Characterization of multiple reflections and phase space properties for a periodically corrugated waveguide

Dynamical properties for a beam light inside a sinusoidally corrugated waveguide are discussed in this paper. The beam is confined inside two-mirrors: one is flat and the other one is sinusoidally corrugated. The evolution of the system is described by the use of a two-dimensional and nonlinear mapping. The phase space of the system is of mixed type therefore exhibiting a large chaotic sea, periodic islands and invariant KAM curves. A careful discussion of the numerical method to solve the transcendental equations of the mapping is given. We characterize the probability of observing successive reflections of the light by the corrugated mirror and show that it is scaling invariant with respect to the amplitude of the corrugation. Average properties of the chaotic sea are also described by the use of scaling arguments.

A theoretical contribution characterizing a potentially new molecular species: MgAs

A new molecular species, MgAs, is investigated theoretically for the first time at the CASSCF/MRCI level using quintuple-zeta quality basis sets. Potential energy curves for the lowest-lying electronic states are presented as well as the associated spectroscopic constants. Dipole and transition moment functions for selected states complement this characterization. Estimates of transition probabilities and radiative life-times for the most important transitions are also reported. The effect of spin-orbit interactions is clearly reflected on the potential energy curves. Comparisons with BeAs, BeN, and BeP are made where pertinent. (C) 2011 Elsevier B.V. All rights reserved.

Theoretical study of the XP3 (X = Al, B, Ga) clusters

The lowest singlet and triplet states of AlP3, GaP3 and BP3 molecules with C-s, C-2v and C-3v symmetries were characterized using the B3LYP functional and the aug-cc-pVTZ and aug-cc-pVQZ correlated consistent basis sets. Geometrical parameters and vibrational frequencies were calculated and compared to existent experimental and theoretical data. Relative energies were obtained with single point CCSD(T) calculations using the aug-cc-pVTZ, aug-cc-pVQZ and aug-cc-pV5Z basis sets, and then extrapolating to the complete basis set (CBS) limit. (C) 2011 Elsevier B.V. All rights reserved.

Bilipid membrane phase characterization by reflectance anisotropy spectroscopy (RAS)

In this work we propose the use of experimental and theoretical reflectance anisotropy spectra (RAS) as a new tool to identify structural and dynamical aspects of the bilipid membrane and its various constituent molecules. The role of geometric details at the atomic level and macroscopic quantities, such as the membrane curvature and tilt for the different gel phases, in the theoretical RAS spectra (using Kohn-Sham density functional theory (KS-DFT)) are presented. Then the results are compared to the experimentally measured spectra taken from other techniques.

Bilipid Membrane Phase Characterization by Reflectance Anisotropy Spectroscopy (RAS)

In this work we propose the use of experimental and theoretical reflectance anisotropy spectra (RAS) as a new tool to identify structural and dynamical aspects of the bilipid membrane and its various constituent molecules. The role of geometric details at the atomic level and macroscopic quantities, such as the membrane curvature and tilt for the different gel phases, in the theoretical RAS spectra (using Kohn-Sham density functional theory (KS-DFT)) are presented. Then the results are compared to the experimentally measured spectra taken from other techniques.

Synthesis, multiscale-multiphase characterization and applications of thiophene-based biohybrids

Biohybrid derivatives of π-conjugated materials are emerging as powerful tools to study biological events through the (opto)electronic variations of the π-conjugated moieties, as well as to direct and govern the self-assembly properties of the organic materials through the organization principles of the bio component. So far, very few examples of thiophene-based biohybrids have been reported. The aim of this Ph. D thesis has been the development of oligothiophene-oligonucleotide hybrid derivatives as tools, on one side, to detect DNA hybridisation events and, on the other, as model compounds to investigate thiophene-nucleobase interactions in the solid state. To obtain oligothiophene bioconjugates with the required high level of purity, we first developed new synthetic ecofriendly protocols for the synthesis of thiophene oligomers. Our innovative heterogeneous Suzuki coupling methodology, carried out in EtOH/water or isopropanol under microwave irradiation, allowed us to obtain alkyl substituted oligothiophenes and thiophene based co-oligomers in high yields and very short reaction times, free from residual metals and with improved film forming properties. These methodologies were subsequently applied in the synthesis of oligothiophene-oligonucleotide conjugates. Oligothiophene-5-labeled deoxyuridines were synthesized and incorporated into 19-meric oligonucletide sequences. We showed that the oligothiophene-labeled oligonucletide sequences obtained can be used as probes to detect a single nucleotide polymorphism (SNP) in complementary DNA target sequences. In fact, all the probes showed marked variations in emission intensity upon hybridization with a complementary target sequence. The observed variations in emitted light were comparable or even superior to those reported in similar studies, showing that the biohybrids can potentially be useful to develop biosensors for the detection of DNA mismatches. Finally, water-soluble, photoluminescent and electroactive dinucleotide-hybrid derivatives of quaterthiophene and quinquethiophene were synthesized. By means of a combination of spectroscopy and microscopy techniques, electrical characterizations, microfluidic measurements and theoretical calculations, we were able to demonstrate that the self-assembly modalities of the biohybrids in thin films are driven by the interplay of intra and intermolecular interactions in which the π-stacking between the oligothiophene and nucleotide bases plays a major role.

