Ab-initio determination of x-ray absorption near edge structure (xanes) spectra in an ultrasoft and norm conserving pseudopotentials scheme

X-ray absorption spectroscopy (XAS) is a powerful means of investigation of structural and electronic properties in condensed -matter physics. Analysis of the near edge part of the XAS spectrum, the so – called X-ray Absorption Near Edge Structure (XANES), can typically provide the following information on the photoexcited atom: - Oxidation state and coordination environment. - Speciation of transition metal compounds. - Conduction band DOS projected on the excited atomic species (PDOS). Analysis of XANES spectra is greatly aided by simulations; in the most common scheme the multiple scattering framework is used with the muffin tin approximation for the scattering potential and the spectral simulation is based on a hypothetical, reference structure. This approach has the advantage of requiring relatively little computing power but in many cases the assumed structure is quite different from the actual system measured and the muffin tin approximation is not adequate for low symmetry structures or highly directional bonds. It is therefore very interesting and justified to develop alternative methods. In one approach, the spectral simulation is based on atomic coordinates obtained from a DFT (Density Functional Theory) optimized structure. In another approach, which is the object of this thesis, the XANES spectrum is calculated directly based on an ab – initio DFT calculation of the atomic and electronic structure. This method takes full advantage of the real many-electron final wavefunction that can be computed with DFT algorithms that include a core-hole in the absorbing atom to compute the final cross section. To calculate the many-electron final wavefunction the Projector Augmented Wave method (PAW) is used. In this scheme, the absorption cross section is written in function of several contributions as the many-electrons function of the finale state; it is calculated starting from pseudo-wavefunction and performing a reconstruction of the real-wavefunction by using a transform operator which contains some parameters, called partial waves and projector waves. The aim of my thesis is to apply and test the PAW methodology to the calculation of the XANES cross section. I have focused on iron and silicon structures and on some biological molecules target (myoglobin and cytochrome c). Finally other inorganic and biological systems could be taken into account for future applications of this methodology, which could become an important improvement with respect to the multiscattering approach.

Studies of pure rotational spectra of isolated molecules and molecular adducts using pulsed jet Fourier transform microwave (PJ-FTM) spectroscopy

This thesis focuses on studying molecular structure and internal dynamics by using pulsed jet Fourier transform microwave (PJ-FTMW) spectroscopy combined with theoretical calculations. Several kinds of interesting chemical problems are investigated by analyzing the MW spectra of the corresponding molecular systems. First, the general aspects of rotational spectroscopy are summarized, and then the basic theory on molecular rotation and experimental method are described briefly. ab initio and density function theory (DFT) calculations that used in this thesis to assist the assignment of rotational spectrum are also included. From chapter 3 to chapter 8, several molecular systems concerning different kind of general chemical problems are presented. In chapter 3, the conformation and internal motions of dimethyl sulfate are reported. The internal rotations of the two methyl groups split each rotational transition into several components line, allowing for the determination of accurate values of the V3 barrier height to internal rotation and of the orientation of the methyl groups with respect to the principal axis system. In chapter 4 and 5, the results concerning two kinds of carboxylic acid bi-molecules, formed via two strong hydrogen bonds, are presented. This kind of adduct is interesting also because a double proton transfer can easily take place, connecting either two equivalent or two non-equivalent molecular conformations. Chapter 6 concerns a medium strong hydrogen bonded molecular complex of alcohol with ether. The dimer of ethanol-dimethylether was chosen as the model system for this purpose. Chapter 7 focuses on weak halogen…H hydrogen bond interaction. The nature of O-H…F and C-H…Cl interaction has been discussed through analyzing the rotational spectra of CH3CHClF/H2O. In chapter 8, two molecular complexes concerning the halogen bond interaction are presented.

