Numerical simulations of magma chamber dynamics at Campi Flegrei, and associated seismicity, deformation and gravity changes

Understanding the complex relationships between quantities measured by volcanic monitoring network and shallow magma processes is a crucial headway for the comprehension of volcanic processes and a more realistic evaluation of the associated hazard. This question is very relevant at Campi Flegrei, a volcanic quiescent caldera immediately north-west of Napoli (Italy). The system activity shows a high fumarole release and periodic ground slow movement (bradyseism) with high seismicity. This activity, with the high people density and the presence of military and industrial buildings, makes Campi Flegrei one of the areas with higher volcanic hazard in the world. In such a context my thesis has been focused on magma dynamics due to the refilling of shallow magma chambers, and on the geophysical signals detectable by seismic, deformative and gravimetric monitoring networks that are associated with this phenomenologies. Indeed, the refilling of magma chambers is a process frequently occurring just before a volcanic eruption; therefore, the faculty of identifying this dynamics by means of recorded signal analysis is important to evaluate the short term volcanic hazard. The space-time evolution of dynamics due to injection of new magma in the magma chamber has been studied performing numerical simulations with, and implementing additional features in, the code GALES (Longo et al., 2006), recently developed and still on the upgrade at the Istituto Nazionale di Geofisica e Vulcanologia in Pisa (Italy). GALES is a finite element code based on a physico-mathematical two dimensional, transient model able to treat fluids as multiphase homogeneous mixtures, compressible to incompressible. The fundamental equations of mass, momentum and energy balance are discretised both in time and space using the Galerkin Least-Squares and discontinuity-capturing stabilisation technique. The physical properties of the mixture are computed as a function of local conditions of magma composition, pressure and temperature.The model features enable to study a broad range of phenomenologies characterizing pre and sin-eruptive magma dynamics in a wide domain from the volcanic crater to deep magma feeding zones. The study of displacement field associated with the simulated fluid dynamics has been carried out with a numerical code developed by the Geophysical group at the University College Dublin (O’Brien and Bean, 2004b), with whom we started a very profitable collaboration. In this code, the seismic wave propagation in heterogeneous media with free surface (e.g. the Earth’s surface) is simulated using a discrete elastic lattice where particle interactions are controlled by the Hooke’s law. This method allows to consider medium heterogeneities and complex topography. The initial and boundary conditions for the simulations have been defined within a coordinate project (INGV-DPC 2004-06 V3_2 “Research on active volcanoes, precursors, scenarios, hazard and risk - Campi Flegrei”), to which this thesis contributes, and many researchers experienced on Campi Flegrei in volcanological, seismic, petrological, geochemical fields, etc. collaborate. Numerical simulations of magma and rock dynamis have been coupled as described in the thesis. The first part of the thesis consists of a parametric study aimed at understanding the eect of the presence in magma of carbon dioxide in magma in the convection dynamics. Indeed, the presence of this volatile was relevant in many Campi Flegrei eruptions, including some eruptions commonly considered as reference for a future activity of this volcano. A set of simulations considering an elliptical magma chamber, compositionally uniform, refilled from below by a magma with volatile content equal or dierent from that of the resident magma has been performed. To do this, a multicomponent non-ideal magma saturation model (Papale et al., 2006) that considers the simultaneous presence of CO2 and H2O, has been implemented in GALES. Results show that the presence of CO2 in the incoming magma increases its buoyancy force promoting convection ad mixing. The simulated dynamics produce pressure transients with frequency and amplitude in the sensitivity range of modern geophysical monitoring networks such as the one installed at Campi Flegrei . In the second part, simulations more related with the Campi Flegrei volcanic system have been performed. The simulated system has been defined on the basis of conditions consistent with the bulk of knowledge of Campi Flegrei and in particular of the Agnano-Monte Spina eruption (4100 B.P.), commonly considered as reference for a future high intensity eruption in this area. The magmatic system has been modelled as a long dyke refilling a small shallow magma chamber; magmas with trachytic and phonolitic composition and variable volatile content of H2O and CO2 have been considered. The simulations have been carried out changing the condition of magma injection, the system configuration (magma chamber geometry, dyke size) and the resident and refilling magma composition and volatile content, in order to study the influence of these factors on the simulated dynamics. Simulation results allow to follow each step of the gas-rich magma ascent in the denser magma, highlighting the details of magma convection and mixing. In particular, the presence of more CO2 in the deep magma results in more ecient and faster dynamics. Through this simulations the variation of the gravimetric field has been determined. Afterward, the space-time distribution of stress resulting from numerical simulations have been used as boundary conditions for the simulations of the displacement field imposed by the magmatic dynamics on rocks. The properties of the simulated domain (rock density, P and S wave velocities) have been based on data from literature on active and passive tomographic experiments, obtained through a collaboration with A. Zollo at the Dept. of Physics of the Federici II Univeristy in Napoli. The elasto-dynamics simulations allow to determine the variations of the space-time distribution of deformation and the seismic signal associated with the studied magmatic dynamics. In particular, results show that these dynamics induce deformations similar to those measured at Campi Flegrei and seismic signals with energies concentrated on the typical frequency bands observed in volcanic areas. The present work shows that an approach based on the solution of equations describing the physics of processes within a magmatic fluid and the surrounding rock system is able to recognise and describe the relationships between geophysical signals detectable on the surface and deep magma dynamics. Therefore, the results suggest that the combined study of geophysical data and informations from numerical simulations can allow in a near future a more ecient evaluation of the short term volcanic hazard.

