Apport de la microscopie à effet tunnel à la caractérisation d'interfaces molécule-métal à fort transfert de charge

Cette thèse est une investigation sur les propriétés électroniques et structurales des interfaces molécule-métal à fort transfert de charge. La maîtrise des aspects fondamentaux qui entourent ce type d'interface est nécessaire au développement de dispositifs moléculaires, surtout dans l'optique de former des contacts molécule-métal de qualité. Parmi ces aspects fondamentaux, on retrouve l'adsorption de molécules sur une surface métallique qui implique généralement un mécanisme de transfert de charge bidirectionnel. Ce mécanisme se décrit par un mélange complexe entre les orbitales de la molécule organique et celles des atomes métalliques de la surface. Ce mélange d'orbitales peut induire l'accumulation de charge partielle sur l'un des constituants et provoquer la déformation structurale de l'interface molécule-surface. Il existe plusieurs exemples dans la littérature qui témoignent de déformations moléculaires voire parfois de reconstruction de surface dont l'amplitude semble être reliée à la force de l'interaction molécule-surface ainsi qu'au transfert de charge constaté au sein de cette interface. Afin d'aborder l'importance du transfert de charge sur les propriétés de l'interface, nous avonsétudié l'interaction de la molécule de tétracyanoéthylène (TCNE) avec différentes surfaces de cuivre. Concernant le TCNE, une molécule fortement électrophile, il apparaît comme un candidat idéal pour investiguer l'influence de fort transfert de charge sur les propriétés électroniques et structurales d'interfaces molécule-surface. En effet, les complexes de TCNE avec plusieurs métaux de transition exhibent un comportement magnétique à température ambiante qui corrobore un changement très significatif de la charge résiduelle sur la molécule de TCNE. L'adsorption des molécules de TCNE sur les surfaces de Cu(100) et de Cu(111) a été étudiée par imagerie à effet tunnel (STM) et par calculs de la théorie de la fonctionnelle de la densité (DFT) avec l'approximation de la densité locale (LDA). Les calculs DFT-LDA ont permis de déterminer la structure géométrique et la structure électronique des interfaces étudiées. Une analyse de Mulliken a permis d'évaluer la charge nette partielle sur les espèces adsorbées. Les diagrammes de densité d'états (DOS) ont fourni l'information nécessaire sur la nature des orbitales frontières impliquées dans le transfert de charge à l'interface molécule-métal. Afin de valider les observations théoriques, une étude comparative a été réalisée entre des images STM obtenues par simulation et des images STM expérimentales produites par nos collaborateurs. Les images STM théoriques ont été calculées avec le logiciel spags-stm en utilisant le formalisme de transport électronique de Landauer-Büttiker avec un hamiltonien semi-empirique basé sur la théorie d'Hückel étendue (EHT) et paramétrisé à l'aide de calculs DFT. Dans le développement du logiciel spags-stm, nous avons créé un module de discrétisation du domaine d'imagerie et permet une génération rapide des images STM. Ce module est basé sur un----------Abstract This thesis invetigates the electronic and structural properties of molecule-metal interfaces with strong charge-transfer. Fundamental aspects of these interfaces need to be understood to promote the development of molecular devices, especially in view of forming good molecule-metal contacts. Among the various fundamental aspects studied here, we nd that the adsorption of molecules on a metallic surface generally implies a bidirectional charge-transfer mechanism, and is described by a complex mixture between the orbitals of the organic molecule and that of metal atoms from the surface. This orbital mixture can induce partial net charge accumulation to one of the components, and cause structural deformation of the molecule-surface interface. Several examples of molecular deformation and surface reconstruction are reported in the literature. The magnitude of these deformations has been attributed to the strength of the molecule-surface interaction and the charge-transfer found at the interface. To assess the importance of charge-transfer on the interface properties, we studied the interaction of the tetracyanoethylene (TCNE) molecule with various copper surfaces. TCNE, a highly electrophilic molecule, appears as an ideal candidate to study the in uence of high charge-transfer on the electronic and structural properties of molecule-surface interfaces. Indeed, various TCNEtransition metal complexes exhibit magnetism at room temperature, which is in agreement with a very signicant change of the residual charge on the TCNE molecule. The adsorption of TCNE molecules on Cu(100) and Cu(111) surfaces was studied by scanning tunneling microscopy (STM) and by density functional theory (DFT) calculations with a local density approximation (LDA). DFT-LDA calculations were performed to determine the geometric and electronic structure of the studied interfaces. Mulliken analysis was used to evaluate the partial net charge on the adsorbed species. The density of states (DOS) diagrams provided informations on the nature of the frontier orbitals involved in the charge-transfer at molecule-metal interfaces. To validate the theoretical observations, a comparative study was conducted between our simulated STM images and experimental STM images provided by our collaborators. The theoretical STM images were obtained with the spags-stm software using the Landauer-B�uttiker formalism with a semi-empirical Hamiltonian based on the extended H�uckel theory (EHT) and parameterized using DFT calculations. During the development of the spags-stm software, we have created a discretization module allowing rapid generation of STM images. This module is based on an adaptive Delaunay meshing scheme to minimize the amount of tunneling current to be computed. The general idea consists into rening the mesh, and therefore the calculations, near large contrast zones rather than over the entire image. The adapted mesh provides an STM image resolution equivalent to that obtained with a conventional Cartesian grid but with a signicantly smaller number of calculated pixels