Generating vegetation-spectra as a basis for global monitoring of annual vegetation cycles using DOAS satellite observations

Vegetation-cycles are of general interest for many applications. Be it for harvest-predictions, global monitoring of climate-change or as input to atmospheric models.rnrnCommon Vegetation Indices use the fact that for vegetation the difference between Red and Near Infrared reflection is higher than in any other material on Earth’s surface. This gives a very high degree of confidence for vegetation-detection.rnrnThe spectrally resolving data from the GOME and SCIAMACHY satellite-instrumentsrnprovide the chance to analyse finer spectral features throughout the Red and Near Infrared spectrum using Differential Optical Absorption Spectroscopy (DOAS). Although originally developed to retrieve information on atmospheric trace gases, we use it to gain information on vegetation. Another advantage is that this method automatically corrects for changes in the atmosphere. This renders the vegetation-information easily comparable over long time-spans.rnThe first results using previously available reference spectra were encouraging, but also indicated substantial limitations of the available reflectance spectra of vegetation. This was the motivation to create new and more suitable vegetation reference spectra within this thesis.rnThe set of reference spectra obtained is unique in its extent and also with respect to its spectral resolution and the quality of the spectral calibration. For the first time, this allowed a comprehensive investigation of the high-frequency spectral structures of vegetation reflectance and of their dependence on the viewing geometry.rnrnThe results indicate that high-frequency reflectance from vegetation is very complex and highly variable. While this is an interesting finding in itself, it also complicates the application of the obtained reference spectra to the spectral analysis of satellite observations.rnrnThe new set of vegetation reference spectra created in this thesis opens new perspectives for research. Besides refined satellite analyses, these spectra might also be used for applications on other platforms such as aircraft. First promising studies have been presented in this thesis, but the full potential for the remote sensing of vegetation from satellite (or aircraft) could bernfurther exploited in future studies.

Wavelet estimation in diffusions with periodicity

Wir betrachten einen zeitlich inhomogenen Diffusionsprozess, der durch eine stochastische Differentialgleichung gegeben wird, deren Driftterm ein deterministisches T-periodisches Signal beinhaltet, dessen Periodizität bekannt ist. Dieses Signal sei in einem Besovraum enthalten. Wir schätzen es mit Hilfe eines nichtparametrischen Waveletschätzers. Unser Schätzer ist von einem Wavelet-Dichteschätzer mit Thresholding inspiriert, der 1996 in einem klassischen iid-Modell von Donoho, Johnstone, Kerkyacharian und Picard konstruiert wurde. Unter gewissen Ergodizitätsvoraussetzungen an den Prozess können wir nichtparametrische Konvergenzraten angegeben, die bis auf einen logarithmischen Term den Raten im klassischen iid-Fall entsprechen. Diese Raten werden mit Hilfe von Orakel-Ungleichungen gezeigt, die auf Ergebnissen über Markovketten in diskreter Zeit von Clémencon, 2001, beruhen. Außerdem betrachten wir einen technisch einfacheren Spezialfall und zeigen einige Computersimulationen dieses Schätzers.

Pre-edge analysis of X-rays absorption spectra in TiO2 modified films

The thesis is mainly focused on the pre-edge analysis of XAS spectra of Ti HCF sample hexacyanocobaltate and hexacyanoferrate samples doped on a Indium Tin Oxide (ITO) thin film. The work is aimed at the determination of Ti oxidation state, as well as indication of various coordination number in the studied samples. The experiment have been conducted using XAFS (X-ray absorption fine structure)beamline at Elettra synchrotron, Trieste (Italy) under supervision of Professor Marco Giorgetti, Department of Industrial Chemistry, University of Bologna. The Master thesis accreditation to fullfill the ASC Master of Advanced Spectroscopy in Chemistry Degree requirement.

