All living organisms must organize their genome so that it not only fits within the cell, but remains accessible for cellular processes. In bacteria, an arsenal of nucleoid-associated proteins contributes to chromosome condensation. A novel nucleoid-associated protein was recently discovered in actinobacteria, and is essential in Mycobacterium. It was classified as an integration host factor protein (IHF); however, it does not share sequence or structural homology with the well characterized Escherichia coli IHF. In this study, we characterize the structure and function of Streptomyces coelicolor IHF (sIHF). We have used a combination of biochemistry and structural biology to characterize the role of sIHF in DNA binding and DNA topology. We have solved crystal structures of sIHF bound to various double-stranded DNA substrates, and show that sIHF is able to contact DNA at multiple surfaces. Furthermore, sIHF inhibits the activity of TopA, impacting DNA topology in vitro. Our work demonstrates that sIHF is a novel nucleoid-associated protein with key roles in condensing DNA. We believe that sIHF performs its function by differentially using multiple nucleic-acid binding surfaces. Further characterization is required to confirm this hypothesis in vivo. Given that the Mycobacterium homolog of sIHF (mIHF) is essential, our studies lay the foundation to explore novel drug targets for Mycobacterium tuberculosis and Mycobacterium leprae. / Thesis / Master of Science (MSc) / Unconstrained, the bacterial genome exceeds the size of the cell by 1 000- 10 000 times; thus, compacting it into a condensed structure, known as the nucleoid, is essential for life. An arsenal of nucleoid-associated proteins contributes to this process. In this study, we characterize the structure and function of a novel nucleoid–associated protein from the soil dwelling organism Streptomyces coelicolor. We used a combination of genetics, biochemistry, and structural biology to characterize the role of this protein in DNA binding and nucleoid organization. Since this protein is also found in important human pathogens, this work lays the foundation to explore the use of nucleoid-associated proteins as antimicrobial drug targets.

The phase diagrams for the thermoreversible gelation of poly(ether ether ketone) (PEEK) in dichloroacetic acid (DCA) and 4-chlorophenol (4CP) were constructed over broad temperature and concentration ranges, revealing that PEEK is capable of dissolving and forming gels in DCA and 4CP up to a weight fraction of 25 wt.%. Highly porous aerogels of PEEK were prepared through simple solvent exchange and solvent removal of the PEEK/DCA or PEEK/4CP gels. Solvent removal utilized freeze-drying (sublimation) methods or supercritical CO2 drying methods. Varying the weight fraction of PEEK dissolved in solution determined PEEK aerogel density. Mechanical properties (in compression) were shown to improve with increasing density, resulting in equivalent compressive moduli at comparable density regardless of preparation method (concentration variation, gelation solvent, solvent removal method, or annealing parameters). Additionally, density-matched aerogels from various MW PEEK showed a correlation between increasing MW and increasing compressive modulus. Contact angle and contact angle hysteresis revealed that PEEK aerogels have a high contact angle, exceeding the conditions necessary to be classified as superhydrophobic materials. PEEK aerogel contact angle decreases with increasing density and a very low contact angle hysteresis that increases with increasing density, regardless of gelation solvent or drying method. Small angle neutron scattering (SANS) contrast-matching experiments were used to elucidate the morphological origin of scattering features, wherein it was determined that the origin of the scattering feature present in the small angle scattering region was stacked crystalline lamella. Ultra-small angle X-ray scattering (USAXS)/SAXS/Wide angle X-ray scattering (WAXS) was then used to probe the hierarchical nanostructure of PEEK aerogels across a broad range of length scales. The Unified Fit Model was used to extract structural information, which was then used to determine the specific surface areas of PEEK aerogels. Regardless of gelation solvent, gel concentration, or solvent removal method, all PEEK aerogels display high surface areas as determined by SAXS and high surface areas as determined by nitrogen adsorption methods. Surface area values determined from SAXS data were consistently higher than that measured directly using nitrogen adsorption, suggesting that pore densification diminishes the accessible aerogel surface area. / Ph. D. / Poly(ether ether ketone) (PEEK) is a semicrystalline polymer with high temperature thermal transitions and excellent mechanical strength, making it an ideal candidate for many high-performance polymer applications. When PEEK is dissolved in particular solvents, it will form a 3-dimensional network where crystalline polymer is the cross-linking unit of the network. Careful solvent removal does not significantly perturb the gel network structure and produces a low-density aerogel. This work details the first reported instance of the monolithic gelation of PEEK and the first examples of PEEK aerogels. The nanostructure of these gels and aerogels is fully characterized to relate structural features to physical properties such as mechanical stiffness and wettability.

