Recent studies of the relationship between protein sequence and protein structure are reviewed. A detailed discussion of past attempts to predict the structure of a protein from its amino acid sequence, the protein folding problem, is presented and the strengths and weaknesses of these methods are examined. The root-mean-square deviation is studied and a benchmark for structural comparisons is established. A combinatorial approach to the protein folding problem is outlined and its advantages over existing methods is discussed. Specific algorithms based on the combinatorial approach are developed and applied to a variety of proteins. The success of this approach in terms of the root-mean-square deviation benchmark as well as the drawbacks of this method are presented.

The Pseudomonas aeruginosa VIM-4 metallo-β-lactamase is a member of the subclass B1. It belongs to the VIM-type β-lactamases encoded by genetic mobile element such as class 1 integrons. This particularity enhances the relevance of VIM type enzymes since these enzymes are now disseminated among important nosocomial strains such as Klebsiella pneumoniae and Pseudomonas aeruginosa. In consequence, the study of VIM-4 was performed to determine its kinetic parameters, its 3D structure and the dependence of its activity on Zn2+ concentration. VIM-4 has been described as an efficient enzyme able to hydrolyze all the β-lactam compounds. We observed that VIM-4 activity is dependent on the Zn2+ concentration in the buffer, with a maximal activity obtained at 50 µM. Two different forms of VIM-4 were observed by X-ray crystallography in the presence or absence of Zn2+ in the crystallogenesis buffer. The first form contains two Zn2+ and the second possesses only one Zn2+ in the histidine site. The apoenzyme form was obtained. Its study revealed that this form was poorly stable with a less structured shape. The active form is not restored even in presence of a large Zn2+ excess. In order to determine the Zn2+ stoechiometry in VIM-4, ICPMS (Inductively coupled plasma mass spectrometry) experiments were performed. The results of this study indicated that the mono-zinc form of VIM-4 is favored in absence of Zn2+ ions in the buffer and the di-zinc form appears in the presence of added Zn2+ ions. The dissociation constants of the Zn2+ ions with VIM-4 enzyme were determined using benzylpenicillin. The dissociation constants of the first, the second and the third Zn2+ are respectively KD1 which is clearly below 1 µM, KD2 equal to 8.5 µM and KD3 within a range of 200 to 500 µM. A complementary titration of the free Zn2+ ions from denatured VIM-4 with a chromophore chelating agent seems to confirm this feature as only one Zn2+ could be titrated. Then with no added Zn2+, VIM-4 would be in a mono-zinc form and with a Zn2+ concentration higher than 10 µM, the di-zinc form of VIM-4 would be present. In the last decade, numerous studies have reported an increasing mortality among patients in intensive care due to multiresistant pathogens. These strains are producing at least two different classes of β-lactamases. In the eighties, a strategy of combination of β-lactamase inactivator and β-lactam antibiotics was developed against serine β-lactamases. Some of the members of this family have already developed variants resistant to these inhibitors; however this combination remains efficient. In the case of the MBLs, extensive studies have been performed to find a generic inhibitor. Unfortunately, due to the heterogeneity of this enzyme group, no solution has been found. The development of a metallo-β-lactamase inhibitor, particularly active against acquired MBLs, which are the most relevant enzymes, is thus needed. Our second purpose was the identification of new molecules that could be developed as broad spectrum MBLs inhibitors. We found a new class of compounds, mercaptophosphonates derivatives, which can be used as leads for finding generic MBL inhibitors.