Stochastic models and dynamic measures for the characterization of bistable circuits

During the last few years, a great deal of interest has risen concerning the applications of stochastic methods to several biochemical and biological phenomena. Phenomena like gene expression, cellular memory, bet-hedging strategy in bacterial growth and many others, cannot be described by continuous stochastic models due to their intrinsic discreteness and randomness. In this thesis I have used the Chemical Master Equation (CME) technique to modelize some feedback cycles and analyzing their properties, including experimental data. In the first part of this work, the effect of stochastic stability is discussed on a toy model of the genetic switch that triggers the cellular division, which malfunctioning is known to be one of the hallmarks of cancer. The second system I have worked on is the so-called futile cycle, a closed cycle of two enzymatic reactions that adds and removes a chemical compound, called phosphate group, to a specific substrate. I have thus investigated how adding noise to the enzyme (that is usually in the order of few hundred molecules) modifies the probability of observing a specific number of phosphorylated substrate molecules, and confirmed theoretical predictions with numerical simulations. In the third part the results of the study of a chain of multiple phosphorylation-dephosphorylation cycles will be presented. We will discuss an approximation method for the exact solution in the bidimensional case and the relationship that this method has with the thermodynamic properties of the system, which is an open system far from equilibrium.In the last section the agreement between the theoretical prediction of the total protein quantity in a mouse cells population and the observed quantity will be shown, measured via fluorescence microscopy.

Electrosynthesis and characterization of structured catalysts

In this research work the optimization of the electrochemical system of LDHs as catalytic precursors on FeCrAlY foams was carried out. Preliminary sintheses were performed on flat surfaces in order to easily characterize the deposited material. From the study of pH evolution vs time at different cathodic potentials applied to a Pt electrode, the theoretical best working conditions for the synthesis of single hydroxides and LDH compounds was achieved. In order to define the optimal potential for the synthesis of a particular LDH compound, the collected data were compared with the interval of precipitation determined by titration with NaOH. However, the characterization of the deposited material on Pt surfaces did not confirm the deposition of a pure and homogeneous LDH phase during the synthesis. Instead a sequential deposition linked to the pH of precipitation of the involved elements is observed. The same behavior was observed during the synthesis of the RhMgAl LDH on FeCrAlY foam as catalytic precursor. Several parameters were considered in order to optimize the synthesis.. The development of electrochemical cells with different feature, such as the counter electrode dimensions or the contact between the foam and the potentiostat, had been carried out in order to obtain a better coating of the foam. The influence of the initial pH of the electrolyte solution, of the applied potential, of the composition of the electrolytic solution were investigated in order to improve a better coating of the catalyst support. Catalytic tests were performed after the calcination of the deposited foam for the CPO and SR reactions, showing an improve of performances along with optimization of the precursors synthesis conditions.

