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.

Interconnection systems for highly integrated computation devices

The sustained demand for faster,more powerful chips has beenmet by the availability of chip manufacturing processes allowing for the integration of increasing numbers of computation units onto a single die. The resulting outcome, especially in the embedded domain, has often been called SYSTEM-ON-CHIP (SOC) or MULTI-PROCESSOR SYSTEM-ON-CHIP (MPSOC). MPSoC design brings to the foreground a large number of challenges, one of the most prominent of which is the design of the chip interconnection. With a number of on-chip blocks presently ranging in the tens, and quickly approaching the hundreds, the novel issue of how to best provide on-chip communication resources is clearly felt. NETWORKS-ON-CHIPS (NOCS) are the most comprehensive and scalable answer to this design concern. By bringing large-scale networking concepts to the on-chip domain, they guarantee a structured answer to present and future communication requirements. The point-to-point connection and packet switching paradigms they involve are also of great help in minimizing wiring overhead and physical routing issues. However, as with any technology of recent inception, NoC design is still an evolving discipline. Several main areas of interest require deep investigation for NoCs to become viable solutions: • The design of the NoC architecture needs to strike the best tradeoff among performance, features and the tight area and power constraints of the on-chip domain. • Simulation and verification infrastructure must be put in place to explore, validate and optimize the NoC performance. • NoCs offer a huge design space, thanks to their extreme customizability in terms of topology and architectural parameters. Design tools are needed to prune this space and pick the best solutions. • Even more so given their global, distributed nature, it is essential to evaluate the physical implementation of NoCs to evaluate their suitability for next-generation designs and their area and power costs. This dissertation focuses on all of the above points, by describing a NoC architectural implementation called ×pipes; a NoC simulation environment within a cycle-accurate MPSoC emulator called MPARM; a NoC design flow consisting of a front-end tool for optimal NoC instantiation, called SunFloor, and a set of back-end facilities for the study of NoC physical implementations. This dissertation proves the viability of NoCs for current and upcoming designs, by outlining their advantages (alongwith a fewtradeoffs) and by providing a full NoC implementation framework. It also presents some examples of additional extensions of NoCs, allowing e.g. for increased fault tolerance, and outlines where NoCsmay find further application scenarios, such as in stacked chips.

Luminescent Systems for Genomics and Proteomics

The present PhD project was focused on the development of new tools and methods for luminescence-based techniques. In particular, the ultimate goal was to present substantial improvements to the currently available technologies for both research and diagnostic in the fields of biology, proteomics and genomics. Different aspects and problems were investigated, requiring different strategies and approaches. The whole work was thus divided into separate chapters, each based on the study of one specific aspect of luminescence: Chemiluminescence, Fluorescence and Electrochemiluminescence. CHAPTER 1, Chemiluminescence The work on luminol-enhancer solution lead to a new luminol solution formulation with 1 order of magnitude lower detection limit for HRP. This technology was patented with Cyanagen brand and is now sold worldwide for Western Blot and ELISA applications. CHAPTER 2, Fluorescescence The work on dyed-doped silica nanoparticles is marking a new milestone in the development of nanotechnologies for biological applications. While the project is still in progress, preliminary studies on model structures are leading to very promising results. The improved brightness of these nano-sized objects, their simple synthesis and handling, their low toxicity will soon turn them, we strongly believe, into a new generation of fluorescent labels for many applications. CHAPTER 3, Electrochemiluminescence The work on electrochemiluminescence produced interesting results that can potentially turn into great improvements from an analytical point of view. Ru(bpy)3 derivatives were employed both for on-chip microarray (Chapter 3.1) and for microscopic imaging applications (Chapter 3.2). The development of these new techniques is still under investigation, but the obtained results confirm the possibility to achieve the final goal. Furthermore the development of new ECL-active species (Chapter 3.3, 3.4, 3.5) and their use in these applications can significantly improve overall performances, thus helping to spread ECL as powerful analytical tool for routinary techniques. To conclude, the results obtained are of strong value to largely increase the sensitivity of luminescence techniques, thus fulfilling the expectation we had at the beginning of this research work.

