La coloration de graphes est un problème central de l’optimisation combinatoire. C’est un domaine très attractif par ses nombreuses applications. Différentes variantes et généralisations du problème de la coloration de graphes ont été proposées et étudiées. La coloration d’arêtes d’un graphe consiste à attribuer une couleur à chaque arête du graphe de sorte que deux arêtes ayant un sommet commun n’ont jamais la même couleur, le tout en utilisant le moins de couleurs possibles. Dans la première partie de cette thèse, nous étudions le problème de la coloration d’arêtes ℓ-distance, qui est une généralisation de la coloration d’arêtes classique. Nous menons une étude combinatoire et algorithmique du paramètre. L’étude porte sur les classes de graphes suivantes : les chaines, les grilles, les hypercubes, les arbres et des graphes puissances. Le paramètre de la coloration d’arêtes ℓ-distance permet de modéliser des problèmes dans des réseaux assez grands. Cependant, avec la multiplication du nombre de nœuds, les réseaux sont de plus en plus vulnérables aux défaillances (ou pannes). Dans la deuxième partie, nous nous intéressons aux algorithmes tolérants aux pannes et en particulier les algorithmes auto-stabilisants. Nous proposons un algorithme auto-stabilisant pour la coloration propre d’arêtes. Notre solution se base sur le résultat de vizing pour utiliser un minimum de couleurs possibles. Par la suite, nous proposons un algorithme auto-stabilisant de clustering destine a des applications dans le domaine de la sécurité dans les réseaux mobiles Ad hoc. La solution que nous proposons est un partitionnement en clusters base sur les relations de confiance qui existent entre nœuds. Nous proposons aussi un algorithme de gestion de clés de groupe dans les réseaux mobiles ad hoc qui s’appuie sur la topologie de clusters préalablement construite. La sécurité de notre protocole est renforcée par son critère de clustering qui surveille en permanence les relations de confiance et expulse les nœuds malveillants de la session de diffusion. / Graph coloring is a famous combinatorial optimization problem and is very attractive for its numerous applications. Many variants and generalizations of the graph-coloring problem have been introduced and studied. An edge-coloring assigns a color to each edge so that no two adjacent edges share the same color. In the first part of this thesis, we study the problem of the ℓ-distance-edge-coloring, which is a generalization of the classical edge-coloring. The study focuses on the following classes of graphs : paths, grids, hypercubes, trees and some power graphs. We are conducting a combinatorial and algorithmic study of the parameter. We give a sequential coloring algorithm for each class of graph. The ℓ-distance-edge-coloring is especially considered in large-scale networks. However, with the increasing number of nodes, networks are increasingly vulnerable to faults. In the second part, we focus on fault-tolerant algorithms and in particular self-stabilizing algorithms. We propose a self-stabilizing algorithm for proper edge-coloring. Our solution is based on Vizing’s result to minimize number of colors. Subsequently, we propose a selfstabilizing clustering algorithm for applications in the field of security in mobile ad hoc networks. Our solution is a partitioning into clusters based on trust relationships between nodes. We also propose a group key-management algorithm in mobile ad hoc networks based on the topology of clusters previously built. The security of our protocol is strengthened by its clustering criterion which constantly monitors trust relationships and expels malicious nodes out of the multicast session.

Les films de ZrO2 pur sont déposés par MOCVD (Metal-Organic Chemical Vapor Deposition) en variant de nombreux paramètres du processus. L'influence des conditions de dépôt sur l'évolution de la microstructure (morphologies, structure cristalline/phase, texture et contrainte résiduelle) a été étudiée et clarifiée. Par des analyses approfondies des résultats expérimentaux, trois mécanismes typiques de croissance de dépôt de ZrO2 ont été proposées. Les contraintes de croissance de compression sont en relation directe avec la diffusion atomique et la quantité d'espèces piégées dans les films. La formation de la texture cristallographique est complexe et deux types de textures ont été analysées dans la phase tétragonale : la texture de fibre {1 1 0}t est contribuée par l'effet superplastique des nano-cristallites de ZrO2 et par la contrainte de croissance de compression ; tandis que la morphologie en facette est due à la croissance concurrentielle de différents plans cristallographiques. La stabilisation de la phase tétragonale de ZrO2 a été analysée et discutée. En plus de la taille critique des cristallites, la stabilisation de la phase tétragonale est favorisée par deux autres mécanismes : la grande quantité des défauts cristallins et la morphologie des cristallites.

