In this work a reversible transition between CeO2/Cu(111) and Ce2O3/Cu(111) was studied by metalic ceria evaporation and oxygen exposition. Prepared layers were characterised by XPS, ISS (and its angle resolved modification), LEED and XPD combined with computer modelling using EDAC code. Four reconstructi- on were identified within the transition - ( √ 7 × √ 7)R19.1◦ , ( √ 3 × √ 3)R30◦ , 3 × 3 and 4 × 4 - for which structural models were suggested. Prepared layers of Ce2O3/Cu(111) exhibiting the 4×4 reconstruction were identified as a cubic pha- se of Ce2O3 by the combination of all methods. The photoelectron spectroscopy study of the chemical state of layers revealed that reduction proceedes from the surface and oxidation is realised by oxygen diffusion into the volume.

Doctoral thesis is dealing with the methods for analysis of surfaces by photoelectrons being emitted by X-ray radiation. The methods are: X-ray Photoelectron Spectroscopy - XPS, Angle-resolved XPS - ARXPS and X-ray Photoelectron Diffraction - XPD. The work is especially focused on a method of ARXPS, which is used for the depth compositional analysis of sample surfaces. To obtain an information about the depth composition from the measured ARXPS spectra, a calculation software in the Matlab environment has been developed. The software has been tested both for simulated and real sample data. For an experimental implementation of these methods, a complete manipulation system has been developed. It ensures the transport of samples inside a vacuum apparatus and the experiment itself. The system is controlled mainly by a software and enables to run the experiments automatically.

L'objectif de cette thèse est d'étudier les propriétés physico-chimiques des surfaces et des interfaces des couches minces par spectroscopie de photoémission (XPS), diffraction des photoélectrons (XPD), et la photoémission résolue en temps (PTR). Les expériences sont réalisées en utilisant une source standard des rayons X AlKa à l'INL ou les rayons X mous auprès du synchrotron Soleil. La première étude sur le système Pt/ Gd203/ Si(111) a montré que le transfert de charge entre le Pt et 0 à l'interface Pt/Gd203 implique un déplacement chimique de niveau Pt4f sans modification des caractéristiques de la composante métallique des spectres XPS. L'étude XPD montre que Pt se cristallise partiellement en deux domaines : [110] Pt(111) // [110] Gd203 (111) et [101] Pt(111) / / [110] Gd203 (111). De plus, une autre phase ordonnée d'oxyde de platine Pt02 à l'interface a été observée. A travers la caractérisation de la morphologie déterminée par la technique AFM et XPD, nous avons discuté l'adhésion aux interfaces métal/oxyde. La deuxième étude traite l'évolution d'interface d'un système modèle : métal non réactive/ semi-conducteur, dépendent fortement des conditions thermodynamiques. Nous avons étudié la couche mince d'Au déposée sur le substrat Si(001) par photoémission résolue en temps (TEMPO- synchrotron Soleil). L'étude XPS, montre avant le recuit la formation de l'oxyde native Si02 sur l'heterostructure à température ambiante. La désorption de cet oxyde se produit à faible température et induit une décroissance de l'intensité des photoélectrons durant le temps de recuit. La désorption de l'oxyde Si02 et la formation de l'alliage AuSi sont responsables de la gravure et la formation des puits de forme cubique à la surface de Si due à l'activité catalytique de l'Au. La troisième étude concerne la croissance du graphène à partir de cristal de SiC(0001)- face Si par décomposition thermique. Le niveau de coeur C1s résolu en trois composantes principales sont associées au carbone de 6H-SiC, de graphène, et l'interface graphène/ 6H-SiC (0001). L'intensité de chaque composante est rapportée en fonction de l'angle polaire (azimutale) pour différents angles azimutales (polaire). Les mesures XPD fournissent des informations cristallographiques qui indiquent clairement que les feuillets de graphène sont organisés en structure graphite sur le substrat 6H-SiC (0001). Cette organisation résulte de l’effondrement de la maille de substrat. Enfin, le découplage à l'interface graphène/ 6H-SiC (0001) par l'oxygène a été étudié par XPS. La dernière étude concerne la croissance du film mince d'InP par MBE sur le substrat SrTi03 (001). L'intégration des semi-conducteurs III-V sur le Si, en utilisant la