Les phases concentrées de protéines sont au centre de nombreuses études visant à identifier et caractériser les interactions et transitions de phases mises en jeu, en utilisant le large corpus de connaissances acquis sur les phases concentrées de colloïdes. Ces phases concentrées de protéines possèdent en outre une grande importance dans des domaines aussi variés que l’industrie agroalimentaire, l’industrie pharmaceutique et la médecine. L’établissement d’équations d’état présentant la pression osmotique (Π) en fonction de la fraction volumique (Φ) est une méthode efficace de caractérisation des interactions entre les composants d’un système. Nous l’avons appliquée à des solutions de deux protéines globulaires, le lysozyme et l’ovalbumine, en balayant une gamme de fractions volumiques allant d’une phase diluée (Φ < 0,01) à une phase concentrée, solide (Φ > 0,62). Les équations d’état obtenues, couplées à d’autres techniques (SAXS, simulations numériques), ont permis de mettre en évidence un comportement très différent des deux protéines lors de la concentration et ont montré leur complexité en comparaison avec des colloïdes modèles. La mise en relation des équations d’état et du comportement interfacial de ces deux protéines a montré des points de convergence et permis de formuler une nouvelle hypothèse expliquant certaines observations portant sur l’adsorption des protéines à l’interface air-eau. / Concentrated phases of proteins are the subject of numerous studies aiming at identifying and characterizing the interactions and phase transitions at play, using the large corpus of knowledge in the field of concentrated colloids. Those concentrated phases of proteins have, in addition, a great importance in various fields, such as food industry, pharmaceutical industry and medicine. The establishment of equations of state relating osmotic pressure (Ð) and volume fraction (Φ) is an efficient way of characterization of the interactions between the components of a system. We applied this method to solutions of two globular proteins, lysozyme and ovalbumin, spanning volume fractions ranging from a dilute phase ( Φ < 0,01) to a concentrated, solid phase ( Φ > 0,62). The equations of state, coupled to other methods (SAXS, numerical simulations), enabled us to show that the two proteins carry a very different behavior when submitted to concentration and that their complexity is beyond that of colloids. Relating equations of state and interfacial behavior of these two proteins also showed points of convergence and enabled us to formulate a new hypothesis which explains some of the results obtained in the study of adsorption of proteins at the air-water interface.

Les liquides diffèrent des solides par une réponse retardée à la sollicitation en cisaillement; c’est-à-dire une absence d’élasticité de cisaillement et un comportement d'écoulement à basses fréquences (<1 Hz). Ce postulat pourrait ne pas être vrai à toutes échelles. A l’échelle submillimétrique, les mesures viscoélastiques (VE) réalisées en améliorant l'interaction entre le liquide et le substrat, montrent qu’une élasticité basses-fréquences existe dans des liquides aussi variés que les polymères, les surfondus, les liquides à liaison H, ioniques ou van der Waals. Ce résultat implique que les molécules à l'état liquide ne seraient pas dynamiquement libres, mais élastiquement corrélées.En utilisant les propriétés biréfringentes des fluctuations prétransitionnelles qui coexistent dans la phase isotrope des cristaux liquides, nous montrons qu'il est possible de visualiser ces corrélations « cachées ». Dans des conditionssimilaires aux mesures VE, une biréfringence optique synchrone à la déformation est observée dans la phase isotrope à des fréquences aussi basses que 0.01 Hz et des températures éloignées de toute transition. Le comportement dela biréfringence basses-fréquences a des similitudes avec l'élasticité; elle est en phase avec la déformation à faibles amplitudes de déformation, puis en phase avec le taux de déformation à plus grandes amplitudes. La biréfringence basses- fréquences est forte, sans défaut et réversible. Elle indique un ordre à longue portée. La synchronisation de la réponse à la sollicitation en fréquence et l’état ordonné qu’elle produit ne sont pas compatibles avec un état liquide isotrope mais montrent qu’il s’agit d’un état élastique soumis à déformation (entropie élastique). / Liquids differ from solids by a delayed response to a shear mechanical solicitation; i.e. they have no shearelasticity and exhibit a flow behaviour at low frequency (<1 Hz). This postulate might be not verified at thesub-millimeter scale. By optimizing the measurement in particular by improving the liquid/substrate interactions (wetting), a low frequency shear elasticity has been found in liquids including molten polymers, glass-formers, H-bond polar, ionic or van der Waals liquids. This result implies that molecules in the liquid state may not be dynamically free but weaklyelastically correlated. Using the birefringent properties of the pretransitional fluctuations coexisting in the isotropic phase of liquid crystals, we show that it is possible to visualize these “hidden” shear-elastic correlations. We detect a synchronized birefringent optical response in the isotropic phase that is observable at frequencies as low as 0.01 Hz and at temperatures far away from anyphase transition. The low-frequency birefringence exhibits a strain dependence similar to the low frequency elasticity: An optical signal that is in-phase with the strain at low strain amplitudes and in-phase with the strain-rate at larger strain amplitudes. The birefringent response is strong, defect-free, reversible and points out a collective response. This long-range ordering rules out the condition of an isotropic liquid and its synchronized response supports the existenceof long-range elastic (solid-like) correlations. In the light of this, the strain dependence of the harmonic birefringent signal and the shear elasticity may correspond to an entropy-driven transition.