High precision radial velocities with giano spectra

Radial velocities measured from near-infrared (NIR) spectra are a potential tool to search for extrasolar planets around cool stars. High resolution infrared spectrographs now available reach the high precision of visible instruments, with a constant improvement over time. GIANO is an infrared echelle spectrograph and it is a powerful tool to provide high resolution spectra for accurate radial velocity measurements of exo-planets and for chemical and dynamical studies of stellar or extragalactic objects. No other IR instruments have the GIANO's capability to cover the entire NIR wavelength range. In this work we develop an ensemble of IDL procedures to measure high precision radial velocities on a few GIANO spectra acquired during the commissioning run, using the telluric lines as wevelength reference. In Section 1.1 various exoplanet search methods are described. They exploit different properties of the planetary system. In Section 1.2 we describe the exoplanet population discovered trough the different methods. In Section 1.3 we explain motivations for NIR radial velocities and the challenges related the main issue that has limited the pursuit of high-precision NIR radial velocity, that is, the lack of a suitable calibration method. We briefly describe calibration methods in the visible and the solutions for IR calibration, for instance, the use of telluric lines. The latter has advantages and problems, described in detail. In this work we use telluric lines as wavelength reference. In Section 1.4 the Cross Correlation Function (CCF) method is described. This method is widely used to measure the radial velocities.In Section 1.5 we describe GIANO and its main science targets. In Chapter 2 observational data obtained with GIANO spectrograph are presented and the choice criteria are reported. In Chapter 3 we describe the detail of the analysis and examine in depth the flow chart reported in Section 3.1. In Chapter 4 we give the radial velocities measured with our IDL procedure for all available targets. We obtain an rms scatter in radial velocities of about 7 m/s. Finally, we conclude that GIANO can be used to measure radial velocities of late type stars with an accuracy close to or better than 10 m/s, using telluric lines as wevelength reference. In 2014 September GIANO is being operative at TNG for Science Verification and more observational data will allow to further refine this analysis.

Searching for outflows signatures in sdss spectra of x-ray selected, obscured agn in the cosmos field

Partendo dal campione di AGN presente nella survey di XMM-COSMOS, abbiamo cercato la sua controparte ottica nel database DR10 della Sloan Digital Sky Survey (SDSS), ed il match ha portato ad una selezione di 200 oggetti, tra cui stelle, galassie e quasar. A partire da questo campione, abbiamo selezionato tutti gli oggetti con un redshift z<0.86 per limitare l’analisi agli AGN di tipo 2, quindi siamo giunti alla selezione finale di un campione di 30 sorgenti. L’analisi spettrale è stata fatta tramite il task SPECFIT, presente in IRAF. Abbiamo creato due tipi di modelli: nel primo abbiamo considerato un’unica componente per ogni riga di emissione, nel secondo invece è stata introdotta un’ulteriore com- ponente limitando la FWHM della prima ad un valore inferiore a 500 km\s. Le righe di emissione di cui abbiamo creato un modello sono le seguenti: Hβ, [NII]λλ 6548,6581, Hα, [SII]λλ 6716,6731 e [OIII]λλ 4959,5007. Nei modelli costruiti abbiamo tenuto conto della fisica atomica per quel che riguarda i rapporti dei flussi teorici dei doppietti dell’azoto e dell’ossigeno, fissandoli a 1:3 per entrambi; nel caso del modello ad una componente abbiamo fissato le FWHM delle righe di emissione; mentre nel caso a due componenti abbiamo fissato le FWHM delle componenti strette e larghe, separatamente. Tenendo conto del chi-quadro ottenuto da ogni fit e dei residui, è stato possibile scegliere tra i due modelli per ogni sorgente. Considerato che la nostra attenzione è focalizzata sulla cinematica dell’ossigeno, abbiamo preso in considerazione solo le sorgenti i cui spettri mostravano la riga suddetta, cioè 25 oggetti. Su questa riga è stata fatta un’analisi non parametrica in modo da utilizzare il metodo proposto da Harrison et al. (2014) per caratterizzare il profilo di riga. Sono state determinate quantità utili come il 2 e il 98 percentili, corrispondenti alle velocità massime proiettate del flusso di materia, e l’ampiezza di riga contenente l’80% dell’emissione. Per indagare sull’eventuale ruolo che ha l’AGN nel guidare questi flussi di materia verso l’esterno, abbiamo calcolato la massa del gas ionizzato presente nel flusso e il tasso di energia cinetica, tenendo conto solo delle componenti larghe della riga di [OIII] λ5007. Per la caratterizzazione energetica abbiamo considerato l’approccio di Cano-Diaz et al (2012) e di Heckman (1990) in modo da poter ottenere un limite inferiore e superiore della potenza cinetica, adottando una media geometrica tra questi due come valore indicativo dell’energetica coinvolta. Confrontando la potenza del flusso di gas con la luminosità bolometrica dell’AGN, si è trovato che l’energia cinetica del flusso di gas è circa lo 0.3-30% della luminosità dell’AGN, consistente con i modelli che considerano l’AGN come principale responsabile nel guidare questi flussi di gas.

