Reduced-order modelling, circuit-level design and SOI fabrication of microelectromechanical resonators

This thesis deals with two important research aspects concerning radio frequency (RF) microresonators and switches. First, a new approach for compact modeling and simulation of these devices is presented. Then, a combined process flow for their simultaneous fabrication on a SOI substrate is proposed. Compact models for microresonators and switches are extracted by applying mathematical model order reduction (MOR) to the devices finite element (FE) description in ANSYS c° . The behaviour of these devices includes forms of nonlinearities. However, an approximation in the creation of the FE model is introduced, which enables the use of linear model order reduction. Microresonators are modeled with the introduction of transducer elements, which allow for direct coupling of the electrical and mechanical domain. The coupled system element matrices are linearized around an operating point and reduced. The resulting macromodel is valid for small signal analysis around the bias point, such as harmonic pre-stressed analysis. This is extremely useful for characterizing the frequency response of resonators. Compact modelling of switches preserves the nonlinearity of the device behaviour. Nonlinear reduced order models are obtained by reducing the number of nonlinearities in the system and handling them as input to the system. In this way, the system can be reduced using linear MOR techniques and nonlinearities are introduced directly in the reduced order model. The reduction of the number of system nonlinearities implies the approximation of all distributed forces in the model with lumped forces. Both for microresonators and switches, a procedure for matrices extraction has been developed so that reduced order models include the effects of electrical and mechanical pre-stress. The extraction process is fast and can be done automatically from ANSYS binary files. The method has been applied for the simulation of several devices both at devices and circuit level. Simulation results have been compared with full model simulations, and, when available, experimental data. Reduced order models have proven to conserve the accuracy of finite element method and to give a good description of the overall device behaviour, despite the introduced approximations. In addition, simulation is very fast, both at device and circuit level. A combined process-flow for the integrated fabrication of microresonators and switches has been defined. For this purpose, two processes that are optimized for the independent fabrication of these devices are merged. The major advantage of this process is the possibility to create on-chip circuit blocks that include both microresonators and switches. An application is, for example, aswitched filter bank for wireless transceiver. The process for microresonators fabrication is characterized by the use of silicon on insulator (SOI) wafers and on a deep reactive ion etching (DRIE) step for the creation of the vibrating structures in single-crystal silicon and the use of a sacrificial oxide layer for the definition of resonator to electrode distance. The fabrication of switches is characterized by the use of two different conductive layers for the definition of the actuation electrodes and by the use of a photoresist as a sacrificial layer for the creation of the suspended structure. Both processes have a gold electroplating step, for the creation of the resonators electrodes, transmission lines and suspended structures. The combined process flow is designed such that it conserves the basic properties of the original processes. Neither the performance of the resonators nor the performance of the switches results affected by the simultaneous fabrication. Moreover, common fabrication steps are shared, which allows for cheaper and faster fabrication.

Biochemistry in healthy and neoplastic human tissues: metabolic alteration revealed by HR-MAS nuclear magnetic resonance spectroscopy