This thesis explores and expands upon theoretical means of quantifying a number of nonlinear spectroscopies, including two-photon absorption, resonant-inelastic x-ray scattering, Jones birefringence, and magnetic circular dichroism. On top of that, detailed information is given for the derivation and program implementation of damped cubic response functions. Complex-valued cubic response functions have been implemented in the quantum chemistry package DALTON, based on working equations formulated for an approximate-state wave function. An assessment of the implementation, such that for small frequencies the second-order hyperpolarizability should behave according to an analytic function that depends quadratically on the optical frequencies. It is demonstrated how two-photon absorption (TPA) can be described either through second-order transition moments or via the damped cubic response function. A few calculated TPA profiles are produced for a set of smaller molecules, in order to display the capability of the cubic response function in the x-ray frequency region. Resonance-inelastic x-ray scattering (RIXS) is explored in a similar manner as two-photon absorption. It is shown how the second-order hyperpolarizability can represent RIXS in the limit of intermediate-state and final-state resonances. Complications emerging from the complex dispersion of the hyperpolarizability are discussed. Moreover, linear birefringences, with focus on the Jones birefringence, are investigated for noble gases, monosubstituted benzenes, furan homologues, and a pure acetonitrile liquid. A linear relation between the Jones birefringence and the empirical para-Hammett constant as well as the permanent electric dipole moment is presented. Estimations of three linear birefringences --- Kerr, Cotton--Mouton, and Jones ---are obtained by averaging over a set of liquid snapshots. The Jones effect for acetonitrile turns out to be unusually large inmparison to the other two investigated linear birefringences. The final chapter of the thesis investigates magnetically induced circular dichroism (MCD). A question regarding relative stability of the first set of excited states for DNA-related molecular systems is resolved through MCD by exploiting the signed nature of circular dichroisms. Furthermore, to what extent solvent contributions affect MCD spectra is explored. The effect on uracil MCD spectrum due to thionation is studied, for which the degree of redshifting for systems 2-thiouracil and 4-thiouracil can be seen to be addative as compared to the 2,4-dithiouracil system. / <p>QC 20171129</p>

Die heterogene Struktur von aus Rattenhirn isolierten Synaptischen Vesikeln wird untersucht mittels Daten aus Kleinwinkel-Röntgenstreuexperimenten unter Berücksichtigung von Daten erhalten durch cryogene Elektronenmikroskopie, dynamische Lichtstreuung und biochemische Analysen. Es werden niedrig aufgelöste Strukturmodelle des funktionellen Synaptischen Vesikels unter quasi-physiologischen Bedingungen vorgeschlagen. Details des Dichteprofils der Membran, einschließlich Beiträgen von Lipiden und Proteinen werden bestimmt. Die typische Konformation und die allgemeine laterale Organisation der Proteine in Mikrodomänen werden ermittelt. Entropische Beiträge zur freien Energie aufgrund möglicher Bildung und Auflösung der Proteinmikrodomänen auf dem Synaptischen Vesikel werden untersucht. Ferner werden zellfreie Fusionssysteme mittels dynamischer Lichtstreudaten charakterisiert und mögliche Anwendungen von Kleinwinkel-Röntgenstreuung für die Untersuchung von Membran-Fusionsprozessen erörtert.

