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This dissertation will have three chapters. In chapter one, a comprehensive review on defects in two dimensional materials will be presented. The aim of this review is to elaborate on different types of defects in two dimensional (2D) materials like graphene and transition metal dichalcogenides (TMDs). First, different types of point and line defects, e.g. vacancies, anti-sites, guest elements, adatoms, vacancy clusters, grain boundaries, and edges, in these materials are categorized in terms of structure. Second, interactions among defects are discussed in terms of their rearrangement for low-energy configurations. Before studying the electronic and magnetic properties of defective 2D materials, some of the structures are considered in order to see how defect structure evolves to a stable defect configuration. Next, the influence of defects on electronic and magnetic properties of 2D materials is discussed. Finally, the dynamic behavior of defects and 2D structures under conditions such as electron beam irradiation, heat treatment, and ambient conditions, is discussed. Later as a case study, defects in a two dimensional transition metal dichalcogenide will be presented. Among two-dimensional (2D) transition metal dichalcogenides (TMDs), platinum diselenide (PtSe2) stands at a unique place in the sense that it undergoes a phase transition from type-II Dirac semimetal to indirect-gap semiconductor as thickness decreases. Defects in 2D TMDs are ubiquitous and play crucial roles in understanding and tuning electronic, optical, and magnetic properties. Here intrinsic point defects in ultrathin 1T-PtSe2 layers grown on mica were investigated through the chemical vapor transport (CVT) method, using scanning tunneling microscopy and spectroscopy (STM/STS) and first-principles calculations. Five types of distinct defects were observed from STM topography images and the local density of states of the defects were obtained. By combining the STM results with first-principles calculations, the types and characteristics of these defects were identified, which are Pt vacancies at the topmost and next monolayers, Se vacancies in the topmost monolayer, and Se antisites at Pt sites within the topmost monolayer. Our study shows that the Se antisite defects are the most abundant with the lowest formation energy in a Se-rich growth condition, in contrast to cases of 2D molybdenum disulfide (MoS2) family. Our findings would provide critical insight into tuning of carrier mobility, charge carrier relaxation, and electron-hole recombination rates by defect engineering or varying growth condition in few-layer 1T-PtSe2 and other related 2D materials. Also, in order to investigate the layer dependency of vibrational and electronic properties of two dimensional materials, 2M-WS2 material was selected. Raman spectroscopy and DFT calculation proved that all Raman active modes have a downshift when material is thinned to few layers (less than 5 layers). It was proven that there is a strong interaction between layers such that by decreasing the number of layers, the downshift in Raman active modes is mostly for the ones which belong to out-of-plane atomic movements and the most downshift is for the Ag2 Raman active mode. Also, I investigated the effect of number of layers on the band structure and electronic properties of this material. As the number of layers decreases, band gap does not change until the materials is thinned down to only a single monolayer. For a single monolayer of 2M-WS2, there is an indirect band gap of 0.05eV; however, with applying in-plane strain to this monolayer, the material takes a metallic behavior as the strain goes beyond ±1%. / Doctor of Philosophy / Graphite (consisting of graphene as building blocks) and TMDS in bulk form are layered and with exfoliation one can reach to few layers which is called two-dimension. Two dimensional materials like graphene have been used in researches vastly due to their unique properties, e.g. high carrier mobility, and tunable electronic properties. Transition metal dichalcogenides (TMDs) with a general formula of MX2, where M represents transition metal elements (groups 4-10) and X represents chalcogen elements (S, Se or Te), are another family of two-dimensional materials which have been extensively studied in the past few years. Besides exfoliation, there are also synthesis methods to produce two dimensional materials, e.g. chemical vapor deposition and chemical vapor transport. Normally, after synthesizing these materials, researchers investigate structure and electronic properties of these materials. There might be some atoms which no longer exist in the structure; hence, those are replaced by either vacancies or other elements which all of them are called defects. In chapter 1, defects in graphene and transition metal dichacolgenides were investigated, carefully. Later, dynamic behavior of defects in these materials were investigated and finally, the