This thesis is focused on the metabolomic study of human cancer tissues by ex vivo High Resolution-Magic Angle Spinning (HR-MAS) nuclear magnetic resonance (NMR) spectroscopy. This new technique allows for the acquisition of spectra directly on intact tissues (biopsy or surgery), and it has become very important for integrated metabonomics studies. The objective is to identify metabolites that can be used as markers for the discrimination of the different types of cancer, for the grading, and for the assessment of the evolution of the tumour. Furthermore, an attempt to recognize metabolites, that although involved in the metabolism of tumoral tissues in low concentration, can be important modulators of neoplastic proliferation, was performed. In addition, NMR data was integrated with statistical techniques in order to obtain semi-quantitative information about the metabolite markers. In the case of gliomas, the NMR study was correlated with gene expression of neoplastic tissues. Chapter 1 begins with a general description of a new “omics” study, the metabolomics. The study of metabolism can contribute significantly to biomedical research and, ultimately, to clinical medical practice. This rapidly developing discipline involves the study of the metabolome: the total repertoire of small molecules present in cells, tissues, organs, and biological fluids. Metabolomic approaches are becoming increasingly popular in disease diagnosis and will play an important role on improving our understanding of cancer mechanism. Chapter 2 addresses in more detail the basis of NMR Spectroscopy, presenting the new HR-MAS NMR tool, that is gaining importance in the examination of tumour tissues, and in the assessment of tumour grade. Some advanced chemometric methods were used in an attempt to enhance the interpretation and quantitative information of the HR-MAS NMR data are and presented in chapter 3. Chemometric methods seem to have a high potential in the study of human diseases, as it permits the extraction of new and relevant information from spectroscopic data, allowing a better interpretation of the results. Chapter 4 reports results obtained from HR-MAS NMR analyses performed on different brain tumours: medulloblastoma, meningioms and gliomas. The medulloblastoma study is a case report of primitive neuroectodermal tumor (PNET) localised in the cerebellar region by Magnetic Resonance Imaging (MRI) in a 3-year-old child. In vivo single voxel 1H MRS shows high specificity in detecting the main metabolic alterations in the primitive cerebellar lesion; which consist of very high amounts of the choline-containing compounds and of very low levels of creatine derivatives and N-acetylaspartate. Ex vivo HR-MAS NMR, performed at 9.4 Tesla on the neoplastic specimen collected during surgery, allows the unambiguous identification of several metabolites giving a more in-depth evaluation of the metabolic pattern of the lesion. The ex vivo HR-MAS NMR spectra show higher detail than that obtained in vivo. In addition, the spectroscopic data appear to correlate with some morphological features of the medulloblastoma. The present study shows that ex vivo HR-MAS 1H NMR is able to strongly improve the clinical possibility of in vivo MRS and can be used in conjunction with in vivo spectroscopy for clinical purposes. Three histological subtypes of meningiomas (meningothelial, fibrous and oncocytic) were analysed both by in vivo and ex vivo MRS experiments. The ex vivo HR-MAS investigations are very helpful for the assignment of the in vivo resonances of human meningiomas and for the validation of the quantification procedure of in vivo MR spectra. By using one- and two dimensional experiments, several metabolites in different histological subtypes of meningiomas, were identified. The spectroscopic data confirmed the presence of the typical metabolites of these benign neoplasms and, at the same time, that meningomas with different morphological characteristics have different metabolic profiles, particularly regarding macromolecules and lipids. The profile of total choline metabolites (tCho) and the expression of the Kennedy pathway genes in biopsies of human gliomas were also investigated using HR-MAS NMR, and microfluidic genomic cards. 1H HR-MAS spectra, allowed the resolution and relative quantification by LCModel of the resonances from choline (Cho), phosphorylcholine (PC) and glycerolphorylcholine (GPC), the three main components of the combined tCho peak observed in gliomas by in vivo 1H MRS spectroscopy. All glioma biopsies depicted an increase in tCho as calculated from the addition of Cho, PC and GPC HR-MAS resonances. However, the increase was constantly derived from augmented GPC in low grade NMR gliomas or increased PC content in the high grade gliomas, respectively. This circumstance allowed the unambiguous discrimination of high and low grade gliomas by 1H HR-MAS, which could not be achieved by calculating the tCho/Cr ratio commonly used by in vivo 1H MR spectroscopy. The expression of the genes involved in choline metabolism was investigated in the same biopsies. The present findings offer a convenient procedure to classify accurately glioma grade using 1H HR-MAS, providing in addition the genetic background for the alterations of choline metabolism observed in high and low gliomas grade. Chapter 5 reports the study on human gastrointestinal tract (stomach and colon) neoplasms. The human healthy gastric mucosa, and the characteristics of the biochemical profile of human gastric adenocarcinoma in comparison with that of healthy gastric mucosa were analyzed using ex vivo HR-MAS NMR. Healthy human mucosa is mainly characterized by the presence of small metabolites (more than 50 identified) and macromolecules. The adenocarcinoma spectra were dominated by the presence of signals due to triglycerides, that are usually very low in healthy gastric mucosa. The use of spin-echo experiments enable us to detect some metabolites in the unhealthy tissues and to determine their variation with respect to the healthy ones. Then, the ex vivo HR-MAS NMR analysis was applied to human gastric tissue, to obtain information on the molecular steps involved in the gastric carcinogenesis. A microscopic investigation was also carried out in order to identify and locate the lipids in the cellular and extra-cellular environments. Correlation of the morphological changes detected by transmission (TEM) and scanning (SEM) electron microscopy, with the metabolic profile of gastric mucosa in healthy, gastric atrophy autoimmune diseases (AAG), Helicobacter pylori-related gastritis and adenocarcinoma subjects, were obtained. These ultrastructural studies of AAG and gastric adenocarcinoma revealed lipid intra- and extra-cellularly accumulation associated with a severe prenecrotic hypoxia and mitochondrial degeneration. A deep insight into the metabolic profile of human healthy and neoplastic colon tissues was gained using ex vivo HR-MAS NMR spectroscopy in combination with multivariate methods: Principal Component Analysis (PCA) and Partial Least Squares Discriminant Analysis (PLS-DA). The NMR spectra of healthy tissues highlight different metabolic profiles with respect to those of neoplastic and microscopically normal colon specimens (these last obtained at least 15 cm far from the adenocarcinoma). Furthermore, metabolic variations are detected not only for neoplastic tissues with different histological diagnosis, but also for those classified identical by histological analysis. These findings suggest that the same subclass of colon carcinoma is characterized, at a certain degree, by metabolic heterogeneity. The statistical multivariate approach applied to the NMR data is crucial in order to find metabolic markers of the neoplastic state of colon tissues, and to correctly classify the samples. Significant different levels of choline containing compounds, taurine and myoinositol, were observed. Chapter 6 deals with the metabolic profile of normal and tumoral renal human tissues obtained by ex vivo HR-MAS NMR. The spectra of human normal cortex and medulla show the presence of differently distributed osmolytes as markers of physiological renal condition. The marked decrease or disappearance of these metabolites and the high lipid content (triglycerides and cholesteryl esters) is typical of clear cell renal carcinoma (RCC), while papillary RCC is characterized by the absence of lipids and very high amounts of taurine. This research is a contribution to the biochemical classification of renal neoplastic pathologies, especially for RCCs, which can be evaluated by in vivo MRS for clinical purposes. Moreover, these data help to gain a better knowledge of the molecular processes envolved in the onset of renal carcinogenesis.

