No description available.

Ces travaux de thèse concernent la conception et l'étude d'algorithmes, d'une part pourprédire les quantités thermodynamiques et la structure secondaire des ARN, d'autre part pour l'alignement de séquences.Dans une première partie, nous appliquons un algorithme de Monte-Carlo pour approximer la densité d'états d'énergie des structures secondaires d'une séquence d'ARN, ou d'une hybridation de deux molécules d'ARN données. Nous montrons d'abord que la densité estimée par notre programme est aussi bonne que la densité exacte, et le temps d'exécution de notre programme est beaucoup plus rapide. Nous calculons ensuite la température de dénaturation d'une hybridation de deux molécules d'ARN. Nous montrons que nos températures de dénaturation sont plus proches des valeurs expérimentales que celles des deux autres programmes existants.Puis, dans une deuxième partie, nous implémentons un algorithme de programmation dynamique qui engendre des structures sous-optimales, dédié principalement à la prédiction des deux structures fonctionnelles des riboswitchs. Nous appliquons d'abord notre programme sur un riboswitch TPP dans lequel nous avons réussi à détecter les deux structures fonctionnelles. Nous montrons ensuite que les structures prédites par notre programme sont plus proches de la structure réelle par rapport aux cinq autres programmes existants, sur un échantillon de riboswitch purine.Enfin, dans une troisième partie, nous présentons un algorithme de recherche des alignements sous-optimaux de séquences pour améliorer la qualité d'alignement des séquences. Nous comparons d'abord nos alignement à ceux produits par l'algorithme de Needdleman-Wunsch. Nous prédissons plus d'alignements de référrence par rapport l'algorithme de Needdleman-Wunsch. Nous calculons ensuite les fréquences des paires de bases alignées et les entropies de position spécifique dans nos alignements sous-optimaux. Nous montrons que les entropies calculées à partir de notre programme sont plus corrélées que celles des autres programmes avec les positions des paires de résidus fiablement alignées selon BAliBASE. / This thesis concerns the design and study of algorithms, on the one hand to predict the thermodynamic quantities and the secondary structure of RNA, the other for sequence alignment.In the first part, we apply a Monte Carlo algorithm to approximate the density of states for secondary structures of a given RNA sequence, and for hybridizations of two RNA sequences. We first show that the density estimated by our program is as good as the exact density, and the execution time of our program is much faster. We then calculate the melting temperature for a hybridization of two RNA sequences. We show that our melting temperatures are closer to experimental values than the other two programs.Then in the second part, we implement a dynamic programming algorithm that generates sub-optimal structures, mainly dedicated to the prediction of functional structures of riboswitchs. We first apply our program on a TPP riboswitch in which we were able to detect both functional structures. We then show that the structures predicted by our program are closer to the real structure compared to five other existing programs, on a sample of purine riboswitch.Finally, in the third part, we present a novel algorithm to produce sub-optimal pairwise alignments. We first compare our alignments to those produced by the algorithm of Needdleman-Wunsch. We predict more reference alignments than the algorithm of Needdleman-Wunsch. We then calculate the frequencies and position-specific entropies from our sub-optimal alignments. We show that entropies calculated from our program are more correlated than other programs with locations in the core block of BAliBASE reference alignments.

No description available.

In the last few years a renewed interest has reappeared in materials that were highly investigated in the 50s-70s, like manganese perovskites, spinel chalcogenides and vanadium oxides. The first two classes of materials are nowadays intensively studied due to the colossal magnetoresistance effect, which is the magnetoresistance associated with a ferromagnetic-paramagnetic transition. Vanadium oxides are known to form many compounds and most of them undergo metal-to-insulator phase transitions, with a high increase in the electrical conductivity (MIT). Many technological applications derive from the variation of the physical properties around the phase transition temperature. Although many efforts have been done in order to understand their electronic structures and to elucidate the MIT mechanisms, the vanadium oxides are still matter of debate in science.The present study has been performed in order to understand the electronic structure of these very intriguing materials. The role of different dopants that induce strong changes in the electronic and magnetic properties has been investigated making use of two spectroscopic techniques, namely X-ray photoelectron and X-ray emission spectroscopy.