effect of defects on the electronic properties of the two dimensional materials were investigated. Chapter two talks about a case study which is two dimensional 1T-PtSe2. In this chapter, 5 different kinds of defects were studied using scanning tunneling microscopy and spectroscopy investigations and density functional theory was used to prove our assumptions of the origin of defects. Also, another thing which is investigated by researcher is that how atoms in two dimensional materials vibrate and how the number of layers in the two dimensional material influences vibrations of atoms. Other than this, electronic properties of these materials is dependent upon the number of layers. When these materials are synthesized, there is a stress applied to the material due the mismatch between the material and its substrate, so it is worth investigating the effect of stress (strain) on the structure, and electronic properties of the material of interest. For this purpose, 2M-WS2 was exfoliated on Si/SiO2 substrate and the layer dependency of its vibrational modes was investigated using Raman spectroscopy and density functional theory calculation. Also, in order to investigate the influence of stress (strain) on the electronic properties of two dimensional 2M-WS2, a single monolayer of this materials underwent a series of strains in density functional theory calculations and the effect of strain on the electronic properties of this material was investigated.

This thesis presents investigations on hydrogenated graphene by scanning tunneling microscopy and spectroscopy (STM/STS) as well as the implementation of spin-polarized STM. Preparation processes for a magnetic standard sample and spin-sensitive chromium tips are developed. The measurements on graphene reveal specific hydrogen adsorption sites in low coverage and the formation of a pattern at higher coverage. Both is found to be in agreement with previous predictions and calculations. Upon hydrogenation, an impurity midgap state emerges in the density of states which is measured directly for the first time. Complementing angle resolved photoemission experiments confirm that this state is dispersionless over the whole Brillouin zone. A routine is developed to prepare the standard sample system of ultra-thin iron films on tungsten (Fe/W(110)). Investigations on this system confirm the magnetic properties known from literature, including the presence of a spin spiral, and prove that it is well suited for the characterization of spin-polarized tips. Different approaches for the preparation of tips from the antiferromagnetic material chromium are tested. Among these, a promising new method is presented: The coating of crystalline chromium tips with fresh chromium material suggests reproducibility of the tip characteristics. The performance of the produced tips in STM measurements is excellent in regard to a fixed spin-polarization, high resolution and stability. Especially, a recovery of the tip magnetization direction proposed in this thesis makes this new preparation method superior to all processes yielding antiferromagnetic tips reported so far. / Inhalt der vorliegenden Arbeit sind Untersuchungen von hydogeniertem Graphen mittels Rastertunnelmikroskopie und -spektroskopie (RTM/RTS) sowie die Einführung spin-polarisierter RTM. Im Rahmen dessen wurden Präparationsprozesse für magnetische Standardproben und spin-sensitive Chrom-Spitzen entwickelt. Die Messungen an Graphen zeigen spezifische Wasserstoff-Adsorptionsstellen bei geringer Bedeckung und die Ausbildung eines Musters bei höherer Bedeckung, jeweils in Übereinstimmung mit Vorhersagen und Berechnungen. Der durch Hydrogenierung entstehende Störstellenzustand in der Bandlücke der Zustandsdichte wurde zum ersten Mal direkt gemessen. Ergänzende winkelaufgelöste Photoelektronenspektroskopieexperimente bestätigen, dass dieser Zustand in der gesamten Brillouinzone dispersionsfrei ist. Ein Verfahren zur Herstellung magnetischer Standardproben aus ultradünnen Eisenfilmen auf Wolfram (Fe/W(110)) wurde entwickelt. RTM-Untersuchungen an diesem System bestätigen die bereits aus der Literatur bekannten magnetischen Eigenschaften, insbesondere das Vorhandensein einer Spinspirale. Damit ist Fe/W(110) hervorragend geeignet für die Charakterisierung spin-polarisierter Spitzen. Verschiedene Ansätze, die zur Herstellung von Spitzen aus dem antiferromagnetischen Material Chrom verfolgt wurden, werden präsentiert, darunter auch eine vielversprechende neue Methode: Das Aufwachsen eines frischen Chromfilms auf kristalline Spitzen desselben Materials verspricht eine Reproduzierbarkeit von Spitzeneigenschaften. Der Einsatz von so hergestellten Spitzen in RTMMessungen ist geprägt von einer festgelegten Spin-Polarisation, hohem Auflösungsvermögen und Stabilität. Insbesondere die mögliche Reproduzierbarkeit der Magnetisierungsrichtung, die in dieser Arbeit diskutiert wird, macht diese Methode allen bisher berichteten Herstellungprozessen antiferromagnetischer Spitzen überlegen.