Study of the thermal effects induced by magnetic resonance on endocardial leads: numerical models and experimental validation

Magnetic resonance imaging (MRI) is today precluded to patients bearing active implantable medical devices AIMDs). The great advantages related to this diagnostic modality, together with the increasing number of people benefiting from implantable devices, in particular pacemakers(PM)and carioverter/defibrillators (ICD), is prompting the scientific community the study the possibility to extend MRI also to implanted patients. The MRI induced specific absorption rate (SAR) and the consequent heating of biological tissues is one of the major concerns that makes patients bearing metallic structures contraindicated for MRI scans. To date, both in-vivo and in-vitro studies have demonstrated the potentially dangerous temperature increase caused by the radiofrequency (RF) field generated during MRI procedures in the tissues surrounding thin metallic implants. On the other side, the technical evolution of MRI scanners and of AIMDs together with published data on the lack of adverse events have reopened the interest in this field and suggest that, under given conditions, MRI can be safely performed also in implanted patients. With a better understanding of the hazards of performing MRI scans on implanted patients as well as the development of MRI safe devices, we may soon enter an era where the ability of this imaging modality may be more widely used to assist in the appropriate diagnosis of patients with devices. In this study both experimental measures and numerical analysis were performed. Aim of the study is to systematically investigate the effects of the MRI RF filed on implantable devices and to identify the elements that play a major role in the induced heating. Furthermore, we aimed at developing a realistic numerical model able to simulate the interactions between an RF coil for MRI and biological tissues implanted with a PM, and to predict the induced SAR as a function of the particular path of the PM lead. The methods developed and validated during the PhD program led to the design of an experimental framework for the accurate measure of PM lead heating induced by MRI systems. In addition, numerical models based on Finite-Differences Time-Domain (FDTD) simulations were validated to obtain a general tool for investigating the large number of parameters and factors involved in this complex phenomenon. The results obtained demonstrated that the MRI induced heating on metallic implants is a real risk that represents a contraindication in extending MRI scans also to patient bearing a PM, an ICD, or other thin metallic objects. On the other side, both experimental data and numerical results show that, under particular conditions, MRI procedures might be consider reasonably safe also for an implanted patient. The complexity and the large number of variables involved, make difficult to define a unique set of such conditions: when the benefits of a MRI investigation cannot be obtained using other imaging techniques, the possibility to perform the scan should not be immediately excluded, but some considerations are always needed.

