We present the development of a novel, UHV-compatible device fabrication strategy for the realisation of nano- and atomic-scale devices in silicon by harnessing the atomic-resolution capability of a scanning tunnelling microscope (STM). We develop etched registration markers in the silicon substrate in combination with a custom-designed STM/ molecular beam epitaxy system (MBE) to solve one of the key problems in STM device fabrication ??? connecting devices, fabricated in UHV, to the outside world. Using hydrogen-based STM lithography in combination with phosphine, as a dopant source, and silicon MBE, we then go on to fabricate several planar Si:P devices on one chip, including control devices that demonstrate the efficiency of each stage of the fabrication process. We demonstrate that we can perform four terminal magnetoconductance measurements at cryogenic temperatures after ex-situ alignment of metal contacts to the buried device. Using this process, we demonstrate the lateral confinement of P dopants in a delta-doped plane to a line of width 90nm; and observe the cross-over from 2D to 1D magnetotransport. These measurements enable us to extract the wire width which is in excellent agreement with STM images of the patterned wire. We then create STM-patterned Si:P wires with widths from 90nm to 8nm that show ohmic conduction and low resistivities of 1 to 20 micro Ohm-cm respectively ??? some of the highest conductivity wires reported in silicon. We study the dominant scattering mechanisms in the wires and find that temperature-dependent magnetoconductance can be described by a combination of both 1D weak localisation and 1D electron-electron interaction theories with a potential crossover to strong localisation at lower temperatures. We present results from STM-patterned tunnel junctions with gap sizes of 50nm and 17nm exhibiting clean, non-linear characteristics. We also present preliminary conductance results from a 70nm long and 90nm wide dot between source-drain leads which show evidence of Coulomb blockade behaviour. The thesis demonstrates the viability of using STM lithography to make devices in silicon down to atomic-scale dimensions. In particular, we show the enormous potential of this technology to directly correlate images of the doped regions with ex-situ electrical device characteristics.

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We present the development of a novel, UHV-compatible device fabrication strategy for the realisation of nano- and atomic-scale devices in silicon by harnessing the atomic-resolution capability of a scanning tunnelling microscope (STM). We develop etched registration markers in the silicon substrate in combination with a custom-designed STM/ molecular beam epitaxy system (MBE) to solve one of the key problems in STM device fabrication ??? connecting devices, fabricated in UHV, to the outside world. Using hydrogen-based STM lithography in combination with phosphine, as a dopant source, and silicon MBE, we then go on to fabricate several planar Si:P devices on one chip, including control devices that demonstrate the efficiency of each stage of the fabrication process. We demonstrate that we can perform four terminal magnetoconductance measurements at cryogenic temperatures after ex-situ alignment of metal contacts to the buried device. Using this process, we demonstrate the lateral confinement of P dopants in a delta-doped plane to a line of width 90nm; and observe the cross-over from 2D to 1D magnetotransport. These measurements enable us to extract the wire width which is in excellent agreement with STM images of the patterned wire. We then create STM-patterned Si:P wires with widths from 90nm to 8nm that show ohmic conduction and low resistivities of 1 to 20 micro Ohm-cm respectively ??? some of the highest conductivity wires reported in silicon. We study the dominant scattering mechanisms in the wires and find that temperature-dependent magnetoconductance can be described by a combination of both 1D weak localisation and 1D electron-electron interaction theories with a potential crossover to strong localisation at lower temperatures. We present results from STM-patterned tunnel junctions with gap sizes of 50nm and 17nm exhibiting clean, non-linear characteristics. We also present preliminary conductance results from a 70nm long and 90nm wide dot between source-drain leads which show evidence of Coulomb blockade behaviour. The thesis demonstrates the viability of using STM lithography to make devices in silicon down to atomic-scale dimensions. In particular, we show the enormous potential of this technology to directly correlate images of the doped regions with ex-situ electrical device characteristics.

Dans ce travail de thèse, nous avons étudié la structure et les propriétés magnétiques de nanoparticules CoxPt1-x épitaxiées sur une surface Au(111). Notre étude de la croissance des nanostructures, réalisée par microscopie à effet tunnel, a montré que l'utilisation d'une surface auto-organisée Au(111) permettait d'obtenir une croissance organisée d'ilots pour des concentrations en platine allant jusqu'à 50%. Nous avons également mis en évidence une modification de la morphologie des nanostructures en fonction de leur composition. En effet, les ilots d'alliage CoxPt1-x présentent une morphologie ambicouche (i.e. la présence simultanée de parties monocouche et bicouche) qui semble propre aux nanostructures d'alliage. Des simulations de dynamique moléculaire nous ont permis de démontrer que cette morphologie résultait de considérations cinétiques. En effet, le cobalt présente un désaccord de paramètre de maille important avec l'or, ce qui lui permet de monter en 2e couche via une faible énergie d'activation. Ainsi, malgré la forte enthalpie de mélange du système (Co,Pt) il se produit une démixtion partielle au sein des nanostructures, avec un enrichissement en cobalt des couches supérieures. L'ajustement de cycles d'aimantation (obtenus par dichroïsme magnétique circulaire des rayons X) en fonction de la température et de l'angle d'application du champ nous a permis de montrer la diminution de l'anisotropie magnétique des ilots en fonction de l'augmentation de la concentration en platine. Nous avons interprété ce résultat via un modèle phénoménologique de paires qui montre que le rapport d'aspect très anisotrope des nanostructures (un ou deux plans atomiques) est à l'origine de cette variation.