Les nanoparticules métalliques et bimétalliques supportées par des oxydes sont de plus en plus utilisées comme catalyseur modèle. Cependant, leur potentiel en vue des applications en catalyse n’est pas complètement exploité à cause d’un manque de connaissance de leurs propriétés fondamentales. Ainsi, pour comprendre les mécanismes de la catalyse hétérogène, il est important d’élaborer ces catalyseurs en contrôlant différents paramètres comme la taille, la distribution spatiale et la composition chimique des agrégats supportés. Nous avons montré qu’en utilisant un film ultramince d’alumine nanostructurée comme gabarit, il était possible d’élaborer des réseaux réguliers d’agrégats mono ou bimétalliques en contrôlant indépendamment leur taille et leur composition chimique. Ces réseaux de particules sont obtenus, sous ultravide, par condensation successive des deux métaux (Au, Pd) sur un film ultramince d’alumine nanostructurée. / Metallic and bimetallic nanoparticles supported on oxides become increasingly used as model catalysts. However, their potential toward applications is not fully achieved because of a lack of knowledge of the nanoparticles properties. In order to understand the mechanisms of heterogeneous catalysis it is important to elaborate these model catalysts in controlling simultaneously the size, spatial distribution and chemical composition of these particles. Recently, we have shown that by using nanostructured ultrathin alumina film as a template, it was possible to obtain regular arrays of metallic and bimetallic nanoparticles with independent control of size and chemical composition. These arrays of clusters are prepared by successive atomic deposition of two metals (Au, Pd), under UHV, on a nanostructured ultrathin alumina film

Cette thèse aborde le problème de la vérification automatique de systèmesparamétrés complexes. Cette approche est importante car elle permet de garantircertaines propriétés sans connaître a priori le nombre de composants dusystème. On s'intéresse en particulier à la sûreté de ces systèmes et on traitele côté paramétré du problème avec des méthodes symboliques. Ces travauxs'inscrivent dans le cadre théorique du model checking modulo théories et ontdonné lieu à un nouveau model checker : Cubicle.Une des contributions principale de cette thèse est une nouvelle technique pourinférer des invariants de manière automatique. Le processus de générationd'invariants est intégré à l'algorithme de model checking et permet de vérifieren pratique des systèmes hors de portée des approches symboliquestraditionnelles. Une des applications principales de cet algorithme estl’analyse de sûreté paramétrée de protocoles de cohérence de cache de tailleindustrielle.Enfin, pour répondre au problème de la confiance placée dans le model checker,on présente deux techniques de certification de notre outil Cubicle utilisantla plate-forme Why3. La première consiste à générer des certificats dont lavalidité est évaluée de manière indépendante tandis que la seconde est uneapproche par vérification déductive du cœur de Cubicle. / This thesis tackles the problem of automatically verifying complexparameterized systems. This approach is important because it can guarantee thatsome properties hold without knowing a priori the number of components in thesystem. We focus in particular on the safety of such systems and we handle theparameterized aspect with symbolic methods. This work is set in the theoreticalframework of the model checking modulo theories and resulted in a new modelchecker: Cubicle.One of the main contribution of this thesis is a novel technique forautomatically inferring invariants. The process of invariant generation isintegrated with the model checking algorithm and allows the verification inpractice of systems which are out of reach for traditional symbolicapproaches. One successful application of this algorithm is the safety analysisof industrial size parameterized cache coherence protocols.Finally, to address the problem of trusting the answer given by the modelchecker, we present two techniques for certifying our tool Cubicle based on theframework Why3. The first consists in producing certificates whose validity canbe assessed independently while the second is an approach by deductiveverification of the heart of Cubicle.