Electrothermal characterization and nonlinear modelling of GaN transistors for telecommunication circuit design

This thesis starts showing the main characteristics and application fields of the AlGaN/GaN HEMT technology, focusing on reliability aspects essentially due to the presence of low frequency dispersive phenomena which limit in several ways the microwave performance of this kind of devices. Based on an equivalent voltage approach, a new low frequency device model is presented where the dynamic nonlinearity of the trapping effect is taken into account for the first time allowing considerable improvements in the prediction of very important quantities for the design of power amplifier such as power added efficiency, dissipated power and internal device temperature. An innovative and low-cost measurement setup for the characterization of the device under low-frequency large-amplitude sinusoidal excitation is also presented. This setup allows the identification of the new low frequency model through suitable procedures explained in detail. In this thesis a new non-invasive empirical method for compact electrothermal modeling and thermal resistance extraction is also described. The new contribution of the proposed approach concerns the non linear dependence of the channel temperature on the dissipated power. This is very important for GaN devices since they are capable of operating at relatively high temperatures with high power densities and the dependence of the thermal resistance on the temperature is quite relevant. Finally a novel method for the device thermal simulation is investigated: based on the analytical solution of the tree-dimensional heat equation, a Visual Basic program has been developed to estimate, in real time, the temperature distribution on the hottest surface of planar multilayer structures. The developed solver is particularly useful for peak temperature estimation at the design stage when critical decisions about circuit design and packaging have to be made. It facilitates the layout optimization and reliability improvement, allowing the correct choice of the device geometry and configuration to achieve the best possible thermal performance.

Modeling and simulation of a synthetic genetic circuit that implements a multicelled behavior in a growing microcolony of E. coli

Synthetic Biology is a relatively new discipline, born at the beginning of the New Millennium, that brings the typical engineering approach (abstraction, modularity and standardization) to biotechnology. These principles aim to tame the extreme complexity of the various components and aid the construction of artificial biological systems with specific functions, usually by means of synthetic genetic circuits implemented in bacteria or simple eukaryotes like yeast. The cell becomes a programmable machine and its low-level programming language is made of strings of DNA. This work was performed in collaboration with researchers of the Department of Electrical Engineering of the University of Washington in Seattle and also with a student of the Corso di Laurea Magistrale in Ingegneria Biomedica at the University of Bologna: Marilisa Cortesi. During the collaboration I contributed to a Synthetic Biology project already started in the Klavins Laboratory. In particular, I modeled and subsequently simulated a synthetic genetic circuit that was ideated for the implementation of a multicelled behavior in a growing bacterial microcolony. In the first chapter the foundations of molecular biology are introduced: structure of the nucleic acids, transcription, translation and methods to regulate gene expression. An introduction to Synthetic Biology completes the section. In the second chapter is described the synthetic genetic circuit that was conceived to make spontaneously emerge, from an isogenic microcolony of bacteria, two different groups of cells, termed leaders and followers. The circuit exploits the intrinsic stochasticity of gene expression and intercellular communication via small molecules to break the symmetry in the phenotype of the microcolony. The four modules of the circuit (coin flipper, sender, receiver and follower) and their interactions are then illustrated. In the third chapter is derived the mathematical representation of the various components of the circuit and the several simplifying assumptions are made explicit. Transcription and translation are modeled as a single step and gene expression is function of the intracellular concentration of the various transcription factors that act on the different promoters of the circuit. A list of the various parameters and a justification for their value closes the chapter. In the fourth chapter are described the main characteristics of the gro simulation environment, developed by the Self Organizing Systems Laboratory of the University of Washington. Then, a sensitivity analysis performed to pinpoint the desirable characteristics of the various genetic components is detailed. The sensitivity analysis makes use of a cost function that is based on the fraction of cells in each one of the different possible states at the end of the simulation and the wanted outcome. Thanks to a particular kind of scatter plot, the parameters are ranked. Starting from an initial condition in which all the parameters assume their nominal value, the ranking suggest which parameter to tune in order to reach the goal. Obtaining a microcolony in which almost all the cells are in the follower state and only a few in the leader state seems to be the most difficult task. A small number of leader cells struggle to produce enough signal to turn the rest of the microcolony in the follower state. It is possible to obtain a microcolony in which the majority of cells are followers by increasing as much as possible the production of signal. Reaching the goal of a microcolony that is split in half between leaders and followers is comparatively easy. The best strategy seems to be increasing slightly the production of the enzyme. To end up with a majority of leaders, instead, it is advisable to increase the basal expression of the coin flipper module. At the end of the chapter, a possible future application of the leader election circuit, the spontaneous formation of spatial patterns in a microcolony, is modeled with the finite state machine formalism. The gro simulations provide insights into the genetic components that are needed to implement the behavior. In particular, since both the examples of pattern formation rely on a local version of Leader Election, a short-range communication system is essential. Moreover, new synthetic components that allow to reliably downregulate the growth rate in specific cells without side effects need to be developed. In the appendix are listed the gro code utilized to simulate the model of the circuit, a script in the Python programming language that was used to split the simulations on a Linux cluster and the Matlab code developed to analyze the data.