La structure et les interactions qui stabilisent des empilements lamellaires lyotropes de bicouches lipidiques "poilues" (et dépourvues de charge électrique nette) dans leur état fluide sont principalement étudiées par diffusion de rayons X aux petits angles. Les empilements lamellaires sont utilisés comme matrices hôtes afin de confiner et d’encapsuler des nano-bâtonnets d’ADN qui s’auto-assemblent en différentes structures en fonction du confinement réalisé. L’objectif fixé est de comprendre l’origine des mécanismes qui sont responsables de la formation de tels assemblages supramoléculaires. Dans ce but,on s’intéresse aux mécanismes entropiques et interfaciaux, sensibles expérimentalement à la physico-chimie du système, cette dernière affectant notamment le caractère "lié"ou "non lié" des systèmes lamellaires à haute dilution. Un modèle thermodynamique est utilisé afin d’interpréter la décroissance exponentielle "classique" observée dans les profils de pression osmotique en fonction de l’hydratation, sans faire appel à la force"d’hydratation". Une transition structurale est mise en évidence, à faible hydratation,entre deux phases lamellaires "liées". Le changement structural de la bicouche est discuté en termes de couplage entre confinements vertical et latéral. La caractérisation de la matrice lamellaire hôte autorise finalement une description des organisations des bâtonnets d’ADN qui semblent directement corrélées aux propriétés physiques des bicouches, faisant ainsi apparaître quelques perspectives pour leur encapsulation au sein "d’ognons". / Structure and interactions stabilizing the lyotropic lamellar stack of (electrically-neutral)mixed "hairy" lipid bilayers in their fluid state are mainly investigated by means of small angleX-ray scattering. The lamellar stacks are used as hosts to confine and encapsulate DNA nanorods which organize themselves into different structures depending on the confinement.The challenge here is to understand the mechanisms responsible for the formation of these supramolecular assemblies. In this aim, we are interested in entropic and interfacial mechanisms which are both experimentally sensitive to the physical-chemistry of the system, changing in particular the “bound” or “unbound” character of the waters wollen systems. A thermodynamic model is then used for interpreting the “classical”exponential decay obtained in osmotic profiles as a function of hydration, without resorting to “hydration forces”. A structural transition between two different “bound” lamellar phases is brought out at low hydration. The bilayer structural changes are discussed as resulting from a coupling between lateral and vertical confinements. The lamellar host characterization finally allows a description of the DNA nanorods organizations which seem to be directly correlated to the physical properties of the bilayers, leaving some perspectives for the encapsulation inside “onions”. / A estrutura e as interações, que estabilizam os empilhamentos lamelares liotrópicos dasmembranas lipídicas em seu estado fluido, são estudadas principalmente por espalhamento de raios-x a baixos ângulos. As membranas “peludas” (eletricamente neutras) são compostas de uma mistura em diversas proporções de lecitina, um fosfolipídio zwiteriônico, ede simulsol, um cotensoativo etoxilado não iônico similar a um copolímero dibloco (curto). Esses empilhamentos lamelares são utilizados como matrizes hospedeiras, com o intuito deconfinar e de encapsular nanobastões de DNA que se auto organizam em diferentes estruturas,em função do confinamento aplicado. O objetivo fixado é de compreender aorigem dos mecanismos responsáveis pela formação dessas organizações supramoleculares,não regidas pelas interações eletrostáticas. Dessa forma, nos interessamos aos mecanismos entrópicos e interfaciais, que são ligados à elasticidade membranar e às interações mais específicas que intervêm nas interfaces membrana-membrana ou DNA-membrana. Aabordagem experimental consiste em modificar os diferentes parâmetros físico-químicosda matriz hospedeira, como a hidratação do sistema, a natureza química do cotensoativo (blocos hidrofóbicos e/ou hidrofílicos) e a proporção de cotensoativo no interior da membrana.O cotensoativo tem então uma função chave para modificar os dois mecanismos,perturbando o estado “ligado” ou “não-ligado” em sistemas lamelares altamente diluídos.Um modelo termodinâmico é utilizado para interpretar o decréscimo exponencial “clássico”observado para os perfis de pressão osmótica, quando se aumenta a hidratação, semutilizar a “força de hidratação”. Uma transição estrutural é evidenciada, à baixahidratação, entre duas fases lamelares “ligadas”. A mudança estrutural da membranaé discutida graças ao acoplamento entre confinamento lateral e vertical, em analogia àconhecida transição “escova-cogumelo” induzida pelo confinamento lateral, relevante paralongos polímeros lineares funcionalizados em superfícies rígidas [10]. A caracterizaçãoda matriz lamelar hospedeira permite, finalmente, uma descrição das organizações dosbastões de DNA que parecem diretamente correlacionados com as propriedades físicasdas membranas, deixando, então, algumas perspectivas para sua encapsulação no interiorde estruturas semelhantes a ”cebolas”.