A large body of literature exists regarding linear and nonlinear dynamic absorbers, but the vast majority of it deals with linear primary structures. However, nonlinearity is a frequency occurrence in engineering applications. Therefore, the present thesis focuses on the mitigation of vibrations of nonlinear primary systems using nonlinear dynamic absorbers. Because most existing contributions about their design rely on optimization and sensitivity analysis procedures, which are computationally demanding, or on analytic methods, which may be limited to small-amplitude motions, this thesis sets the emphasis on a tuning procedure of nonlinear vibration absorbers that can be computationally tractable and treat strongly nonlinear regimes of motion. The proposed methodology is a two-step procedure relying on a frequency-energy based approach followed by a bifurcation analysis. The first step, carried out in the free vibration case, imposes the absorber to possess a qualitatively similar dependence on energy as the primary system. This gives rise to an optimal nonlinear functional form and an initial set of absorber parameters. Based upon these initial results, the second step, carried out in the forced vibration case, exploits the relevant information contained within the nonlinear frequency response functions, namely, the bifurcation points. Their tracking in parameter space enables the adjustment of the design parameter values to reach a suitable tuning of the absorber. The use of the resulting integrated tuning methodology on nonlinear vibration absorbers coupled to systems with nonlinear damping is then investigated. The objective lies in determining an appropriate functional form for the absorber so that the limit cycle oscillation suppression is maximized. Finally, the proposed tuning methodology of nonlinear vibration absorbers may impose the use of complicated nonlinear functional forms whose practical realization, using mechanical elements, may be difficult. In this context, an electro-mechanical nonlinear vibration absorber relying on piezoelectric shunting possesses attractive features as various functional forms for the absorber nonlinearity can be achieved through proper circuit design. The foundation of this new approach are laid down and the perspectives are discussed.

Mechanical behaviour of variably saturated clay fills VLADISLAVA KOSTKANOVÁ Ph.D. Thesis - English Abstract The excavated overburden from open-cast coal mines is end-dumped in fills. Clay type soil prevails among the filled soils in North-western Bohemia. As a consequence of the character and state of the soil, together with the mining and dumping technology, a typical lumpy structure of the clay fill is formed. The filled lumps range in size and vary in mechanical properties, but stiff to solid lumps up to 0.5 m in size are prevalent. Large and open macrovoids between the single lumps are a characteristic feature of the clay fills. Clay fills exhibit a double porosity structure, consisting of intergranular porosity between the lumps and intragranular porosity inside them. The total porosity of the freshly filled soils can reach 70%. This type of clay fill structure is metastable. This thesis focuses on the problematic behaviour of clay fill soils due to their metastable structure and their partly saturated state. Long-term monitoring of matric suction at depths up to 2 metres in two reclaimed clay fills revealed two different trends. Seasonally-dependent suction oscillations were recorded in the moderate slope of the clay fill in the Bílina mine, while no suction pointing to fully saturated conditions was...

RESUME A partir de lanalyse des incidents des FSOs de type CALM Soft Yoke de Vietsovpetro aux gisements White Tiger (Tigre Blanc) et Dragon, on saperçoit du besoin de développer des structures offshore (y compris les FPSOs) installées et opérées «en sécurité» dans les conditions spéciales des états de mer du Vietnam, où apparaissent de nombreux vents violents et de fréquents typhons tropicaux. Dans le cadre de cette thèse, une recherche générale sur les systèmes dancrage des FPSO a été réalisée en considérant divers problèmes : efforts hydrodynamiques du second ordre, réponses dynamiques aléatoires des systèmes dancrage des FPSO, analyses du dommage de fatigue aléatoire et estimation de la durée de vie des lignes dancrage. Plus spécialement, une étude plus approfondie avec un nouveau concept a été proposée pour estimer la fiabilité totale dun système de lignes d'ancrage des FSPO. La fiabilité totale a été déterminée selon les conditions de mer extrêmes (ULS), elle diminue avec le temps à cause de la prise en compte de l'accumulation du dommage en fatigue des lignes d'ancrage (FLS). Dans la dernière part de thèse, cette méthode a été appliquée aux conditions de mer sévères du Vietnam, surtout dans les états limites extrêmes, prenant en compte l'accumulation du dommage en fatigue. En application numérique, deux FSOs existants au Vietnam ont été analysés. Le contenu principal des études de la thèse a également contribué à réaliser un Projet National de Recherche du Vietnam (intitulé code KC.09.15/06-10), dont lun des membres est lauteur de cette thèse./ ABSTRACT From analyzing incidents of the CALM Yoke FSOs of Vietsovpetro in the White Tiger and Dragon fields, we can identify the need to develop offshore structures (including FPSO) installed and operated in safety in most severe Vietnamese sea states, with many and frequent strong winds and tropical typhoons. In this thesis, a general research on the FPSO mooring systems has been carried out by considering various problems: second order hydrodynamic efforts, random dynamic responses of the FPSO mooring systems, analyzing random damage of fatigue and estimating the durability of the mooring lines. In particular, a thorough study with a new concept was proposed to estimate the total reliability of FSPO mooring line systems. The total reliability was estimated for extreme sea conditions (ULS), which decreases with the time due to the accumulation of the damage by fatigue of the moorings lines (FLS). In the last part of thesis, this method was applied to the severe sea conditions of Vietnam, especially considering the ultimate limit states and taking into account the accumulation of the fatigue damage. For numerical application, two FSOs existing now in Vietnam were analyzed. The main studies in this thesis have also contributed to develop a National Research Project in Vietnam (entitled code KC.09.15/06-10), in which the author acts as a research team member.