The adsorption of biologically active molecules, such as the DNA bases, amino acids, on solid surfaces has been the subject of a number of experimental and theoretical studies in the past years. The understanding of the self-assembly mechanism of bioactive molecules on surfaces not only is fundamentally important in the preparation of bioactive surfaces, but also provides us insight into the origins of life and homo-chirality in nature. In this thesis, the adsorption behaviour of adenine and phenylglycine molecules on the Cu(110) surface has been investigated in order to understand the effect of experimental parameters like coverage, annealing temperature etc. on the molecular orientation and the ordering of the adlayer structures. The thesis is organised in six parts: Chapter I gives an introduction to the relevance of surface sciences studies, describing the phenomena of surface chirality and molecular adsorption behaviours on surfaces. Chapter II gives an overview of the experimental techniques and introduces basic concepts of theoretical calculation. Chapter III investigates the effect of experimental parameters, e.g. surface coverage, annealing temperature and substrate temperature on molecular diffusion, molecular orientation and ordering of the adlayer structures. LT-STM examination of the contrast variations of adenine chains and isolated adsorbate as a function of the tip-sample bias voltage is also presented with the aim to understand the tunnelling mechanism. Chapter IV shows RAIR spectra studies of the evolution of phenylglycine molecular orientation as a function of surface coverage at room temperature. The adsorption geometry and binding nature of phenylglycine is discussed. Chapter V concerns with the adsorption behaviours of phenylglycine and adenine on Cu(110) surface pre-covered with oxygen. Chapter VI summarises the conclusions and describes the outlook of some future work.

In this thesis, graphene (i.e. monolayer carbon film) and carbon clusters supported on a transition metal surface are systematically studied by local probe techniques, with respect to their structures, electronic properties and formation mechanisms. The main tools used are low-temperature scanning tunnelling microscopy and spectroscopy (STM and STS), which are introduced in Chapter 2. The mechanism of the resonance tunnelling at electron energies higher than the work function of the surface is discussed in detail, and a qualitative explanation of the Gundlach oscillations in the corresponding spectroscopy is presented. Epitaxial graphene synthesised on the Rh(111) surface by ethylene dehydrogenation is investigated by STM in Chapter 4. Such carbon film exhibits a hexagonal Moiré pattern due to a lattice mismatch between graphene and the rhodium substrate. The periodicity and local registries of the graphene/Rh(111) superstructure are carefully analysed. Based on a thorough discussion about the “commensurate vs. incommensurate” nature of the Moiré pattern in surface science field, the graphene/Rh(111) system is identified to have a non-simple-commensurate superstructure. The surface electronic properties and geometric buckling of graphene/Rh(111) are investigated by resonance tunnelling spectroscopy (RTS) and density functional theory (DFT) calculations in Chapter 5. Spectroscopy measurements reveal a modulation of the electronic surface potential (or work function Φ) across the supercell of epitaxial graphene. Based on the microscopy/spectroscopy data and the extended DFT calculations, we examined the electronic coupling of the various local C-Rh registries, and identified both experimentally and theoretically the local atomic configurations of maximum and minimum chemical bonding between graphene and the rhodium substrate. We studied in Chapter 6 the growth mechanism of graphene on Rh(111) at elevated temperatures. This part starts by investigating the dehydrogenation of ethylene into ethylidyne. When the dehydrogenation process is complete, monodispersed carbon species, identified as 7C6, are found to dominate the cluster population on the rhodium terraces. A significant coalescence of the 7C6 clusters into graphene islands occurs at temperatures higher than 873 K. The structural and electronic properties of the 7C6 carbon clusters are examined by high-resolution STM and STS, and compared with coronene molecules, i.e. the hydrogenated analogues of 7C6. DFT calculations are further used to explain the stability of 7C6 supported on the Rh(111) surface, and also the structural characteristics of such magic-sized carbon clusters.