Wavetrack, implementazione ottimizzata di un algoritmo di pitch tracking basato su wavelet

WaveTrack é un'implementazione ottimizzata di un algoritmo di pitch tracking basato su wavelet, nello specifico viene usata la trasformata Fast Lifting Wavelet Transform con la wavelet di Haar. La libreria è stata scritta nel linguaggio C e tra le sue peculiarità può vantare tempi di latenza molto bassi, un'ottima accuratezza e una buona flessibilità d'uso grazie ad alcuni parametri configurabili.

COSMIC-LAB: Unexpected Results from High-resolution Spectra of AGB Stars in Globular Clusters

We have used high-resolution spectra, acquired with UVES@ESO-VLT, to determine the chemical abundances of different samples of AGB and RGB stars in 4 Galactic globular clusters, namely 47Tuc, NGC3201, M22 and M62. For almost all the analyzed AGB stars we found a clear discrepancy between the iron abundance measured from neutral lines and that obtained from single ionized lines, while this discrepancy is not obtained for the RGB samples observed in the same clusters and analyzed with the same procedure. Such a behavior exactly corresponds to what expected in the case of Non-Local Thermodynamical Equilibrium (NLTE) in the star atmosphere. These results have a huge impact on the proper determination of GC chemistry. In fact, one of the most intriguing consequences is that, at odds with previous claims, no iron spread is found in NGC3201 and M22 if the iron abundance is obtained from ionized lines only.

Trasformate wavelet

La presente tesi vuole dare una descrizione delle Trasformate Wavelet indirizzata alla codifica dell’immagine in formato JPEG2000. Dopo aver quindi descritto le prime fasi della codifica di un’immagine, procederemo allo studio dei difetti derivanti dall’analisi tramite la Trasformata Discreta del Coseno (utilizzata nel formato predecessore JPEG). Dopo aver quindi descritto l’analisi multirisoluzione e le caratteristiche che la differenziano da quest’ultima, analizzeremo la Trasformata Wavelet dandone solo pochi accenni teorici e cercando di dedurla, in una maniera più indirizzata all’applicazione. Concluderemo la tesi descrivendo la codifica dei coefficienti calcolati, e portando esempi delle innumerevoli applicazioni dell’analisi multirisoluzione nei diversi campi scientifici e di trasmissione dei segnali.

Analyse zur Auswirkung der irreversiblen Wavelet-Kompression (JPEG2000) auf CT-Bildverarbeitungs- und Darstellungsalgorithmen