<p>Laser-based absorption spectroscopy (AS) is a powerful technique for qualitative and quantitative studies of atoms and molecules. An important field of use of AS is the detection of species in trace concentrations, which has applications not only in physics and chemistry but also in biology and medicine, encompassing environmental monitoring, regulation of industrial processes and breath analysis. Although a large number of molecular species can successfully be detected with established AS techniques, there are some applications that require higher sensitivity, selectivity and accuracy, yet robust and compact instrumentation.</p><p>Various approaches have been made during the years to improve on the performance of AS, usually based on modulation spectrometry or external cavities. The most sensitive absorption technique of today is, however, noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS). This technique elegantly combines several approaches: external cavities (for optical path length enhancement), modulation techniques (for noise reduction) and saturation spectroscopy (for enhanced selectivity). However, due to its complexity, the technique has so far not been applied to practical trace species detection.</p><p>This thesis provides the background for an understanding of NICE-OHMS and describes the construction of a first compact NICE-OHMS spectrometer based on a narrowband fiber laser. Moreover, it gives theoretical expressions for NICE-OHMS signal lineshapes, measured in various modes of detection, which can be fitted to the experimental data and thereby facilitate the assessment of species concentration. The sensitivity of the instrumentation is demonstrated by detection of acetylene (C₂H₂) and carbon dioxide (CO₂) in the 1.5 μm region. A fractional absorption sensitivity of 3*10^-9 (integrated absorption of 5*10^-11 cm^-1), could be achieved using a cavity with a finesse of 4800 and an acquisition time of 0.7 s. This results in a detection limit for C₂H₂ of 4.5 ppt (4.5*10^-12 atm).</p><p>In addition, the thesis revives the idea of using an accurate (frequency) measurement of the free-spectral-range (FSR) of an external cavity for sensitive and calibration-free concentration assessment. A theoretical description of the expected signal lineshapes is given, and in a first experimental demonstration the FSR could be measured with a resolution of 5 Hz, resulting in a fractional absorption sensitivity of 1*10^-7, and subsequently in a detection limit for C₂H₂ of 180 ppt (12.5 s acquisition time).</p><p>The thesis, finally, also contributes to the continuously ongoing development of conventional AS and wavelength modulated AS by addressing concepts related to when the light optically saturates the transition.</p>

<p>The mouse xenobiotic-inducible <i>Cyp2a5</i> gene is both transcriptionally and posttranscriptionally regulated. One of the most potent <i>Cyp2a5</i> inducers, the hepatotoxin pyrazole, increases the CYP2A5 mRNA half-life. The induction is accomplished through the interaction of a pyrazole-inducible protein with a 71 nt long, putative hairpin-loop region in the 3' UTR of the CYP2A5 mRNA.</p><p>The aims of this thesis have been to identify the pyrazole-inducible protein, to investigate its role in the <i>Cyp2a5</i> expression and the significance of the 71 nt hairpin-loop region for the <i>Cyp2a5</i> expression, and to examine a possible coupling between transcriptional and posttranscriptional processes in <i>Cyp2a5</i> expression.</p><p>The pyrazole-inducible protein was identified as the heterogeneous nuclear ribonucleoprotein (hnRNP) A1. Studies performed in mouse primary hepatocytes overexpressing hnRNP A1, and in mouse erythroleukemia derived cells lacking hnRNP A1, revealed that the 71 nt region in the 3' UTR of the CYP2A5 mRNA is essential for <i>Cyp2a5</i> expression.</p><p>The hnRNP A1 is a multifunctional nucleocytoplasmic shuttling protein, with the ability to bind both RNA and DNA. These properties make it an interesting candidate mediating a coupling between nuclear and cytoplasmic gene regulatory events, which was investigated for the <i>Cyp2a5</i>. In conditions of cellular stress hnRNP A1 translocates from the nucleus to the cytoplasm. The accumulation of cytoplasmic hnRNP A1 after RNA polymerase II transcription inhibition, resulted in an increased binding of hnRNP A1 to the CYP2A5 mRNA, parallel with a stabilization of the CYP2A5 mRNA.</p><p>Treating primary mouse hepatocytes with phenobarbital (PB), a <i>Cyp2a5</i> transcriptional inducer, resulted in a mainly nuclear localization of the hnRNP A1. Electrophoretic mobility shift assays with nuclear extracts from control or PB-treated mice, revealed that hnRNP A1 interacts with two regions in the <i>Cyp2a5</i> proximal promoter, and that the interaction to one of the regions was stimulated by PB treatment.</p><p>In conclusion, the change in hnRNP A1 subcellular localization after transcriptional inhibition or activation, together with the effects on the interaction of hnRNP A1 with the CYP2A5 mRNA and <i>Cyp2a5</i> promoter, suggest that hnRNP A1 could couple the nuclear and cytoplasmic events of the <i>Cyp2a5</i> expression.</p><p>The presented studies are the first showing involvement of an hnRNP protein in the regulation of a <i>Cyp</i> gene. Moreover, it is the first time an interconnected transcriptional and posttranscriptional regulation has been suggested for a member of the <i>Cyp</i> gene family.</p>