Investigations on formation and specification of neural precursor cells in the central nervous system of the Drosophila melanogaster embryo

Investigations on formation and specification of neural precursor cells in the central nervous system of the Drosophila melanogaster embryoSpecification of a unique cell fate during development of a multicellular organism often is a function of its position. The Drosophila central nervous system (CNS) provides an ideal system to dissect signalling events during development that lead to cell specific patterns. Different cell types in the CNS are formed from a relatively few precursor cells, the neuroblasts (NBs), which delaminate from the neurogenic region of the ectoderm. The delamination occurs in five waves, S1-S5, finally leading to a subepidermal layer consisting of about 30 NBs, each with a unique identity, arranged in a stereotyped spatial pattern in each hemisegment. This information depends on several factors such as the concentrations of various morphogens, cell-cell interactions and long range signals present at the position and time of its birth. The early NBs, delaminating during S1 and S2, form an orthogonal array of four rows (2/3,4,5,6/7) and three columns (medial, intermediate, and lateral) . However, the three column and four row-arrangement pattern is only transitory during early stages of neurogenesis which is obscured by late emerging (S3-S5) neuroblasts (Doe and Goodman, 1985; Goodman and Doe, 1993). Therefore the aim of my study has been to identify novel genes which play a role in the formation or specification of late delaminating NBs.In this study the gene anterior open or yan was picked up in a genetic screen to identity novel and yet unidentified genes in the process of late neuroblast formation and specification. I have shown that the gene yan is responsible for maintaining the cells of the neuroectoderm in an undifferentiated state by interfering with the Notch signalling mechanism. Secondly, I have studied the function and interactions of segment polarity genes within a certain neuroectodermal region, namely the engrailed (en) expressing domain, with regard to the fate specification of a set of late neuroblasts, namely NB 6-4 and NB 7-3. I have dissected the regulatory interaction of the segment polarity genes wingless (wg), hedgehog (hh) and engrailed (en) as they maintain each other’s expression to show that En is a prerequisite for neurogenesis and show that the interplay of the segmentation genes naked (nkd) and gooseberry (gsb), both of which are targets of wingless (wg) activity, leads to differential commitment of NB 7-3 and NB 6-4 cell fate. I have shown that in the absence of either nkd or gsb one NB fate is replaced by the other. However, the temporal sequence of delamination is maintained, suggesting that formation and specification of these two NBs are under independent control.