Der technische Fortschritt konfrontiert die medizinische Bildgebung wie keine andere Sparte der Medizin mit einem rasanten Anstieg zu speichernder Daten. Anschaffung, Wartung und Ausbau der nötigen Infrastruktur entwickeln sich zunehmend zu einem ökonomischen Faktor. Ein Verfahren, welches diesem Trend etwas entgegensetzten könnte ist die irreversible Bilddatenkompression. Sie ist seit über 10 Jahren Gegenstand vieler Studien, deren Ergebnisse sich wiederum in Empfehlungen zum Einsatz irreversibler Kompression mehrerer nationaler und internationaler Organisation, wie CAR, DRG, RCR und ESR wiederspiegeln. Tenor dieser Empfehlungen ist, dass der Einsatz von moderater irreversibler Bilddatenkompression sicher und sinnvoll ist. Teil dieser Empfehlungen sind auch Angaben über das Maß an Kompression, ausgedrückt in Kompressionsraten, welche je nach Untersuchung und anatomischer Region als sicher anwendbar gelten und keinen diagnostisch relevanten Verlust der komprimierten Bilder erzeugen.rnVerschiedene Kompressionsalgorithmen wurden vorgeschlagen. Letztendlich haben sich vor allem die beiden weit verbreiteten Algorithmen JPEG und JPEG2000 bewährt. Letzterer erfährt in letzter Zeit zunehmen Anwendung, aufgrund seiner einfacheren Handhabung und seiner umfangreichen Zusatzfunktionen.rnAufgrund rechtlich-ethischer Bedenken hat die irreversible Kompression keine breite praktische Anwendung finden können. Dafür verantwortlich ist unter anderem auch die Unklarheit, wie sich irreversible Kompression auf Nach- und Weiterverarbeitung (sog. Postprocessing) medizinischer Bilder, wie Segmentierung, Volumetrie oder 3D-Darstellung, auswirkt. Bisherige Studien zu diesem Thema umfassen vier verschiedene Postprocessing-Algorithmen. Die untersuchten Algorithmen zeigten sich bei verlustbehafteter Kompression im Bereich der erwähnten, publizierten Kompressionsraten weitgehend unbeeinflusst. Lediglich die computergestützte Messung von Stenosegraden in der digitalen Koronarangiographie kollidiert mit den in Großbritannien geltenden Empfehlungen. Die Verwendung unterschiedlicher Kompressionsalgorithmen schränkt die allgemeinernAussagekraft dieser Studienergebnisse außerdem ein.rnZur Erweiterung der Studienlage wurden vier weitere Nach- und Weiterverarbeitungsalgorithmen auf ihre Kompressionstoleranz untersucht. Dabei wurden die Kompressionsraten von 8:1, 10:1 und 15:1 verwendet, welche um die empfohlenen Kompressionsraten von CAR, DRG, RCR und ESR liegen und so ein praxisnahes Setting bieten. Als Kompressionsalgorithmus wurde JPEG2000 verwendet, aufgrund seiner zunehmenden Nutzung in Studien sowie seiner bereits erwähnten Vorzüge in Sachen Handhabung und Zusatzfunktionen. Die vier Algorithmen umfassten das 3D-Volume rendering von CT-Angiographien der Becken-Bein-Gefäße, die Computer-assistierte Detektion von Lungenrundherden, die automatisierte Volumetrie von Leberrundherden und die funktionelle Bestimmung der Ejektionsfraktion in computertomographischen Aufnahmen des Herzens.rnAlle vier Algorithmen zeigten keinen Einfluss durch irreversibler Bilddatenkompression in denrngewählten Kompressionsraten (8:1, 10:1 und 15:1). Zusammen mit der bestehenden Literatur deuten die Ergebnisse an, dass moderate irreversible Kompression im Rahmen aktueller Empfehlungen keinen Einfluss auf Nach- und Weiterverarbeitung medizinischer Bilder hat. Eine explizitere Vorhersage zu einem bestimmten, noch nicht untersuchten Algorithmus ist jedoch aufgrund der unterschiedlichen Funktionsweisen und Programmierungen nicht sicher möglich.rnSofern ein Postprocessing Algorithmus auf komprimiertes Bildmaterial angewendet werden soll, muss dieser zunächst auf seine Kompressionstoleranz getestet werden. Dabei muss der Test eine rechtlich-ethische Grundlage für den Einsatz des Algorithmus bei komprimiertem Bildmaterial schaffen. Es sind vor allem zwei Optionen denkbar, die Testung institutsintern, eventuell unter Zuhilfenahme von vorgefertigten Bibliotheken, oder die Testung durch den Hersteller des Algorithmus.