Étude des artefacts en tomodensitométrie par simulation Monte Carlo

En radiothérapie, la tomodensitométrie (CT) fournit l’information anatomique du patient utile au calcul de dose durant la planification de traitement. Afin de considérer la composition hétérogène des tissus, des techniques de calcul telles que la méthode Monte Carlo sont nécessaires pour calculer la dose de manière exacte. L’importation des images CT dans un tel calcul exige que chaque voxel exprimé en unité Hounsfield (HU) soit converti en une valeur physique telle que la densité électronique (ED). Cette conversion est habituellement effectuée à l’aide d’une courbe d’étalonnage HU-ED. Une anomalie ou artefact qui apparaît dans une image CT avant l’étalonnage est susceptible d’assigner un mauvais tissu à un voxel. Ces erreurs peuvent causer une perte cruciale de fiabilité du calcul de dose. Ce travail vise à attribuer une valeur exacte aux voxels d’images CT afin d’assurer la fiabilité des calculs de dose durant la planification de traitement en radiothérapie. Pour y parvenir, une étude est réalisée sur les artefacts qui sont reproduits par simulation Monte Carlo. Pour réduire le temps de calcul, les simulations sont parallélisées et transposées sur un superordinateur. Une étude de sensibilité des nombres HU en présence d’artefacts est ensuite réalisée par une analyse statistique des histogrammes. À l’origine de nombreux artefacts, le durcissement de faisceau est étudié davantage. Une revue sur l’état de l’art en matière de correction du durcissement de faisceau est présentée suivi d’une démonstration explicite d’une correction empirique.Computed tomography (CT) is widely used in radiotherapy to acquire patient-specific data for an accurate dose calculation in radiotherapy treatment planning. To consider the composition of heterogeneous tissues, calculation techniques such as Monte Carlo method are needed to compute an exact dose distribution. To use CT images with dose calculation algorithms, all voxel values, expressed in Hounsfield unit (HU), must be converted into relevant physical parameters such as the electron density (ED). This conversion is typically accomplished by means of a HU-ED calibration curve. Any discrepancy (or artifact) that appears in the reconstructed CT image prior to calibration is susceptible to yield wrongly-assigned tissues. Such tissue misassignment may crucially decrease the reliability of dose calculation. The aim of this work is to assign exact physical values to CT image voxels to insure the reliability of dose calculation in radiotherapy treatment planning. To achieve this, origins of CT artifacts are first studied using Monte Carlo simulations. Such simulations require a lot of computational time and were parallelized to run efficiently on a supercomputer. An sensitivity study on HU uncertainties due to CT artifacts is then performed using statistical analysis of the image histograms. Beam hardening effect appears to be the origin of several artifacts and is specifically addressed. Finally, a review on the state of the art in beam hardening correction is presented and an empirical correction is exposed in detail

Strongly reshaped organic-metal interfaces: Tetracyanoethylene on Cu(100)

The interaction of the strong electron-acceptor tetracyanoethylene (TCNE) with the Cu(100) surface has been studied with scanning tunneling microscopy experiments and first-principles density functional theory calculations. We compare two different adsorption models with the experimental results and show that the molecular self-assembly is caused by a strong structural modification of the Cu(100) surface rather than the formation of a coordination network by diffusing Cu adatoms. Surface atoms become highly buckled and the chemisorption of TCNE is accompanied by a partial charge-transfer.Comment: 4 pages, 3 figures, to appear in Physical Review Letter