Application of reactive fluid transport modeling to hydrothermal systems

A one-dimensional multi-component reactive fluid transport algorithm, 1DREACT (Steefel, 1993) was used to investigate different fluid-rock interaction systems. A major short coming of mass transport calculations which include mineral reactions is that solid solutions occurring in many minerals are not treated adequately. Since many thermodynamic models of solid solutions are highly non-linear, this can seriously impact on the stability and efficiency of the solution algorithms used. Phase petrology community saw itself faced with a similar predicament 10 years ago. To improve performance and reliability, phase equilibrium calculations have been using pseudo compounds. The same approach is used here in the first, using the complex plagioclase solid solution as an example. Thermodynamic properties of a varying number of intermediate plagioclase phases were calculated using ideal molecular, Al-avoidance, and non-ideal mixing models. These different mixing models can easily be incorporated into the simulations without modification of the transport code. Simulation results show that as few as nine intermediate compositions are sufficient to characterize the diffusional profile between albite and anorthite. Hence this approach is very efficient, and can be used with little effort. A subsequent chapter reports the results of reactive fluid transport modeling designed to constrain the hydrothermal alteration of Paleoproterozoic sediments of the Southern Lake Superior region. Field observations reveal that quartz-pyrophyllite (or kaolinite) bearing assemblages have been transformed into muscovite-pyrophyllite-diaspore bearing assemblages due to action of fluids migrating along permeable flow channels. Fluid-rock interaction modeling with an initial qtz-prl assemblage and a K-rich fluid simulates the formation of observed mineralogical transformation. The bulk composition of the system evolves from an SiO2-rich one to an Al2O3+K2O-rich one. Simulations show that the fluid flow was up-temperature (e.g. recharge) and that fluid was K-rich. Pseudo compound approach to include solid solutions in reactive transport models was tested in modeling hydrothermal alteration of Icelandic basalts. Solid solutions of chlorites, amphiboles and plagioclase were included as the secondary mineral phases. Saline and fresh water compositions of geothermal fluids were used to investigate the effect of salinity on alteration. Fluid-rock interaction simulations produce the observed mineral transformations. They show that roughly the same alteration minerals are formed due to reactions with both types of fluid which is in agreement with the field observations. A final application is directed towards the remediation of nitrate rich groundwaters. Removal of excess nitrate from groundwater by pyrite oxidation was modeled using the reactive fluid transport algorithm. Model results show that, when a pyrite-bearing, permeable zone is placed in the flow path, nitrate concentration in infiltrating water can be significantly lowered, in agreement with proposals from the literature. This is due to nitrogen reduction. Several simulations investigate the efficiency of systems with different mineral reactive surface areas, reactive barrier zone widths, and flow rates to identify the optimum setup.

Atomistic simulations of cosolvent/water mixtures

In this thesis, atomistic simulations are performed to investigate hydrophobic solvation and hydrophobic interactions in cosolvent/water binary mixtures. Many cosolvent/water binary mixtures exhibit non-ideal behavior caused by aggregation at the molecular scale level although they are stable and homogenous at the macroscopic scale. Force-field based atomistic simulations provide routes to relate atomistic-scale structure and interactions to thermodynamic solution properties. The predicted solution properties are however sensitive to the parameters used to describe the molecular interactions. In this thesis, a force field for tertiary butanol (TBA) and water mixtures is parameterized by making use of the Kirkwood-Buff theory of solution. The new force field is capable of describing the alcohol-alcohol, water-water and alcohol-water clustering in the solution as well as the solution components’ chemical potential derivatives in agreement with experimental data. With the new force field, the preferential solvation and the solvation thermodynamics of a hydrophobic solute in TBA/water mixtures have been studied. First, methane solvation at various TBA/water concentrations is discussed in terms of solvation free energy-, enthalpy- and entropy- changes, which have been compared to experimental data. We observed that the methane solvation free energy varies smoothly with the alcohol/water composition while the solvation enthalpies and entropies vary nonmonotonically. The latter occurs due to structural solvent reorganization contributions which are not present in the free energy change due to exact enthalpy-entropy compensation. It is therefore concluded that the enthalpy and entropy of solvation provide more detailed information on the reorganization of solvent molecules around the inserted solute. Hydrophobic interactions in binary urea/water mixtures are next discussed. This system is particularly relevant in biology (protein folding/unfolding), however, changes in the hydrophobic interaction induced by urea molecules are not well understood. In this thesis, this interaction has been studied by calculating the free energy (potential of mean force), enthalpy and entropy changes as a function of the solute-solute distance in water and in aqueous urea (6.9 M) solution. In chapter 5, the potential of mean force in both solution systems is analyzed in terms of its enthalpic and entropic contributions. In particular, contributions of solvent reorganization in the enthalpy and entropy changes are studied separately to better understand what are the changes in interactions in the system that contribute to the free energy of association of the nonpolar solutes. We observe that in aqueous urea the association between nonpolar solutes remains thermodynamically favorable (i.e., as it is the case in pure water). This observation contrasts a long-standing belief that clusters of nonpolar molecules dissolve completely in the presence of urea molecules. The consequences of our observations for the stability of proteins in concentrated urea solutions are discussed in the chapter 6 of the thesis.