The synthesis and characterization of a variety of ammonium ionenes from water-soluble coatings to high-performance elastomers are discussed. Water-soluble random copolymer ionenes were synthesized using the Menshutkin reaction from 1,12-dibromododecane, N,N,Nâ ²,Nâ ²-tetramethyl-1,6-hexanediamine, and 1,12-bis(N,N-dimethylamino)dodecane. The absolute molecular weights were determined for the first time using a multiangle laser light scattering detector in aqueous size exclusion chromatography and the weight-average molecular weights of these ionenes were in the range of 17,000-20,000 g/mol. Charge density increased with increasing molar ratio of N,N,Nâ ²,Nâ ²-tetramethyl-1,6-hexanediamine and the glass transition temperature (Tg) increased from 69 °C to 90 °C as the charge density increased. Small angle x-ray scattering (SAXS) showed isotropic scattering patterns for these ionenes. A limited study on cytotoxicity of these ionenes showed no direct correlation between charge density and cell viability for human brain microvascular endothelial cell line. A series of low hard segment (HS) content, poly(propylene glycol) (PPG)-based ammonium ionenes were synthesized using a Menshutkin reaction from bromine end-capped PPG oligomers (prepared using acid-chloride reactions) and N,N,Nâ ²,Nâ ²-tetramethyl-1,6-hexanediamine. Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry, titration analyses, and ¹H NMR spectroscopy, confirmed the difunctionality of bromine end-capped PPG oligomers. Thermal analysis revealed Tg's of -60 °C, comparable to pure PPG, using differential scanning calorimetery (DSC), dynamic mechanical analysis (DMA) confirming microphase separation, and an onset of degradation (Td) at 240 °C. Synthesis of a series of random block copolymer ammonium ionenes with an aliphatic 1,12-dibromododecane as part of the hard segment (33 wt% HS) enhanced film formation and supported microphase separation property. The Td and Tg did not change compared to PPG-ionenes with lower HS content. DMA and tensile testing demonstrated the influence of soft segment (SS) molecular weight and hard segment (HS) content on the mechanical properties of segmented ammonium ionenes. DMA showed the onset of flow, ranging from 100-140 ºC for 1K and 2K g/mol PPG-based ionenes respectively. SAXS revealed a Bragg distance scaled with soft segment molecular weight and ranged from 6.6 to 23.4 nm for 1K to 4K g/mol PPG-based ionenes, respectively. An investigation of the salt-responsive solubility property of random block copolymer PPG-ionenes revealed a dependence on PPG molecular weight. The 1K g/mol PPG-based ionenes with a hydrophilic (HPL)/hydrophobic (HPB) value ranging from one to three showed solubility in both water and one wt% NaCl aqueous solutions. The 2K g/mol PPG-based ionenes containing HPL/HPB value of two to 15 showed cloudy dispersions in water and one wt% NaCl solutions. The 4K g/mol PPG-based ionenes possessed the salt-responsive character; 4K g/mol PPG-based ionenes with HPL/HPB values of one to 12 showed milky dispersions in water, suspended particles in one wt% NaCl solutions and film precipitation at a HPL/HPB molar ratio of 19. / Master of Science

No description available.

