Physics and Astronomy electronic theses and dissertations (MU)
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The items in this collection are the theses and dissertations written by students of the Department of Physics and Astronomy. Some items may be viewed only by members of the University of Missouri System and/or University of Missouri-Columbia. Click on one of the browse buttons above for a complete listing of the works.
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Item Time-dependent exciton dynamics : insights from 1- and 2-dimensional model systems(University of Missouri--Columbia, 2024) Williams, Jared Robert; Ullrich, CarstenTime-Dependent Density-Functional Theory (TDDFT) has become a promising alternative to the Bethe-Salpeter Equation (BSE) in terms of the calculation of optical spectra, including excitoinic features, due to its significantly lower computational cost. TDDFT brings with it the advantage of, in principle, access to the Time-Dependent (TD) exciton wave function and the ability to study ultra-fast TD phenomena. One promising family of Exchange & Correlation (XC) functionals for capturing excitonic effects in TDDFT are the Long-Range Corrected (LRC) functionals. In order to test the LRC functionals, we have written programs to do calculations in both a One-Dimensional (1D) and Two-Dimensional (2D) model systems. We used the 1D model system to explore avenues of TD exciton wave function visualization to facilitate the study and understanding of the TD dynamics of excitons. Likewise, we used the 2D model system to study various methods of correction to the LRC in hopes of better capturing excitonic effects and improving stability for Real-Time (RT) calculations. We show examples of exciton wave functions visualized with various techniques, including waterfall plots and heat maps. We have also used our 1D model system to explore how RT calculations performed using TDDFT can be used to gain insight into novel systems, as exemplified by our study of charge-transfer excitations. Using our 2D model system we have explored two possible avenues of correction to the LRC: adding a 'counter' term to the XC functional and 'generalizing' the differential equation which defines the LRC. The first avenue we explored is the addition of a new term to the XC potential, explicitly constructed to cancel out the error produced by the LRC's violation of the zero-force theorem, leading to the introduction of spurious, nonphysical, internal forces. This approach, in the end, does not seem to make a substantial impact on the optical absorption spectra or the stability of the LRC. The second avenue, using the so-called "Proca" equation, adds terms to the equation of motion in order to stabilize the calculations-again with limited success. We have successfully demonstrated in our model systems that the RT methods for TDDFT are promising tools for the exploration of TD phenomena in electronic systems. We have also explored these techniques using some illustrative situations and avenues for improving the accuracy and stability of these calculations.Item Theoretical and computational modeling of the interactions of peptides and proteins with lipid bilayer surfaces(University of Missouri--Columbia, 2024) Smith, Ryan; Kosztin, IoanThis dissertation combines computational and theoretical modeling with experimental data to advance our understanding of peptide-lipid interactions, leveraging coarse-grained (CG) molecular dynamics (MD) simulations and atomic force microscopy (AFM)-based force spectroscopy to elucidate these essential biological processes. We investigated the impact of polypeptide length on membrane interactions using a series of short, homologous peptides, revealing a linear dependence of free energy barriers and intrinsic dissociation rates on peptide length. Another study examined the effect of primary structure by varying guest residue species and positions within host-guest pentapeptides, finding significant effects of terminal residues on interactions with zwitterionic and anionic lipid bilayers and identifying multiple dissociation pathways. Additionally, we applied and compared several computational techniques for analyzing AFM force spectroscopy data, proposing machine learning methods for improved analysis. These findings suggest that peptide-membrane interactions might be more complex than previously understood, often requiring multiple dissociation pathways. Finally, we extended CG MD simulations to study a large peripheral membrane protein, providing insights into interactions at the lipid membrane surface from its dominant binding regions. This study highlights limitations in current methods and suggests alternative approaches for studying complete proteins.Item Structural and electronic properties of hybrid halide perovskites : insights into chemical vapor deposited films(University of Missouri--Columbia, 2024) Burns, Randy Daniel; Guha, SuchismitaIn the past several years, hybrid perovskite semiconductors that have been incorporated into solar cells have experienced an extremely rapid increase in power conversion efficiency that now rivals traditional silicon based devices. Hybrid organic-inorganic (HOIP) halide perovskites combine inorganic, metallic materials such as lead and tin, with organic compound groups such as methylammonium or formamidinium along with halogen atoms such as iodine, chlorine, or bromine. The combination of ions based off of those elements culminates in thin films with a variety of fortuitous characteristics. HOIP materials exhibit high absorption coefficients, tunable band gaps, extremely high defect tolerance in comparison to silicon, and allow for low-temperature