Hybrid Methods for Resource Allocation and Scheduling Problems in Deterministic and Stochastic Environments

This work presents exact, hybrid algorithms for mixed resource Allocation and Scheduling problems; in general terms, those consist into assigning over time finite capacity resources to a set of precedence connected activities. The proposed methods have broad applicability, but are mainly motivated by applications in the field of Embedded System Design. In particular, high-performance embedded computing recently witnessed the shift from single CPU platforms with application-specific accelerators to programmable Multi Processor Systems-on-Chip (MPSoCs). Those allow higher flexibility, real time performance and low energy consumption, but the programmer must be able to effectively exploit the platform parallelism. This raises interest in the development of algorithmic techniques to be embedded in CAD tools; in particular, given a specific application and platform, the objective if to perform optimal allocation of hardware resources and to compute an execution schedule. On this regard, since embedded systems tend to run the same set of applications for their entire lifetime, off-line, exact optimization approaches are particularly appealing. Quite surprisingly, the use of exact algorithms has not been well investigated so far; this is in part motivated by the complexity of integrated allocation and scheduling, setting tough challenges for ``pure'' combinatorial methods. The use of hybrid CP/OR approaches presents the opportunity to exploit mutual advantages of different methods, while compensating for their weaknesses. In this work, we consider in first instance an Allocation and Scheduling problem over the Cell BE processor by Sony, IBM and Toshiba; we propose three different solution methods, leveraging decomposition, cut generation and heuristic guided search. Next, we face Allocation and Scheduling of so-called Conditional Task Graphs, explicitly accounting for branches with outcome not known at design time; we extend the CP scheduling framework to effectively deal with the introduced stochastic elements. Finally, we address Allocation and Scheduling with uncertain, bounded execution times, via conflict based tree search; we introduce a simple and flexible time model to take into account duration variability and provide an efficient conflict detection method. The proposed approaches achieve good results on practical size problem, thus demonstrating the use of exact approaches for system design is feasible. Furthermore, the developed techniques bring significant contributions to combinatorial optimization methods.

Structural and functional analysis of centromeric chromatin

Animal neocentromeres are defined as ectopic centromeres that have formed in non-centromeric locations and avoid some of the features, like the DNA satellite sequence, that normally characterize canonical centromeres. Despite this, they are stable functional centromeres inherited through generations. The only existence of neocentromeres provide convincing evidence that centromere specification is determined by epigenetic rather than sequence-specific mechanisms. For all this reasons, we used them as simplified models to investigate the molecular mechanisms that underlay the formation and the maintenance of functional centromeres. We collected human cell lines carrying neocentromeres in different positions. To investigate the region involved in the process at the DNA sequence level we applied a recent technology that integrates Chromatin Immuno-Precipitation and DNA microarrays (ChIP-on-chip) using rabbit polyclonal antibodies directed against CENP-A or CENP-C human centromeric proteins. These DNA binding-proteins are required for kinetochore function and are exclusively targeted to functional centromeres. Thus, the immunoprecipitation of DNA bound by these proteins allows the isolation of centromeric sequences, including those of the neocentromeres. Neocentromeres arise even in protein-coding genes region. We further analyzed if the increased scaffold attachment sites and the corresponding tighter chromatin of the region involved in the neocentromerization process still were permissive or not to transcription of within encoded genes. Centromere repositioning is a phenomenon in which a neocentromere arisen without altering the gene order, followed by the inactivation of the canonical centromere, becomes fixed in population. It is a process of chromosome rearrangement fundamental in evolution, at the bases of speciation. The repeat-free region where the neocentromere initially forms, progressively acquires extended arrays of satellite tandem repeats that may contribute to its functional stability. In this view our attention focalized to the repositioned horse ECA11 centromere. ChIP-on-chip analysis was used to define the region involved and SNPs studies, mapping within the region involved into neocentromerization, were carried on. We have been able to describe the structural polymorphism of the chromosome 11 centromeric domain of Caballus population. That polymorphism was seen even between homologues chromosome of the same cells. That discovery was the first described ever. Genomic plasticity had a fundamental role in evolution. Centromeres are not static packaged region of genomes. The key question that fascinates biologists is to understand how that centromere plasticity could be combined to the stability and maintenance of centromeric function. Starting from the epigenetic point of view that underlies centromere formation, we decided to analyze the RNA content of centromeric chromatin. RNA, as well as secondary chemically modifications that involve both histones and DNA, represents a good candidate to guide somehow the centromere formation and maintenance. Many observations suggest that transcription of centromeric DNA or of other non-coding RNAs could affect centromere formation. To date has been no thorough investigation addressing the identity of the chromatin-associated RNAs (CARs) on a global scale. This prompted us to develop techniques to identify CARs in a genome-wide approach using high-throughput genomic platforms. The future goal of this study will be to focalize the attention on what strictly happens specifically inside centromere chromatin.