The mouse xenobiotic-inducible Cyp2a5 gene is both transcriptionally and posttranscriptionally regulated. One of the most potent Cyp2a5 inducers, the hepatotoxin pyrazole, increases the CYP2A5 mRNA half-life. The induction is accomplished through the interaction of a pyrazole-inducible protein with a 71 nt long, putative hairpin-loop region in the 3' UTR of the CYP2A5 mRNA. The aims of this thesis have been to identify the pyrazole-inducible protein, to investigate its role in the Cyp2a5 expression and the significance of the 71 nt hairpin-loop region for the Cyp2a5 expression, and to examine a possible coupling between transcriptional and posttranscriptional processes in Cyp2a5 expression. The pyrazole-inducible protein was identified as the heterogeneous nuclear ribonucleoprotein (hnRNP) A1. Studies performed in mouse primary hepatocytes overexpressing hnRNP A1, and in mouse erythroleukemia derived cells lacking hnRNP A1, revealed that the 71 nt region in the 3' UTR of the CYP2A5 mRNA is essential for Cyp2a5 expression. The hnRNP A1 is a multifunctional nucleocytoplasmic shuttling protein, with the ability to bind both RNA and DNA. These properties make it an interesting candidate mediating a coupling between nuclear and cytoplasmic gene regulatory events, which was investigated for the Cyp2a5. In conditions of cellular stress hnRNP A1 translocates from the nucleus to the cytoplasm. The accumulation of cytoplasmic hnRNP A1 after RNA polymerase II transcription inhibition, resulted in an increased binding of hnRNP A1 to the CYP2A5 mRNA, parallel with a stabilization of the CYP2A5 mRNA. Treating primary mouse hepatocytes with phenobarbital (PB), a Cyp2a5 transcriptional inducer, resulted in a mainly nuclear localization of the hnRNP A1. Electrophoretic mobility shift assays with nuclear extracts from control or PB-treated mice, revealed that hnRNP A1 interacts with two regions in the Cyp2a5 proximal promoter, and that the interaction to one of the regions was stimulated by PB treatment. In conclusion, the change in hnRNP A1 subcellular localization after transcriptional inhibition or activation, together with the effects on the interaction of hnRNP A1 with the CYP2A5 mRNA and Cyp2a5 promoter, suggest that hnRNP A1 could couple the nuclear and cytoplasmic events of the Cyp2a5 expression. The presented studies are the first showing involvement of an hnRNP protein in the regulation of a Cyp gene. Moreover, it is the first time an interconnected transcriptional and posttranscriptional regulation has been suggested for a member of the Cyp gene family.