Automated Segmentation and Non-Rigid Registration for the Quantitative Evaluation of Myocardial Perfusion from Magnetic Resonance Images

Myocardial perfusion quantification by means of Contrast-Enhanced Cardiac Magnetic Resonance images relies on time consuming frame-by-frame manual tracing of regions of interest. In this Thesis, a novel automated technique for myocardial segmentation and non-rigid registration as a basis for perfusion quantification is presented. The proposed technique is based on three steps: reference frame selection, myocardial segmentation and non-rigid registration. In the first step, the reference frame in which both endo- and epicardial segmentation will be performed is chosen. Endocardial segmentation is achieved by means of a statistical region-based level-set technique followed by a curvature-based regularization motion. Epicardial segmentation is achieved by means of an edge-based level-set technique followed again by a regularization motion. To take into account the changes in position, size and shape of myocardium throughout the sequence due to out of plane respiratory motion, a non-rigid registration algorithm is required. The proposed non-rigid registration scheme consists in a novel multiscale extension of the normalized cross-correlation algorithm in combination with level-set methods. The myocardium is then divided into standard segments. Contrast enhancement curves are computed measuring the mean pixel intensity of each segment over time, and perfusion indices are extracted from each curve. The overall approach has been tested on synthetic and real datasets. For validation purposes, the sequences have been manually traced by an experienced interpreter, and contrast enhancement curves as well as perfusion indices have been computed. Comparisons between automatically extracted and manually obtained contours and enhancement curves showed high inter-technique agreement. Comparisons of perfusion indices computed using both approaches against quantitative coronary angiography and visual interpretation demonstrated that the two technique have similar diagnostic accuracy. In conclusion, the proposed technique allows fast, automated and accurate measurement of intra-myocardial contrast dynamics, and may thus address the strong clinical need for quantitative evaluation of myocardial perfusion.

Measurement of K(892)*0 resonance production in Pb-Pb collisions with the ALICE experiment at the LHC

The analysis of the K(892)*0 resonance production in Pb–Pb collisions at √sNN = 2.76 TeV with the ALICE detector at the LHC is presented. The analysis is motivated by the interest in the measurement of short-lived resonances production that can provide insights on the properties of the medium produced in heavy-ion collisions both during its partonic (Quark-Gluon Plasma) and hadronic phase. This particular analysis exploits particle identification of the ALICE Time-Of-Flight detector. The ALICE experiment is presented, with focus on the performance of the Time-Of-Flight system. The aspects of calibration and data quality controls are discussed in detail, while illustrating the excellent and very stable performance of the system in different collision environments at the LHC. A full analysis of the K*0 resonance production is presented: from the resonance reconstruction to the determination of the efficiency and the systematic uncertainty. The results show that the analysis strategy discussed is a valid tool to measure the K∗0 up to intermediate momenta. Preliminary results on K*0 resonance production at the LHC are presented and confirmed to be a powerful tool to study the physics of ultra-relativistic heavy-ion collisions.

Measurement of k(892)*0 resonance production in p-pb collisions with the alice experiment at the lhc

̀ qui presentato lo studio della produzione della risonanza K∗0 in collisioni p-Pb con l’esperimento ALICE presso LHC. L’elaborato si compone di una introduzione sulla natura del fenomeno studiato: la formazione del Quark Gluon Plasma (QGP), uno stato della materia fortemente interagente ad alte temperatura e densità d’energia. Vengono descritte le segnature studiate ai fini di identificare il suddetto fenomeno, riportando come esempio concreto i risultati sperimentali. Successivamente l’acceleratore di particelle, LHC, e l’esperimento, ALICE, vengono brevemente introdotti. Più in dettaglio ven- gono descritti i rivelatori di ALICE effettivamente usati per l’analisi, a cui sono dedicate sezioni approfondite. Viene infine introdotta l’analisi e le sue motivazioni. Il metodo utilizzato e lo studio degli errori da associare alla misura sono illustrati in ogni loro passo e supportati dai risultati ottenuti. La discussione finale dei risultati include il confronto con i risultati preceden- temente ottenuti da ALICE in collisioni pp e Pb-Pb e da altri esperimenti.