couche tampon d'oxyde SrTi03 est l'objet des intenses recherches, en raison des applications prometteuses dans le domaine de nano-optoélectronique. Les niveaux de coeur O1s, Sr3d, Ti2p, In3d, P2p ont été analysés et rapportés en fonction de l'angle azimutale à différents angles polaires. La comparaison des courbes XPD azimutales de Sr3d et In3d montre que les ilots InP sont orientées (001) avec la relation d'épitaxie; [110]InP(001 )/ / [100]! SrTi03 (001). La caractérisation morphologique par AFM montre des ilots InP facettés régulièrement dispersée à la surface. / The main objective of this thesis is to study the chemical and physical properties at the surface or at the interface between thin layers by photoemission spectroscopy (XPS), photoelectron diffraction (XPD), and time resolved photoemission (PTR) . The experiments were conducted using an Alka source at INL or soft -X ray synchrotron radiation at Soleil, the French national Synchrotron facility. The first photoemission study has been performed on platinum deposited on thin Gd2(h layers grown by Molecular Bearn Epitaxy (MBE) on Si (111) substrate. The charge transfer between Pt and 0 at the interface causes a chemical shift to higher binding energies without changing the characteristic shape of the metal XPS peak. The XPD study shows that Pt is partially crystallized into two (111)-oriented do mains on Gd20 3 (111) with the in-plane epitaxial relationships [11 0] Pt (111) / / [11 0] Gd203 (111) and [101] Pt(111)/ / [11 0] Gd20 3 (111). In addition to bi-domains formation of platinum Pt (111) on Gd20 3 (111), a new ordered phase of platinum oxide Pt02 at the Pt/ Gd203 interface have been observed. The study of the background of the polar curves depending of the morphology has shown, that the film of Pt does not wet on the oxide, due to the low energy of interaction at the interface compared to the Pt thin layer. The second study has been interested to the photoemission time-resolved study of non-reactive metal / semiconductor model system. We have studied the thin layer gold (Au) growth on silicon (Si) substrate before and during annealing in TEMPO beam line (synchrotron Soleil).The XPS study, shows before annealing the formation of silicon native oxide on heterostructure at ambient temperature. The desorption of silicon oxide during annealing at low temperature induce photoemission intensity decreases with time. The desorption of oxide and alloy formation (AuSi) induce distribution of pits with cubic form at silicon surface due to gold etching activity. The third photoemission study has concerned thin films of a few layers of graphene obtained by solid-state graphitization from 6H-SiC (0001) substrates have been studied by X-ray photoelectron spectroscopy (XPS) and X-ray photoelectron diffraction (XPD). The Cls core-level has been resolved into components, which have been associated with carbon from bulk SiC, carbon from graphene and carbon at the interface graphene/ 6H-SiC (0001). Then, the intensity of each of these components has been recorded as a function of polar (azimuth) angle for several azimuth (polar) angles. These XPD measurements provide crystallographic information which clearly indicates that the graphene sheets are organized in graphite-like structure on 6H-SiC(0001), an organization that results of the shrinking of the 6H-SiC (0001) lattice after Si depletion. Finally the decoupling of graphene from 6H-SiC (0001) substrate by oxygen intercalation has been studied from the XPS point of view. Finally, photoemission study has concerned thin film of InP (phosphor indium ) islands grown by Molecular Bearn Epitaxy (MBE) on SrTi03 (001) bulk substrate have been investigated by X-ray photoelectron spectroscopy and diffraction (XPS/ XPD).Integration of III-V semi-conductor on silicon wafer, via SrTi03 buffer is currently the subject of intense research because of its potentially interesting applications in future nano-optoelectronics. The Ols, Sr3d, Ti2p, In3d, and P 2p core level area have been studied as function of azimuth angle for different polar angles. Comparison of the XPD azimuth curves of Sr3d and In3d shows that islands InP are oriented (001) with an in-plane epitaxial relationship [110] InP(001 ) // [100] SrTi03 (001). AFM images shows that InP islands are regularly dispersed on the surface. Their shape is a regularly facetted half-sphere.