Design, Synthesis and Characterization of N-Containing Organic Compounds

The needed of new intermediates/products for screening in the fields of drug discovery and material science is the driving force behind the development of new methodologies and technologies. Organic scaffolds are privileged targets for this scouting. Among them a priority place must be attributed to those including nitrogen functionalities in their scaffolds. It comes out that new methodologies, allowing the introduction of the nitrogen atom for the synthesis of an established target or for the curiosity driven researches, will always be welcome. The target of this PhD Thesis’ work is framed within this goal. Accordingly, Chapter 1 reports the preparation of new N-Heteroarylmethyl 3-carboxy-5-hydroxy piperidine scaffold, as potential and selective α-glucosidase inhibitors. The proposed reversible uncompetitive mechanism of inhibition makes them attractive as interesting candidate for drug development. Chapter 2 is more environmentally method-driven research. Eco-friendly studies on the synthesis of enantiomerically pure 1,4-dihydropyridines using “solid” ammonia (magnesium nitride) is reported via classical Hantzch method. Chapter 3 and Chapter 4 may be targeted as the core of the Thesis’s research work. Chapter 3 reports the studies addressed to the synthesis of N-containing heterocycles by using N-trialkylsilylimine/hetero-Diels–Alder (HAD) approach. New eco-friendly methodology as MAOS (Microwave Assisted Organic Synthesis) has been used as witness of our interest to a sustainable chemistry. Theoretical calculations were adopted to fully clarify the reaction mechanism. Chapter 4 is dedicated to picture the most recent studies performed on the application of N-Metallo-ketene imines (metallo= Si, Sn, Al), relatively new intermediates which are becoming very popular, in the preparation of highly functionalized N-containing derivatives, accordingly to the Thesis’ target. Derivatives obtained are designed in such a way that they could be of interest in the field of drug and new material chemistry.

Characterization of fold-related fractures in the carbonate rocks of the Cingoli anticline, northern Apennines, Italy

Thrust fault-related folds in carbonate rocks are characterized by deformation accommodated by different structures, such as joints, faults, pressure solution seams, and deformation bands. Defining the development of fracture systems related to the folding process is significant both for theoretical and practical purposes. Fracture systems are useful constrains in order to understand the kinematical evolution of the fold. Furthermore, understanding the relationships between folding and fracturing provides a noteworthy contribution for reconstructing the geodynamic and the structural evolution of the studied area. Moreover, as fold-related fractures influence fluid flow through rocks, fracture systems are relevant for energy production (geothermal studies, methane and CO2 , storage and hydrocarbon exploration), environmental and social issues (pollutant distribution, aquifer characterization). The PhD project shows results of a study carried out in a multilayer carbonate anticline characterized by different mechanical properties. The aim of this study is to understand the factors which influence the fracture formation and to define their temporal sequence during the folding process. The studied are is located in the Cingoli anticline (Northern Apennines), which is characterized by a pelagic multilayer characterized by sequences with different mechanical stratigraphies. A multi-scale analysis has been made in several outcrops located in different structural positions. This project shows that the conceptual sketches proposed in literature and the strain distribution models outline well the geometrical orientation of most of the set of fractures observed in the Cingoli anticline. On the other hand, the present work suggests the relevance of the mechanical stratigraphy in particular controlling the type of fractures formed (e.g. pressure solution seams, joints or shear fractures) and their subsequent evolution. Through a multi-scale analysis, and on the basis of the temporal relationship between fracture sets and their orientation respect layering, I also suggest a conceptual model for fracture systems formation.

Development and characterization of micromachined devices for separation techniques

Nowadays microfluidic is becoming an important technology in many chemical and biological processes and analysis applications. The potential to replace large-scale conventional laboratory instrumentation with miniaturized and self-contained systems, (called lab-on-a-chip (LOC) or point-of-care-testing (POCT)), offers a variety of advantages such as low reagent consumption, faster analysis speeds, and the capability of operating in a massively parallel scale in order to achieve high-throughput. Micro-electro-mechanical-systems (MEMS) technologies enable both the fabrication of miniaturized system and the possibility of developing compact and portable systems. The work described in this dissertation is towards the development of micromachined separation devices for both high-speed gas chromatography (HSGC) and gravitational field-flow fractionation (GrFFF) using MEMS technologies. Concerning the HSGC, a complete platform of three MEMS-based GC core components (injector, separation column and detector) is designed, fabricated and characterized. The microinjector consists of a set of pneumatically driven microvalves, based on a polymeric actuating membrane. Experimental results demonstrate that the microinjector is able to guarantee low dead volumes, fast actuation time, a wide operating temperature range and high chemical inertness. The microcolumn consists of an all-silicon microcolumn having a nearly circular cross-section channel. The extensive characterization has produced separation performances very close to the theoretical ideal expectations. A thermal conductivity detector (TCD) is chosen as most proper detector to be miniaturized since the volume reduction of the detector chamber results in increased mass and reduced dead volumes. The microTDC shows a good sensitivity and a very wide dynamic range. Finally a feasibility study for miniaturizing a channel suited for GrFFF is performed. The proposed GrFFF microchannel is at early stage of development, but represents a first step for the realization of a highly portable and potentially low-cost POCT device for biomedical applications.