Atlas multi-couches pour robot mobile

En cherchant à connaitre les origines de la vie sur Terre, on se demande également si elle peut se trouver ailleurs. Malgré le fait que Mars nous est voisine et qu'elle ne semble pas en démontrer la présence, on désire toutefois l'étudier et la comparer avec la Terre. Pour y arriver, l'Homme a recours à la technologie : les télescopes, satellites, sondes et robots servent à observer Mars. À chacune des expéditions d'observation de Mars, nous cherchons à en connaître davantage et améliorons en conséquence la technologie utilisée. C'est pour cela que la prochaine génération de véhicules d'exploration planétaire nécessitera une plus grande autonomie de navigation. De tels requis impliquent une gestion adéquate de données géoréférencées potentiellement volumineuses et denses, représentées sous la forme de cartes. Ce mémoire présente l'état des recherches faites sur un système de gestion de données utilisable dans un contexte d'exploration planétaire autonome. Pour valider un tel système, il a fallu utiliser, mais ,également constituer, un répertoire de cartes en trois dimensions ayant été géoréférencées. Afin d'obtenir un répertoire représentatif du contexte d'utilisation, il a également été nécessaire de développer un comportement d'exploration et de navigation sur une plateforme robotisée, capable d'acquérir les cartes requises. À l'aide de ce répertoire, il a été possible de vérifier les capacités, les performances ainsi que l'exactitude des opérations effectuées à l'aide du système de gestion proposé. Un article intégré au mémoire présente la conception d'un tel système de gestion de données, ainsi qu'une solution permettant de gérer dynamiquement une variété de données, l'incertitude des relations spatiales entre deux cartes, de procurer un mécanisme de planification de chemins au travers des cartes, ainsi que la corrélation des cartes pour les opérations de localisation. Cet article présente également les résultats expérimentaux sur l'utilisation du système de gestion atlas par un véhicule d'exploration autonome. En plus de démontrer la faisabilité et l'utilité d'un tel gestionnaire de données en navigation autonome, le système pourrait également être utilisé comme plateforme d'analyse afin de comparer les performances de différents algorithmes de recalage de surfaces

Citalopram inhibits platelet function independently of SERT-mediated 5-HT transport.

Citalopram prevents serotonin (5-HT) uptake into platelets by blocking the serotonin reuptake transporter (SERT). Although some clinical data suggest that selective serotonin reuptake inhibitors (SSRIs) may affect haemostasis and thrombosis, these poorly-characterised effects are not well understood mechanistically and useful in vitro data is limited. We sought to determine whether the inhibitory effects of citalopram on platelets are mediated via its pharmacological inhibition of 5-HT transport. We quantified the inhibitory potency of (RS)-, (R)- and (S)-citalopram on platelet function. If SERT blockade is the primary mechanism for citalopram-mediated platelet inhibition, these potencies should show quantitative congruence with inhibition of 5-HT uptake. Our data show that citalopram inhibits platelet aggregation, adhesion and thromboxane production with no difference in potency between (R)- and (S)-isomers. By contrast, citalopram had a eudysmic ratio of approximately 17 (S > R) for SERT blockade. Furthermore, nanomolar concentrations of citalopram inhibited 5-HT uptake into platelets but had no effect on other platelet functions, which were inhibited by micromolar concentrations. Our data indicate that citalopram-induced inhibition of platelets in vitro is not mediated by blockade of 5-HT transport. This raises a new question for future investigation: by what mechanism(s) does citalopram inhibit platelets

Schistosomiasis and the risk of bladder cancer in Alexandria, Egypt.