Ma thèse porte sur l’étude par simulations numériques à l’échelle atomique de l’adsorption de molécules uniques et d’auto-assemblages moléculaires sur la surface de silicium Si(111) dopée bore notée Si(111) (√(3 ) x√3)R30°-B. Après un premier chapitre de présentation des méthodes de calcul, puis un chapitre consacré à la surface Si(111)-B, la thèse se divise en deux grandes parties : l’une concernant l’adsorption de molécules uniques et l’autre consacrée à l’adsorption de tapis moléculaire.La première partie concerne l’adsorption de molécules uniques sur la surface de Si(111) (√(3 ) x√3)R30°-B. Nous avons plus particulièrement étudié trois molécules présentant des mécanismes d’adsorption différents : la molécule de pyridile-azobenzène, une molécule de la famille des porphyrines (Cu-TBPP) et deux molécules appartenant à la famille des phtalocyanines (H2Pc et CuPc). Dans chaque étude, nous avons effectué une étude énergétique, structurale et électronique. Dans la plupart des cas, nous avons complété l’étude par un calcul d’image STM pour comparer avec les résultats expérimentaux. A partir de cette étude, nous avons montré que les molécules interagissent différemment avec la surface via des interactions électrostatiques, des liaisons datives, des liaisons ioniques et un mécanisme de cycloaddition. La deuxième partie de la thèse est dédiée à l’étude de l’auto-assemblage de molécules organiques sur la surface Si(111) (√(3 ) x√3)R30°-B. L’auto-assemblage moléculaire est une technique permettant la fabrication d’architectures hautement organisées à l’échelle atomique. Nous avons étudié trois molécules différentes formant un auto-assemblage sur la surface de Si(111)-B : 1,3,5-tri(4-bromophényle benzène) notée TBB, 1,3,5-tri(4-iodophényle benzène) notée TIB et 1,3,5-triphenylbenzene notée THB. Comme la formation d’un réseau auto-organisé est la conséquence d’un équilibre entre les interactions molécule-molécule et molécules-substrat, nous avons évalué les énergies d’interaction mises en jeu en utilisant différentes approximations (LDA, GGA et GGA+D). Nous avons étudié, ensuite, les propriétés électroniques de ces assemblages par le calcul des densités d’états projetées, de la différence de la densité de charge, du Laplacien de la charge ou de la fonction ELF. Afin de comparer nos résultats avec les résultats expérimentaux, nous avons effectué un calcul d’image STM en utilisant deux approches : l’approche de Tersoff-Hamann et l’approche multidiffusion proposée par le code bSKAN. Dans une dernière étape, nous avons étudié la recroissance de molécules de fullerène C60 sur le réseau auto-organisé de molécules de TBB déposées sur la surface Si(111) (√(3 ) x√3)R30° -B. Nous avons effectué une étude énergétique des molécules de C60 qui se déposent préférentiellement dans les nanopores de forme hexagonale en accord avec les expériences STM. / My thesis presents the study of the adsorption of single molecules and molecular self-assembly, by numerical simulations at the atomic scale, on a boron doped silicon surface denoted Si(111)(√(3 ) x√3)R30°-B. After presenting the calculation methods and describing the surface model, this thesis is made of two parts: the first one is about the adsorption of single molecules and the second one is devoted to the formation of supramolecular network. In the first part, I studied the adsorption of single molecules on the silicon surface doped boron Si (111)(√(3 ) x√3)R30°-B. I have investigated the adsorption mechanisms of three different molecules: a molecule of pyridyl-azobenzene, a molecule of the family of porphyrin (Cu-TBBP) and two molecules which belong to the family of phtalocyanine (H2Pc and CuPc). For every molecule, I conducted energetic, structural and electronic studies. In most of the cases, I completed this work by calculating STM images in order to compare with experimental results. The second part of this thesis deals with the study of self assembly of organic molecules on the surface of Si(111)(√(3 ) x√3)R30°-B. Molecular self assembly is a technique which allows the formation of highly organized architectures at the atomic scale. I have studied three different molecules forming self assembly on the surface of Si (111)(√(3 ) x√3)R30°-B : 1,3,5-tri(4-bromophenyl benzene) denoted TBB, 1,3,5-tri(4-iodophenyle benzene) denoted TIB et 1,3,5-triphenylbenzene denoted THB. As the formation of a self organized network is a result of equilibrium between molecule-molecule interaction and molecule-substrate one, I have evaluated the interaction energies by using different approximations (LDA, GGA and GGA+D). Then, I have studied the electronic properties of these assemblies by calculating the projected density of states, the charge difference and the Laplacien of the charge or the ELF function (Electronic Localization Function). In order to compare our results with experimental ones, STM images calculations were performed by using two different approaches: the approach of Tersoff-Hamann and the multi-scattering approach proposed by bSKAN code. Finally, I have studied the growth of C60 molecules on the self organized network formed by the TBB molecules deposited on the Si (111)(√(3 ) x√3)R30°-B surface. The energetic study shows that C60 molecules are adsorbed preferentially in the hexagonal nanopores in agreement with the STM observations.