Transcriptional dynamics of the human DMD locus

The human DMD locus encodes dystrophin protein. Absence or reduced levels of dystrophin (DMD or BMD phenotype, respectively) lead to progressive muscle wasting. Little is known about the complex coordination of dystrophin expression and its transcriptional regulation is a field of intense interest. In this work we found that DMD locus harbours multiple long non coding RNAs which orchestrate and control transcription of muscle dystrophin mRNA isoforms. These lncRNAs are tissue-specific and highly expressed during myogenesis, suggesting a possible role in tissue-specific expression of DMD gene isoforms. Their forced ectopic expression in human muscle and neuronal cells leads to a specific and negative regulation of endogenous dystrophin full lenght isoforms. An intriguing aspect regarding the transcription of the DMD locus is the gene size (2.4Mb). The mechanism that ensures the complete synthesis of the primary transcript and the coordinated splicing of 79 exons is still completely unknown. By ChIP-on-chip analyses, we discovered novel regions never been involved before in the transcription regulation of the DMD locus. Specifically, we observed enrichments for Pol II, P-Ser2, P-Ser5, Ac-H3 and 2Me-H3K4 in an intronic region of 3Kb (approximately 21Kb) downstream of the end of DMD exon 52 and in a region of 4Kb spanning the DMD exon 62. Interestingly, this latter region and the TSS of Dp71 are strongly marked by 3Me-H3K36, an histone modification associated with the regulation of splicing process. Furthermore, we also observed strong presence of open chromatin marks (Ac-H3 and 2Me-H3K4) around intron 34 and the exon 45 without presence of RNA pol II. We speculate that these two regions may exert an enhancer-like function on Dp427m promoter, although further investigations are necessary. Finally, we investigated the nuclear-cytoplasmic compartmentalization of the muscular dystrophin mRNA and, specifically, we verified whether the exon skipping therapy could influence its cellular distribution.

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.

Chemiluminescence DNA-based Nanotechnologies for Bioanalytical Applications

DNA as powerful building molecule, is widely used for the assembly of molecular structures and dynamic molecular devices with different potential applications, ranging from synthetic biology to diagnostics. The feature of sequence programmability, which makes it possible to predict how single stranded DNA molecules fold and interact with one another, allowed the development of spatiotemporally controlled nanostructures and the engineering of supramolecular devices. The first part of this thesis addresses the development of an integrated chemiluminescence (CL)-based lab-on-chip sensor for detection of Adenosine-5-triphosphate (ATP) life biomarker in extra-terrestrial environments.Subsequently, we investigated whether it is possible to study the interaction and the recognition between biomolecules and their targets, mimicking the intracellular environment in terms of crowding, confinement and compartmentalization. To this purpose, we developed a split G-quadruplex DNAzyme platform for the chemiluminescent and quantitative detection of antibodies based on antibody-induced co-localization proximity mechanism in which a split G-quadruplex DNAzyme is led to reassemble into the functional native G-quadruplex conformation as the effect of a guided spatial nanoconfinement.The following part of this thesis aims at developing chemiluminescent nanoparticles for bioimaging and photodynamic therapy applications.In chapter5 a realistic and accurate evaluation of the potentiality of electrochemistry and chemiluminescence (CL) for biosensors development (i.e., is it better to “measure an electron or a photon”?), has been achieved.In chapter 6 the emission anisotropy phenomenon for an emitting dipole bound to the interface between two media with different refractive index has been investigated for chemiluminescence detection.