Model reduction techniques in flexible multibody dynamics with application to engine cranktrain simulation

The development of a multibody model of a motorbike engine cranktrain is presented in this work, with an emphasis on flexible component model reduction. A modelling methodology based upon the adoption of non-ideal joints at interface locations, and the inclusion of component flexibility, is developed: both are necessary tasks if one wants to capture dynamic effects which arise in lightweight, high-speed applications. With regard to the first topic, both a ball bearing model and a journal bearing model are implemented, in order to properly capture the dynamic effects of the main connections in the system: angular contact ball bearings are modelled according to a five-DOF nonlinear scheme in order to grasp the crankshaft main bearings behaviour, while an impedance-based hydrodynamic bearing model is implemented providing an enhanced operation prediction at the conrod big end locations. Concerning the second matter, flexible models of the crankshaft and the connecting rod are produced. The well-established Craig-Bampton reduction technique is adopted as a general framework to obtain reduced model representations which are suitable for the subsequent multibody analyses. A particular component mode selection procedure is implemented, based on the concept of Effective Interface Mass, allowing an assessment of the accuracy of the reduced models prior to the nonlinear simulation phase. In addition, a procedure to alleviate the effects of modal truncation, based on the Modal Truncation Augmentation approach, is developed. In order to assess the performances of the proposed modal reduction schemes, numerical tests are performed onto the crankshaft and the conrod models in both frequency and modal domains. A multibody model of the cranktrain is eventually assembled and simulated using a commercial software. Numerical results are presented, demonstrating the effectiveness of the implemented flexible model reduction techniques. The advantages over the conventional frequency-based truncation approach are discussed.

Efficient methodologies for system matrix modelling in iterative image reconstruction for rotating high-resolution PET

A fully 3D iterative image reconstruction algorithm has been developed for high-resolution PET cameras composed of pixelated scintillator crystal arrays and rotating planar detectors, based on the ordered subsets approach. The associated system matrix is precalculated with Monte Carlo methods that incorporate physical effects not included in analytical models, such as positron range effects and interaction of the incident gammas with the scintillator material. Custom Monte Carlo methodologies have been developed and optimized for modelling of system matrices for fast iterative image reconstruction adapted to specific scanner geometries, without redundant calculations. According to the methodology proposed here, only one-eighth of the voxels within two central transaxial slices need to be modelled in detail. The rest of the system matrix elements can be obtained with the aid of axial symmetries and redundancies, as well as in-plane symmetries within transaxial slices. Sparse matrix techniques for the non-zero system matrix elements are employed, allowing for fast execution of the image reconstruction process. This 3D image reconstruction scheme has been compared in terms of image quality to a 2D fast implementation of the OSEM algorithm combined with Fourier rebinning approaches. This work confirms the superiority of fully 3D OSEM in terms of spatial resolution, contrast recovery and noise reduction as compared to conventional 2D approaches based on rebinning schemes. At the same time it demonstrates that fully 3D methodologies can be efficiently applied to the image reconstruction problem for high-resolution rotational PET cameras by applying accurate pre-calculated system models and taking advantage of the system's symmetries.

Search strategies and the automated control of plant diseases

We propose the use of the "infotaxis" search strategy as the navigation system of a robotic platform, able to search and localize infectious foci by detecting the changes in the profile of volatile organic compounds emitted by and infected plant. We builded a simple and cost effective robot platform that substitutes odour sensors in favour of light sensors and study their robustness and performance under non ideal conditions such as the exitence of obstacles due to land topology or weeds.

Evaluating a web-based clinical decision support system for language disorders screening in a nursery school

Background: Early and effective identification of developmental disorders during childhood remains a critical task for the international community. The second highest prevalence of common developmental disorders in children are language delays, which are frequently the first symptoms of a possible disorder. Objective: This paper evaluates a Web-based Clinical Decision Support System (CDSS) whose aim is to enhance the screening of language disorders at a nursery school. The common lack of early diagnosis of language disorders led us to deploy an easy-to-use CDSS in order to evaluate its accuracy in early detection of language pathologies. This CDSS can be used by pediatricians to support the screening of language disorders in primary care. Methods: This paper details the evaluation results of the ?Gades? CDSS at a nursery school with 146 children, 12 educators, and 1 language therapist. The methodology embraces two consecutive phases. The first stage involves the observation of each child?s language abilities, carried out by the educators, to facilitate the evaluation of language acquisition level performed by a language therapist. Next, the same language therapist evaluates the reliability of the observed results. Results: The Gades CDSS was integrated to provide the language therapist with the required clinical information. The validation process showed a global 83.6% (122/146) success rate in language evaluation and a 7% (7/94) rate of non-accepted system decisions within the range of children from 0 to 3 years old. The system helped language therapists to identify new children with potential disorders who required further evaluation. This process will revalidate the CDSS output and allow the enhancement of early detection of language disorders in children. The system does need minor refinement, since the therapists disagreed with some questions from the CDSS knowledge base (KB) and suggested adding a few questions about speech production and pragmatic abilities. The refinement of the KB will address these issues and include the requested improvements, with the support of the experts who took part in the original KB development. Conclusions: This research demonstrated the benefit of a Web-based CDSS to monitor children?s neurodevelopment via the early detection of language delays at a nursery school. Current next steps focus on the design of a model that includes pseudo auto-learning capacity, supervised by experts.

