens are modified by the bacterial cell in order to become major players in causing disease.

Variability analysis of discrete event series and wavefront patterns in surface electrocardiogram: contributions to psychophysiological and clinical research

The surface electrocardiogram (ECG) is an established diagnostic tool for the detection of abnormalities in the electrical activity of the heart. The interest of the ECG, however, extends beyond the diagnostic purpose. In recent years, studies in cognitive psychophysiology have related heart rate variability (HRV) to memory performance and mental workload. The aim of this thesis was to analyze the variability of surface ECG derived rhythms, at two different time scales: the discrete-event time scale, typical of beat-related features (Objective I), and the “continuous” time scale of separated sources in the ECG (Objective II), in selected scenarios relevant to psychophysiological and clinical research, respectively. Objective I) Joint time-frequency and non-linear analysis of HRV was carried out, with the goal of assessing psychophysiological workload (PPW) in response to working memory engaging tasks. Results from fourteen healthy young subjects suggest the potential use of the proposed indices in discriminating PPW levels in response to varying memory-search task difficulty. Objective II) A novel source-cancellation method based on morphology clustering was proposed for the estimation of the atrial wavefront in atrial fibrillation (AF) from body surface potential maps. Strong direct correlation between spectral concentration (SC) of atrial wavefront and temporal variability of the spectral distribution was shown in persistent AF patients, suggesting that with higher SC, shorter observation time is required to collect spectral distribution, from which the fibrillatory rate is estimated. This could be time and cost effective in clinical decision-making. The results held for reduced leads sets, suggesting that a simplified setup could also be considered, further reducing the costs. In designing the methods of this thesis, an online signal processing approach was kept, with the goal of contributing to real-world applicability. An algorithm for automatic assessment of ambulatory ECG quality, and an automatic ECG delineation algorithm were designed and validated.

Phytoplankton Response to Environmental Variables and Organic Pollutants. Laboratory Cultures and Numerical Simulations Experiments

Herbicides are becoming emergent contaminants in Italian surface, coastal and ground waters, due to their intensive use in agriculture. In marine environments herbicides have adverse effects on non-target organisms, as primary producers, resulting in oxygen depletion and decreased primary productivity. Alterations of species composition in algal communities can also occur due to the different sensitivity among the species. In the present thesis the effects of herbicides, widely used in the Northern Adriatic Sea, on different algal species were studied. The main goal of this work was to study the influence of temperature on algal growth in the presence of the triazinic herbicide terbuthylazine (TBA), and the cellular responses adopted to counteract the toxic effects of the pollutant (Chapter 1 and 2). The development of simulation models to be applied in environmental management are needed to organize and track information in a way that would not be possible otherwise and simulate an ecological prospective. The data collected from laboratory experiments were used to simulate algal responses to the TBA exposure at increasing temperature conditions (Chapter 3). Part of the thesis was conducted in foreign countries. The work presented in Chapter 4 was focused on the effect of high light on growth, toxicity and mixotrophy of the ichtyotoxic species Prymnesium parvum. In addition, a mesocosm experiment was conducted in order to study the synergic effect of the pollutant emamectin benzoate with other anthropogenic stressors, such as oil pollution and induced phytoplankton blooms (Chapter 5).

Atmospheric plasma processes for microbial inactivation: food applications and stress response in Listeria monocytogenes

This PhD thesis is focused on cold atmospheric plasma treatments (GP) for microbial inactivation in food applications. In fact GP represents a promising emerging technology alternative to the traditional methods for the decontamination of foods. The objectives of this work were to evaluate: - the effects of GP treatments on microbial inactivation in model systems and in real foods; - the stress response in L. monocytogenes following exposure to different GP treatments. As far as the first aspect, inactivation curves were obtained for some target pathogens, i.e. Listeria monocytogenes and Escherichia coli, by exposing microbial cells to GP generated with two different DBD equipments and processing conditions (exposure time, material of the electrodes). Concerning food applications, the effects of different GP treatments on the inactivation of natural microflora and Listeria monocytogenes, Salmonella Enteritidis and Escherichia coli on the surface of Fuji apples, soya sprouts and black pepper were evaluated. In particular the efficacy of the exposure to gas plasma was assessed immediately after treatments and during storage. Moreover, also possible changes in quality parameters such as colour, pH, Aw, moisture content, oxidation, polyphenol-oxidase activity, antioxidant activity were investigated. Since the lack of knowledge of cell targets of GP may limit its application, the possible mechanism of action of GP was studied against 2 strains of Listeria monocytogenes by evaluating modifications in the fatty acids of the cytoplasmic membrane (through GC/MS analysis) and metabolites detected by SPME-GC/MS and 1H-NMR analyses. Moreover, changes induced by different treatments on the expression of selected genes related to general stress response, virulence or to the metabolism were detected with Reverse Transcription-qPCR. In collaboration with the Scripps Research Institute (La Jolla, CA, USA) also proteomic profiles following gas plasma exposure were analysed through Multidimensional Protein Identification Technology (MudPIT) to evaluate possible changes in metabolic processes.

Modelling UV response of biomolecules: from electronic structure to ab-initio dynamics.

The interaction of organic chromophores with light initiates ultrafast processes in the timescale of femtoseconds. An atomistic understanding of the mechanism driving such photoinduced reactions opens up the door to exploit them for our benefit. This thesis studies the interactions of ultraviolet light with the DNA/RNA molecules and the amino-acid tryptophan. Using some of the most accurate electronic structure methods and sophisticated environmental modelling, the works documented herein enable quantitative comparisons with cutting-edge experimental data. The relaxation pathways undertaken by the excited molecule are revealed through static and dynamical investigations of the excited-state potential energy surface. The profound role played by the dynamic response of the environment to guide the excitation in these timescales is addressed thoroughly.

The role of the Rocky Mountains in shaping the atmospheric mean state and the response to tropical forcing in idealised simulations.

Understanding the natural and forced variability of the atmospheric general circulation and its drivers is one of the grand challenges in climate science. It is of paramount importance to understand to what extent the systematic error of climate models affects the processes driving such variability. This is done by performing a set of simulations (ROCK experiments) with an intermediate complexity atmospheric model (SPEEDY), in which the Rocky Mountains orography is increased or decreased to influence the structure of the North Pacific jet stream. For each of these modified-orography experiments, the climatic response to idealized sea surface temperature anomalies of varying intensity in the El Niño Southern Oscillation (ENSO) region is studied. ROCK experiments are characterized by variations in the Pacific jet stream intensity whose extension encompasses the spread of the systematic error found in Coupled Model Intercomparison Project (CMIP6) models. When forced with ENSO-like idealised anomalies, they exhibit a non-negligible sensitivity in the response pattern over the Pacific North American region, indicating that the model mean state can affect the model response to ENSO. It is found that the classical Rossby wave train response to ENSO is more meridionally oriented when the Pacific jet stream is weaker and more zonally oriented with a stronger jet. Rossby wave linear theory suggests that a stronger jet implies a stronger waveguide, which traps Rossby waves at a lower latitude, favouring a zonal propagation of Rossby waves. The shape of the dynamical response to ENSO affects the ENSO impacts on surface temperature and precipitation over Central and North America. A comparison of the SPEEDY results with CMIP6 models suggests a wider applicability of the results to more resources-demanding climate general circulation models (GCMs), opening up to future works focusing on the relationship between Pacific jet misrepresentation and response to external forcing in fully-fledged GCMs.