Made available in DSpace on 2014-12-17T15:32:32Z (GMT). No. of bitstreams: 1 JoabeSP_TESE.pdf: 3616540 bytes, checksum: 2904dbfc0f83145c9569635cf5feba21 (MD5) Previous issue date: 2013-09-16 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / Oral squamous cell carcinoma (OSCC) is an important cause of morbidity and mortality worldwide despite recent advances in treatment. There are several studies aiming to find markers that may improve the assessment of this disease prognosis. Studies about genetic polymorphisms have gained prominence due to their influence on individual susceptibility to cancer development. The aim of this study was to evaluate the association between the frequency of polymorphisms XPD Lys751Gln and XRCC3 Thr241Met and clinicopathological features of OSCC cases, including age, sex, presence or absence of metastases, and histological grading of malignancy according to Bryne (1998). Sample consisted of 54 cases of OSCC and 40 cases of inflammatory fibrous hyperplasia (IFH). OSCC cases were classified as low or high grade. DNA samples were previously extracted from paraffin blocks. Genotypes for each case were determined through PCR-RFLP (polymerase chain reaction - restriction fragment length polymorphism). Results were analyzed by Fisher s exact test and Chi-square test and the odds ratio was calculated considering p < 0.05 to indicate statistical significance. For XPD, Lys/Gln genotype was more common in IFHs (n=28; 70%) than in OSCCs (n=24; 44.4%) (OR: 0.3; p<0.05). Frequency of Gln allele was higher in high-grade lesions when compared to low grade lesions (0.48 and 0.21, respectively) (OR: 3.4; p<0.05). For XRCC3, Met allele was more common in OSCC than in IFH (0.49 and 0.35, respectively) (OR: 2.6; p<0.05). Met/Met genotype was associated with presence of metastases (OR: 8.1; p<0.05). There was no statistically significant association between the genotypes and the age or sex of patients. In the present sample, the higher frequency of XPD Gln allele in IFH reveals a possible protective role of this variant against the development of OSCC. However, its association with high-grade lesions indicates that this allele could influence the tumor progression after the neoplasia development. The presence of XRCC3 Met allele, in turn, seems to contribute to the development of OSCC and metastases / O carcinoma oral de c?lulas escamosas (COCE) ? importante causa de morbidade e mortalidade em todo o mundo a despeito dos recentes avan?os nas formas de tratamento. Diante disto, v?rias s?o as pesquisas no intuito de se encontrar marcadores que possam melhorar o progn?stico desta doen?a. Neste sentido t?m se destacado os estudos dos polimorfismos gen?ticos, os quais podem influenciar a suscetibilidade individual para o desenvolvimento do c?ncer. O objetivo deste estudo foi avaliar a associa??o entre a frequ?ncia dos polimorfismos XPD Lys751Gln e XRCC3 Thr241Met e o perfil clinicopatol?gico em casos de COCE, incluindo idade, sexo, presen?a ou n?o de met?stase e grada??o histol?gica de malignidade de Bryne (1998). A amostra foi composta por 54 casos de COCE e 40 casos de hiperplasia fibrosa inflamat?ria (HFI). Os casos de COCE foram classificados como les?es de baixo ou de alto grau de malignidade. Foram utilizadas amostras de DNA previamente extra?do de blocos de parafina. Os gen?tipos para cada caso foram determinados atrav?s da t?cnica de PCR-RFLP (rea??o em cadeia da polimerase - polimorfismos de comprimento de fragmentos de restri??o). Os resultados foram submetidos aos testes estat?sticos Exato de Fisher e Qui-quadrado de Pearson e foi calculada a raz?o de chance (odds ratio) considerando o n?vel de signific?ncia quando p<0,05. Para o XPD, o gen?tipo Lys/Gln foi mais comum nas HFIs (n=28; 70%) que nos COCEs (n=24; 44,4%) (OR: 0,3; p<0,05). A frequ?ncia do alelo Gln foi maior nas les?es de alto grau, em compara??o ?s de baixo grau (0,48 e 0,21, respectivamente) (OR: 3,4; p<0,05). Para o XRCC3, o alelo Met foi mais frequente no COCE que na HFI (0,49 e 0,35, respectivamente) (OR: 2,6; p<0,05). O gen?tipo Met/Met foi associado ? presen?a de met?stases (OR: 8,1; p<0,05). N?o houve associa??o estat?stica significativa entre os gen?tipos e a idade ou sexo dos pacientes. Na amostra analisada, a maior frequ?ncia do alelo XPD Gln na HIF revela um poss?vel papel protetor dessa variante contra o desenvolvimento do COCE. Todavia, sua associa??o com les?es de alto grau, indica que esse alelo poderia influenciar no processo de progress?o ap?s o tumor instalado. A presen?a do alelo XRCC3 Met, por sua vez, parece contribuir com o desenvolvimento do COCE e de met?stases nessas les?es