Direct observation of a single proton in a Penning trap

In der vorgelegten Doktorarbeit werden Experimente vorgestellt, die an einem einzelnen Proton in einer Penningfalle durchgeführt worden sind. Die Eigenbewegung eines isoliert gespeicherten, freien Protons konnte elektronisch durch Kopplung an einen Resonanzschwingkreis nachgewiesen werden. Dies stellt eine nicht-destruktive Messung dar, d. h. das Teilchen geht während der Messung nicht verloren. Die freie Zyklotronfrequenz, die aus den drei gemessenen Eigenfrequenzen hervorgeht, ist eine von zwei zur Bestimmung des magnetischen Moments notwendigen Frequenzen. So wird im Gegensatz zu den existierenden Arbeiten eine direkte Bestimmung des g-Faktors ermöglicht. Planung, Entwicklung und Inbetriebnahme des experimentellen Aufbaus wurden im Rahmen dieser Arbeit durchgeführt, womit eine Messgenauigkeit von 10-7 erreicht wurde. Die dabei zu bewältigenden technischen Herausforderungen zur Bestimmung der zweiten Frequenz (der Larmorfrequenz) ergeben sich aus der Kleinheit des magnetischen Moments. Bei dem für diese Messung benötigten Spinzustand des Teilchens handelt es sich um einen internen Freiheitsgrad, der nur über eine Kopplung des magnetischen Moments an die Eigenbewegung bestimmt werden kann. Eine neuartige, hybride Penningfalle wird in dieser Arbeit vorgestellt, die als Quantensprung-Spektrometer die Spininformation auf die Eigenbewegung abbildet. Damit liegt der aus der magnetischen Kopplung resultierende Frequenzunterschied in den beiden Spinzuständen erstmalig in einem elektronisch detektierbaren Bereich.

Advanced schemes for surface plasmon resonance and plasmon-enhanced fluorescence biosensors

Advanced optical biosensor platforms exploiting long range surface plasmons (LRSPs) and responsive N-isopropylacrylamide (NIPAAm) hydrogel binding matrix for the detection of protein and bacterial pathogen analytes were carried out. LRSPs are optical waves that originate from coupling of surface plasmons on the opposite sites of a thin metallic film embedded between two dielectrics with similar refractive indices. LRSPs exhibit orders of magnitude lower damping and more extended profile of field compared to regular surface plasmons (SPs). Their excitation is accompanied with narrow resonance and provides stronger enhancement of electromagnetic field intensity that can advance the sensitivity of surface plasmon resonance (SPR) and surface plasmon-enhanced fluorescence spectroscopy (SPFS) biosensors. Firstly, we investigated thin gold layers deposited on fluoropolymer surface for the excitation of LRSPs. The study indicates that the morphological, optical and electrical properties of gold film can be changed by the surface energy of fluoropolymer and affect the performance of a SPFS biosensor. A photo-crosslinkable NIPAAm hydrogel was grafted to the sensor surface in order to serve as a binding matrix. It was modified with bio-recognition elements (BREs) via amine coupling chemistry and offered the advantage of large binding capacity, stimuli responsive properties and good biocompatibility. Through experimental observations supported by numerical simulations describing diffusion mass transfer and affinity binding of target molecules in the hydrogel, the hydrogel binding matrix thickness, concentration of BREs and the profile of the probing evanescent field was optimized. Hydrogel with a up to micrometer thickness was shown to support additional hydrogel optical waveguide (HOW) mode which was employed for probing affinity binding events in the gel by means of refractometric and fluorescence measurements. These schemes allow to reach limits of detection (LODs) at picomolar and femtomolar levels, respectively. Besides hydrogel based experiments for detection of molecular analytes, long range surface plasmon-enhanced fluorescence spectroscopy (LRSP-FS) was employed for detection of bacterial pathogens. The influence of capture efficiency of bacteria on surfaces and the profile of the probing field on sensor response were investigated. The potential of LRSP-FS with extended evanescent field is demonstrated for detection of pathogenic E. coli O157:H7 on sandwich immunoassays . LOD as low as 6 cfu mL-1 with a detection time of 40 minutes was achieved.rn

In vivo evaluation of the translations of the gleno-humeral joint using Magnetic resonance imaging

Gleno-humeral joint (GHJ) is the most mobile joint of the human body. This is related to theincongr uence between the large humeral head articulating with the much smaller glenoid (ratio 3:1). The GHJ laxity is the ability of the humeral head to be passively translated on the glenoid fossa and, when physiological, it guarantees the normal range of motion of the joint. Three-dimensional GHJ linear displacements have been measured, both in vivo and in vitro by means of different instrumental techniques. In vivo gleno-humeral displacements have been assessed by means of stereophotogrammetry, electromagnetic tracking sensors, and bio-imaging techniques. Both stereophotogrammetric systems and electromagnetic tracking devices, due to the deformation of the soft tissues surrounding the bones, are not capable to accurately assess small displacements, such as gleno-humeral joint translations. The bio-imaging techniques can ensure for an accurate joint kinematic (linear and angular displacement) description, but, due to the radiation exposure, most of these techniques, such as computer tomography or fluoroscopy, are invasive for patients. Among the bioimaging techniques, an alternative which could provide an acceptable level of accuracy and that is innocuous for patients is represented by magnetic resonance imaging (MRI). Unfortunately, only few studies have been conducted for three-dimensional analysis and very limited data is available in situations where preset loads are being applied. The general aim of this doctoral thesis is to develop a non-invasive methodology based on open-MRI for in-vivo evaluation of the gleno-humeral translation components in healthy subjects under the application of external loads.

