Doctor of Philosophy, University of Akron, 2014, Polymer Science

For decades, device design has focused on decreasing length scales. In computer and electronic engineering, small feature sizes allow increasing computational power in ever-smaller packages; in medicine, nanoscale in vivo devices and sensors and coatings have myriad applications. These applications all focus strongly on material/component interfaces. While recent advances in experimental techniques probing interfaces at nanometer and sub-nanometer scales have improved dramatically, computational simulation remains vital to obtaining detailed information about structure and energetics in nanometer-scale interactions at interfaces and the physical properties arising from interactions at larger scales. We start with all-atom molecular dynamics simulations of methane and chloromethane adsorption on the (100) surface of molybdenum to understand adsorbate polarity/geometry and substrate interaction potential effects on interfacial structure, packing and energetics. For featureless substrates, adsorbate geometry and orientation do not influence packing and affinity. Substrates with explicit surface structure show cooperation between substrate and adsorbate geometry via adsorption-site preference. Methane prefers sites over unit cell faces, roughly commensurate with the Mo surface, whereas chloromethane invites disorder, orienting its long axis along ”bridges” between surface Mo atoms. In the second phase, we used a coarse-grained bead-spring model to perform simulations of bottle-brush homopolymers tethered to a wall substrate at long time/length scales. We studied the intra- and intermolecular accumulation of tension in tethered bottle-brush backbones vs. bottle-brush dimensions and surface grafting density. Variations in bond force and bottle-brush/component shape and size descriptors uncovered three tension ”regimes”: (i) an isolated-brush regime (low surface grafting density), where intramolecular interactions dominate and tension is minimal; (ii) a ”soft-contac (open full item for complete abstract)

Committee: Mesfin Tsige Dr. (Advisor); Mark Foster Dr. (Committee Member); Shi-Qing Wang Dr. (Committee Member); Gustavo Carri Dr. (Committee Member); Jutta Luettmer-Strathmann Dr. (Committee Member) Subjects: Condensed Matter Physics; Materials Science; Molecular Physics; Physical Chemistry; Physics; Polymers; Theoretical Physics

Doctor of Philosophy, The Ohio State University, 2023, Biophysics

This dissertation explores the use of applying molecular dynamics (MD) and enhanced sampling methods towards understanding dynamics of the cardiac troponin complex (cTn) and the thermodynamic and functional consequences introduced by cardiomyopathic mutations. Chapter 2 explores an idea from the Davis group at Ohio State that cardiomyopathic mutations in the cTnI inhibitory peptide region (cTnIIP) can cause a reduced effective concentration of the cTnI switch peptide (cTnISP) to the cTnC hydrophobic patch region (cTnCHP). We utilized the Ca2+-unbound cTn structure produced by Yamada and colleagues to simulate both a normal cTn complex (tethered) and a model of the cTn complex with the cTnIIP removed and a free cTnISP (untethered) using molecular dynamics. Our results showed that the tether was essential in producing an effective concentration of cTnISP necessary for physiological function. We also observed that cardiomyopathic mutations did not significantly affect the effective concentration of cTnISP to the cTnCHP but did cause alterations to the dynamics and flexibility of the cTnIIP region. We observed in our simulations from chapter 2 that the cTnCHP never opened for any significant amount of time. Therefore, in the third chapter we sought to produce a trajectory of the transition event between the Ca2+-unbound and Ca2+-bound cTn forms by again using structures produced by Yamada. We successfully performed this using Targeted MD (TMD) and were able to observe a transition from a Ca2+-unbound, cTnCHP closed, cTnISP unbound form of cTn to a Ca2+-bound, cTnCHP open, cTnISP bound cTn. We then selected windows from the trajectory that correlated strongly with the cTnCHP opening and cTnISP binding transition events and performed umbrella sampling (US) simulations. Our results show near perfect replication of NMR studies on the cTnISP binding event and strong correlation with previous computational studies on the cTnCHP opening event. We then introduced mutations to (open full item for complete abstract)