Throughout the last half century of materials science, significant motivations came from, and still do, the industrial applications of these materials. Whether it is electronic, thermal, tribological or chemical in nature, the study of metals, semiconductors and insulators eventually reveals that the surface plays a significant part in the properties of these materials. Understanding metal terminations reveals often that an oxide is the stable state of the metallic surface in an ambient atmosphere and the ability to predict and control these oxides has led to significant strides forward in not just the metallic bulk but the oxide as well. Here we add to the understanding of the class of materials known as transition metal oxides by focusing on the structural and chemical nature of their surfaces. Vanadia, chromia and a new mixed metal oxide, VTiO3, all of which form the corundum structure and have physical properties that need further study. Specifically, Cr2O3 has been at the center of much debate over how oxygen chemical potential influences surface terminations and top layer relaxation. Chromia is a wide band gap (~3.4eV) insulator with substantial ligand field interaction and measurements of the 3d states reveal these states split to t2g and eg– consistent with the distorted octahedral. V2O3 is known to be a Mott insulator and paramagnetic, properties that can be modified through dopants, stoichiometry and strain. In this work, solid solutions of V2O3 and Ti2O3 are studied. VTiO3, has been synthesized in a corundum – like structure by epitaxial growth on an isostructural α-Al2O3 substrate. Section I offers a review of corundum like transition metal oxides and their surface properties and motivations of continued research. In section II we describe in detail, the critical components of PLD thin film growth and in the next section a review of the pertinent characterization techniques utilized in the process. Finally, the results are presented of the study of two transition metal oxide structures namely: 1) Novel VTiO3 in a corundum structure has been grown via Pulsed Laser Deposition – Molecular Beam Epitaxy on a single crystal Al2O3(0001) substrate. The sapphire substrate with modest lattice mismatch was utilized in an effort to compel heteroepitaxial growth of the VTiO3 film. Confirmation of the films structure & chemical state were performed by X-Ray diffraction, Transmission Electron Microscopy (HR), X-Ray Photo-electron Diffraction, Ultra-Violet Photo-Electron Diffraction and Reflection High Energy Electron expected that the metal ions exist in a 3+ charge state. While XPS clearly points to a V3+ charge state and this suggests that Ti should as well, however there is also a strong Ti4+ component present. EELS spectra support the existence of a mixed state Ti3+ & 4+. Broadening of the valance band edge as revealed by UPS spectra indicate that the 3d orbitals are occupied and that the a1g molecular states are occupied. The conflict in diffraction data supporting corundum and PES/EELS data suggesting a mixed state implies that additional final state effects are present and/or an oxygen rich structure. 2) Additionally, corundum like Chromium(III) Oxide is formed on a Cr(110) surface and characterized with X-Ray Photoelectron Diffraction, Low Energy Electron Diffraction and XPS for the purpose of characterizing surface termination and terminating layer relaxation. Comparison of the XPD diffraction data with known and previously discussed terminations reveal the as grown film does not conform. Consequently, we propose a new, stoichiometric termination with oxygen termination and 1st layer chromium interstitials. Atop this structure was grown an ultra-thin film of V2O3 by vanadium e-beam evaporation in background oxygen. This final structure supports the previously proposed vanadyl structured surface

The isolation of single layers of van der Waals materials has shown that their properties can be significantly different compared to their bulk counterparts. These observations, illustrates the importance of interface interactions for determining the materials properties even in weakly interacting materials and raise the question if materials properties of single layer van der Waals materials can be controlled by appropriate hetero-interfaces. To study interface effects in monolayer systems, surface science techniques, such as photoemission spectroscopy and scanning probe microscopy/spectroscopy, are ideally suited. However, before these characterization methods can be employed, approaches for the synthesis of hetero-van der Waals systems must be developed, preferably in-situ with the characterization methods, i.e. in ultra-high vacuum. Therefore, in this thesis, we explored novel approaches for creating van der Waals heterostructures and characterized fundamental structural and electronic properties of such systems. Specifically, we developed an approach to decouple graphene from a Ir(111) growth