In order to produce predictable and robust systems forprotein purification and detection, well characterized, small,folded domains descending from bacterial receptors have beenused. These bacterial receptors, staphylococcal protein A (SPA)and streptococcal protein G (SPG), possess high affinity to IgGand / or HSA. They are composed of repetitive units in whicheach one binds the ligand independently. The domains foldindependently and are very stable. Since the domains also havewellknown three-dimensional structures and do not containcysteine residues, they are very suitable as frameworks forfurther protein engineering. Streptococcal protein G (SPG) is a multidomain proteinpresent on the cell surface ofStreptococcus. X-ray crystallography has been used todetermine the binding site of the Ig-binding domain. In thisthesis the region responsible for the HSA affinity of ABD3 hasbeen determined by directed mutagenesis followed by functionaland structural analysis. The analysis shows that the HSAbindinginvolves residues mainly in the second α-helix. Most protein-based affinity chromatography media are verysensitive towards alkaline treatment, which is the preferredmethod for regeneration and removal of contaminants from thepurification devices in industrial applications. Here, aprotein engineering strategy has been used to improve thetolerance to alkaline conditions of different domains fromprotein G, ABD3 and C2. Amino acids known to be susceptibletowards high pH were substituted for less alkali susceptibleresidues. The new, engineered variants of C2 and ABD shownhigher stability towards alkaline pH. Also, very important forthe potential use as affinity ligands, these mutated variantsretained the secondary structure and the affinity to HSA andIgG, respectively. Moreover, dimerization was performed toinvestigate whether a higher binding capacity could be obtainedby multivalency. For ABD, binding studies showed that divalentligands coupled using non-directed chemistry demonstrated anincreased molar binding capacity compared to monovalentligands. In contrast, equal molar binding capacities wereobserved for both types of ligands when using a directed ligandcoupling chemistry involving the introduction and recruitmentof a unique C-terminal cysteine residue. The staphylococcal protein A-derived domain Z is also a wellknown and thoroughly characterized fusion partner widely usedin affinity chromatography systems. This domain is consideredto be relatively tolerant towards alkaline conditions.Nevertheless, it is desirable to further improve the stabilityin order to enable an SPA-based affinity medium to withstandeven longer exposure to the harsh conditions associated withcleaning in place (CIP) procedures. For this purpose adifferent protein engineering strategy was employed. Smallchanges in stability due to the mutations would be difficult toassess. Hence, in order to enable detection of improvementsregarding the alkaline resistance of the Z domain, a by-passmutagenesis strategy was utilized, where a mutated structurallydestabilized variant, Z(F30A) was used as a surrogateframework. All eight asparagines in the domain were exchangedone-by-one. The residues were all shown to have differentimpact on the alkaline tolerance of the domain. By exchangingasparagine 23 for a threonine we were able to remarkablyincrease the stability of the Z(F30A)-domain towards alkalineconditions. Also, when grafting the N23T mutation to the Zscaffold we were able to detect an increased tolerance towardsalkaline treatment compared to the native Z molecule. In allcases, the most sensitive asparagines were found to be locatedin the loops region. In summary, the work presented in this thesis shows theusefulness of protein engineering strategies, both to explorethe importance of different amino acids regarding stability andfunctionality and to improve the characteristics of aprotein. <b>Keywords:</b>binding, affinity, human serum albumin (HSA),albumin-binding domain (ABD), affinity chromatography,deamidation, protein A, stabilization, Z-domain, capacity,protein G, cleaning-in-place (CIP), protein engineering, C2receptor.

Motion planning and control synthesis are challenging problems for underactuated mechanical systems due to the presence of passive (non-actuated) degrees of freedom. For those systems that are additionally not feedback linearizable and with unstable internal dynamics there are no generic methods for planning trajectories and their feedback stabilization. For fully actuated mechanical systems, on the other hand, there are standard tools that provide a tractable solution. Still, the problem of generating efficient and optimal trajectories is nontrivial due to actuator limitations and motion-dependent velocity and acceleration constraints that are typically present. It is especially challenging for manipulators with kinematic redundancy. A generic approach for solving the above-mentioned problems is described in this work. We explicitly use the geometry of the state space of the mechanical system so that a synchronization of the generalized coordinates can be found in terms of geometric relations along the target motion with respect to a path coordinate. Hence, the time evolution of the state variables that corresponds to the target motion is determined by the system dynamics constrained to these geometrical relations, known as virtual holonomic constraints. Following such a reduction for underactuated mechanical systems, we arrive at integrable second-order dynamics associated with the passive degrees of freedom. Solutions of this reduced dynamics, together with the geometric relations, can be interpreted as a motion generator for the full system. For fully actuated mechanical systems the virtually constrained dynamics provides a tractable way of shaping admissible trajectories. Once a feasible target motion is found and the corresponding virtual holonomic constraints are known, we can describe dynamics transversal to the orbit in the state space and analytically compute a transverse linearization. This results in a linear time-varying control system that allows us to use linear control theory for achieving orbital stabilization of the nonlinear mechanical system as well as to conduct system analysis in the vicinity of the motion. The approach is applicable to continuous-time and impulsive mechanical systems irrespective of the degree of underactuation. The main contributions of this thesis are analysis of human movement regarding a nominal behavior for repetitive tasks, gait synthesis and stabilization for dynamic walking robots, and description of a numerical procedure for generating and stabilizing efficient trajectories for kinematically redundant manipulators.

Ziel der Arbeit war die Nutzbarmachung von Bioethanol zur Wandlung in Strom und Wärme in einer Hochtemperaturbrennstoffzelle. Dazu waren neben der Entwicklung eines langzeitstabilen, effektiven Katalysators zur Synthesegaserzeugung und dessen Testung sowie der Übertragung gewonnener Erkenntnisse auf in einem Reformer einsetzbare Konzepte die Verifizierung kommerzieller Katalysatorsysteme für die partielle Oxidation von Ethanol notwendig. Außerdem ist für die Entwicklung eines ethanolbetriebenen SOFC-Systems eine pulsations- und ablagerungsfreie Verdampfung von unvergälltem und vergälltem Ethanol – welche nicht Stand der Technik ist – erforderlich, für die ein geeignetes Verdampferkonzept entwickelt und getestet wurde. Experimentell konnte die Betreibbarkeit eines SOFC-Systems mit Ethanol an einem für den Betrieb mit LPG ausgelegten System nachgewiesen werden.