Thin films of polythiophene: Linear and nonlinear optical characterization

Wir haben die linearen und nichtlinearen optischen Eigenschaften von dünnen Schichten und planaren Wellenleitern aus mehreren konjugierten Polymeren (MEH-PPV und P3AT) und Polymeren mit -Elektronen Systemen in der Seitenkette (PVK und PS) untersucht und verglichen. PVK und PS haben relativ kleine Werte des nichtlinearen Brechungsindex n2 bei 532 nm, nämlich (1,2 ± 0,5)10-14 cm2/W und (2,6 ± 0,5) 10-14 cm2/W.rnWir haben die linearen optischen Konstanten von mehreren P3ATs untersucht, insbesondere den Einfluss der Regioregularität und Kettenlänge der Alkylsubstituenten. Wir haben das am besten geeignete Polymere für Wellenleiter Anwendungen identifiziert, welches P3BT-ra genannt ist. Wir haben die linearen optischen Eigenschaften dünner Schichten des P3BT-ra untersucht, die mit Spincoating aus verschiedenen Lösungsmitteln mit unterschiedlichen Siedetemperaturen präparieret wurden. Wir haben festgestellt, dass P3BT-ra Filme aus Toluol-Lösungen die am besten geeigneten Wellenleiter für die intensitätsabhängigen Prismen-Kopplungs Experimente sind, weil diese geringe Wellenleiterdämpfungsverluste bei = 1064 nm haben. rnWir haben die Dispersionen des Wellenleiterdämfungsverlustes gw, des nichtlinearen Brechungsindex n2 und des nichtlinearen Absorptionskoeffizienten 2 von Wellenleitern aus P3BT-ra im Bereich von 700 - 1500 nm gemessen. Wir haben große Werte des nichtlinearen Brechungsindex bis 1,5x10-13 cm2/W bei 1150 nm beobachtet. Wir haben gefunden, dass die Gütenkriterien (“figures of merit“) für rein optische Schalter im Wellenlängebereich 1050 - 1200 nm erfüllt sind. Dieser Bereich entspricht dem niederenergetischen Ausläufer der Zwei-Photonen-Absorption. Die Gütekriterien von P3BT-ra gehören zu den besten der bisher bekannten Werte von konjugierten Polymeren.rnWir haben gefunden, dass P3BT-ra ein vielversprechender Kandidat für integriert-optische Schalter ist, weil es eine gute Kombination aus großer Nichtlinearität dritter Ordnung, geringen Wellenleiterdämpfungverlusten und ausreichender Photostabilität zeigt. rnWir haben einen Vergleich der gemessenen Dispersion von gw, n2 und 2 mit der Theorie durchgeführt. Durch Kurvenanpassung der Dispersion von gw haben wir gefunden, dass Rayleigh-Streuung der dominierende Dämpfungsmechanismus in MEH-PPV und P3BT-ra Wellenleitern ist. Ein quantenmechanischer Ansatz wurde zur Berechnung der nichtlinearen Suszeptibilität dritter Ordnung (3) verwendet, um die gemessenen Spektren von n2 und 2 von P3BT-ra und MEH-PPV zu simulieren. Dies kann erklären, dass sättigbare Absorption und Zwei-Photonen Absorption die hauptsächlichen Effekte sind, welche die Dispersion von n2 und 2 verursachen. rn

Design and experimental characterization of antennas and wireless systems for innovative wearable and implantable ultra low–power applications