solution processing and vapor deposition growth methods. Unfortunately, the main obstacle preventing mass commercialization of hybrid perovskite solar cells is stability. Moisture, heat, and light induce substantial stress onto perovskite materials and cause irreversible, destructive degradation. As such, research is now focused on developing perovskite thin films that can withstand external stimuli that may cause degradation mechanisms to occur in perovskite based devices. Many methods exist that help improve perovskite stability including modifications to the growth technique to improve the intrinsic sample quality, composition engineering of the perovskite material, encapsulation with polymers or glass, post-treatment annealing or vapor assisted defect passivation, and many more. This work primarily focuses on developing and describing precisely how chemical vapor deposition (CVD) as a growth technique, in contrast to many solution-based methods such as spin coating, greatly impacts the downstream characteristics of the perovskite thin films by enhancing stability, favorable charge transport, and shifting the structural phase diagram of the material. Furthermore, this work demonstrates that many characteristics of perovskite materials that are conventionally thought of as intrinsic are actually greatly dependent, in practice, on the growth environment that ultimately produces the thin films as opposed to idealized models which assume very low defect densities. This work demonstrates air stable perovskite thin films through CVD that exist in the ideal cubic phase at room temperature with increased electronic transport. High hydrostatic pressure was used as a probe to elucidate the phase diagram and optical pressure response of 3D perovskites. Additionally, the CVD method can be augmented to produce chlorine incorporated perovskite thin films that exhibit a single phase structure across a wide temperature range where chlorine acts as a defect passivator. More exotic forms of the material such as 2D Ruddlesden-Popper (RP) were grown with improved columnar alignment in comparison to spin coated films. Finally, a post-deposition electron-beam irradiation treatment is explored and shows how low doses of radiation of CVD grown films can improve optical and electrical performance.Item Probing membrane protein dynamics and interactions with lipids at the single molecule level(University of Missouri--Columbia, 2024) Weaver, Dylan Ross; King, Gavin M.Membrane proteins are difficult to characterize via traditional techniques, yet they constitute [approx]30 percent of proteins expressed in cells and perform critical functions. It is also essential to study the interactions with these proteins and membrane interfaces, as they can help shed light on protein stability and folding processes. The challenge in studying these interactions resides in not only the complexity of the biochemical system in question, but the length and time scales these dynamics/interactions take place in. At the single molecule level, atomic force microscopy (AFM) has become increasingly useful for direct imaging of membrane proteins in near-native conditions. Though the past decades have seen significant enhancements in scanning speed, AFM remains a serial imaging process in which a single tip is physically raster-scanned in x and y over a region of interest. AFM-based single molecule force spectroscopy (SMFS) can also be applied to studying the interactions between certain peptide sequences and supported lipid bilayers, which help to determine the energy landscapes for these peptides. However, this approach can lead to low throughput of high-quality data, as mechanical limitations of AFM cantilevers can reduce the amount of detectable interactions above a certain noise level. A long-standing question is,"How can one improve the spatial and/or temporal resolution without sacrificing precision?" This work probes this question for both AFM and force spectroscopy by studying two different systems, respectively: (1) protein translocation in bacteria, and (2) dissociation pathways of oligopeptide-lipid interactions. Translocation of polypeptide chains across membranes is an essential activity of all life forms. The general secretory (Sec) system is a primary method of exporting unfolded proteins from the cytosol of E. coli and all eubacteria. Integral membrane protein complex SecDF is a translocation factor that enhances the polypeptide secretion process that is driven by the Sec translocase, consisting of translocon SecYEG and peripheral ATPase SecA. Working models have been developed to describe the structure and functions of SecDF, but important mechanistic questions remain unanswered. Here, we acquired AFM images of SecDF protrusions in supported lipid bilayers, and compared the resulting height distriubtion to simulated images based on reported crystal structures. Orientational assignment was bolstered via imaging certain mutations of SecDF lacking critical domains. As a complement, we acquire kymographs ([greater than] 100 ms resolution) to probe the conformational dynamics of SecDF across time. Conformational shifts and increased transition rates between states were observed upon interaction with SecYEG. The method of kymograph analysis is further analyzed using simulated images of SecDF, studying the effect of certain imaging artifacts such as instrument drift. Taken together, the data provides a novel vista of SecDF dynamics in physiologically relevant conditions. Protein-lipid interfaces are a fundamental component of biology. A multitude of membraneactive peptides are known to partition into membranes and develop higher order structures. The