Data analysis and simulations of VIRTIS venus spectra

VIRTIS, a bordo di Venus Express, è uno spettrometro in grado di operare da 0.25 a 5 µm. Nel periodo 2006-2011 ha ricavato un'enorme mole di dati ma a tutt'oggi le osservazioni al lembo sono poco utilizzate per lo studio delle nubi e delle hazes, specialmente di notte. Gli spettri al lembo a quote mesosferiche sono dominati dalla radianza proveniente dalle nubi e scatterata in direzione dello strumento dalle hazes. L'interpretazione degli spettri al lembo non può quindi prescindere dalla caratterizzazione dell'intera colonna atmosferica. L'obiettivo della tesi è di effettuare un’analisi statistica sulle osservazioni al nadir e proporre una metodologia per ricavare una caratterizzazione delle hazes combinando osservazioni al nadir e al lembo. La caratterizzazione delle nubi è avvenuta su un campione di oltre 3700 osservazioni al nadir. È stato creato un ampio dataset di spettri sintetici modificando, in un modello iniziale, vari parametri di nube quali composizione chimica, numero e dimensione delle particelle. Un processo di fit è stato applicato alle osservazioni per stabilire quale modello potesse descrivere gli spettri osservati. Si è poi effettuata una analisi statistica sui risultati del campione. Si è ricavata una concentrazione di acido solforico molto elevata nelle nubi basse, pari al 96% in massa, che si discosta dal valore generalmente utilizzato del 75%. Si sono poi integrati i risultati al nadir con uno studio mirato su poche osservazioni al lembo, selezionate in modo da intercettare nel punto di tangenza la colonna atmosferica osservata al nadir, per ricavare informazioni sulle hazes. I risultati di un modello Monte Carlo indicano che il numero e le dimensioni delle particelle previste dal modello base devono essere ridotte in maniera significativa. In particolare si osserva un abbassamento della quota massima delle hazes rispetto ad osservazioni diurne.

Trasformata di Fourier e trasformata Wavelet

Questo elaborato si concentra sullo studio della trasformata di Fourier e della trasformata Wavelet. Nella prima parte della tesi si analizzano gli aspetti fondamentali della trasformata di Fourier. Si definisce poi la trasformata di Fourier su gruppi abeliani finiti, richiamando opportunamente la struttura di tali gruppi. Si mostra che calcolare la trasformata di Fourier nel quoziente richiede un minor numero di operazioni rispetto a calcolarla direttamente nel gruppo di partenza. L'ultima parte dell'elaborato si occupa dello studio delle Wavelet, dette ondine. Viene presentato quindi il sistema di Haar che permette di definire una funzione come serie di funzioni di Haar in alternativa alla serie di Fourier. Si propone poi un vero e proprio metodo per la costruzione delle ondine e si osserva che tale costruzione è strettamente legata all'analisi multirisoluzione. Un ruolo cruciale viene svolto dall'identità di scala, un'identità algebrica che permette di definire certi coefficienti che determinano completamente le ondine. Interviene poi la trasformata di Fourier che riduce la ricerca dei coefficienti sopra citati, alla ricerca di certe funzioni opportune che determinano esplicitamente le Wavelet. Non tutte le scelte di queste funzioni sono accettabili. Ci sono vari approcci, qui viene presentato l'approccio di Ingrid Daubechies. Le Wavelet costituiscono basi per lo spazio di funzioni a quadrato sommabile e sono particolarmente interessanti per la decomposizione dei segnali. Sono quindi in relazione con l'analisi armonica e sono adottate in un gran numero di applicazioni. Spesso sostituiscono la trasformata di Fourier convenzionale.

Two-dimensional linear-combination model fitting of magnetic resonance spectra to define the macromolecule baseline using FiTAID, a Fitting Tool for Arrays of Interrelated Datasets

To propose the determination of the macromolecular baseline (MMBL) in clinical 1H MR spectra based on T(1) and T(2) differentiation using 2D fitting in FiTAID, a general Fitting Tool for Arrays of Interrelated Datasets.

Magnetization exchange with water and T(1) relaxation of the downfield resonances in human brain spectra at 3.0 T

The use of water suppression for in vivo proton MR spectroscopy diminishes the signal intensities from resonances that undergo magnetization exchange with water, particularly those downfield of water. To investigate these exchangeable resonances, an inversion transfer experiment was performed using the metabolite cycling technique for non-water-suppressed MR spectroscopy from a large brain voxel in 11 healthy volunteers at 3.0 T. The exchange rates of the most prominent peaks downfield of water were found to range from 0.5 to 8.9 s(-1), while the T(1) relaxation times in absence of exchange were found to range from 175 to 525 ms. These findings may help toward the assignments of the downfield resonances and a better understanding of the sources of contrast in chemical exchange saturation transfer imaging.