This study tested the performance of classification, regression, and ordination techniques to evaluate the spatiotemporal dynamics of threats to big sagebrush ecological sites. The research was focused on invasion by annual exotic grasses and encroachment by woodlands. We sought to identify those areas that have had a persistent coverage of cheatgrass (Bromus tectorum) in big sagebrush ecological sites. We took advantage of the contrast in greenness between multi-temporal (within one year) remotely sensed vegetation indices captured in the spring and summer to find a distinct phenological signature that allowed mapping cheatgrass. We utilized support vector machines (SVM) to classify three temporal scenarios for which field data sets were available. SVM performed very well with accuracies of 70% (producer's) and 95% (user's) for the class of interest (presence of cheatgrass). This was the focus of chapter 2. In chapter 3 we report the development of vegetation continuous fields (VCF) for three years of interest 1996, 2001, and 2007 in order to detect active woodland encroachment. We prepared VCF for shrubs, trees, herbaceous vegetation, and bare ground using a suite of remotely sensed spectral reflectance, vegetation indices, and transformations. We compared the performance of multivariate regression trees (MRT) and random forests (RF) to develop the VCF multi-temporal series. RF outperformed MRT in both accuracy and ability to appropriately map the continuum of percent cover across large landscapes. We estimate that 17,570 hectares of big sagebrush lands showed encroachment by woodlands. Our goal in chapter 4 was to develop a similarity index for large rangeland landscapes. Trend assessments field sites and a long-term annual series (1984 - 2008) of remotely sensed imagery were used in conjunction with multidimensional scaling (MDS) to measure ecological distance to undesired states such as invasion by exotic annuals and encroachment by woodlands. In this chapter our units of analysis were soil-mapping units, which were predominantly composed of one ecological site (>60%). Our MDS results show that different ecological sites can be identified in the reduced MDS statistical space. The observed transitions and trajectories of mountain, Wyoming, and basin big sagebrush sites correlated well with the ecological expectation in semiarid lands. We anticipate that managers can use our protocols to update ecological site descriptions and state and transition models from a remotely sensed perspective.

De manière ultime, l'électronique moléculaire aspire à utiliser une molécule unique comme partie active d'un composant. Une telle réalisation fusionnerait l'énorme potentiel de la chimie aux technologies les plus avancées des nanosciences. Cependant, les propriétés de transport électronique d'une seule molécule restent, aujourd'hui, l'enjeu de débats animés qui s'appuient sur des calculs et sur de trop rares expériences. Les expériences sont, en effet, difficiles car elles nécessitent de pouvoir fabriquer des électrodes de contact dont l'écartement correspond à la taille de la molécule. Notre travail contribue au développement de telles techniques instrumentales dont l'intérêt dépasse celui de l'électronique moléculaire et englobe, plus généralement, le transport électronique à l'échelle nanométrique. Dans la première partie, nous décrivons d'abord la technique. Elle fait appel à un microscope à effet tunnel modifié pour fabriquer des électrodes nanométriques (technique des jonctions brisées). Cette approche combine en fait deux domaines de recherche qui sont d'une part, les mesures de conductance moléculaire et, d'autre part, les contacts atomiques ponctuels. Plus précisément, la physique de la formation et du transport d'électrons dans ces derniers est particulièrement étudiée. Après avoir décrit l'instrumentation développée, nous présentons donc des résultats à la fois sur des contacts atomiques ponctuels (jonction Au-Au) et sur des contacts moléculaires (jonction Au-molécule-Au). Notamment, la quantification de la conductance et le transport balistique sont mis en évidence. Cela montre que la présence d'une seule molécule peut être décelée électriquement. Nous soulignons qu'en dépit des énormes progrès apportés par cette technique à la détermination de la conductance d'une molécule, la disparité des résultats expérimentaux reportés reste importante. Nous clôturons la première partie en insistant sur l'impérieuse nécessité d'études statistiques rigoureuses à partir des nombreuses données expérimentales. Nous effectuons ce travail pour les jonctions Au-Au. Dans la seconde partie nous développons des outils d'analyse statistique. Ils permettent d'extraire de chaque mesure de conductance d'une nanojonction d'Au les paramètres indispensables à leur étude (le temps de vie par exemple). La statistique de ces paramètres sur des dizaines de milliers de mesures dans différentes conditions expérimentales est discutée et, outre les aspects de transport, donne des informations sur la mécanique de ces nanosystèmes (i.e. sur des mécanismes de rupture de la nanojonction). Les outils développés permettent d'observer des effets fins. Il est montré qu'une petite fraction des électrons échappe au transport balistique. Enfin, nous montrons l'existence de fluctuations bistables et discutons de leur effet sur le transport balistique et de leur rapport avec les mouvements atomiques.