Design and optimization of optical, fiber based PSK demodulators for high-bit-rate optical networks

El objetivo principal de esta tesis ha sido el diseño y la optimización de receptores implementados con fibra óptica, para ser usados en redes ópticas de alta velocidad que empleen formatos de modulación de fase. En los últimos años, los formatos de modulación de fase (Phase Shift keying, PSK) han captado gran atención debido a la mejora de sus prestaciones respecto a los formatos de modulación convencionales. Principalmente, presentan una mejora de la eficiencia espectral y una mayor tolerancia a la degradación de la señal causada por la dispersión cromática, la dispersión por modo de polarización y los efectos no-lineales en la fibra óptica. En este trabajo, se analizan en detalle los formatos PSK, incluyendo sus variantes de modulación de fase diferencial (Differential Phase Shift Keying, DPSK), en cuadratura (Differential Quadrature Phase Shift Keying, DQPSK) y multiplexación en polarización (Polarization Multiplexing Differential Quadrature Phase Shift Keying, PM-DQPSK), con la finalidad de diseñar y optimizar los receptores que permita su demodulación. Para ello, se han analizado y desarrollado nuevas estructuras que ofrecen una mejora en las prestaciones del receptor y una reducción de coste comparadas con las actualmente disponibles. Para la demodulación de señales DPSK, en esta tesis, se proponen dos nuevos receptores basados en un interferómetro en línea Mach-Zehnder (MZI) implementado con tecnología todo-fibra. El principio de funcionamiento de los MZI todo-fibra propuestos se asienta en la interferencia modal que se produce en una fibra multimodo (MMF) cuando se situada entre dos monomodo (SMF). Este tipo de configuración (monomodo-multimodo-monomodo, SMS) presenta un buen ratio de extinción interferente si la potencia acoplada en la fibra multimodo se reparte, principal y equitativamente, entre dos modos dominantes. Con este objetivo, se han estudiado y demostrado tanto teórica como experimentalmente dos nuevas estructuras SMS que mejoran el ratio de extinción. Una de las propuestas se basa en emplear una fibra multimodo de índice gradual cuyo perfil del índice de refracción presenta un hundimiento en su zona central. La otra consiste en una estructura SMS con las fibras desalineadas y donde la fibra multimodo es una fibra de índice gradual convencional. Para las dos estructuras, mediante el análisis teórico desarrollado, se ha demostrado que el 80 – 90% de la potencia de entrada se acopla a los dos modos dominantes de la fibra multimodo y se consigue una diferencia inferior al 10% entre ellos. También se ha demostrado experimentalmente que se puede obtener un ratio de extinción de al menos 12 dB. Con el objeto de demostrar la capacidad de estas estructuras para ser empleadas como demoduladores de señales DPSK, se han realizado numerosas simulaciones de un sistema de transmisión óptico completo y se ha analizado la calidad del receptor bajo diferentes perspectivas, tales como la sensibilidad, la tolerancia a un filtrado óptico severo o la tolerancia a las dispersiones cromática y por modo de polarización. En todos los casos se ha concluido que los receptores propuestos presentan rendimientos comparables a los obtenidos con receptores convencionales. En esta tesis, también se presenta un diseño alternativo para la implementación de un receptor DQPSK, basado en el uso de una fibra mantenedora de la polarización (PMF). A través del análisi teórico y del desarrollo de simulaciones numéricas, se ha demostrado que el receptor DQPSK propuesto presenta prestaciones similares a los convencionales. Para complementar el trabajo realizado sobre el receptor DQPSK basado en PMF, se ha extendido el estudio de su principio de demodulación con el objeto de demodular señales PM-DQPSK, obteniendo como resultado la propuesta de una nueva estructura de demodulación. El receptor PM-DQPSK propuesto se basa en la estructura conjunta de una única línea de retardo junto con un rotador de polarización. Se ha analizado la calidad de los receptores DQPSK y PM-DQPSK bajo diferentes perspectivas, tales como la sensibilidad, la tolerancia a un filtrado óptico severo, la tolerancia a las dispersiones cromática y por modo de polarización o su comportamiento bajo condiciones no-ideales. En comparación con los receptores convencionales, nuestra propuesta exhibe prestaciones similares y además permite un diseño más simple que redunda en un coste potencialmente menor. En las redes de comunicaciones ópticas actuales se utiliza la tecnología de multimplexación en longitud de onda (WDM) que obliga al uso de filtros ópticos con bandas de paso lo más estrechas posibles y a emplear una serie de dispositivos que incorporan filtros en su arquitectura, tales como los multiplexores, demultiplexores, ROADMs, conmutadores y OXCs. Todos estos dispositivos conectados entre sí son equivalentes a una cadena de filtros cuyo ancho de banda se va haciendo cada vez más estrecho, llegando a distorsionar la forma de onda de las señales. Por