Chemiluminescence – based bioanalytical devices for astrobiological, food safety and clinical applications

At the intersection of biology, chemistry, and engineering, biosensors are a multidisciplinary innovation that provide a cost-effective alternative to traditional laboratory techniques. Due to their advantages, biosensors are used in medical diagnostics, environmental monitoring, food safety and many other fields. The first part of the thesis is concerned with learning the state of the art of paper-based immunosensors with bioluminescent (BL) and chemiluminescent (CL) detection. The use of biospecific assays combined with CL detection and paper-based technology offers an optimal approach to creating analytical tools for on-site applications and we have focused on the specific areas that need to be considered more in order to ensure a future practical implementation of these methods in routine analyses. The subsequent part of the thesis addresses the development of an autonomous lab-on-chip platform for performing chemiluminescent-based bioassays in space environment, exploiting a CubeSat platform for astrobiological investigations. An origami-inspired microfluidic paper-based analytical device has been developed with the purpose of assesses its performance in space and to evaluate its functionality and the resilience of the (bio)molecules when exposed to a radiation-rich environment. Subsequently, we designed a paper-based assay to detect traces of ovalbumin in food samples, creating a user-friendly immunosensing platform. To this purpose, we developed an origami device that exploits a competitive immunoassay coupled with chemiluminescence detection and magnetic microbeads used to immobilize ovalbumin on paper. Finally, with the aim of exploring the use of biomimetic materials, an hydrogel-based chemiluminescence biosensor for the detection of H2O2 and glucose was developed. A guanosine hydrogel was prepared and loaded with luminol and hemin, miming a DNAzyme activity. Subsequently, the hydrogel was modified by incorporating glucose oxidase enzyme to enable glucose biosensing. The emitted photons were detected using a portable device equipped with a smartphone's CMOS (complementary metal oxide semiconductor) camera for CL emission detection.

CMoS lab-on-a-chip devices for individual cell biology

The development of microlectronic lab-on-a-chip devices (LOACs) can now be pursued thanks to the continous advances in silicon technology. LOACs are miniaturized devices whose aim is to perform in a more efficient way specific chemical or biological analysis protocols which are usually carried out with traditional laboratory equipment. In this application area, CMOS technology has the potential to integrate LOAC functionalities for cell biology applications in single chips, e.g. sensors, actuators, signal conditioning and processing circuits. In this work, after a review of the state of the art, the development of a CMOS prototype chip for individual cell manipulation and detection based on dielectrophoresis will be presented. Issues related to the embedded optical and capacitive detection of cells will be discussed together with the main experimental results obtained in manipulation and detection of living cells and microparticles.

An Input-Process-Output Approach to Interorganizational Teams: The Influence of Work Group Diversity, Trust and Shared Leadership on Communication Network and Team Outputs.

The market’s challenges bring firms to collaborate with other organizations in order to create Joint Ventures, Alliances and Consortia that are defined as “Interorganizational Networks” (IONs) (Provan, Fish and Sydow; 2007). Some of these IONs are managed through a shared partecipant governance (Provan and Kenis, 2008): a team composed by entrepreneurs and/or directors of each firm of an ION. The research is focused on these kind of management teams and it is based on an input-process-output model: some input variables (work group’s diversity, intra-team's friendship network density) have a direct influence on the process (team identification, shared leadership, interorganizational trust, team trust and intra-team's communication network density), which influence some team outputs, individual innovation behaviors and team effectiveness (team performance, work group satisfaction and ION affective commitment). Data was collected on a sample of 101 entrepreneurs grouped in 28 ION’s government teams and the research hypotheses are tested trough the path analysis and the multilevel models. As expected trust in team and shared leadership are positively and directly related to team effectiveness while team identification and interorganizational trust are indirectly related to the team outputs. The friendship network density among the team’s members has got positive effects on the trust in team and on the communication network density, and also, through the communication network density it improves the level of the teammates ION affective commitment. The shared leadership and its effects on the team effectiveness are fostered from higher level of team identification and weakened from higher level of work group diversity, specifically gender diversity. Finally, the communication network density and shared leadership at the individual level are related to the frequency of individual innovative behaviors. The dissertation’s results give a wider and more precise indication about the management of interfirm network through “shared” form of governance.