Study of Bone Biomineralization in 2D and 3D Cultures of a Human Osteosarcoma Cell Line As Osteoblast-like Model

This PhD project focuses on the study of the early stages of bone biomineralization in 2D and 3D cultures of osteoblast-like SaOS-2 osteosarcoma cells, exposed to an osteogenic cocktail. The efficacy of osteogenic treatment was assessed on 2D cell cultures after 7 days. A large calcium minerals production, an overexpression of osteogenic markers and of alkaline phosphatase activity occurred in treated samples. TEM microscopy and cryo-XANES micro-spectroscopy were performed for localizing and characterizing Ca-depositions. These techniques revealed a different localization and chemical composition of Ca-minerals over time and after treatment. Nevertheless, the Mito stress test showed in treated samples a significant increase in maximal respiration levels associated to an upregulation of mitochondrial biogenesis indicative of an ongoing differentiation process. The 3D cell cultures were realized using two different hydrogels: a commercial collagen type I and a mixture of agarose and lactose-modified chitosan (CTL). Both biomaterials showed good biocompatibility with SaOS-2 cells. The gene expression analysis of SaOS-2 cells on collagen scaffolds indicated an osteogenic commitment after treatment. and Alizarin red staining highlighted the presence of Ca-spots in the differentiated samples. In addition, the intracellular magnesium quantification, and the X-ray microscopy on mineral depositions, suggested the incorporation of Mg during the early stages of bone formation process., SaOS-2 cells treated with osteogenic cocktail produced Ca mineral deposits also on CTL/agarose scaffolds, as confirmed by alizarin red staining. Further studies are underway to evaluate the differentiation also at the genetic level. Thanks to the combination of conventional laboratory methods and synchrotron-based techniques, it has been demonstrated that SaOS-2 is a suitable model for the study of biomineralization in vitro. These results have contributed to a deeper knowledge of biomineralization process in osteosarcoma cells and could provide new evidences about a therapeutic strategy acting on the reversibility of tumorigenicity by osteogenic induction.

Soil-structure interaction during tunnelling in urban area: observations and 3D numerical modelling

This work illustrates a soil-tunnel-structure interaction study performed by an integrated,geotechnical and structural,approach based on 3D finite element analyses and validated against experimental observations.The study aims at analysing the response of reinforced concrete framed buildings on discrete foundations in interaction with metro lines.It refers to the case of the twin tunnels of the Milan (Italy) metro line 5,recently built in coarse grained materials using EPB machines,for which subsidence measurements collected along ground and building sections during tunnelling were available.Settlements measured under freefield conditions are firstly back interpreted using Gaussian empirical predictions. Then,the in situ measurements’ analysis is extended to include the evolving response of a 9 storey reinforced concrete building while being undercrossed by the metro line.In the finite element study,the soil mechanical behaviour is described using an advanced constitutive model. This latter,when combined with a proper simulation of the excavation process, proves to realistically reproduce the subsidence profiles under free field conditions and to capture the interaction phenomena occurring between the twin tunnels during the excavation. Furthermore, when the numerical model is extended to include the building, schematised in a detailed manner, the results are in good agreement with the monitoring data for different stages of the twin tunnelling. Thus, they indirectly confirm the satisfactory performance of the adopted numerical approach which also allows a direct evaluation of the structural response as an outcome of the analysis. Further analyses are also carried out modelling the building with different levels of detail. The results highlight that, in this case, the simplified approach based on the equivalent plate schematisation is inadequate to capture the real tunnelling induced displacement field. The overall behaviour of the system proves to be mainly influenced by the buried portion of the building which plays an essential role in the interaction mechanism, due to its high stiffness.

Slope stability analysis by multi-temporal DEMs and 3D modelling: The 2002 and 2007 Stromboli landslide events