substrate by intercalation growth of a 2D-FeO layer, and we investigate van der Waals epitaxy of MoSe2 on graphite and other transition metal dichalcogenide substrates. For the Ir(111)/2D-FeO/graphene heterostructure system, we first demonstrated the growth of 2D-FeO on Ir(111). The FeO monolayer on Ir(111) exhibits a long range moiré structure indicating the locally varying change of the coordination of the Fe atoms with respect to the substrate Ir atoms. This variation also gives rise to modulations in the Fe2+-O2- separation, and thus in the monolayer dipole. We demonstrated that this structure can be intercalated underneath of graphene grown on Ir(111) by chemical vapor deposition. The modulation of the dipole in the 2D-FeO moiré structure consequently gives rise to a modulated charge doping in the graphene. This effect has been studied by C-1s core level broadening. In general, this study demonstrates that modulated substrates can be used to periodically modify 2D materials. Growth of transition metal dichalcogenides (TMDCs) by molecular beam epitaxy (MBE) is a very versatile approach for growing TMDC heterostructures. However, there may be unforeseen challenges in the synthesis of some of these materials. Here we show that in MBE growth of MoSe2, the formation of twin grain boundaries is very abundant. While this is detrimental in our efforts for characterizing interface properties of TMDC heterostructures, however the twin grain boundaries have exciting properties. Since the twin grain boundaries are aligned in an epitaxial film we were able to characterize their properties by angle resolved photoemission spectroscopy (ARPES), which may be the first time a material’s line defects could be studied by this method. We demonstrate that the line defects are metallic and exhibit a parabolic dispersing band. Because of the 1D nature of the metallic lines, embedded in a semiconducting matrix, the electronic structure follows a Tomonaga Luttinger formalism and our studies showed strong evidence of the predicted so-called spin charge separation in such 1D electron systems. Moreover, a metal-to-insulator Peierls transition has been observed in this system by scanning tunneling microscopy as well as in transport measurements. Finally, we have shown that the defect network that forms at the surface also lends itself for decoration with metal clusters. Although unexpected, the formation of grain boundary networks in MoSe2 marks the discovery of a new material with exciting quantum properties.

Internet of Things (IoT) is a phenomenon that involves providing things or objects with sensors and internet connection. The field of IoT is growing rapidly and there are strong incentives for companies to follow the trend to develop and create an IoT. However, the proportion of IoT initiatives considered to be successful has been shown to be low. This study therefore investigates how a project methodology can support a concept development and secure the business value for IoT initiatives. The project methodology developed in this study is named eXtreme PoC Development (XPD). XPD is based on existing project methodologies from literature and interviews from consulting companies within the field in the Stockholm region. It was evaluated by a case study where fault detection in street lighting was investigated and implemented. The evaluation of the methodology highlighted the importance of defining problems and solutions that are anchored in the business value, calculating a potential of an IoT initiative that determines the continuation of a project, involving stakeholders at an early stage and developing a PoC to validate and evaluate a concept with stakeholders. / Internet of Things (IoT) är ett fenomen som innebär att förse saker eller objekt med sensorer och internetförbindelse. Området för IoT är starkt växande och det finns starka incitament hos företag att följa trenden att utveckla och skapa en IoT. Andelen IoT-initiativ som anses vara framgångsrika har däremot visats sig vara låg. Denna studie undersöker hur en projektmetodik kan stödja en konceptutveckling och säkra affärsnyttan för IoT-initiativ. Projektmetodiken som tagits fram i denna studie benämns eXtreme PoC Development (XPD). XPD baseras på befintliga projektmetodiker från litteratur och intervjuer från konsultbolag i Stockholmsregionen. Den utvärderades genom en fallstudie där feldetektering i ljuspunkter i utomhusmiljö undersöktes och implementerades. Utvärderingen av metodiken belyste vikten av att definiera problem och lösningar som är förankrade i affärsnyttan, att beräkna en potential av ett IoT-initiativ som bestämmer ett projekts fortsättning, att involvera intressenter i ett tidigt stadie och att utveckla en PoC för att validera och utvärdera ett koncept med intressenterna.