Committee: Steffen Lindert (Advisor); Mark Ziolo (Committee Member); Marcos Sotomayor (Committee Member); Xiaolin Cheng (Committee Member) Subjects: Biophysics

Doctor of Philosophy, Miami University, 2025, Chemistry and Biochemistry

The purpose of this dissertation is to observe physical properties of molecules in solution. Structural dynamics information is provided for three systems: a cobalt-centered complex converting between three coordination states at low temperature, a lanthanide complex adopting two NMR-active enantiomers according to identity of the metal center, and a chaperone protein interaction determining binding symmetry. These systems are investigated using a variety of analytical methods – including crystallography, NMR spectroscopy, Density Functional Theory calculations, and Molecular Dynamics simulations. Chapter 2 examines the dynamics of TpPh,Me Cobalt (II) NO3 (TpPh,MeCoNO3) [TpPh,Me = tris-3-phenyl-5-methylpyrazolylborate]. Solid-state XRD structure of TpPh,MeCoNO3 is presented for the first time, showing a five-coordinate Co (II) complex with TpPh,Me with NO3 bound as a bidentate ligand. Variable temperature NMR spectra are complicated at low temperature, with signals coalescing as temperature is increased. The high temperature NMR spectra indicate a four-coordinate structure above room temperature. Spectral analysis demonstrates the TpPh,MeCoNO3 complex occupies three concurrent structures at low temperatures. These three structures are analyzed using Density Functional Theory (DFT) calculations of four- and five-coordinate structures generated in silica from the crystal structure. In Chapter 3, the conformational interconversion of two NMR-active LnDOTAM structures (Ln=La-Lu; DOTAM=1,4,7,10-tetrakis(acetamido)-1,4,7,10-tetraaza-cyclododecane) are examined using a series of 13 lanthanide ions. Variable-temperature 1H NMR spectra demonstrate the concentration of the two identifiable conformations in solution depends on the identity of the metal ion. At low temperature, early LnDOTAM (Ce-Nd) have a high concentration of the twisted square antiprismatic geometry (TSAP), and later LnDOTAM (Sm, Eu, Tb-Yb) have a higher concentration of the square antiprismatic geomet (open full item for complete abstract)

Committee: David Tierney (Advisor); Rick Page (Committee Chair); Michael Crowder (Committee Member); Dominik Konkolewicz (Committee Member); Luis Actis (Committee Member) Subjects: Chemistry; Inorganic Chemistry; Molecular Biology; Physical Chemistry

Master of Science (M.S.), University of Dayton, 2024, Materials Engineering

Rare earth elements (REEs) are essential to many modern-day technological applications. Due to their difficult and environmentally harmful refining methods, many of these REEs are imported to the U.S. from various other countries. With countries like China dominating the market, the U.S. supply chain is at risk. A potential solution to this issue would involve the use of proteins to extract these REEs in an environmentally sustainable manner. Custom proteins would be designed to extract specific REEs from their mixed metal ores through computer simulations, namely molecular dynamics. Currently the design process is stymied by the lack of working force fields for REEs within many molecular dynamics programs. This work seeks to address this issue by creating custom force fields designed around replicating basic experimental properties the REE ions have with water, counterions, and REE binding proteins. This is done utilizing a Bayesian optimization algorithm which can efficiently and accurately choose new parameters to test and verify for a wide variety of systems.

Committee: Kevin Hinkle (Advisor); Michael Elsass (Committee Member); Rajiv Berry (Committee Member) Subjects: Biochemistry; Bioinformatics; Materials Science; Molecular Biology; Molecular Chemistry; Molecular Physics