Natural hazard related to the volcanic activity represents a potential risk factor, particularly in the vicinity of human settlements. Besides to the risk related to the explosive and effusive activity, the instability of volcanic edifices may develop into large landslides often catastrophically destructive, as shown by the collapse of the northern flank of Mount St. Helens in 1980. A combined approach was applied to analyse slope failures that occurred at Stromboli volcano. SdF slope stability was evaluated by using high-resolution multi-temporal DTMMs and performing limit equilibrium stability analyses. High-resolution topographical data collected with remote sensing techniques and three-dimensional slope stability analysis play a key role in understanding instability mechanism and the related risks. Analyses carried out on the 2002–2003 and 2007 Stromboli eruptions, starting from high-resolution data acquired through airborne remote sensing surveys, permitted the estimation of the lava volumes emplaced on the SdF slope and contributed to the investigation of the link between magma emission and slope instabilities. Limit Equilibrium analyses were performed on the 2001 and 2007 3D models, in order to simulate the slope behavior before 2002-2003 landslide event and after the 2007 eruption. Stability analyses were conducted to understand the mechanisms that controlled the slope deformations which occurred shortly after the 2007 eruption onset, involving the upper part of slope. Limit equilibrium analyses applied to both cases yielded results which are congruent with observations and monitoring data. The results presented in this work undoubtedly indicate that hazard assessment for the island of Stromboli should take into account the fact that a new magma intrusion could lead to further destabilisation of the slope, which may be more significant than the one recently observed because it will affect an already disarranged deposit and fractured and loosened crater area. The two-pronged approach based on the analysis of 3D multi-temporal mapping datasets and on the application of LE methods contributed to better understanding volcano flank behaviour and to be prepared to undertake actions aimed at risk mitigation.

The physical city and the urban structure: detecting amenity zones and applying urban morphology to New York

The city is a collection of built structures and infrastructure embedded in socio-cultural processes: any investigation into a city’s transformations involves considerations on the degree to which its composite elements respond to socio-economical changes. The main purpose of this research is to investigate how transformations in the functional requirements of New York’s society have spurred, since the 1970s, changes in both the city’s urban structure and physical form. The present work examines the rise of Amenity Zones in New York, and investigates the transformations that have occurred in New York’s built environment since the 1970s. By applying qualitative measures and analyzing the relationship between urban amenities and the creative class, the present work has investigated changes in the urban structure and detected a hierarchical series of amenity zones classes, namely, Super Amenity Zones (SAZs), Nodal Amenity Zones (NAZs) and Peripheral Amenity Zones (PAZs). This series allows for a more comprehensive reading of the urban structure in a complex city like New York, bringing advancements to the amenity zone’s methodology. In order to examine the manner in which the other component of the city, the physical form, has changed or adapted to the new socio-economic condition, the present research has applied Conzenian analysis to a select study area, Atlantic Avenue. The results of this analysis reveal that, contrary to the urban structure, which changes rapidly, the physical form of New York is hard to modify completely, due to the resilience of the town plan and its elements, and to preservation laws; the city rather adapts to socio-economical changes through process of adaptive reuses or conversion. Concluding, this research has examined the dialectic between the ever-changing needs of society and the complexity of the built environment and urban structure, showing the different degrees to which the urban landscape modifies, reacts and sometimes adapts to the population’s functional requirements.

Theoretical and numerical study of the laser-plasma ion acceleration

The laser driven ion acceleration is a burgeoning field of resarch and is attracting a growing number of scientists since the first results reported in 2000 obtained irradiating thin solid foils by high power laser pulses. The growing interest is driven by the peculiar characteristics of the produced bunches, the compactness of the whole accelerating system and the very short accelerating length of this all-optical accelerators. A fervent theoretical and experimental work has been done since then. An important part of the theoretical study is done by means of numerical simulations and the most widely used technique exploits PIC codes (“Particle In Cell'”). In this thesis the PIC code AlaDyn, developed by our research group considering innovative algorithms, is described. My work has been devoted to the developement of the code and the investigation of the laser driven ion acceleration for different target configurations. Two target configurations for the proton acceleration are presented together with the results of the 2D and 3D numerical investigation. One target configuration consists of a solid foil with a low density layer attached on the irradiated side. The nearly critical plasma of the foam layer allows a very high energy absorption by the target and an increase of the proton energy up to a factor 3, when compared to the ``pure'' TNSA configuration. The differences of the regime with respect to the standard TNSA are described The case of nearly critical density targets has been investigated with 3D simulations. In this case the laser travels throughout the plasma and exits on the rear side. During the propagation, the laser drills a channel and induce a magnetic vortex that expanding on the rear side of the targer is source of a very intense electric field. The protons of the plasma are strongly accelerated up to energies of 100 MeV using a 200PW laser.