esto, además de analizar el impacto del filtrado óptico en las señales de 40 Gbps DQPSK y 100 Gbps PM-DQPSK, este trabajo de tesis se completa estudiando qué tipo de filtro óptico minimiza las degradaciones causadas en la señal y analizando el número máximo de filtros concatenados que permiten mantener la calidad requerida al sistema. Se han estudiado y simulado cuatro tipos de filtros ópticos;Butterworth, Bessel, FBG y F-P. ABSTRACT The objective of this thesis is the design and optimization of optical fiber-based phase shift keying (PSK) demodulators for high-bit-rate optical networks. PSK modulation formats have attracted significant attention in recent years, because of the better performance with respect to conventional modulation formats. Principally, PSK signals can improve spectrum efficiency and tolerate more signal degradation caused by chromatic dispersion, polarization mode dispersion and nonlinearities in the fiber. In this work, many PSK formats were analyzed in detail, including the variants of differential phase modulation (Differential Phase Shift Keying, DPSK), in quadrature (Differential Quadrature Phase Shift Keying, DQPSK) and polarization multiplexing (Polarization Multiplexing Differential Quadrature Phase Shift Keying, PM-DQPSK), in order to design and optimize receivers enabling demodulations. Therefore, novel structures, which offer good receiver performances and a reduction in cost compared to the current structures, have been analyzed and developed. Two novel receivers based on an all-fiber in-line Mach-Zehnder interferometer (MZI) were proposed for DPSK signal demodulation in this thesis. The operating principle of the all-fiber MZI is based on the modal interference that occurs in a multimode fiber (MMF) when it is located between two single-mode fibers (SMFs). This type of configuration (Single-mode-multimode-single-mode, SMS) can provide a good extinction ratio if the incoming power from the SMF could be coupled equally into two dominant modes excited in the MMF. In order to improve the interference extinction ratio, two novel SMS structures have been studied and demonstrated, theoretically and experimentally. One of the two proposed MZIs is based on a graded-index multimode fiber (MMF) with a central dip in the index profile, located between two single-mode fibers (SMFs). The other one is based on a conventional graded-index MMF mismatch spliced between two SMFs. Theoretical analysis has shown that, in these two schemes, 80 – 90% of the incoming power can be coupled into the two dominant modes exited in the MMF, and the power difference between them is only ~10%. Experimental results show that interference extinction ratio of 12 dB could be obtained. In order to demonstrate the capacity of these two structures for use as DPSK signal demodulators, numerical simulations in a completed optical transmission system have been carried out, and the receiver quality has been analyzed under different perspectives, such as sensitivity, tolerance to severe optical filtering or tolerance to chromatic and polarization mode dispersion. In all cases, from the simulation results we can conclude that the two proposed receivers can provide performances comparable to conventional ones. In this thesis, an alternative design for the implementation of a DQPSK receiver, which is based on a polarization maintaining fiber (PMF), was also presented. To complement the work made for the PMF-based DQPSK receiver, the study of the demodulation principle has been extended to demodulate PM-DQPSK signals, resulting in the proposal of a novel demodulation structure. The proposed PM-DQPSK receiver is based on only one delay line and a polarization rotator. The quality of the proposed DQPSK and PM-DQPSK receivers under different perspectives, such as sensitivity, tolerance to severe optical filtering, tolerance to chromatic dispersion and polarization mode dispersion, or behavior under non-ideal conditions. Compared with the conventional receivers, our proposals exhibit similar performances but allow a simpler design which can potentially reduce the cost. The wavelength division multiplexing (WDM) technology used in current optical communications networks requires the use of optical filters with a passband as narrow as possible, and the use of a series of devices that incorporate filters in their architecture, such as multiplexers, demultiplexers, switches, reconfigurable add-drop multiplexers (ROADMs) and optical cross-connects (OXCs). All these devices connected together are equivalent to a chain of filters whose bandwidth becomes increasingly narrow, resulting in distortion to the waveform of the signals. Therefore, in addition to analyzing the impact of optical filtering on signal of 40 Gbps DQPSK and 100 Gbps PM-DQPSK, we study which kind of optical filter minimizes the signal degradation and analyze the maximum number of concatenated filters for maintaining the required quality of the system. Four types of optical filters, including Butterworth, Bessel, FBG and FP, have studied and simulated.