The techniques of small-angle x-ray scattering (SAXS) and grazing-incidence small-angle x-ray scattering (GISAXS) have successfully been used for many years in the analysis of nanostructures in non-crystalline samples, e.g., polymers, metallic alloys, ceramics, and glasses. In many specimens, however, the nanostructure is not distributed homogeneously, but instead varies as a function of position in the sample. Conventional SAXS or GISAXS measurements on such heterogeneous samples merely yield an averaged scattering pattern of all the different structures present along the x-ray beam path. In this thesis, scanning tomography is combined with SAXS and GISAXS, revealing the individual local scattering cross section at each position on a virtual section through the sample. The technique thereby offers unique analytical possibilities in heterogeneous specimens. A brief review of the physics of x rays and x-ray scattering is given, before the methods of tomographic SAXS and GISAXS are introduced. Experimental requirements and limitations of both methods are discussed, including aspects of sampling, local rotational invariance and x-ray beam coherence. Experiments performed at the beamline BW4 at HASYLAB at DESY, Hamburg, Germany are described, illustrating the capabilities of the method. Finally, an outlook on possible future developments in tomographic small-angle x-ray scattering is given. / Die Methoden der Röntgenkleinwinkelstreuung (SAXS) und Röntgenkleinwinkelstreuung unter streifendem Einfall (GISAXS) werden seit vielen Jahren erfolgreich eingesetzt zur Analyse von Nanostrukturen in nicht-kristallinen Proben, z.B. Polymeren, metallischen Legierungen, Keramiken und Gläsern. In vielen Proben ist die Nanostruktur allerdings nicht homogen verteilt, sondern variiert als Funktion des Ortes in der Probe. Konventionelle SAXS- oder GISAXS-Messungen an solch heterogenen Proben liefern lediglich ein über alle unterschiedlichen Strukturen entlang des Röntgenstrahls gemitteltes Streubild. In dieser Arbeit wird Rastertomographie mit SAXS und GISAXS kombiniert und so der lokale Streuquerschnitt an jedem Ort auf einem virtuellen Schnitt durch die Probe gewonnen. Diese Technik bietet so einzigartige Analysemöglichkeiten von heterogenen Proben. Es wird zunächst ein kurzer Überblick über die Physik der Röntgenstrahlung und Röntgenstreuung gegeben, bevor die Methoden der SAXS- und GISAXS-Tomographie eingeführt werden. Die experimentellen Anforderungen und Grenzen beider Methoden werden besprochen, wobei Aspekte der Abtastung, der lokalen Rotationsinvarianz und der Kohärenz im Röntgenstrahl eine Rolle spielen. Experimente, die an der Messstrecke BW4 am HASYLAB bei DESY, Hamburg, durchgeführt wurden, werden beschrieben, um die Möglichkeiten der Methode zu illustrieren. Schließlich wird ein Ausblick auf mögliche zukünftige Entwicklungen der Kleinwinkelstreutomographie gegeben.

In the investigation of correlated electron systems which are characterized by strong spin-orbit coupling, one of the central challenges is the description of the complex interplay of different microscopic energy scales and the elucidation of its influence on the formation of exotic electronic phases like complex ordering phenomena and superconductivity. In the present thesis, exemplary three case studies of iridium-based compounds are presented, in which the effects of such an interplay have been investigated employing state-of-the-art synchrotron-based techniques. The particular focus is set on experimental possibilities to influence this equilibrium utilizing external parameters. In the first study, magnetic excitations are investigated in iridate double perovskites, which exhibit a nonmagnetic ground state. Upon increasing the influence of kinetic contributions, the potential condensation of these excitations is predicted to drive a novel kind of magnetic transitions, called ’excitonic magnetism’. A comprehensive investigation of the dynamics of these excitations via resonant inelastic x-ray scattering allows for an estimation of the relevant energy scales. These results indeed reveal that the influence of kinetic contributions is too small to drive such a transition under ambient conditions. Therefore the influence of excitonic magnetism on the macroscopic properties of the investigated compounds can be excluded. In the second case, the development of a new experimental setup is presented, facilitating the investigation of complex ordering phenomena at low temperatures as a function of pressure via resonant elastic x-ray scattering. This setup has been developed and implemented as part of this work in strong collaboration with the staff of the beamline P09 at the synchrotron PETRAIII (DESY). The functionality of this setup has been illustrated by measurements of the resonant magnetic x-ray scattering in the spin-orbit coupled Mott-insulator Sr 2IrO4. Since the magnetic ground state and magnetic order in iridates result from a complex interplay of different microscopic energy scales, these systems are particularly susceptible to external influences like hydrostatic pressure. In the third case, structural phase transitions are investigated in the iridium-based dichalcogenide IrTe2. Despite the macroscopic itinerant properties of IrTe2, the phase transitions are characterized by the formation of strongly localized states. These transitions have been investigated in the course of this work using single crystal x-ray diffraction experiments as a function of hydrostatic pressure and temperature. The presented experimental data show that these strongly localized states are stabilized with increasing pressure, which is observed as an increased density of Ir-Ir dimer bonds.