Laser-based absorption spectroscopy (AS) is a powerful technique for qualitative and quantitative studies of atoms and molecules. An important field of use of AS is the detection of species in trace concentrations, which has applications not only in physics and chemistry but also in biology and medicine, encompassing environmental monitoring, regulation of industrial processes and breath analysis. Although a large number of molecular species can successfully be detected with established AS techniques, there are some applications that require higher sensitivity, selectivity and accuracy, yet robust and compact instrumentation. Various approaches have been made during the years to improve on the performance of AS, usually based on modulation spectrometry or external cavities. The most sensitive absorption technique of today is, however, noise-immune cavity-enhanced optical heterodyne molecular spectroscopy (NICE-OHMS). This technique elegantly combines several approaches: external cavities (for optical path length enhancement), modulation techniques (for noise reduction) and saturation spectroscopy (for enhanced selectivity). However, due to its complexity, the technique has so far not been applied to practical trace species detection. This thesis provides the background for an understanding of NICE-OHMS and describes the construction of a first compact NICE-OHMS spectrometer based on a narrowband fiber laser. Moreover, it gives theoretical expressions for NICE-OHMS signal lineshapes, measured in various modes of detection, which can be fitted to the experimental data and thereby facilitate the assessment of species concentration. The sensitivity of the instrumentation is demonstrated by detection of acetylene (C2H2) and carbon dioxide (CO2) in the 1.5 μm region. A fractional absorption sensitivity of 3*10-9 (integrated absorption of 5*10-11 cm-1), could be achieved using a cavity with a finesse of 4800 and an acquisition time of 0.7 s. This results in a detection limit for C2H2 of 4.5 ppt (4.5*10-12 atm). In addition, the thesis revives the idea of using an accurate (frequency) measurement of the free-spectral-range (FSR) of an external cavity for sensitive and calibration-free concentration assessment. A theoretical description of the expected signal lineshapes is given, and in a first experimental demonstration the FSR could be measured with a resolution of 5 Hz, resulting in a fractional absorption sensitivity of 1*10-7, and subsequently in a detection limit for C2H2 of 180 ppt (12.5 s acquisition time). The thesis, finally, also contributes to the continuously ongoing development of conventional AS and wavelength modulated AS by addressing concepts related to when the light optically saturates the transition.

Noise-immune cavity-enhanced optical heterodyne molecular spectro-metry (NICE-OHMS) is one of the most sensitive laser-based absorption techniques. The high sensitivity of NICE-OHMS is obtained by a unique combination of cavity enhancement (for increased interaction length with a sample) with frequency modulation spectrometry (for reduction of noise). Moreover, sub-Doppler detection is possible due to the presence of high intensity counter-propagating waves inside an external resonator, which provides an excellent spectral selectivity. The high sensitivity and selectivity make NICE-OHMS particularly suitable for trace gas detection. Despite this, the technique has so far not been often used for practical applications due to its technical complexity, originating primarily from the requirement of an active stabilization of the laser frequency to a cavity mode. The main aim of the work presented in this thesis has been to develop a simpler and more robust NICE-OHMS instrumentation without compro-mising the high sensitivity and selectivity of the technique. A compact NICE-OHMS setup based on a fiber laser and a fiber-coupled electro-optic modulator has been constructed. The main advantage of the fiber laser is its narrow free-running linewidth, which significantly simplifies the frequency stabilization procedure. It has been demonstrated, using acetylene and carbon dioxide as pilot species, that the system is capable of detecting relative absorption down to 3 × 10-9 on a Doppler-broadened transition, and sub-Doppler optical phase shift down to 1.6 × 10-10, the latter corresponding to a detection limit of 1 × 10-12 atm of C2H2. Moreover, the potential of dual frequency modulation dispersion spectrometry (DFM-DS), an integral part of NICE-OHMS, for concentration measurements has been assessed. This thesis contributes also to the theoretical description of Doppler-broadened and sub-Doppler NICE-OHMS signals, as well as DFM-DS signals. It has been shown that the concentration of an analyte can be deduced from a Doppler-broadened NICE-OHMS signal detected at an arbitrary and unknown detection phase, provided that a fit of the theoretical lineshape to the experimental data is performed. The influence of optical saturation on Doppler-broadened NICE-OHMS signals has been described theoretically and demonstrated experimentally. In particular, it has been shown that the Doppler-broadened dispersion signal is unaffected by optical saturation in the Doppler limit. An expression for the sub-Doppler optical phase shift, valid for high degrees of saturation, has been derived and verified experimentally up to degrees of saturation of 100.