Ce travail présente les études, par microscopie à effet tunnel (STM) sous ultravide, d’une part de la formation de réseaux supramoléculaires, résultant de l’auto-assemblage des précurseurs organiques sur les surfaces Cu(111), Au(111), Si(111)-B et HOPG, et d’autre part, de l’étude de réactions chimiques sur les surfaces Cu(111), Au(111) et HOPG. Le premier chapitre décrit l’état de l’art des réseaux supramoléculaires ainsi que les réactions chimiques sur les surfaces. Le deuxième chapitre présente le dispositif expérimental et les théories sous-jacentes, ainsi que les préparations des substrats, de la pointe et la méthode de déposition des molécules.Le troisième chapitre présente les réseaux supramoléculaires formés par les dépositions des molécules fonctionnalisées par des atomes de brome ou d’azote sur les surfaces Cu(111) et Si(111)-B. Dans tous les cas, le rôle de la surface est prédominant lors de la formation des réseaux. Sur Cu(111), deux réseaux linéaires sont stabilisés par des interactions organométalliques entre les adatomes de Cu et les molécules organiques. Sur Si(111)-B, les réseaux formés sont commensurables avec la reconstruction √3 × √3 de la surface. En fonction de la compétition entre les interactions intermoléculaires et molécule-surface, les réseaux peuvent être 2D ou 1D.Le quatrième chapitre présent le premier exemple de polymérisation radicalaire sur une surface. Pour ce faire, quatre molécules de type arylalkyléthers et deux molécules arylalkanes furent synthétisées et déposées sur les surfaces de Cu (111), Au (111) et HOPG. Le mécanisme proposé pour cette réaction débute par une étape d’initialisation grâce à un processus de transfert inélastique d’électron tunnel (IET), générant des radicaux libres qui peuvent ensuite polymérisés par voie radicalaire sur la surface. / This work deals with the investigation, by means of scanning tunneling microscopy under ultra-high vacuum, of supramolecular networks resulting from the self-assembly of organic precursors on surfaces such as Cu(111), Au(111), Si(111)-B and HOPG, but also the investigation of on-surface reactions. The first chapter describes the state-of-the-art of supramolecular networks and on-surface reactions on surfaces. The second chapter presents the experimental setup and theoretical concepts, as well as the preparations of the substrates, the probe tip and the method of molecular deposition.The third chapter presents the supramolecular networks formed by the depositions of molecules functionalized by bromine atoms or nitrogen atoms on the Cu(111) and Si(111)-B surfaces. For both cases, the surface plays a key role in the formation of networks: on Cu(111), the two linear networks are stabilized by metal-organic interactions between the Cu adatoms and the organic molecules; on Si(111)-B, the nanoarchitectures are commensurable with the reconstruction √3 × √3 of the surface. As function of the competition between the intramolecular and intermolecular interactions, the networks could be 2D or 1D.The fourth chapter presents the first example of on-surface radical polymerization, which is developed by the tandem synthetic method. For this end, four arylalkylether molecules and two arylalkane molecules are synthetized and deposited on different types of surfaces such as Cu (111), Au (111) and HOPG. The proposed mechanism suggests that this reaction is initialized by the inelastic electron tunneling (IET) process, which provides the free and stable radicals for the further on surface radical polymerization.