Fast and accurate numerical solutions in some problems of particle and radiation transport: synthetic acceleration for the method of short characteristics, Doppler-broadened scattering kernel, remote sensing of the cryosphere

The aim of this work is to present various aspects of numerical simulation of particle and radiation transport for industrial and environmental protection applications, to enable the analysis of complex physical processes in a fast, reliable, and efficient way. In the first part we deal with speed-up of numerical simulation of neutron transport for nuclear reactor core analysis. The convergence properties of the source iteration scheme of the Method of Characteristics applied to be heterogeneous structured geometries has been enhanced by means of Boundary Projection Acceleration, enabling the study of 2D and 3D geometries with transport theory without spatial homogenization. The computational performances have been verified with the C5G7 2D and 3D benchmarks, showing a sensible reduction of iterations and CPU time. The second part is devoted to the study of temperature-dependent elastic scattering of neutrons for heavy isotopes near to the thermal zone. A numerical computation of the Doppler convolution of the elastic scattering kernel based on the gas model is presented, for a general energy dependent cross section and scattering law in the center of mass system. The range of integration has been optimized employing a numerical cutoff, allowing a faster numerical evaluation of the convolution integral. Legendre moments of the transfer kernel are subsequently obtained by direct quadrature and a numerical analysis of the convergence is presented. In the third part we focus our attention to remote sensing applications of radiative transfer employed to investigate the Earth's cryosphere. The photon transport equation is applied to simulate reflectivity of glaciers varying the age of the layer of snow or ice, its thickness, the presence or not other underlying layers, the degree of dust included in the snow, creating a framework able to decipher spectral signals collected by orbiting detectors.

Physical land degradation and loss of soil fertility: soil structural stability and bio-physical indicators

This study investigates the changes in soil fertility due to the different aggregate breakdown mechanisms and it analyses their relationships in different soil-plant systems, using physical aggregates behavior and organic matter (OM) changes as indicators. Three case studies were investigated: i) an organic agricultural soil, where a combined method, aimed to couple aggregate stability to nutrients loss, were tested; ii) a soil biosequence, where OM chemical characterisation and fractionation of aggregates on the basis of their physical behaviour were coupled and iii) a soils sequence in different phytoclimatic conditions, where isotopic C signature of separated aggregates was analysed. In agricultural soils the proposed combined method allows to identify that the severity of aggregate breakdown affected the quantity of nutrients lost more than nutrients availability, and that P, K and Mg were the most susceptible elements to water abrasion, while C and N were mainly susceptible to wetting. In the studied Chestnut-Douglas fir biosequence, OM chemical properties affected the relative importance of OM direct and indirect mechanisms (i.e., organic and organic-metallic cements, respectively) involved in aggregate stability and nutrient losses: under Douglas fir, high presence of carboxylate groups enhanced OM-metal interactions and stabilised aggregates; whereas under Chestnut, OM directly acted and fresh, more C-rich OM was preserved. OM direct mechanism seemed to be more efficient in C preservation in aggregates. The 13C natural abundance approach showed that, according to phytoclimatic conditions, stable macroaggregates can form both around partially decomposed OM and by organic-mineral interactions. In topsoils, aggregate resistance enhanced 13C-rich OM preservation, but in subsoils C preservation was due to other mechanisms, likely OM-mineral interactions. The proposed combined approach seems to be useful in the understanding of C and nutrients fate relates to water stresses, and in future research it could provide new insights into the complexity of soil biophysical processes.

Understanding, defining and assessing food systems’ social and economic sustainability indicators: implementation of mixed methodologies for policy insights

Sustainability encompasses the presence of three dimensions that must coexist simultaneously, namely the environmental, social, and economic ones. The economic and social dimensions are gaining the spotlight in recent years, especially within food systems. To assess social and economic impacts, indicators and tools play a fundamental role in contributing to the achievements of sustainability targets, although few of them have deepen the focus on social and economic impacts. Moreover, in a framework of citizen science and bottom-up approach for improving food systems, citizen play a key role in defying their priorities in terms of social and economic interventions. This research expands the knowledge of social and economic sustainability indicators within the food systems for robust policy insights and interventions. This work accomplishes the following objectives: 1) to define social and economic indicators within the supply chain with a stakeholder perspective, 2) to test social and economic sustainability indicators for future food systems engaging young generations. The first objective was accomplished through the development of a systematic literature review of 34 social sustainability tools, based on five food supply chain stages, namely production, processing, wholesale, retail, and consumer considering farmers, workers, consumers, and society as stakeholders. The second objective was achieved by defining and testing new food systems social and economic sustainability indicators through youth engagement for informed and robust policy insights, to provide policymakers suggestions that would incorporate young generations ones. Future food systems scenarios were evaluated by youth through focus groups, whose results were analyzed through NVivo and then through a survey with a wider platform. Conclusion addressed the main areas of policy interventions in terms of social and economic aspects of sustainable food systems youth pointed out as in need of interventions, spanning from food labelling reporting sustainable origins to better access to online food services.