Doctor of Philosophy, Case Western Reserve University, 2025, Chemistry

Nonadiabatic molecular dynamics (NAMD) simulations are a powerful tool for uncovering atomic-scale mechanisms of light-driven processes of molecules. However, these processes involve ultrafast nuclear motions that are tightly coupled to electronic motion, and it is uncertain if the feld of NAMD has progressed to the point of being truly predictive. To encourage the development of NAMD methods, the Journal of Chemical Physics arranged for a double-blind test of NAMD predictive capabilities against time-resolved ultrafast electron difraction (UED) experiments on the photodynamics of cyclobutanone. In Chapter 2, we present our contribution to this 2024 prediction challenge special collection. We apply a “workhorse” NAMD methodology of time-dependent density functional theory with trajectory surface hopping to simulate several picoseconds of cyclobutanone after excitation with 200 nm light, generating time-resolved electron difraction patterns to directly compare with yet-to-be-released experimental results.We also include an overview of the prediction outcomes of the full complement of contributions to the prediction challenge. A key component of NAMD simulations is the selection of the electronic structure method used to generate on-the-fy forces and nonadiabatic couplings that determine the motion of nuclei. However, excited states remain a frontier of electronic structure method development. In Chapter 3, we introduce the resonating Hartree-Fock (ResHF) method as a promising candidate for excited state applications. We then present a detailed overview of the nonorthogonal, multiconfgurational ResHF method. In Chapter 4, we present a unique formulation of ResHF that uses the matrix adjugate to remove numeric instabilities of the method.We demonstrate improved convergence to the ResHF wavefunction as a result, and benchmark ResHF against complete active space self-consistent feld in the computation of excited state energy surfaces.

Committee: Shane Parker (Advisor); Clemens Burda (Committee Chair); Robert Warburton (Committee Member); Daniel Scherson (Committee Member); Carlos Crespo-Hernández (Committee Member) Subjects: Chemistry; Physical Chemistry; Physics; Quantum Physics

PHD, Kent State University, 2024, College of Arts and Sciences / Department of Physics

Energy landscape theory of protein folding is based on the “principle of minimum frustration” which states that evolutionary pressure has selected protein sequences with an energetic bias towards native-like conformations. Some simple models (known as native-centric models) emphasize this free energy driving force towards the native state. These models have been used extensively to predict folding mechanics and conformational dynamics of proteins. Native-centric models simplify the interactions in a protein configuration to a set of attractive interactions between residues in proximity in the native structure (native contacts) and repulsive interactions for all others (non-native contacts). While these models ensure that native conformation is a minimum energy configuration, navigating the entropic and energetic tradeoffs along the folding route of a protein is non-trivial. Success of these simple models has led to an understanding that the topology of a folded protein determines the way that it folds. Nevertheless, some proteins with the same topology (and different sequences) have surprisingly distinct behavior. The work in my dissertation considers exploring the extent to which native-centric models can be used to predict properties of such proteins. My research focuses on using structure-based models that are both analytic and simulation based to predict fundamental properties observed in proteins such as folding mechanism, folding rates, binding cooperativity, and binding mechanisms. The structure-based models are applied to two proteins, Calmodulin and α-Spectrin. Both proteins have multiple domains studied individually through experiments. Each domain is topologically similar with subtle differences in mechanism properties. First, I use an analytic variational model developed to predict dominant folding routes of globule proteins. This model is applied to the R15, R16, and R17 domains of α-spectrin due to their topological similarities but diverse folding ki (open full item for complete abstract)

Committee: John Portman (Advisor) Subjects: Biophysics

Doctor of Philosophy (PhD), Ohio University, 2024, Chemical Engineering (Engineering and Technology)

Molecular dynamics simulations and enhanced sampling techniques were employed to investigate adsorption behavior of surfactants at aqueous (metal-water and oil-water) interfaces. Key findings include: (a) Surfactants exhibit a strong affinity for metallic nanoparticles (MNPs), with a tendency of the alkyl tails to wrap around the MNPs. (b) The polar head of surfactants preferentially adsorbs onto the low-coordinated sites on MNPs, while the surfactant tails show no significant preference to adsorb on different MNP facets. (c) Surfactants with longer tails have a higher tendency to aggregate with themselves upon adsorption onto MNPs. (d) On a partially surfactant-covered planar metal-water interfaces, surfactant micelles preferentially adsorb onto bare metal patches. In contrast, on a fully surfactant-covered metal surface, adsorption is primarily driven by hydrophobic interactions, leading to the formation of a hemispherical configuration. (e) Surfactant micelles encounter a free energy barrier to adsorption on metal surfaces, regardless of the extent of surface coverage. (f) At oil-water interfaces with linear oil molecules, surfactants aggregate at the interface along with the oil molecules that align parallel to the orientation of the surfactants' alkyl tail. (g) In the presence of aromatic oil, linear surfactants and linear oils do not form a structured interface layer. (h) The interfacial tension at the oil-water interface decreases with increasing surfactant concentration.