The present PhD thesis exploits the design skills I have been improving since my master thesis’ research. A brief description of the chapters’ content follows. Chapter 1: the simulation of a complete front–end is a very complex problem and, in particular, is the basis upon which the prediction of the overall performance of the system is possible. By means of a commercial EM simulation tool and a rigorous nonlinear/EM circuit co–simulation based on the Reciprocity Theorem, the above–mentioned prediction can be achieved and exploited for wireless links characterization. This will represent the theoretical basics of the entire present thesis and will be supported by two RF applications. Chapter 2: an extensive dissertation about Magneto–Dielectric (MD) materials will be presented, together with their peculiar characteristics as substrates for antenna miniaturization purposes. A designed and tested device for RF on–body applications will be described in detail. Finally, future research will be discussed. Chapter 3: this chapter will deal with the issue regarding the exploitation of renewable energy sources for low–energy consumption devices. Hence the problem related to the so–called energy harvesting will be tackled and a first attempt to deploy THz solar energy in an innovative way will be presented and discussed. Future research will be proposed as well. Chapter 4: graphene is a very promising material for devices to be exploited in the RF and THz frequency range for a wide range of engineering applications, including those ones marked as the main research goal of the present thesis. This chapter will present the results obtained during my research period at the National Institute for Research and Development in Microtechnologies (IMT) in Bucharest, Romania. It will concern the design and manufacturing of antennas and diodes made in graphene–based technology for detection/rectification purposes.

Design and Characterization of Curved and Spherical Flexure Hinges for Planar and Spatial Compliant Mechanisms

A flexure hinge is a flexible connector that can provide a limited rotational motion between two rigid parts by means of material deformation. These connectors can be used to substitute traditional kinematic pairs (like bearing couplings) in rigid-body mechanisms. When compared to their rigid-body counterpart, flexure hinges are characterized by reduced weight, absence of backlash and friction, part-count reduction, but restricted range of motion. There are several types of flexure hinges in the literature that have been studied and characterized for different applications. In our study, we have introduced new types of flexures with curved structures i.e. circularly curved-beam flexures and spherical flexures. These flexures have been utilized for both planar applications (e.g. articulated robotic fingers) and spatial applications (e.g. spherical compliant mechanisms). We have derived closed-form compliance equations for both circularly curved-beam flexures and spherical flexures. Each element of the spatial compliance matrix is analytically computed as a function of hinge dimensions and employed material. The theoretical model is then validated by comparing analytical data with the results obtained through Finite Element Analysis. A case study is also presented for each class of flexures, concerning the potential applications in the optimal design of planar and spatial compliant mechanisms. Each case study is followed by comparing the performance of these novel flexures with the performance of commonly used geometries in terms of principle compliance factors, parasitic motions and maximum stress demands. Furthermore, we have extended our study to the design and analysis of serial and parallel compliant mechanisms, where the proposed flexures have been employed to achieve spatial motions e.g. compliant spherical joints.

Besnoitia besnoiti protein disulfide isomerase (BbPDI): molecular characterization, expression and in silico modelling

Besnoitia besnoiti is an apicomplexan parasite responsible for bovine besnoitiosis, a disease with a high prevalence in tropical and subtropical regions and re-emerging in Europe. Despite the great economical losses associated with besnoitiosis, this disease has been underestimated and poorly studied, and neither an effective therapy nor an efficacious vaccine is available. Protein disulfide isomerase (PDI) is an essential enzyme for the acquisition of the correct three-dimensional structure of proteins. Current evidence suggests that in Neosporacaninum and Toxoplasmagondii, which are closely related to B. besnoiti, PDI play an important role in host cell invasion, is a relevant target for the host immune response, and represents a promising drug target and/or vaccine candidate. In this work, we present the nucleotide sequence of the B. besnoiti PDI gene. BbPDI belongs to the thioredoxin-like superfamily (cluster 00388) and is included in the PDI_a family (cluster defined cd02961) and the PDI_a_PDI_a'_c subfamily (cd02995). A 3D theoretical model was built by comparative homology using Swiss-Model server, using as a template the crystallographic deduced model of Tapasin-ERp57 (PDB code 3F8U chain C). Analysis of the phylogenetic tree for PDI within the phylum apicomplexa reinforces the close relationship among B. besnoiti, N. caninum and T. gondii. When subjected to a PDI-assay based on the polymerisation of reduced insulin, recombinant BbPDI expressed in E. coli exhibited enzymatic activity, which was inhibited by bacitracin. Antiserum directed against recombinant BbPDI reacted with PDI in Western blots and by immunofluorescence with B. besnoiti tachyzoites and bradyzoites.