Temperature of solar cells with regard to photoactive and non-photoactive light absorption in concentrator PV modules

A new method has recently been proposed by us for accurate measurement of the solar cell temperature in any operational regime, in particular, at a maximum power point (MPP) of the I-V curve (T-p-n(MPP)). For this, fast switching of a cell from MPP to open circuit (OC) regime is carried out and open circuit voltage V-oc is measured immediately (within about 1 millisecond), so that this value becomes to be an indicator of T-p-n(MPP). In the present work, we have considered a practical case, when a solar cell is heated not only by absorption of light incident upon its surface (called "photoactive" absorption of power), but also by heat transferred from structural elements surrounding the cell and heated by absorption of direct or diffused sunlight ("non-photoactive" absorption of power with respect to a solar cell). This process takes place in any concentrator module with non-ideal concentrators. Low overheating temperature of the p-n junction (or p-n junctions in a multijunction cell) is a cumulative parameter characterizing the quality of a solar module by the factor of heat removal effectiveness and, at the same time, by the factor of low "non-photoactive" losses.

The Pto kinase mediates a signaling pathway leading to the oxidative burst in tomato

The Pto gene encodes a serine/threonine kinase that confers resistance in tomato to Pseudomonas syringae pv. tomato strains that express the avirulence gene avrPto. Partial characterization of the Pto signal transduction pathway and the availability of transgenic tomato lines (± Pto) make this an ideal system for exploring the molecular basis of disease resistance. In this paper, we test two transgenic tomato cell suspension cultures (±Pto) for production of H2O2 following independent challenge with two strains of P. syringae pv. tomato (±avrPto). Only when Pto and avrPto are present in the corresponding organisms are two distinct phases of the oxidative burst seen, a rapid first burst followed by a slower and more prolonged second burst. In the remaining three plant–pathogen interactions, we observe either no burst or only a first burst, indicating that the second burst is correlated with disease resistance. Further support for this observation comes from the finding that both resistant and susceptible tomato lines produce the critical second oxidative burst when challenged with P. syringae pv. tabaci, a nonhost pathogen that elicits a hypersensitive response on both tomato lines. The Pto kinase is not required, however, for the oxidative burst initiated by non-specific elicitors such as oligogalacturonides or osmotic stress. A model describing a possible role for the Pto kinase in the overall scheme of oxidative burst signaling is proposed.

The maturity-onset diabetes of the young (MODY1) transcription factor HNF4α regulates expression of genes required for glucose transport and metabolism

Hepatocyte nuclear factor 4α (HNF4α) plays a critical role in regulating the expression of many genes essential for normal functioning of liver, gut, kidney, and pancreatic islets. A nonsense mutation (Q268X) in exon 7 of the HNF4α gene is responsible for an autosomal dominant, early-onset form of non-insulin-dependent diabetes mellitus (maturity-onset diabetes of the young; gene named MODY1). Although this mutation is predicted to delete 187 C-terminal amino acids of the HNF4α protein the molecular mechanism by which it causes diabetes is unknown. To address this, we first studied the functional properties of the MODY1 mutant protein. We show that it has lost its transcriptional transactivation activity, fails to dimerize and bind DNA, implying that the MODY1 phenotype is because of a loss of HNF4α function. The effect of loss of function on HNF4α target gene expression was investigated further in embryonic stem cells, which are amenable to genetic manipulation and can be induced to form visceral endoderm. Because the visceral endoderm shares many properties with the liver and pancreatic β-cells, including expression of genes for glucose transport and metabolism, it offers an ideal system to investigate HNF4-dependent gene regulation in glucose homeostasis. By exploiting this system we have identified several genes encoding components of the glucose-dependent insulin secretion pathway whose expression is dependent upon HNF4α. These include glucose transporter 2, and the glycolytic enzymes aldolase B and glyceraldehyde-3-phosphate dehydrogenase, and liver pyruvate kinase. In addition we have found that expression of the fatty acid binding proteins and cellular retinol binding protein also are down-regulated in the absence of HNF4α. These data provide direct evidence that HNF4α is critical for regulating glucose transport and glycolysis and in doing so is crucial for maintaining glucose homeostasis.