The details of the interplay between the electronic structure and the magnetic properties of matter represent a state of the art challenge. In the present work spectroscopic investigations on the electronic structure of some interesting materials are presented. The achieved information has been used in order to answer specific questions related to the magnetic behavior of the investigated materials. For the transition metal dicyanamide compounds it is shown that the electronic states arising from carbon and nitrogen remain roughly unchanged for all compositions. A model for the magnetic superexchange interaction was proposed. In this model the geometry of the crystallographic structure accounts for a particular interaction pattern while the occupancy of the 3d transition metal band is the factor which triggers the changeover from antiferromagnetic to ferromagnetic interaction. In the case of six-membered ferric-wheel molecules the comparison between experimental and theoretical data issued estimations for the magnitude of magnetic exchange interactions. The information on the electronic structure of the LaNi5-xMex (Me=Cu, Al) allowed a better understanding of their magnetic behavior. The changes induced in the electronic structure of the parent compound by partial substitutions of nickel by copper or aluminum are discussed.

Ce travail de thèse a porté sur l’étude des propriétés fondamentales de bâtonnets quantiques InAs/InP formant la zone active de diodes lasers, à l’aide de microscopie et spectroscopie à effet tunnel à balayage. Nous avons pu étudier la nature de la dimensionnalité de ces nanostructures, mesurer la structure électronique de bâtonnets uniques en fonction de leur position dans la jonction PIN et également établir la cartographie de leur fonction d’onde à l’aide de mesures de conductivité différentielle. Nous avons de plus étudié le potentiel de ces bâtonnets quantiques comme milieu à gain de diodes lasers pour applications en détection de gaz. Nous avons optimisé des structures actives qui ont permis une émission laser en continu jusqu’à 2 µm et nos résultats expérimentaux et de modélisation montrent que cette longueur d’onde d’émission peut être étendue encore plus vers le MIR. De plus nous avons conçu et développé un procédé de fabrication de lasers DFB à couplage latéral à base de réseau de Bragg à fort rapport cyclique qui a permis d’améliorer de façon significative le coefficient de couplage (>40 cm-1). Ce procédé ne nécessitant pas de reprise d’épitaxie est très simple et à bas coût dans sa réalisation. Les valeurs élevées du coefficient de couplage sont d’autre part obtenues sans recourir à des réseaux de Bragg métalliques, comme c’est généralement le cas dans la littérature, qui introduisent des pertes de propagation non négligeables. Cette nouvelle approche a été mise en œuvre pour la réalisation d’un laser monofréquence émettant à 1,986 µm, avec une puissance de sortie par face de 4,5 mW, un courant de seuil de 65 mA et un taux de suppression des modes latéraux > 37 dB. Ces paramètres sont parfaitement adaptés à la détection e.g. de NH3, ce qui est très important pour des applications industrielles. Ce type de laser DFB à couplage latéral (LC-DFB), à fort k et faibles pertes de propagation constitue une brique de base pour la réalisation future de composants à deux sections présentant une gamme élevée d’accordabilité en continu pour des applications aussi bien en détection de gaz qu’en télécommunications optiques / During this work, we investigated the fundamental properties of single Qdashes, that were embedded in a diode-laser structure configuration, using cross-sectional scanning tunneling microscopy and spectroscopy. The main results included addressing the open question of the Qdash dimensionality nature, probing the electronic structure of individual nanostructures in respect to their precise location in the p-i-n junction and imaging of the Qdash electronic squared wavefunctions by high-stability differential conductivity mapping. In addition, we investigated Qdashes as the active material of semiconductor lasers, with special attention to the gas sensing application. We optimized Qdash based material at specific emission wavelengths above 1.55 um, and demonstrated CW lasing up to 2 um with high performances. Our experimental and simulation results show to be promising for further pushing the emission wavelength out, towards longer wavelengths in the future, using the same material system. Furthermore, a novel process has been developed, for the fabrication of laterally-coupled DFB lasers, based on high-duty-cycle etched Bragg gratings: The process provides appreciably improved coupling coefficients suitable for practical applications (~40 cm-1), while avoiding the complicated high cost processing steps, that had been employed in previous works (regrowth over corrugated substrates/ FIB lithography) and without using the conventional highly absorbing metal gratings, which introduce significant additional losses. We implemented this approach on our optimized epi-wafer and demonstrated high SMSR (>37dB) LC-DFB lasers emitting at 1.986 um, with an output power per facet up to 4.5 mW and Ith down to 65 mA for a 630 um cavity length, suitable for detection of the NH3 gas. These high-κ, low loss, preliminary results of our LC-DFB lasers, achieved using etched gratings, open the way for the fabrication of a two-section LC-DBR laser using the same technology in the future. Such a laser would combine a significantly simplified process, with sufficient feedback, continuous wide range tunability, and negligible grating-induced losses, finding potential applications both in sensing and telecommunications applications

