Date of Award

May 2026

Document Type

Dissertation

Degree Name

Doctor of Philosophy (PhD)

Department

Physics & Astrophysics

First Advisor

Nuri Oncel

Abstract

In this work we define the methods and experimental techniques that are used in the synthesis, characterization, and development of biophysical and hard matter systems. These efforts encompass six principal areas: Comprehensive characterization of pathogenic bacteria, development of novel chemical methods for probing binding affinities in cellular systems, understanding the electronic properties of silicon/silicon dioxide interfaces, characterization of catalytic perovskite oxide materials, and lastly, heteroepitaxial growth of vanadium nitride thin films on the silicon nitride surface.The Lyme disease spirochete Borrelia burgdorferi (B. burgdorferi) causes an infection with diverse clinical outcomes, which can include arthritis as well as cardiac and neurological manifestations. B. burgdorferi expresses different outer surface lipoproteins at different stages in its infectious cycle, many of which are adhesins. Utilizing atomic force microscopy (AFM), we obtained topography images and force-distance (F-D) curves of wild-type B. burgdorferi and mutant strains encoding different complements of surface lipoproteins. AFM data show that a reduced number of genome encoded lipoproteins correlates with decreased binding probability, weakens unbinding force, and negatively affects cell elasticity. However, these binding affinity assays represent nonspecific interactions at the AFM cantilever-cell interface. Multiple techniques have been developed to probe interfacial sites at the cellular level (i.e., flow assays, micro manipulation, super resolution spectroscopy, microscopy) however, many of these techniques do not have the ability to directly probe cell surface dynamics. Recent developments in AFM techniques have allowed for the direct investigation of receptor-ligand dynamics with high precision. This method, known as dynamic force spectroscopy (DFS) involves affixing ligand probes at the apex of an AFM cantilever (known as functionalization) to probe ligand-receptor interactions on substrates of interest. Many DFS protocols involve the functionalization of single cantilevers with pathogenic lipoproteins, however in this protocol we will present a method for functionalizing the cantilever apex with human fibronectin. This technique was employed to study the interactions of B. burgdorferi proteins to describe ligand-receptor adhesion forces and derive their bond dynamics. In the case of inorganic material systems, we employ techniques that excel in the realm of hard matter or surface chemistry. One such technique is X-ray photoelectron spectroscopy (XPS). In XPS, samples are bombarded with high intensity X-rays that break electrons loose from their atomic orbitals. By classifying the kinetic energy and number of extracted photoelectrons, we can gain information about the chemical and electronic states of the material surface. However, while XPS is generally lauded as non-destructive, ionization of the surface can introduce unwanted charge states or cause damage to poorly conductive samples; oxides are especially susceptible to this effect. In this study, we look at how X-rays affect the electronic properties of silicon oxide films in-situ using different X-ray intensities. Catalyst materials are ubiquitous in their applications and uses, from improving reaction efficiency to facilitating novel synthesis processes and their roles in waste abatement. This broad utility calls for the development of new, available, non-toxic, and efficient catalysts. Among these types of materials are oxygen-deficient (OD) perovskite oxides. OD perovskite oxides are a type of material with the general formula ???3−?, where the A-site in the perovskite lattice is populated by alkaline earth or lanthanide cations and the B-site is populated by a transition metal. OD perovskite oxides have highly tunable chemical and electronic properties, in part due to the ability of transition metal at the B-site to adopt multiple different oxidation states and coordination configurations. This “configurability” present in OD perovskite oxides makes them perfect candidates for catalytic applications that often require custom electronic and chemical configurations. The main goal of this project was to study how changing manganese concentration affects the performance of perovskite-oxides for oxygen evolution reaction (OER). To correlate the performance of perovskite-oxides with their physical and chemical properties, we investigated them using techniques such as scanning electron microscopy (SEM) and scanning transmission electron microscopy (S/TEM). With these techniques, we were able to confirm the successful synthesis of the target perovskite compounds. Additionally, by using techniques such as energy dispersive X-ray spectroscopy (EDS) and XPS we were able to analyze the composition and oxidation states of our synthesized materials. Transition metal nitrides (TMNs) have attracted significant interest due to their chemical stability, complementary metal-oxide semiconductor compatibility, and diverse functional properties, including superconductivity, making them promising candidates for applications in quantum computing, low-loss electronics, catalysis, energy storage, and plasmonics. Among superconducting TMNs such as TiN, NbN, ZrN, and VN, vanadium nitride is particularly compelling, with theoretical predictions suggesting a critical transition temperature as high as 32 K. In this study, we report the successful epitaxial synthesis of VN thin films on Si3N4(0001)/Si(111) substrates using molecular beam epitaxy (MBE). We investigate the mechanisms and growth parameters required to achieve highly crystalline films and demonstrate that increasing nitrogen flow during deposition significantly improves film quality. Structural, morphological, and compositional characterization was performed using reflection high-energy electron diffraction (RHEED), SEM, STEM, AFM, and X-ray diffraction (XRD), along with EDS and XPS. These analyses enabled identification of the crystallographic orientation relationships between VN, Si3N4(0001), and Si, and established correlations between synthesis conditions and film quality. Our results demonstrate a viable pathway for integrating high-quality epitaxial VN with silicon-based platforms, advancing its potential for superconducting and electronic device applications.

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