Les mémoires flash non volatiles - utilisées dans les ordinateurs, les téléphones portables ou les clés USB - peuvent être constituées de nanostructures semiconductrices (SC) ou métalliques insérées dans une matrice isolante. Elles nécessitent l’élaboration d’hétérostructures de type "oxyde/métal/oxyde/SC" et la maîtrise de chaque interface. Dans ce cadre, nous avons étudié les premiers stades de la croissance de nanostructures de Fer élaborées par épitaxie par jet moléculaire (EJM) sur les substrats d’oxyde (high-k) cristallins LaAlO3(001) et LaAlO3(111). Les propriétés chimiques et structurales ont été déterminées, in-situ, par spectroscopie de photoélectrons X (XPS), diffraction de photoélectrons X (XPD) et diffraction d’électrons (RHEED et LEED) puis ex-situ par microscopie électronique en transmission (TEM). Une étude par simulation des profils XPD, basée sur la théorie de la diffusion multiple, a été menée à l’aide du programme de calcul Ms-Spec. L’étude de la croissance de Fe sur LaAlO3(001) à différentes températures de substrat a montré l’existence d’une fenêtre étroite de température, autour de 500 °C, où la croissance de Fe est épitaxique et de type Volmer-Weber (îlots 3D). Les analyses RHEED, XPD et TEM ont mis en évidence une unique relation d’épitaxie, où la maille élémentaire de Fe est tournée de 45° par rapport à celle du substrat. Les résultats XPS ont montré un environnement chimique unique des atomes de Fer (forme atomique), traduisant l’absence de toute inter-diffusion à l’interface Fe/LaAlO3(001). L’étude de la croissance de Fe sur LaAlO3(111) a également mis en évidence un mode de croissance Volmer-Weber et une interface abrupte. Par ailleurs, tout un travail de développement à l'intérieur du code Ms-Spec a été nécessaire afin de surmonter des problèmes de convergence des calculs de diffusion multiple rencontrés dans le cas d’atomes lourds ayant des énergies cinétiques élevées (atomes de La dans LaAlO3). À cette fin, quatre hypothèses ont été formulés:1- Une prise en compte insuffisante des processus inélastiques :2- L’approximation muffin-tin n'est plus suffisante pour décrire correctement le potentiel ;3- Trop de chemins de faible intensité sont négligés ;4- Divergence de la série de diffusion multiple utilisée pour calculer la section efficace.Les calculs ont montré que les trois premières hypothèses n’ont pas d’influence sur la convergence dans le cas présent. En revanche, la quatrième hypothèse a été validée. En effet, on a montré que du fait du fort pouvoir diffuseur des atomes de La, le développement en série de diffusion multiple pouvait diverger (rayon spectral, i.e. la plus grande des valeurs propres en module de la matrice de diffusion, > 1) pour des grandes tailles d'amas de LaAlO3, alors qu’il converge pour des amas de Si et de MgO de taille similaire (les deux systèmes utilisés en comparaison). Par ailleurs, au-delà de quelques centaines d’atomes, le rayon spectral de LaAlO3, même inférieur à 1, reste important ce qui rend la convergence très lente. / Non-volatile flash memories embedding nanocrystals (NC) are promissing devices for use in computers, mobiles phones or USB keys. The insertion of semiconducting (SC) or metal NC in an insulating matrix requires the elaboration of complex "oxide/metal/oxide/SC" heterostructures and the control of the associated successive growth steps. In this context, we have studied the first growth stades of Fe nanostructures elaborated by Molecular Beam Epitaxy (MBE) on the of crystalline oxides (high-k) substrates of LaAlO3(001) and LaAlO3(111). Chemical and structural properties were investigated in-situ, by X-ray photoelectron spectroscopy (XPS), X-ray photoelectron diffraction (XPD) and electron diffraction (RHEED and LEED), and ex-situ by transmission electron spectroscopy (TEM). A simulation study of XPD profiles, based on the theory of multiple scattering, was conducted using the Ms-Spec calculation program. The study of the growth of Fe on LaAlO3(001) at