Alloy nanoparticles have been extensively studied for decades. However, the synthesis and characterization of alloy nanoparticles are still posing significant challenges, leading to an increasing demand for in situ characterization techniques. Small-angle X-ray scattering (SAXS) is a powerful method for structural analysis of nanoparticles. As the SAXS signal is essentially the Fourier transform of the electron distribution, it provides structural information for the entire ensemble of nanoparticles. The development of SAXS has been facilitated by significant advances in synchrotron X-ray sources and data processing methods, leading to the development of the 3D-SAXS method, which enables the reconstruction of the 3D structures of particles from SAXS profiles.Although SAXS has the potential to be a powerful tool for investigating the internal structures of alloy nanoparticles, its application is hindered by the challenges posed by polydispersity, which can cause smearing effects that complicate the geometry recovery process. This dissertation presents a novel approach to overcome the problem of polydispersity in SAXS data analysis, thus demonstrating the utility of SAXS in investigating the internal electron density distributions of alloy nanoparticles. In Chapter 2, the SharPy algorithm is introduced as a size-refocusing program that reduces the smearing effect caused by polydispersity in SAXS data. SharPy is based on a penalized iterative regression approach to fit the pair distance distribution function (PDDF) with an estimated size distribution. It can provide detailed information about the shape of nanoparticles from the smeared SAXS signal under various scenarios and conditions. Chapter 3 investigates the simulated SAXS profiles of AuAg core-shell nanoparticles with varying size distribution, core-shell ratio, and degrees of alloying. It demonstrates the capability of SAXS in observing the electron density distribution of AuAg core-shell structures. These findings provide insights into the potential of SAXS as a reliable method for investigating the internal structures of alloy nanoparticles. Chapter 4 focuses on synthesizing and characterizing AuAg nanoparticles. Their SAXS profiles and PDDF analysis demonstrate that SAXS can distinguish between homogeneous and core-shell nanoparticle structures. In this chapter, the SharPy algorithm is first-time applied to real experimental data, demonstrating its ability to reveal the core-shell structure from a polydisperse nanoparticle system. Chapter 5 investigates the evolution of alloying AuAg nanoparticles through a combination of SAXS/PDDF analysis, 3D reconstruction, and molecular dynamics (MD) simulation. The study presents the 3D electron density distribution of alloying AuAg nanoparticles. The 3D reconstruction with electron density mapping provides a straightforward visualization of the electron density distribution pattern of the alloying AuAg nanoparticles. The success of the SAXS experiment lies in the development of the 3D-SAXS pipeline, which involves the use of SharPy and 3D reconstruction programs, making 3D SAXS a promising alternative to electron microscopy for visualizing the morphology of nanoparticle systems. / Chemistry

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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.

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The Rho family of guanosine triphosphatases (GTPases) function as binary molecular switches, which play an important role in the regulation of actin cytoskeleton rearrangement and are involved in several critical cellular processes including cell adhesion, division and migration. Rho GTPases are specifically activated by their associated guanine nucleotide exchange factors (RhoGEFs). Dysregulation of RhoGEFs function through mutation or overexpression has been implicated in oncogenic transformation of cells and linked to several kinds of invasive and metastatic forms of cancer. T-cell lymphoma invasion and metastasis 1 (Tiam1) is a multi-domain Dbl family GEF protein and specifically activates Rho GTPase Rac1 through the catalytic Dbl homology and Pleckstrin homology (DH-PH) bi-domain. Previous works have shown that the nucleotide exchange function of the full-length Tiam1 is auto-inhibited and can be activated by N-terminal truncation, phosphorylation and protein-protein interactions. However, the molecular mechanisms of Tiam1 GEF auto-inhibition and activation have not yet been determined. In this study, the N-terminal PH-CC-Ex domain of Tiam1 is shown to directly inhibit the GEF function of the catalytic DH-PH domain in vitro. Using fluorescencebased kinetics experiments, we demonstrate that the auto-inhibition of Tiam1 GEF function occurs by a competitive inhibition model. In this model, the maximum velocity of catalytic activity remains unchanged, but the Michaelis-Menten constant of the auto-inhibited Tiam1 (the PH-PH fragment) on the substrate Rac1 is increased compared to the activated Tiam1 (the catalytic DH-PH domain alone). Through small angle X-ray scattering (SAXS), the structure of auto-inhibited Tiam1 (the PH-PH fragment) is shown to form a closed conformation in which the catalytic DH-PH domain is blocked by the N-terminal PH-CC-Ex domain. Taken together, these findings demonstrate the molecular mechanism of Tiam1 GEF autoinhibition in which the PH-CC-Ex domain of Tiam1 inhibits its GEF function by preventing the substrate Rho GTPase Rac1 from accessing the catalytic DH-PH bi-domain.