Nanopartikel auf Basis von NaYF4 erfreuen sich großer Beliebtheit durch ihre vielseitigen Einsatzmöglichkeiten. Durch die Dotierung mit Ytterbium und Erbium im Wirtsgitter ist es beispielsweise möglich, niedrigenergetisches Infrarotlicht in höher-ergetisches, sichtbares Licht umzuwandeln. Zudem lässt sich NaYF4 auch im Nanometermaßstab präparieren, sodass ein Einsatz in Zellen oder lebenden Organismen möglich ist, wo die zur Anregung verwendete infrarote Strahlung ohne Probleme das Gewebe durchdringen kann. Zu Beginn dieser Arbeit zeigten aufwärtskonvertierende Nanomaterialien wie NaYF4 :Yb,Er jedoch auch nach Umhüllen mit einer inaktiven Schale aus undotiertem NaYF4 nur sehr geringe Lumineszenz-Quantenausbeuten und kurze Energieniveau-Lebenszeiten. Im Rahmen dieser Arbeit wurde die Synthesemethode zur Herstellung von aufwärtskonvertierenden NaYF4 -Nanopartikeln durch den Einsatz neuer Eduktmaterialien modifiziert und die Auswirkung der Modifikationen auf die Partikeleigenschaften näher untersucht. So konnte gezeigt werden, dass durch den Einsatz einer alternativen Fluoridquelle (NaHF2) Partikel mit sehr engen Partikelgrößenverteilungen hergestellt werden können. Jedoch zeigte sich auch, dass die mit NaHF2 präparierten Partikel sich nicht mit einer Schale aus undotiertem NaYF4 umhüllen ließen. Im zweiten Teil dieser Arbeit wurde daher der Fokus auf die Verbesserung der optischen Eigenschaften gelegt. Durch die Verwendung von getrockneten Lösungsmitteln und wasserfreien Seltenerdacetaten, sowie NH4F als Fluoridquelle gelang es erstmals, aufwärtskonvertierende Kern/Schale-Nanopartikel (<50 nm) mit einer sehr hohen Lumineszenz-Quantenausbeute, ähnlich dem des makrokristallinen Referenzmaterials, herzustellen. Auch bei sehr kleinen Kern/Schale-Partikeln (≤15 nm) konnten Quantenausbeuten erzielt werden, die nur um einen Faktor 3-4 niedriger sind als beim Referenzmaterial. Dabei zeigte sich durch die Messung der Energieniveau-Lebenszeiten, dass die größten Verlustprozesse durch die Yb3+ Emission bei 940 nm auftraten und diese durch aufbringen einer Schale unterbunden werden konnten.

Lactobacillus kunkeei is one of the most abundant bacteria within the honey crop of the honey bee. Genome sequencing of L. kunkeei isolated from honey bees all over the world showed several genes unique for L. kunkeei. Among these orphan genes, an array of four to five highly conserved genes coding for giant extracellular proteins were found. Cryogenic electron microscopy imaging of a giant-protein preparation from L. kunkeei A00901 showed an overall structure similar to a long string with a knot at the end. Further analysis showed high similarity between the different giants at the N-terminus, and secondary structure predictions showed that the same region was rich in β-sheets.  These results, combined with the knowledge of other large extracellular proteins, led to the hypothesis that the “knot” domain is located at the N-terminus and that these proteins are used by the cell to latch on to the intestine lining or other cells in the honey crop. In this study, predictions were made to locate the N-terminal domains of two of these giant proteins. Four different constructs were made for each protein, where three constructs were designed for expression and purification of the N-terminal domain with different end-positions, and one construct was for a predicted β-solenoid domain located downstream from the N-terminal domain. The protein constructs were recombinantly produced in E. coli, and three of the N-terminal constructs from both proteins were purified. Thermal stability was tested using nano differential scanning fluorimetry (nanoDSF), Thermofluor, and circular dichroism (CD), which all showed characteristic melting curves at low melting temperatures, ranging from 33 °C to 44 °C, for all three constructs. During CD measurements, all three constructs showed refolding after thermal denaturation and a higher abundance of antiparallel β-sheets over α-helices. Looking at the protein structure, small angle X-ray scattering data indicated that all three proteins formed elongated structures. These results indicate that a folded domain has been found for both proteins. Although, further analysis will be required to determine the boundaries of the N-terminal domains, and to elucidate if these domains have anything to do with ligand binding and the L. kunkeei ability to latch onto the honey crop.

No description available.