Les méthodes classiques dans l'étude de la dynamique de réseau, comme la diffusion inélastique des neutrons et des rayons X, sont et vont rester limitées en flux. En conséquence les mesures sont coûteuse en temps. Pour optimiser le rendement de ces techniques, la stratégie de mesure doit être préparée avant l'expérience. Cette stratégie peut être élaborée et optimisé par des calculs de la dynamique de réseau et de la diffusion diffuse. La mesure de la diffusion diffuse thermique est une expérience simple où les régions étendues dans l'espace réciproque peuvent être explorées rapidement et en détails, ce qui permet d'identifier les caractéristiques dans la dynamique de réseau. Une méthode spectroscopique peut être appliquée ensuite sur les régions d'intérêt donnant accès à l'énergie et à l'intensité des vibrations individuelles. Dans certains cas, la diffusion diffuse thermique devient tellement contraignante pour les calculs de la dynamique de réseau (quasi)harmonique, que l'expérience de diffusion inélastique n'est plus un ingrédient nécessaire dans la reconstruction d'une image cohérente de la dynamique. Dans le cadre de ce travail la combinaison des techniques utilisant la diffusion thermique, la diffusion inélastique des rayons X et les calculs réalisés à partir des premiers principes ab initio est proposée pour l'étude de la dynamique de réseau de monocristaux. Les intensités de diffusion diffuse ainsi que les spectres inélastiques observés sont comparés à ceux calculés ab initio. Ces techniques combinées donnent accès à la description complète de la dynamique de réseau en approximation harmonique, et fournissent des informations supplémentaires précieuses. Le lecteur sera initié au formalisme de la dynamique de réseau et à celui de la diffusion inélastique et thermique. Les méthodes de calculs des propriétés vibrationnelles issues des calculs ab initio vont être introduites suivant un ensemble d'étapes menant à la convergence et donc à la validation de l'ensemble des calculs. Les techniques expérimentales utilisées tout au long de cette étude ainsi que les nouvelles possibilités s'ouvrant désormais grâce aux études combinées, serons présentées. La méthodologie sera illustrée par plusieurs systèmes de référence. Dans le cadre des systèmes à liaisons covalentes, deux polymorphes de silice - coésite et cristobalite - sont à l'étude. Les calculs expérimentaux validés sont utilisés pour l'étude des vecteurs propres, des valeurs propres et de leur contributions a la densité d'états vibrationnels (partiel et total). La comparaison avec le polymorphe de silice le plus abondant - alpha-quartz - et l'oxide de germanium en structure de alpha-quartz - révèle des ressemblances et des différences distinctes dans les propriétés vibrationnelles à basse énergie. Les polymorphes d'étain ont été choisis pour étudier l'impact du sous-système électronique sur les interactions inter-ioniques et la dynamique de réseau de monocristaux. L'étain manifeste des propriétés structurelles intéressantes, et une surface de Fermi relativement complexe. On observe une asymétrie inhabituelle au niveau de la diffusion diffuse, propriété qui peut s'expliquer dans le cadre d'une approximation harmonique de la dynamique de réseau. Enfin, la méthode élaborée est appliquée à de la glace, ce qui démontre non seulement une diffusion thermique caractéristique mais également des contributions statiques provenant du désordre de l'hydrogène. La méthodologie proposée fournit un outil puissant pour l'étude de la dynamique de réseau et sera applicable à une large variété de systèmes. Les études peuvent être étendues à des conditions extrêmes impliquant de très hautes pressions et une large gamme de températures. Cette méthodologie peut également être utilisée pour étudier les propriétés localisées de vibrations atomiques dans les systèmes avec des symétries brisées, par exemple des systèmes avec du désordre ou des effets topologiques. / The classical methods in the study of lattice dynamics, such as inelastic neutron and x-ray scattering, are and will remain flux-limited, consequently the measurements are time consuming. To maximise the yield of these techniques, measurement strategies need to be established prior to the experiment. These strategies can be elaborated and optimised by lattice dynamics calculations and thermal diffuse scattering. Measuring thermal diffuse scattering is a simple experiment where extended regions of reciprocal space can be rapidly explored in detail and characteristic features of the lattice dynamics identified. Slower spectroscopy measurements can then be applied on the selected regions of interest to gain access to the energy and intensity of individual vibrations. Moreover, in some cases the input of thermal diffuse scattering may become so constraining for the (quasi)harmonic lattice dynamic calculation, that inelastic scattering experiment will not be a necessary ingredient for the recovery of a self-consistent picture of the dynamics. In the frame of this work, the combination of thermal diffuse scattering, inelastic x-ray scattering and lattice dynamics calculations from first principles ab initio is applied to study the lattice dynamics of single crystals. Both diffuse scattering intensities and inelastic spectra determined by experiment are compared to the ones calculated ab initio. The combination of these three techniques gives access to the full lattice dynamics in the harmonic description and permits valuable new insights into the vibrational properties. The reader will be introduced to the key formalism of lattice dynamics, inelastic and thermal diffuse scattering. Methods for the calculation of vibrational properties from first principles are discussed, followed by a guideline for well converged calculations. The experimental techniques used in this work are presented and new possibilities for combined studies examined. The methodology is illustrated for several benchmark systems. Two silica polymorphs - coesite and alpha-cristobalite – were chosen as examples for covalent systems and investigated in detail. The experimentally validated calculation was used for the analysis of eigenvectors and eigenvalues of different modes, and their contribution to the total and partial density of vibrational states. Comparison with the most abundant silica polymorph - alpha-quartz - and germanium oxide in alpha-quartz structure reveals distinct similarities and differences in the low-energy vibrational properties. Metallic tin polymorphs were chosen to study the influence of the electron subsystem on inter-ionic interactions and the lattice dynamics. Tin exhibits both interesting structural properties and a complex Fermi surface. An unusual asymmetry of thermal diffuse scattering is observed which can be explained within the frame of harmonic lattice dynamics. Finally, the established method is applied to ice which exhibits not only characteristic thermal diffuse scattering but also static contributions from the hydrogen disorder. The methodology proposed in the present work provides a powerful tool in the study of lattice dynamics and will be applicable to a large variety of systems. The studies can be extended to extreme conditions involving very high pressures and a large temperature range. It may be also used to study localised properties of atomic vibrations in systems with broken symmetries, e.g. disorder or surface effects.