The relationship between history of schistosomiasis and bladder cancer risk was investigated using data from a case-control study conducted between January 1994 and July 1996 in Alexandria, Egypt. Cases were 190 subjects with incident, histologically confirmed invasive cancer of the bladder, and controls were 187 subjects admitted to hospital for acute, non-neoplastic, non-urinary tract conditions. Eighty-six cases (45%) vs 69 controls (37%) reported a history of urinary schistosomiasis. The corresponding multivariate odds ratio (OR) of bladder cancer -- after allowance for age, sex, education, smoking, other urinary infections and high-risk occupations -- was 1.72 (95% confidence interval (CI) 1.0-2.9). The ORs were 0.22 (95% CI 0.1-0.4) for intestinal schistosomiasis and 0.32 (95% CI 0.1-1.9) for schistosomiasis of other types. The OR for urinary schistosomiasis was higher in subjects who were younger at first diagnosis (OR of 3.3 for <15 years) and in those with a long time since first diagnosis (OR of 3.0 for > or = 35 years). The ORs were 15.8 for male ever-smokers with a history of urinary schistosomiasis, compared with never-smokers without such a history, and 3.2 for men ever-infected with urinary Schistosoma haematobium and ever-employed in high-risk occupations, compared with those never-infected and with no high-risk occupational history. This study confirms that clinical history of urinary schistosomiasis is significantly, but modestly, associated with increased bladder cancer risk, explaining some 16% of bladder cancer cases in this Egyptian population

Surface state engineering of molecule-molecule interactions

Engineering the electronic structure of organics through interface manipulation, particularly the interface dipole and the barriers to charge carrier injection, is of essential importance to improved organic devices. This requires the meticulous fabrication of desired organic structures by precisely controlling the interactions between molecules. The well-known principles of organic coordination chemistry cannot be applied without proper consideration of extra molecular hybridization, charge transer and dipole formation at the interfaces. Here we identify the interplay between energy level alignment, charge transfer, surface dipole and charge pillow effect and show how these effects collectively determine the net force between adsorbed porphyrin 2H-TPP on Cu(111). We show that the forces between supported porphyrins can be altered by controlling the amount of charge transferred across the interface accurately through the relative alignment of molecular electronic levels with respect to the Shockley surface state of the metal substrate, and hence govern the self-assembly of the molecules

Two-dimensional ketone-driven metal-organic coordination on Cu(111)

Two-dimensional metal-organic nanostructures based on the binding of ketone groups and metal atoms were fabricated by depositing pyrene-4,5,9,10-tetraone (PTO) molecules on a Cu(111) surface. The strongly electronegative ketone moieties bind to either copper adatoms from the substrate or co-deposited iron atoms. In the former case, scanning tunnelling microscopy images reveal the development of an extended metal-organic supramolecular structure. Each copper adatom coordinates two ketone ligands of two neighbouring PTO molecules, forming chains that are linked together into large islands via secondary van der Waals interactions. Deposition of iron atoms leads to a transformation of this assembly resulting from the substitution of the metal centres. Density functional theory calculations reveal that the driving force for the metal substitution is primarily determined by the strength of the ketone-metal bond, which is higher for Fe compared to Cu. This second class of nanostructures displays a structural dependence on the rate of iron deposition

Chromosomal aberrations in benign and malignant Bilharzia-associated bladder lesions analyzed by comparative genomic hybridization

BACKGROUND: Bilharzia-associated bladder cancer (BAC) is a major health problem in countries where urinary schistosomiasis is endemic. Characterization of the genetic alterations in this cancer might enhance our understanding of the pathogenic mechanisms of the disease but, in contrast to nonbilharzia bladder cancer, BAC has rarely been the object of such scrutiny. In the present study, we aimed to characterize chromosomal imbalances in benign and malignant post-bilharzial lesions, and to determine whether their unique etiology yields a distinct cytogenetic profile as compared to chemically induced bladder tumors. METHODS: DNAs from 20 archival paraffin-embedded post-bilharzial bladder lesions (6 benign and 14 malignant) obtained from Sudanese patients (12 males and 8 females) with a history of urinary bilharziasis were investigated for chromosomal imbalances using comparative genomic hybridization (CGH). Subsequent FISH analysis with pericentromeric probes was performed on paraffin sections of the same cases to confirm the CGH results. RESULTS: Seven of the 20 lesions (6 carcinomas and one granuloma) showed chromosomal imbalances varying from 1 to 6 changes. The most common chromosomal imbalances detected were losses of 1p21-31, 8p21-pter, and 9p and gain of 19p material, seen in three cases each, including the benign lesion. CONCLUSION: Most of the detected imbalances have been repeatedly reported in non-bilharzial bladder carcinomas, suggesting that the cytogenetic profiles of chemical- and bilharzia-induced carcinomas are largely similar. However, loss of 9p seems to be more ubiquitous in BAC than in bladder cancer in industrialized countries