This book is devoted to the study of operators on discrete structures. The operators are supposed to be self-adjoint and obey a certain translation invariance property. The discrete structures are given as Cayley graphs via finitely generated groups. Here, sofic groups and amenable groups are in the center of our considerations. Note that every finitely generated amenable group is sofic. We investigate the spectrum of a discrete self-adjoint operator by studying a sequence of finite dimensional analogues of these operators. In the setting of amenable groups we obtain these approximating operators by restricting the operator in question to finite subsets Qn , n ∈ N. These finite dimensional operators are self-adjoint and therefore admit a well-defined normalized eigenvalue counting function. The limit of the normalized eigenvalue counting functions when |Qn | → ∞ (if it exists) is called the integrated density of states (IDS). It is a distribution function of a probability measure encoding the distribution of the spectrum of the operator in question on the real axis. We prove the existence of the IDS in various geometric settings and for different types of operators. The models we consider include deterministic as well as random situations. Depending on the specific setting, we prove existence of the IDS as a weak limit of distribution functions or even as a uniform limit. Moreover, in certain situations we are able to express the IDS via a semi-explicit formula using the trace of the spectral projection of the original operator. This is sometimes referred to as the validity of the Pastur-Shubin trace formula. In the most general geometric setting we study, the operators are defined on Cayley graphs of sofic groups. Here we prove weak convergence of the eigenvalue counting functions and verify the validity of the Pastur-Shubin trace formula for random and non-random operators . These results apply to operators which not necessarily bounded or of finite hopping range. The methods are based on resolvent techniques. This theory is established without having an ergodic theorem for sofic groups at hand. Note that ergodic theory is the usual tool used in the proof of convergence results of this type. Specifying to operators on amenable groups we are able to prove stronger results. In the discrete case, we show that the IDS exists uniformly for a certain class of finite hopping range operators. This is obtained by using a Banach space-valued ergodic theorem. We show that this applies to eigenvalue counting functions, which implies their convergence with respect to the Banach space norm, in this case the supremum norm. Thus, the heart of this theory is the verification of the Banach space-valued ergodic theorem. Proceeding in two steps we first prove this result for so-called ST-amenable groups. Then, using results from the theory of ε-quasi tilings, we prove a version of the Banach space-valued ergodic theorem which is valid for all amenable groups. Focusing on random operators on amenable groups, we prove uniform existence of the IDS without the assumption that the operator needs to be of finite hopping range or bounded. Moreover, we verify the Pastur-Shubin trace formula. Here we present different techniques. First we show uniform convergence of the normalized eigenvalue counting functions adapting the technique of the Banach space-valued ergodic theorem from the deterministic setting. In a second approach we use weak convergence of the eigenvalue counting functions and additionally obtain control over the convergence at the jumps of the IDS. These ingredients are applied to verify uniform existence of the IDS. In both situations we employ results from the theory of large deviations, in order to deal with long-range interactions.

Despite the increased interest among local governments in collecting data on performance measurement, empirical evidence is still limited regarding the extent to which these data are utilized to assess the impact on efficiency of economies of scale and uncontrollable factors. Data envelopment analysis (DEA) is a linear programming method designed to estimate the relative efficiency of decision-making units. In addition to assessing relative efficiency, DEA can estimate scale efficiency and incorporate the impact of uncontrollable factors. Using data from the International City/County Association (ICMA), this study utilized DEA to evaluate the impact of economies of scale and uncontrollable factors on the relative efficiency of municipal service delivery in the United States. The findings from this doctoral dissertation show that uncontrollable variables such as population density, unemployment, and household income suppress the relative efficiency of local governments. Moreover, the findings imply that the prevalence of economies of scale in city governments depends on the types of services these governments provide.