different substrate temperatures showed the existence of a narrow temperature window, around 500 °C, where Fe has epitaxial growth with Volmer-Weber type (3D islands). The RHEED, XPD and TEM analysis showed a single epitaxial relationship, where the Fe unit cell is rotated by 45° compared to the substrate one. The XPS results showed a unique chemical environment of Fe atoms (atomic form), reflecting the absence of inter-diffusion in the Fe/LaAlO3(001) interface. The study of the Fe grown on LaAlO3(111) also showed a Volmer-Weber growth mode and an abrupt interface.Moreover, further development work within the Ms-Spec code was needed to overcome the issue of multiple scattering calculations convergence usually encountered in the case of heavy atoms with high kinetic energies (La atoms in the LaAlO3). In this regard, four hypotheses were formulated : 1- Insufficient consideration of the inelastic processes ;2- The muffin-tin approximation is no longer sufficient to adequately describe the potential ;3- Unduly low intensity paths are neglected ;4- Divergence of multile scattering series used to calculate the cross section.The calculations allowed us to rule out the first three hypothesis, since no influence on convergence was found in this case. However, the fourth hypothesis was validated. Indeed, it was shown that due to the high power diffuser of the La atoms, the multiple scattering series expansion could diverge (spectral radius, i.e. the largest eigenvalue modulus of the scattering matrix,> 1) for large sizes of LaAlO3 clusters. Whereas, it converges to the clusters of Si and MgO of similar size (both systems used in comparison). Furthermore, even less than 1, spectral radius of LaAlO3 remains important beyond few hundred atoms, thus rendering the convergence very slow.

DNA is constantly damaged by a variety of exogenous and endogenous sources. To maintain the integrity of the genome, different DNA repair mechanisms have evolved, which deal with different kinds of DNA damage. One of the DNA repair pathways, Nucleotide Excision Repair (NER), is highly conserved throughout the three kingdoms of life and deals mainly with lesions arising in the DNA duplex after exposure to UV-light. The NER pathway in archaea is more closely related to that of eukarya, although the overall process is not yet well understood. This thesis describes the isolation and characterisation of one of the repair factors, XPD, from the crenarchaeon Sulfolobus acidocaldarius (SacXPD). SacXPD was first identified due to its homology with the eukaryal XPD protein. In eukarya XPD is the 5a' -> 3a' helicase involved in opening the DNA duplex around a damaged site. In eukarya, XPD is part of a 10-subunit complex, where it fulfils important structural roles and takes part in NER, transcription initiation from RNA polymerase II promoters and cell cycle regulation. The archaeal protein on the contrary is a monomer and a 5a' -> 3a' SF2 DNA helicase as its eukaryal counterpart. Its cellular functions, however, are unclear. Upon purification of SacXPD, it was discovered that the protein binds an ironsulphur cluster (FeS), which is essential for its helicase activity, but not for any other enzymatic functions, such as the ATP hydrolysing activity. The FeS cluster domain was not only identified in archaeal XPD, but also in eukaryal XPD and other related eukaryal helicases, such as FancJ. The presence of the FeS cluster was confirmed in the eukaryotic XPD homologue Rad3 from Saccharomyces cerevisiae. Mutagenesis studies were used to investigate a possible function of the FeS cluster, which may be used to engage ssDNA during the duplex unwinding process. This would actively distort the ss/ ds DNA junction. In addition, the resulting bending of the clamped single DNA strand could be used to avoid reannealing. The consequences of some human mutations introduced into the SacXPD gene were investigated and could contribute to our understanding of the development of human diseases.