ability to quantitatively characterize the interaction strength between peptides and lipids would be beneficial in studying the folding and stability of certain membrane proteins. When studying these interactions via bulk biochemical assays, one can extract salient information about the peptide(s) being studied, such as their free energy of transfer (bilayer to solution). However, asynchronous activity resulting from these ensembles prevent us from probing more mechanical details about the interactions. In an attempt the complement these results, we applied AFM-based force spectroscopy to two classes of peptides, both of which stem from the hydrophobicity scale developed by Wimley and White: (1) Polyleucines W-Ln and (2) Host-guest Pentapeptides W - L - L - L - X (X is a guest residue). By studying the rupture force distributions P(F) and dissociation rate k(F), we can study the peptide-lipid interactions' dependence on both peptide length and amino acid sequence. These results were coupled with coarse-grained (CG) MD simulations, allowing us to construct the free energy profile for certain peptide-lipid systems. The proposed methods can extract from the AFM data the P(F) corresponding to a single peptide, regardless of the number of peptides attached to the AFM tip. We also compare manual vs. automated methods of analyzing rupture force data in order to reduce potential user bias. These investigations will help shed light on the kinetics underlying interactions between membranes and smaller peptides, paving the way for future experiments with more complex amino acid sequences.Item Elucidation of quantum magnetic dynamics in semi-classical honeycomb lattice(University of Missouri--Columbia, 2023) Guo, Jiasen; Singh, Deepak K.[EMBARGOED UNTIL 12/1/2024] The artificial spin ice systems are essentially arrays of single domain nanomagnets with specifically designed patterns, e.g. squares, honeycombs, etc. As a natural extension of the classical spin ice system found in rare earth pyrochlore compounds, artificial spin ice systems are initially designed to mimic the tetrahedral geometry in the pyrochlore lattice. The geometrically frustrated spin configuration in classical spin ice often leads to novel electric and magnetic properties, in particular, the intriguing magnetic charge physics under the dumbbell formalism, so does the artificial spin ice. In fact, artificial spin ice has been proved a more versatile platform for such studies, both of scientific and technological importance. This is largely benefited from its easily tunable design parameters, including those related to the periodic lattice as well as those related to the individual building element, the nanomagnet. Hence a plethora of artificial spin ice has been designed and explored. Conventionally, artificial spin ice systems are often prepared via electric beam lithography which yields large element size typically in the range from hundreds of nanometers to micrometers. The large element size unavoidably leads to strong dipolar inter-elemental interaction energy in the order of 104 K, thus prohibiting the redistribution of magnetic charges via moment flipping without appealing to external stimulus. However, it is the aim of this thesis to explore a newly realized artificial magnetic honeycomb lattice through a hierarchical nanofabrication process. The as-mentioned magnetic honeycomb lattice features ultra small connected elements that have typically 11 nm in length and 4 nm in width and a variable thickness. The resulting small inter-elemental interaction energy ? 40 K thus enables the rearrangement of magnetic charges in a large temperature range, hence temperature dependent magnetic phases. In this thesis, we have extensively studied the as-mentioned artificial magnetic honeycomb lattice using a combination of neutron scattering techniques, electric mea- surements as well as theoretical calculations. Specifically, we have focused on the exploration of the dynamic properties of magnetic charge defects in the as-mentioned artificial magnetic honeycomb lattice of permalloy as well as the topological con- sequence imparted onto its transport properties by the ordering of these magnetic charges. We found that the magnetic charge defects resemble quasi-particles of quan- tum mechanical nature, and persistently move around the honeycomb lattice effort- lessly, exhibiting a temperature independent relaxation rate. On the other hand, an usual quasi-oscillatory Hall anomaly was detected in the Hall probe measurements, which can be attributed to the Berry phase effect invoked by the gauge potential due to the vortex magnetism. In a separate venue, Neodymium based honeycomb systems have also been studied extensively. In a remarkable observation, we have observed planar hall effect induced by the local spin ice order in a thin Nd-Sn hon- eycomb. More recently, neutron spin echo measurements reveals dynamic behavior of magnetic origin in the Nd-based honeycomb, that is, in many ways, similar to the dynamics of the magnetic charges defects in the Py-based honeycomb, despite the rather different magnetic properties of these two systems. Further experimental and theoretical investigation in this dynamic behavior is currently going on. In addition to the studies on artificial magnetic honeycomb systems, we also high- light two complementary studies on bulk magnetic materials, namely, Cr-doped ZnTe and NiSi. In both cases, we have utilized single crystal neutron scattering methods to elucidate the magnetic structure as well as its order parameter. Specifically, The study on Cr-doped ZnTe is supplemented by detailed theoretical calculation based on the density functional theory.