Chemo-physical and biological mechanisms behind the anticancer activity of plasma activated Ringer's Lactate solution for the treatment of peritoneal carcinosis from primitive epithelial ovarian/tubular tumor

Cancer research and development of targeting agents in this field is based on robust studies using preclinical models. The failure rate of standardized treatment approaches for several solid tumors has led to the urgent need to fine-tune more sophisticated and faithful preclinical models able to recapitulate the features of in vivo human tumors, with the final aim to shed light on new potential therapeutic targets. Epithelial Ovarian Cancer (EOC) serous histotype (HGSOC) is one of the most lethal diseases in women due to its high aggressiveness (75% of patients diagnosed at FIGO III-IV state) and poor prognosis (less of 50% in 5 years), whose therapy often fails as chemoresistance sets in. This thesis aimed at using the novel perfusion-based bioreactor U-CUP that provides direct perfusion throughout the tumor tissue seeking to obtain an EOC 3D ex vivo model able to recapitulate the features of the original tumor including the tumor microenvironment and maintaining its cellular heterogeneity. Moreover, we optimized this approach so that it can be successfully applied to slow-frozen tumoral tissues, further extending the usefulness of this tool. We also investigated the effectiveness of Plasma Activated Ringer’s Lactate solution (PA-RL) against Epithelial Ovarian Cancer (EOC) serous histotype in both 2D and 3D cultures using ex-vivo specimens from HGSOC patients. We propose PA-RL as a novel therapy with local intraperitoneal administration, which could act on primary or metastatic ovarian tumors inducing a specific cancer cell death with reduced damage on the surrounding healthy tissues.

TCAD approaches to multidimensional simulation of advanced semiconductor devices

Technology scaling increasingly emphasizes complexity and non-ideality of the electrical behavior of semiconductor devices and boosts interest on alternatives to the conventional planar MOSFET architecture. TCAD simulation tools are fundamental to the analysis and development of new technology generations. However, the increasing device complexity is reflected in an augmented dimensionality of the problems to be solved. The trade-off between accuracy and computational cost of the simulation is especially influenced by domain discretization: mesh generation is therefore one of the most critical steps and automatic approaches are sought. Moreover, the problem size is further increased by process variations, calling for a statistical representation of the single device through an ensemble of microscopically different instances. The aim of this thesis is to present multi-disciplinary approaches to handle this increasing problem dimensionality in a numerical simulation perspective. The topic of mesh generation is tackled by presenting a new Wavelet-based Adaptive Method (WAM) for the automatic refinement of 2D and 3D domain discretizations. Multiresolution techniques and efficient signal processing algorithms are exploited to increase grid resolution in the domain regions where relevant physical phenomena take place. Moreover, the grid is dynamically adapted to follow solution changes produced by bias variations and quality criteria are imposed on the produced meshes. The further dimensionality increase due to variability in extremely scaled devices is considered with reference to two increasingly critical phenomena, namely line-edge roughness (LER) and random dopant fluctuations (RD). The impact of such phenomena on FinFET devices, which represent a promising alternative to planar CMOS technology, is estimated through 2D and 3D TCAD simulations and statistical tools, taking into account matching performance of single devices as well as basic circuit blocks such as SRAMs. Several process options are compared, including resist- and spacer-defined fin patterning as well as different doping profile definitions. Combining statistical simulations with experimental data, potentialities and shortcomings of the FinFET architecture are analyzed and useful design guidelines are provided, which boost feasibility of this technology for mainstream applications in sub-45 nm generation integrated circuits.

Numerical models of trench migration for lateral heterogeneous subducting plates

The aim of this Thesis is to investigate the effect of heterogeneities within the subducting plate on the dynamics of subduction. In particular, I study the motion of the trench for oceanic and continental subduction, first, separately, and, then, together in the same system to understand how they interact. The understanding of these features is fundamental to reconstruct the evolution of complex subduction zones, such as the Central Mediterranean. For this purpose, I developed 2D and 3D numerical models of oceanic and continental subduction where the rheological, geometrical and compositional properties of the plates are varied. In these models, the trench and the overriding plate move self-consistently as a function of the dynamics of the system. The effect of continental subduction on trench migration is largely investigated. Results from a parametric study showed that despite different rheological properties of the plates, all models with a uniform continental crust share the same kinematic behaviour: the trench starts to advance once the continent arrives at the subduction zone. Hence, the advancing mode in continental collision scenarios is at least partly driven by an intrinsic feature of the system. Moreover, the presence of a weak lower crust within the continental plate can lead to the occurrence of delamination. Indeed, by changing the viscosity of the lower crust, both delamination and slab detachment can occur. Delamination is favoured by a low viscosity value of the lower crust, because this makes the mechanical decoupling easier between crust and lithospheric mantle. These features are observed both in 2D and 3D models, but the numerical results of the 3D models also showed that the rheology of the continental crust has a very strong effect on the dynamics of the whole system, since it influences not only the continental part of plate but also the oceanic sides.