Investigation of dangling bonds in al2o3 passivated si surface using electron paramagnetic resonance (epr)

Nel presente lavoro di tesi magistrale sono stati depositati e caratterizzati sottili film di ossido di alluminio, Al2O3, (di spessore compreso tra 3-30 nm) su un substrato di FZ-Si drogato p. La deposizione è avvenuta mediante plasma ALD (Atomic Layer Depostion). La tecnica spettroscopica EPR (Electron Paramagnetic Resonance) è stata utilizzata per studiare l’interfaccia Si/Al2O3 con lo scopo di scoprire l’origine della formazione di densità di carica negativa Qf all’interfaccia: tale carica negativa induce una passivazione per effetto di campo ed è quindi la ragione per cui il dielettrico Al2O3 risulta essere un ottimo materiale passivante. Si è deciso di variare alcuni parametri, come lo spessore dello strato di Al2O3, lo spessore dello strato intermedio di ossido di silicio, depositato mediante ossidazione termica (dry thermal oxidation), e la superficie del substrato di silicio. Sono stati realizzati cinque differenti gruppi di campioni: per ciascuno di essi sono state impiegate varie tecniche di caratterizzazione, come la QSSPC (Quasi Steady State Photoconuctance) e la tecnica di spettroscopia ottica SE (spettroscopic ellipsometry). Per ogni gruppo sono stati riportati gli spettri EPR ottenuti ed i rispettivi fit, da cui è stato possibile risalire ai fattori giromagnetici di spin g, riportati in tabelle con le loro possibili attribuzioni. E’ stato dimostrato che la presenza di uno strato di ossido di silicio tra il substrato di silicio e lo strato di ossido di alluminio risulta essere fondamentale per la formazione di densità di carica negativa all’interfaccia: aumentando lo spessore dello strato di SiOx (nel range 1-30 nm) si assiste ad una diminuzione di carica negativa Qf. Analizzando gli spettri EPR, è stato possibile concludere che all’interfaccia Si/Al2O3 sono presenti difetti caratteristici dell’interfaccia Si/SiOx. Le nostre osservazioni, dunque, sono coerenti con la formazione di uno strato di ossido di silicio tra Si e Al2O3.

Silicon Photonics Integrated Circuits for Flexible Optical Systems

This dissertation deals with the design and the characterization of novel reconfigurable silicon-on-insulator (SOI) devices to filter and route optical signals on-chip. Design is carried out through circuit simulations based on basic circuit elements (Building Blocks, BBs) in order to prove the feasibility of an approach allowing to move the design of Photonic Integrated Circuits (PICs) toward the system level. CMOS compatibility and large integration scale make SOI one of the most promising material to realize PICs. The concepts of generic foundry and BB based circuit simulations for the design are emerging as a solution to reduce the costs and increase the circuit complexity. To validate the BB based approach, the development of some of the most important BBs is performed first. A novel tunable coupler is also presented and it is demonstrated to be a valuable alternative to the known solutions. Two novel multi-element PICs are then analysed: a narrow linewidth single mode resonator and a passband filter with widely tunable bandwidth. Extensive circuit simulations are carried out to determine their performance, taking into account fabrication tolerances. The first PIC is based on two Grating Assisted Couplers in a ring resonator (RR) configuration. It is shown that a trade-off between performance, resonance bandwidth and device footprint has to be performed. The device could be employed to realize reconfigurable add-drop de/multiplexers. Sensitivity with respect to fabrication tolerances and spurious effects is however observed. The second PIC is based on an unbalanced Mach-Zehnder interferometer loaded with two RRs. Overall good performance and robustness to fabrication tolerances and nonlinear effects have confirmed its applicability for the realization of flexible optical systems. Simulated and measured devices behaviour is shown to be in agreement thus demonstrating the viability of a BB based approach to the design of complex PICs.