Résumé : Lobjectif des travaux entrepris au cours de cette thèse visait à mettre en place un procédé global de conservation des graines de grenade (Punica granatum L.). Ce procédé se base essentiellement sur une déshydratation osmotique (DO), associée à un pré-traitement de congélation et un post-traitement de séchage par entrainement. Dans ce contexte, plusieurs paramètres d'optimisation du transfert de masse ont été étudiés, tels que la nature de la solution dimmersion (saccharose, glucose, glucose/saccharose et jus de datte « sous-produit » enrichi en saccharose), la température (30, 40, et 50°C) et létat du fruit (frais, congelé). En outre, nous avons mis en relation ces conditions avec certaines propriétés des graines : leur texture, leur structure, et leur couleur. Létude des paramètres de déshydratation (perte en eau (WL), gain en solides (SG), et réduction en poids (WR)) a montré quen utilisant des graines congelées et indépendamment de la température et de la solution utilisée, la majorité du transfert de masse seffectue pendant les vingt premières minutes de traitement. A lissue de cette période, la perte en eau est estimée à 46%, 41%, 39%, et 37% respectivement dans les solutions de saccharose, glucose/saccharose, de jus de datte et du glucose. La DO des graines fraîches est caractérisée par une cinétique plus lente, mais une perte finale en eau plus importante. Comme le montrent les analyses en microscopie électronique, cela sexplique par une déstructuration cellulaire survenant à la suite de la congélation des graines, ce qui vient conforter les résultats des observations microscopiques. Les mêmes techniques ont également indiqué une modification de texture/structure induite par le processus de DO. Dautre part, lutilisation dune solution de saccharose (55°Brix) et dune température de 50°C favorise un meilleur transfert de masse. La détermination des différentes fractions deau dans la graine par calorimétrie différentielle (DSC) a montré une augmentation dun facteur ~2,5 fois de la fraction deau non congelable (eau liée) et une réduction de ~3,5 fois de la fraction deau congelable (eau libre) favorisant ainsi une meilleure conservation du fruit. Le suivi de la qualité intrinsèque des graines au cours de la DO a montré une perte dune quantité non négligeable de certains composés (protéines, cendres) de la graine vers la solution, ce qui pourrait avoir une influence majeure sur la qualité organoleptique et nutritionnelle du fruit. La DO seule ne pourrait pas maintenir une stabilité du produit au cours de la conservation. En effet, lactivité deau du produit fini après DO est proche de 0,90. Ainsi, dans un but plus appliqué, un traitement complémentaire de séchage par entrainement (2 m/s durant 4 heures) a été mis en place, à différentes températures (40, 50, et 60°C), afin de réduire lactivité deau à une valeur inférieure à 0,65. Afin doptimiser le traitement de séchage, nous avons étudié en premier lieu leffet de la température sur lévolution de la matière sèche, de lactivité deau et du pourcentage de séchage des graines. Dautre part, plusieurs paramètres de qualité des graines de grenade (lactivité antioxydante, la teneur en composés phénoliques, les anthocyanines, la couleur, et la texture) ont été étudiés à différentes températures. Ce travail est une contribution à létude des propriétés physico-chimiques des graines de grenade (Punica granatum L.) au cours des procédés de congélation, de déshydratation et de séchage. Les caractéristiques du produit fini peuvent justifier de nouvelles voies de transformation et dexploitation des graines de grenade. Abstract: The aim of this work was to create a complete conservation process of pomegranate seeds (Punica granatum L.). This process is essentially based on osmotic dehydration (OD), which was associated to freezing and air-drying process. Several parameters were studied to optimize the process such as osmotic solution (sucrose, glucose, and sucrose/glucose and date juice with sucrose added), temperature (30, 40, and 50°C) and state of the fruit (fresh and frozen). All these conditions were linked to seed proprieties (texture, structure, and colour). The study of osmotic dehydration parameters (water loss (WL), solids gain (SG) and weight reduction (WR)) showed that most significant changes of mass transfer took place during the first 20 min of dewatering using frozen seeds, independently of temperature and sugar type. During this period, seeds water loss was estimated at 46% in sucrose, 41% in sucrose/glucose