Numerical modeling of the Alto Tiberina low angle normal fault

The aim of this Thesis is to obtain a better understanding of the mechanical behavior of the active Alto Tiberina normal fault (ATF). Integrating geological, geodetic and seismological data, we perform 2D and 3D quasi-static and dynamic mechanical models to simulate the interseismic phase and rupture dynamic of the ATF. Effects of ATF locking depth, synthetic and antithetic fault activity, lithology and realistic fault geometries are taken in account. The 2D and 3D quasi-static model results suggest that the deformation pattern inferred by GPS data is consistent with a very compliant ATF zone (from 5 to 15 km) and Gubbio fault activity. The presence of the ATF compliant zone is a first order condition to redistribute the stress in the Umbria-Marche region; the stress bipartition between hanging wall (high values) and footwall (low values) inferred by the ATF zone activity could explain the microseismicity rates that are higher in the hanging wall respect to the footwall. The interseismic stress build-up is mainly located along the Gubbio fault zone and near ATF patches with higher dip (30°3D rupture dynamic models demonstrate that the magnitude expected, after that an event is simulated on the ATF, can decrease if we consider the fault plane roughness.

Application of Submerged Grouted Anchors in Sheet Pile Quay Walls

Sheet pile walls are one of the oldest earth retention systems utilized in civil engineering projects. They are used for various purposes; such as excavation support system, cofferdams, cut-off walls under dams, slope stabilization, waterfront structures, and flood walls. Sheet pile walls are one of the most common types of quay walls used in port construction. The worldwide increases in utilization of large ships for transportation have created an urgent need of deepening the seabed within port areas and consequently the rehabilitation of its wharfs. Several methods can be used to increase the load-carrying capacity of sheet-piling walls. The use of additional anchored tie rods grouted into the backfill soil and arranged along the exposed wall height is one of the most practical and appropriate solutions adopted for stabilization and rehabilitation of the existing quay wall. The Ravenna Port Authority initiated a project to deepen the harbor bottom at selected wharves. An extensive parametric study through the finite element program, PLAXIS 2D, version 2012 was carried out to investigate the enhancement of using submerged grouted anchors technique on the load response of sheet-piling quay wall. The influence of grout-ties area, length of grouted body, anchor inclination and anchor location were considered and evaluated due to the effect of different system parameters. Also a comparative study was conducted by Plaxis 2D and 3D program to investigate the behavior of these sheet pile quay walls in terms of horizontal displacements induced along the sheet pile wall and ground surface settlements as well as the anchor force and calculated factor of safety. Finally, a comprehensive study was carried out by using different constitutive models to simulate the mechanical behavior of the soil to investigate the effect of these two models (Mohr-Coulomb and Hardening Soil) on the behavior of these sheet pile quay walls.

Statistical analysis of the error associated with the simplification of the stratigraphy in geotechnical models

The uncertainties in the determination of the stratigraphic profile of natural soils is one of the main problems in geotechnics, in particular for landslide characterization and modeling. The study deals with a new approach in geotechnical modeling which relays on a stochastic generation of different soil layers distributions, following a boolean logic – the method has been thus called BoSG (Boolean Stochastic Generation). In this way, it is possible to randomize the presence of a specific material interdigitated in a uniform matrix. In the building of a geotechnical model it is generally common to discard some stratigraphic data in order to simplify the model itself, assuming that the significance of the results of the modeling procedure would not be affected. With the proposed technique it is possible to quantify the error associated with this simplification. Moreover, it could be used to determine the most significant zones where eventual further investigations and surveys would be more effective to build the geotechnical model of the slope. The commercial software FLAC was used for the 2D and 3D geotechnical model. The distribution of the materials was randomized through a specifically coded MatLab program that automatically generates text files, each of them representing a specific soil configuration. Besides, a routine was designed to automate the computation of FLAC with the different data files in order to maximize the sample number. The methodology is applied with reference to a simplified slope in 2D, a simplified slope in 3D and an actual landslide, namely the Mortisa mudslide (Cortina d’Ampezzo, BL, Italy). However, it could be extended to numerous different cases, especially for hydrogeological analysis and landslide stability assessment, in different geological and geomorphological contexts.