Detection and determination of oligonucleotide triplex formation-mediated transcription-coupled DNA repair in HeLa nuclear extracts

Transcription-coupled repair (TCR) plays an important role in removing DNA damage from actively transcribed genes. It has been speculated that TCR is the most important mechanism for repairing DNA damage in non-dividing cells such as neurons. Therefore, abnormal TCR may contribute to the development of many age-related and neurodegenerative diseases. However, the molecular mechanism of TCR is not well understood. Oligonucleotide DNA triplex formation provides an ideal system to dissect the molecular mechanism of TCR since triplexes can be formed in a sequence-specific manner to inhibit transcription of target genes. We have recently studied the molecular mechanism of triplex-forming oligonucleotide (TFO)-mediated TCR in HeLa nuclear extracts. Using plasmid constructs we demonstrate that the level of TFO-mediated DNA repair activity is directly correlated with the level of transcription of the plasmid in HeLa nuclear extracts. TFO-mediated DNA repair activity was further linked with transcription since the presence of rNTPs in the reaction was essential for AG30-mediated DNA repair activity in HeLa nuclear extracts. The involvement of individual components, including TFIID, TFIIH, RNA polymerase II and xeroderma pigmentosum group A (XPA), in the triplex-mediated TCR process was demonstrated in HeLa nuclear extracts using immunodepletion assays. Importantly, our studies also demonstrated that XPC, a component involved in global genome DNA repair, is involved in the AG30-mediated DNA repair process. The results obtained in this study provide an important new understanding of the molecular mechanisms involved in the TCR process in mammalian cells.

Nervous and muscle system development in Phascolion strombus (Sipuncula)

Recent interpretations of developmental gene expression patterns propose that the last common metazoan ancestor was segmented, although most animal phyla show no obvious signs of segmentation. Developmental studies of non-model system trochozoan taxa may shed light on this hypothesis by assessing possible cryptic segmentation patterns. In this paper, we present the first immunocytochemical data on the ontogeny of the nervous system and the musculature in the sipunculan Phascolion strombus. Myogenesis of the first anlagen of the body wall ring muscles occurs synchronously and not subsequently from anterior to posterior as in segmented spiralian taxa (i.e. annelids). The number of ring muscles remains constant during the initial stages of body axis elongation. In the anterior-posteriorly elongated larva, newly formed ring muscles originate along the entire body axis between existing myocytes, indicating that repeated muscle bands do not form from a posterior growth zone. During neurogenesis, the Phascolion larva expresses a non-metameric, paired, ventral nerve cord that fuses in the mid-body region in the late-stage elongated larva. Contrary to other trochozoans, Phascolion lacks any larval serotonergic structures. However, two to three FMRFamide-positive cells are found in the apical organ. In addition, late larvae show commissure-like neurones interconnecting the two ventral nerve cords, while early juveniles exhibit a third, medially placed FMRFamidergic ventral nerve. Although we did not find any indications for cryptic segmentation, certain neuro-developmental traits in Phascolion resemble the conditions found in polychaetes (including echiurans) and myzostomids and support a close relationship of Sipuncula and Annelida.

Noise in detection of qubit states using a quantum point contact

We present a model for detection of the states of a coupled quantum dots (qubit) by a quantum point contact. Most proposals for measurements of states of quantum systems are idealized. However in a real laboratory the measurements cannot be perfect due to practical devices and circuits. The models using ideal devices are not sufficient for describing the detection information of the states of the quantum systems. Our model therefore includes the extension to a non-ideal measurement device case using an equivalent circuit. We derive a quantum trajectory that describes the stochastic evolution of the state of the system of the qubit and the measuring device. We calculate the noise power spectrum of tunnelling events in an ideal and a non-ideal quantum point contact measurement respectively. We found that, for the strong coupling case it is difficult to obtain information of the quantum processes in the qubit by measurements using a non-ideal quantum point contact. The noise spectra can also be used to estimate the limits of applicability of the ideal model.