mix, 39% in date juice, and 37% in glucose. Mass transfer was slower starting from fresh fruit but led to a higher rate of WL at the end of the process. This fact can be explained by scanning electron microscopy, which showed damage of seed cell structure after freezing. This has practical consequences in terms of the modification of seeds texture. The same process also revealed a modification of seed texture and cell structure after osmotic dehydration. Using a sucrose solution and a temperature of 50°C favoured the best mass transfer. The determination of different water fractions of seed by differential scanning calorimetry (DSC) showed that the % of frozen water decreased 3.5 times contrary the % of unfreezable water that increased 2.5 times. This favours a better seeds conservation. During osmotic dehydration, there was a non negligible leaching of natural solutes from seeds into the solution, which might have an important impact on the sensorial and nutritional value of seeds. Using only osmotic dehydration could not maintain the stability of seeds during conservation. In fact, after the osmotic process, water activity of seeds was found to be higher than 0.9, allowing to the development of microorganisms and some undesirable reactions. As a consequence, a drying of the pomegranate seeds (during four hours) was investigated at three different temperatures (40, 50, and 60 °C) with air flow rate of 2 ms-1. Prior to the drying process, seeds were osmodehydrated in a sucrose solution (55°Brix) during 20 min at 50°C. The drying kinetics and the effects of OD and air-drying temperature on antioxidant capacity, total phenolic, colour, and texture were determined. This work is a contribution to the study of physico-chemical properties of pomegranate seeds (Punica granatum L.) during freezing, osmotic dehydration and drying. After the global process, the pomegranate seed characteristics lead to new industrial developments.

Monolayers of the cationic surfactant hexadecyltrimethylammonium halide (CTAX, where X = F¯, Cl¯, Br¯, and I¯) have been studied at the air-water and oilwater interfaces. At the air-water interface, the effects of the halide counterion and the addition of counterion were investigated. Sum-frequency spectroscopy (SFS), ellipsometry, and surface tensiometry indicated that the counterion changed the efficiency and effectiveness of the surfactant, both decreasing in the order of Br¯> Cl¯>F¯. The addition of salt in the form of 0.1 M KX was found to reduce the cmc but had little effect on the limiting area per molecule attained at the cmc, which increased from 44 Ų for CTAB to 65 Ų for CTAC and ca. 94 Ų for CTAF. Neither SFS nor ellipsometry provided any firm evidence for specific effects of the halide ions on the structure of the surfactant monolayers. For CTAB monolayers in the absence of excess electrolyte, the effect of area per molecule on the sum-frequency (SF) spectra was studied. Mixed monolayers of CTAB and tetradecane at the air-water interface exhibit a first-order phase transition from a conformationally disordered to a conformationally ordered state as the temperature is lowered. The phase transition occurs ca. 11 °C above the bulk melting point of tetradecane. A new experimental arrangement is described for acquiring SF spectra from surfactants at the oil-water interface. The key features of this approach are the stabilisation of a thin oil film between a sapphire prism and an aqueous phase, and the use of total internal reflection to enhance the total signal and discriminate against signals from other interfaces in the system. With this new methodology, the first SF vibrational spectra of surfactant monolayers at an alkane-water interface were obtained. Surface tensiometry was used to characterise the monolayers further. The structure of CTAB monolayers at the hexadecane-water interface was determined by SFS and compared with monolayers of CTAB at the air-water interface. At low concentrations, CTAB/hexadecane showed the expected features in the C-H stretching region, characteristic of a conformationally disordered monolayer. As the bulk concentration approached the critical micelle concentration, the spectra changed to one characteristic of a more ordered, upright conformation. Ellipsometric measurements supported this conclusion. This qualitative structural change is not observed in analogous monolayers at the air-water interface or CCl₄-water interface, or in surfactant solutions in contact with a hydrophobic solid surface.