Valorisation of organic waste: new developments from proton nuclear magnetic resonance characterization

The last half-century has seen a continuing population and consumption growth, increasing the competition for land, water and energy. The solution can be found in the new sustainability theories, such as the industrial symbiosis and the zero waste objective. Reducing, reusing and recycling are challenges that the whole world have to consider. This is especially important for organic waste, whose reusing gives interesting results in terms of energy release. Before reusing, organic waste needs a deeper characterization. The non-destructive and non-invasive features of both Nuclear Magnetic Resonance (NMR) relaxometry and imaging (MRI) make them optimal candidates to reach such characterization. In this research, NMR techniques demonstrated to be innovative technologies, but an important work on the hardware and software of the NMR LAGIRN laboratory was initially done, creating new experimental procedures to analyse organic waste samples. The first results came from soil-organic matter interactions. Remediated soils properties were described in function of the organic carbon content, proving the importance of limiting the addition of further organic matter to not inhibit soil processes as nutrients transport. Moreover NMR relaxation times and the signal amplitude of a compost sample, over time, showed that the organic matter degradation of compost is a complex process that involves a number of degradation kinetics, as a function of the mix of waste. Local degradation processes were studied with enhanced quantitative relaxation technique that combines NMR and MRI. The development of this research has finally led to the study of waste before it becomes waste. Since a lot of food is lost when it is still edible, new NMR experiments studied the efficiency of conservation and valorisation processes: apple dehydration, meat preservation and bio-oils production. All these results proved the readiness of NMR for quality controls on a huge kind of organic residues and waste.

Studies of degradation of organic solar cell materials using electrical scanning probe microscopy

Intense research is being done in the field of organic photovoltaics in order to synthesize low band-gap organic molecules. These molecules are electron donors which feature in combination with acceptor molecules, typically fullerene derivarntives, forming an active blend. This active blend has phase separated bicontinuous morphology on a nanometer scale. The highest recorded power conversionrnefficiencies for such cells have been 10.6%. Organic semiconductors differ from inorganic ones due to the presence of tightly bonded excitons (electron-hole pairs)resulting from their low dielectric constant (εr ≈2-4). An additional driving force is required to separate such Frenkel excitons since their binding energy (0.3-1 eV) is too large to be dissociated by an electric field alone. This additional driving force arises from the energy difference between the lowest unoccupied molecular orbital (LUMO) of the donor and the acceptor materials. Moreover, the efficiency of the cells also depends on the difference between the highest occupied molecular orbital (HOMO) of the donor and LUMO of the acceptor. Therefore, a precise control and estimation of these energy levels are required. Furthermore any external influences that change the energy levels will cause a degradation of the power conversion efficiency of organic solar cell materials. In particular, the role of photo-induced degradation on the morphology and electrical performance is a major contribution to degradation and needs to be understood on a nanometer scale. Scanning Probe Microscopy (SPM) offers the resolution to image the nanometer scale bicontinuous morphology. In addition SPM can be operated to measure the local contact potential difference (CPD) of materials from which energy levels in the materials can be derived. Thus SPM is an unique method for the characterization of surface morphology, potential changes and conductivity changes under operating conditions. In the present work, I describe investigations of organic photovoltaic materials upon photo-oxidation which is one of the major causes of degradation of these solar cell materials. SPM, Nuclear Magnetic Resonance (NMR) and UV-Vis spectroscopy studies allowed me to identify the chemical reactions occurring inside the active layer upon photo-oxidation. From the measured data, it was possible to deduce the energy levels and explain the various shifts which gave a better understanding of the physics of the device. In addition, I was able to quantify the degradation by correlating the local changes in the CPD and conductivity to the device characteristics, i.e., open circuit voltage and short circuit current. Furthermore, time-resolved electrostatic force microscopy (tr-EFM) allowed us to probe dynamic processes like the charging rate of the individual donor and acceptor domains within the active blend. Upon photo-oxidation, it was observed, that the acceptor molecules got oxidized first preventing the donor polymer from degrading. Work functions of electrodes can be tailored by modifying the interface with monomolecular thin layers of molecules which are made by a chemical reaction in liquids. These modifications in the work function are particularly attractive for opto-electronic devices whose performance depends on the band alignment between the electrodes and the active material. In order to measure the shift in work function on a nanometer scale, I used KPFM in situ, which means in liquids, to follow changes in the work function of Au upon hexadecanethiol adsorption from decane. All the above investigations give us a better understanding of the photo-degradation processes of the active material at the nanoscale. Also, a method to compare various new materials used for organic solar cells for stability is proposed which eliminates the requirement to make fully functional devices saving time and additional engineering efforts.