Submitted by Automa??o e Estat?stica (sst@bczm.ufrn.br) on 2016-02-29T22:55:50Z No. of bitstreams: 1 StefaniaJeronimoFerreira_TESE.pdf: 1963411 bytes, checksum: 83b197f2ea9b0bdbd5ac4b4732412733 (MD5) / Approved for entry into archive by Arlan Eloi Leite Silva (eloihistoriador@yahoo.com.br) on 2016-03-02T19:57:46Z (GMT) No. of bitstreams: 1 StefaniaJeronimoFerreira_TESE.pdf: 1963411 bytes, checksum: 83b197f2ea9b0bdbd5ac4b4732412733 (MD5) / Made available in DSpace on 2016-03-02T19:57:46Z (GMT). No. of bitstreams: 1 StefaniaJeronimoFerreira_TESE.pdf: 1963411 bytes, checksum: 83b197f2ea9b0bdbd5ac4b4732412733 (MD5) Previous issue date: 2015-02-24 / Conselho Nacional de Desenvolvimento Cient?fico e Tecnol?gico - CNPq / As vias de reparo por excis?o de base (BER) e por excis?o de nucleot?deo (NER) desempenham um papel crucial na manuten??o da integridade gen?mica. Polimorfismos em genes das vias BER e NER, que modulam a capacidade de reparo do DNA, podem estar relacionados ao risco de desenvolvimento e progn?stico do c?ncer oral. O presente trabalho teve como objetivo investigar a frequ?ncia de polimorfismos de nucleot?deos simples, em dois genes da via de reparo do DNA por excis?o de base (XRCC1 ? rs25487 e APEX1 ? rs1130409) e dois genes da via de reparo por excis?o de nucleot?deo (XPD ? rs13181 e XPF ? rs1799797), em pacientes com carcinoma de c?lulas escamosas oral (CCEO), buscando associa??es com o risco de desenvolver esta neoplasia maligna e o seu progn?stico. Um total de 92 amostras de DNA de pacientes com CCEO e 130 controles foram genotipadas utilizando o m?todo da rea??o em cadeia da polimerase em tempo real. O software estat?stico GraphPad Prism version 6.0.1. foi utilizado para a aplica??o dos testes apropriados. Odds ratio (OR) e hazard ratio (HR), e seus intervalos de confian?a (IC) de 95%, foram calculados pela regress?o log?stica. A avalia??o do progn?stico foi realizada por meio da curva de Kaplan-Meier e an?lise multivariada de Cox. A presen?a das variantes polim?rficas nos genes XRCC1, APEX1, XPD, e XPF n?o foram associadas ao risco de desenvolver CCEO. A intera??o da presen?a da variante polim?rfica com o h?bito de fumar n?o foi significativa para nenhum dos polimorfismos analisados. J? a presen?a do polimorfismo em XPD, somada ao h?bito de beber, aumentou o risco de desenvolver CCEO (OR 1,86, 95% IC: 0,86 ? 4,01, p=0,03). Apenas o SNP do APEX1 (rs1130409) esteve associado a uma diminui??o da sobrevida espec?fica (HR 3,94, 95% IC: 1,31 ? 11,88, p=0,01). O presente estudo sugere uma intera??o entre o consumo de ?lcool e a presen?a do polimorfismo estudado no gene XPD. Al?m disso, indica um pior progn?stico para pacientes que possuem o polimorfismo estudado em APEX1. / Base excision repair (BER) and nucleotide excision repair (NER) pathways play critical role in maintaining genome integrity. Polymorphisms in BER and NER genes which modulate the DNA repair capacity may affect the susceptibility and prognosis of oral cancer. This study was conducted with genomic DNA from 92 patients with oral squamous cell carcinomas (OSCC) and 130 controls. The cases were followed up to explore the associations between BER and NER genes polymorphisms and the risk and prognosis of OSCC. Four single-nucleotide polymorphisms (SNPs) in XRCC1 (rs25487), APEX1 (rs1130409), XPD (rs13181) and XPF (rs1799797) genes were tested by polymerase chain reaction ? quantitative real time method. The GraphPad Prism version 6.0.1 statistical software was applied for statistical analysis of association. Odds ratio (OR), hazard ratio (HR), and their 95 % confidence intervals (CIs) were calculated by logistic regression. Kaplan-Meier curve and Cox proportional hazard model were used for prognostic analysis. The presence of polymorphic variants in XRCC1, APEX1, XPD and XPF genes were not associated with an increased risk of OSCC. Gene-environment interactions with smoking were not significant for any polymorphism. The presence of polymorphic variants of the XPD gene in association with alcohol consumption conferred an increased risk of 1.86 (95% CI: 0.86 ? 4.01, p=0.03) for OSCC. Only APEX1 was associated with decreased specific survival (HR 3.94, 95% CI: 1.31 ? 11.88, p=0.01). These results suggest an interaction between polymorphic variants of the XPF gene and alcohol consumption. Additionally APEX1 may represent a prognostic marker for OSCC.