Vanderghem Caroline. (2009). La membrane du globule gras du lait : études physico-chimiques et sa valorisation technofonctionnelle dans les babeurres (Thèse de doctorat en Anglais). Gembloux, Belgique, Faculté Universitaire des Sciences Agronomiques de Gembloux. 198p., 14 tabl., 59 fig. Résumé La membrane du globule gras du lait (MGGL) est une structure complexe qui enveloppe, protège et délivre des composants bioactifs et des nutriments dune façon efficace au nouveau-né. Sa structure est unique par rapport à dautres systèmes biologiques de transport de lipides. Lobjectif général de ce travail a été de contribuer à augmenter les connaissances et la compréhension de cet émulsifiant naturel. La première partie de cette thèse concerne létude de la structure de la MGGL. Limportance des protéines membranaires concernant la stabilité et leur disposition dans la MGGL ont été étudiés. Les protéines de la MGGL sont présentes en petite quantité dans le lait et une technique de pré-fractionnement simpose afin de les isoler par rapport aux autres protéines du lait (caséines et protéines du lactosérum). Une technique dextraction qui a été développée dans notre laboratoire a été testée afin disoler la MGGL de la crème laitière. Une analyse détaillée a révélé que cette procédure est très bien adaptée pour lélimination dun maximum de protéines du lait écrémé. Une approche protéomique a été établie et a permis lidentification de protéines majeures de la MFGM ainsi que dautres protéines mineures (GTP-binding proteins, annexins, actin) afin de compléter le protéome. Par la suite, différentes protéases ont été testées en vue dobtenir différents degrés et/ou sélectivité dhydrolyse des protéines de la MGGL. La distribution asymétrique des protéines de la MGGL a été étudiée par une approche basée sur lattaque protéolytique du globule gras natif. Sur base de nos résultats et des données bibliographiques récentes, un nouveau modèle de la structure de la MGGL est proposé. La deuxième partie de cette thèse est consacrée à évaluer les propriétés technofonctionnelles de la MGGL dans les babeurres. Les propriétés interfaciales, moussantes et émulsifiantes du babeurre sont comparées à dautres ingrédients laitiers comme le lait écrémé et le concentré protéique de lactosérum. Nos résultats montrent le bon pouvoir émulsifiant du babeurre en comparaison des autres ingrédients laitiers. Dans les émulsions recombinées, la stabilité envers le crémage a été améliorée et les membranes ont présenté une meilleure résistance face à la coalescence. Les résultats sur la tension interfaciale et les propriétés rhéologiques interfaciales ont été mis en relation avec certaines propriétés des mousses et des émulsions. Vanderghem Caroline. (2009). The milk fat globule membrane: physico-chemical studies and its techno-functional valorisation in buttermilk (Thèse de doctorat). Gembloux, Belgium, Gembloux Agricultural University, 198p., 14 tabl., 59 fig. Summary The milk fat globule membrane (MFGM) is a complex structure that surrounds, protects and delivers bioactive compounds and nutrients in an efficient manner to the neonate. Its structure is unique in relation with any other biological lipid transport system. The overall aim of this work was to contribute to increase the knowledge and comprehension of this natural emulsifier. The first part of this thesis concerned the study of the structure of the MFGM. Membrane proteins were targeted and their importance regarding stability and disposition in the MFGM was studied. MFGM proteins are present at low concentrations in milk and a pre-fractionation of the sample is required in order of MFGM proteins to be visible among other milk proteins (caseins and whey proteins). A mild procedure developed in our laboratory was tested in order to isolate MFGM from cream. Detailed analysis revealed that this procedure is very well suited for the elimination of a maximum of skim milk proteins. A proteomic approach was established and allowed the identification of the most important MFGM proteins and additional minor MFGM proteins for additional completion of the proteome (GTP-binding proteins, annexins, actin). Subsequently, different proteases were screened in an attempt to obtain different degrees and/or selective proteolysis of MFGM proteins. Asymmetric arrangement of MFGM proteins was studied with an approach based on the proteolytic attack on the native fat globule. Based on our results and recent bibliographic data, an updated model of the MFGM structure was proposed. The second part of this thesis was devoted to assess the techno-functional properties of the MFGM in buttermilks. Interfacial, foaming and emulsifying properties of buttermilk were assessed and compared to classic milk ingredients such as skim milk and whey protein concentrate. Our results highlighted that buttermilk possesses good emulsifying power compared to other milk ingredients. In buttermilk recombined emulsions stability towards creaming was improved and the recombined membrane presented a great resistance to coalescence. Results of the interfacial pressure and the interfacial rheological properties were related to some foams and emulsions properties.