Physically assembled gels are widely applicable in the food industry, biomedical devices, drug delivery, and soft robotics due to their tunable mechanical properties and thermoreversibility. The mechanical responses of these gels originate from their microstructure. Therefore, factors affecting the gel microstructure like polymer molecular weight, solvent quality, and polymer concentration play a significant role in determining their mechanical behavior. Gel microstructure also changes during the deformations resulting in a deviation from the structure-property relationship established for the low deformations. During large deformations, other factors like stress relaxation, poroelasticity, and polymer chain entanglement contribute significantly to the gel response. This complexity extends to the understanding of their failure behavior that occurs at large deformations. The low strain mechanical behavior of gels is governed by load-bearing chain density. They are often represented with non-linear elastic models, which ignore the contribution from viscous dissipation, polymer entanglements, surface tension, and bond dissociation. In addition, the available theoretical models cannot capture the experimental conditions like boundary confinement, therefore, numerical simulations are useful to test the developed model by comparing with experimental observations. With this objective, the present dissertation is focused on understanding the failure of physically assembled gels that consists of an ABA-type triblock copolymer dissolved in a B-block (midblock) selective solvent. Here, gelation occurs as a result of relative difference in the solubility of A-blocks (endblocks) and B-blocks (midblocks) with solvent. The thermo-mechanical characterization of these gels was performed using rheology, cavitation rheology, and DSC. A custom-built experimental set-up was developed to conduct large deformation experiments like tensile tests, creep failure experiments, and fracture experiments with a predefined crack. To characterize the gel microstructure, small-angle x-ray/neutron techniques were used. A change in the gel microstructure during deformation was also captured. The microstructure of gels was tuned by varying temperature, polymer volume fraction, midblock length, and by addition of midblock homopolymer. Finite element simulations have been used to understand the effect of boundary confinement, surface tension, and viscous dissipation. The present work provides a better understanding of failure behavior in physically assembled gels through the polymer dynamics at nano-scale level.

Thermal and morphological studies of the segmented multiblock copolyesters containing 2,2,4,4-tetramethyl-1,3-cyclobutanediol and dimethyl-1,4-cyclohexane dicarboxylate were carried out using differential scanning calorimetry, small angle X-ray scattering, wide angle X-ray diffraction and dynamic mechanical analysis. Molecular origins of the thermal transitions appearing in copolyesters were assigned by the copolyester analysis at different temperatures. The hard segments in copolyesters underwent short-range and long-range ordering (crystallization) during cooling or annealing above glass transition temperature, as concluded from thermal and wide angle X-ray diffraction analysis. Annealing process affected the ordering in hard segments and annealing temperatures of 160 °C and above led to increased microphase mixing. The small angle X-ray scattering studies confirmed the microphase separated morphology of copolyesters and supported the argument of increased microphase mixing in copolyesters annealed at higher temperatures. The amount of sulfonate containing co-monomer and its presence in either hard or soft microphase affected the morphology of the copolyesters. Introduction of the sulfonate groups led to increased microphase mixing in copolyesters as well as destruction of long-range order in the hard segments. / Master of Science

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

No description available.

No description available.

No description available.

No description available.

No description available.

No description available.

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.