Density functional theory (DFT) calculations of polyethylene (PE) HVDC cable insulation have been performed for systems containing four different chemical impurities: acetophenone, cumene, $\alpha$-methyl styrene and $\alpha$-cumyl alcohol. Systems were generated by molecular dynamics (MD) equilibration at four different temperatures relevant for cable insulation applications: 277 K, 293 K, 343 K and 363 K. With the goal of gaining better measure of variations in hole and electron traps energies, four initial configurations were also stochastically generated at each temperature, which yielded four different final configurations after equilibration. The counterpoise correction scheme was implemented for DFT calculations, by distributing ghost atoms thought any empty pockets of space in between the PE chains. The PBE functional was selected for DFT simulations. The resulting band gaps were in agreement with those of earlier GGA-based studies, and thus lower by 3 eV than empirical band gaps. For all impurities, the first HOMO state and the first two LUMO states were generally located on the impurity molecule, forming one hole trap and two electron traps, but certain configurations generated increased electron trap numbers, or eliminated hole traps. No dependence could be derived between temperature and trap depth for either electron or hole traps. Mean electron trap energies were largely in agreement with results from earlier studies, they were deepest for acetophenone, and they varied by as much as 0.6 eV between different configurations. Hole traps are universally shallow and vary by up to 0.7 eV between configurations, and are similar in depth for all impurities. Results suggest that electron trap depths correlate with the presence of molecular features such as oxygen atoms and conjugated double bonds. The dependence of trap depth on the spatial configuration of the impurity molecule suggests that results could be improved by more precise quantum mechanical treatment of the dynamics of the impurity. / Täthetsfunktionalteori (DFT) har använts för beräkningar av isolering till HVDC kablar som består av polyeten innehållande fyra olika kemiska orenheter: acetofenon, kumen, alfa-metylstyren och alfa-kumylalkohol. System att studera genererades genom molekylärdynamisk ekvilibrering vid fyra olika temperaturer relevanta för tillämning till kabelisolering: 277 K, 293 K, 343 K och 363 K. För att få ett mått på de variationer som existerar i energierna på hål- och elektronfällor genererades stokastiskt fyra initialkonfigurationer vid varje temperatur, vilket fyra olika konfigurationer efter relaxering. Motviktskorrigering implementerades för DFT-beräkningar, genom att fördela "spökatomer" i de tomrum som bildas mellan PE-kedjorna i den amorfa fasen. PBE-funktionalen användes för DFT-simuleringar. De resulterande bandgapen stämde överens med tidigare GGA-baserade studier, och var därmed runt 3 eV smalare än empiriskt uppmätta bandgap. För alla orenheter var det första HOMO-tillståndet och de två första LUMO-tillstånden i allmänhet placerade på orenheten, vilket resulterade i en hålfälla och två elektronfällor, men vissa konfigurationer gav upphov till fler elektronfällor, eller eliminerade hålfällorna. Inget samband kunde härledas mellan temperaturen och djupet på fällorna för vare sig elektron- eller hålfällor. Medelvärdet på elektronfällornas energier överensstämde till stor del med resultat från tidigare studier, energierna var högst för acetofenon, och de varierade med så mycket som 0,6 eV mellan olika konfigurationer. Hålfällorna var genomgående grunda, varierade med upp till 0,7 eV mellan olika konfigurationer, och hade likartat djup för alla orenheter. Resultaten indikerar att variationerna elektronfällornas medeldjup uppstår på grund av orenheternas olika molekylära uppbyggnad: förekomst av syreatomer och konjugerade dubbelbindningar i orenheterna leder till djupare elektronfällor. Det faktum att djupet på elektron- och hålfällor varierar mellan olika rumsliga konfigurationer av av orenheten och polyetenstrukturen ger en antydan om att resultaten kan komma att förbättras om dynamiken hos orenheten simuleras med mer exakta kvantmekanisk metoder.

Um einen besseren Zugang zum Verständnis struktureller Eigenschaften von den ternären Verbindungen des Systems Yb–Pd–Ga zu bekommen, wurden zunächst die Ordnungs- und Unordnungsbeziehungen sowie die chemische Bindung in den Kristallstrukturen binärer Pd–Ga- bzw. Yb–Ga-Verbindungen analysiert. Im Rahmen der phasenanalytischen Untersuchungen des binären Systems Yb–Ga konnte eine neue Verbindung charakterisiert werden (Ytterbiumpentagallid). Für den galliumreichen Teil des ternären Phasendiagramms Yb–Pd–Ga wurde ein isothermer Schnitt bei 600 °C erstellt (> 50 At.-% Ga). Die Homogenitätsbereiche der untersuchten Verbindungen wurden metallographisch bzw. röntgenographisch bestimmt. Die Kristallstrukturen wurden aus Röntgen-Einkristalldaten bestimmt. In den Kristallstrukturen wurden drei unterschiedliche Arten von Unordnung beobachtet (Substitutionsunordnung, Symmetrie-Brechung, Positionsunordnung). Für eine Reihe von Verbindungen des Systems Yb–Pd–Ga wurde der elektronische Zustand von Yb bestimmt. Dies gelang mit Hilfe von Messungen der magnetischen Suszeptibilität bzw. mit der Röntgen-Absorptionsnahkantenspektroskopie.