This thesis addresses the investigation of doubly excited 2l´nl states in helium atoms and double core excitations in solid lithium compounds. Measurements on He are made in field free environments and under the influence of electric and magnetic fields, using synchrotron based inelastic photon scattering. Cross sections for scattering to singly excited final states are directly determined and compared to theoretical results and are found to be in excellent agreement. Radiative and spin-orbit effects are quantified and are shown to play an important role in the overall characterization of highly excited He states below the N =2 threshold. A dramatic electric field dependence is also observed in the flourecence yield already for relatively weak fields. This signal increase, induced by electric as well as magnetic fields, is interpreted in terms of mixing with states of higher fluorescence branching ratios. Double core excitations at the lithium site in solid lithium compounds are investigated using resonant inelastic x-ray scattering (RIXS). The lithium halides LiF, LiCl, LiBr and LiI are studied as well as the molecular compounds Li2O, Li2CO3 and LiBF4. States with one, as well as both, of the excited electrons localized at the site of the bare lithium nucleus are identified, and transitions which involve additional band excitations are observed. A strong influence of the chemical surrounding is found, and it is discussed in terms of the ionic character of the chemical bond.

No description available.

No description available.

Neste trabalho estudamos a influência do tamanho molecular médio sobre a natureza da transição de fase esmética A (SA)-colestérica (C) líquido-cristalina para os compostos termotrópicos de miristato de colesterila (C14), nonanoato de colesterila (C9) e misturas binárias de C14 e C9 e caproato de colesterila (C6) e C9. Medidas de microscopia óptica foram realizadas para determinar as temperaturas de transição de fase SA C e C-isotrópica (I). Isto possibilitou a escolha dos intervalos de temperatura próximos às transições de fases, como referências para as outras técnicas utilizadas no trabalho. A natureza das transições de fase (descontínua, também denominada de primeira ordem, ou contínua) foi inferida através das análises de medidas de densidade e entálpicas. Os resultados evidenciaram que a transição passa de primeira ordem para contínua quando o tamanho molecular médio e a temperatura reduzida, r (definida como a razão entre as temperaturas de transição de fases SA C e C I ), decrescem no sistema. A ocorrência de uma transição de fase SA C contínua foi observada para a concentração de 65% de C9 na mistura C6 C9, para o valor de r ~ 0, 92. Propriedades mesoscópicas dos compostos estudados, como a distância entre as camadas esméticas na fase SA, dSA, o tamanho molecular médio, , no domínio C, e o comportamento do tamanho de correlação, , ao longo das transições de fase, foram determinadas da análise dos picos de difração de raios X. Os dados revelaram que dSA diminui com o decréscimo do tamanho molecular médio, como era esperado. Além disso, os valores de obtidos na fase C, próximos à transição I C, concordam com os tamanhos moleculares médios calculados supondo que as moléculas estejam em conformação estendida. Mais ainda, foi observado um aumento no tamanho de correlação na fase C quando a temperatura é reduzida da fase I para a fase SA, representando um aumento no grau de ordem orientacional. Contudo, o parâmetro troca abruptamente na transição C SA. Tal descontinuidade diminui com o decréscimo do tamanho molecular médio (e assim com r). Para o sistema particular composto por 65% C9 : 35% C6, onde identificamos um transição de fase contínua SA C, observamos um comportamento de (T TSAC)0,5 no domínio da fase C, em bom acordo com a teoria de campo médio. / The influence of the mean molecular length on the nature of the smectic A (SA)- cholesteric (C) liquid crystal phase transition has been studied for cholesteryl myristate (C14), cholesteryl nonanoate (C9) and binary mixtures of C14 and C9 and cholesteryl caproate (C6) and C9. Optical microscopy was carried out to determine the temperatures of the SAC as weel as the C - isotropic (I) phase transitions. This allowed the choice of the optimum temperature interval near the phase transitions. Information concerning the nature of the transitions (descontinuous, also referred to as first order, or continuous) was evaluated through the analysis of the density and enthalpic measurements. The results have evidenced that the transition crosses over from first order to continuous when both the mean molecular length and the reduced temperature, r (ratio between SAC and CI phase transition temperatures), decrease in the system. The occurrence of a continuous SA C phase transition is observed for a concentration very near 63.1 molar percent of C9 in the C6 C9 mixture (65 wt% C9 : 35 wt% C6), at r ~ 0.92. Mesoscopic properties of the systems, as the distance between the smectic layers in the SA phase, dSA, the mean molecular length, , in the C domain, and the correlation length, , behavior along the phase transitons, were determined from the X-ray difraction peaks. The data have revealed that dSA decreases as the mean molecular length is reduced, as it was expected. Moreover, values obtained in the C phase near the I C phase transition agree with the mean molecular lengths calculated from the corresponding extended molecule lengths. In addition, an increase in the correlation length in the C phase is observed, as the temperature is reduced from I to SA phases, representing an increase in the orientational order. Nevertheless, the parameter jumps in the C SA phase transition. Such discontinuity decreases as the mean molecular length (and hence the reduced temperature) diminishes. For the particular system composed of 65 wt% C9 : 35 wt% C6, where a continuous SA C phase transition was identified, a behavior of (T TSAC)0,5 in the C domain was observed, in good agreement with the mean field theory.

Iron oxide nanoparticles (NPs) are promising materials for use in many applications, including new cancer treatments and in cleaning water, because they exhibit size-dependent magnetic and absorptive properties. NP properties are caused by structural attributes of the NPs, like surface disorder and cation vacancies. However, NP synthetic methods also impact structure, therefore properties, of NPs. Furthermore, the synthetic method is often changed in order to change the core diameter of NPs. Determining if properties are caused by the dimensions of the NP is impossible if there are also structural features present in the NP caused by the synthetic method, like grain boundaries or polycrystalline shells. In Chapter II of this dissertation, we show a new continuous growth synthesis of spinel iron oxide where the diameter of NPs is changed by the amount of precursor added to the reaction, meaning the only structural feature changing between the NPs is size. Continuous growth, therefore, can be used to probe the impact that size has on NP structure and properties. We report that saturation magnetization of NPs produced from continuous growth is size-dependent and higher in magnitude than NPs of the same core diameter made by other syntheses. In chapter III of this dissertation we determine nanoscale structure by Pair Distribution Function (PDF) analysis of Total X-ray Scattering data of NPs isolated from the reaction with core diameters between 3-10 nm. In Chapter IV of this dissertation we monitored the growth of NPs in situ with Total X-ray Scattering to gain insight on the structures of NPs while forming. In situ measurements of Total X-ray Scattering data gave insights into how precursor oxidation state influences the structures formed during formation of NPs, with more oxidized precursor giving a more oxidized product and a reduced precursor yielding a more reduced product even though the NPs formed by either method are indistinguishable by ex situ analysis. This dissertation includes previously published and unpublished co-authored material. / 2021-04-30