Committee: Sumit Sharma (Advisor) Subjects: Chemical Engineering; Engineering

Doctor of Philosophy, The Ohio State University, 2024, Chemistry

Nobel prize winner Jean-Marie Lehn defined supramolecular chemistry nearly 40 years ago as “the chemistry beyond the molecule.” This field strives to not only build novel molecular structures, but also to investigate their interactions with other molecules. Within this field, host-guest chemistry specifically focuses on the ability of a molecule called a “host” to covalently interact, encapsulating a “guest” molecule. In the 40-50 years since the birth of supramolecular chemistry as a field, a wide variety of cavitands, or molecules with cavities, have been synthesized. This large chemical space constitutes a myriad of potential host molecules which are now being applied in areas such as medicine, consumer goods, and sensors. In the Badjic group at OSU, a benzocyclotrimer known as the molecular basket has been extensively researched, showing affinities for molecules such as anti-cancer agents and nerve agent mimics. In the past, the groups work has been focused on the development of synthetic routes toward these molecular baskets, after which guest molecules are sought out which bind to the synthesized hosts. In recent years, the synthesis of molecular baskets has become more feasible with decagram scale preparations becoming the norm. Further advancement of these methods culminated in the ability for a tris-differentiated and chiral molecular basket to be synthesized in efforts to more accurately mimic the asymmetric environments of proteins (Chapter 2) As the focus of the group has moved from synthesis to application, the need has arisen for targeted selection of guest molecules to take place. While one can imagine designing molecular baskets on paper with some idea of chemical complementarity, this is burdensome and may result in the synthesis of hosts without affinities for target guest. Seeing a gap in the design process, it was suggested that computational chemical methods could potentially be used to investigate libraries of molecular baskets affinities (open full item for complete abstract)

Committee: Jovica Badjic (Advisor); Christo Sevov (Committee Member); Christopher Hadad (Committee Member) Subjects: Chemistry

Doctor of Philosophy, The Ohio State University, 2024, Biophysics

Here we present investigations on the structure and mechanics of molecular force sensors and DNA nanodevices using a combination of computational and experimental approaches. This work implements a range of methods from all-atom and coarse-grained molecular dynamics to cryogenic and transmission electron microscopy. All-atom molecular dynamics simulations were employed to characterize the mechanical properties of peptide-based and DNA-based molecular force sensors. The simulations revealed that the stiffness of peptide-based sensors, derived from spider silk or synthetic peptides, is consistent with theoretical predictions and experimental measurements. However, the formation of transient secondary structures in spider silk-based sensors and overstretching in DNA-based sensors can influence their elastic responses, highlighting the importance of considering these factors in sensor design. The research also explored the use of DNA origami nanostructures for delivering gene templates for homology-directed repair (HDR) in human cells. Coarse-grained simulations (oxDNA) guided the design of DNA nanostructures, and experiments demonstrated their efficacy in enhancing HDR efficiency compared to unstructured DNA, particularly when delivered using Cas9 virus-like particles (VLPs). This finding suggests the potential of DNA nanostructures for targeted gene delivery and genome editing applications. Furthermore, the dissertation explored the development of DNA-origami-protein hybrid devices for cryogenic electron microscopy characterization of protein interactions and force spectroscopy applications. Preliminary data demonstrated the feasibility of integrating peptide-based force sensors into DNA nanostructures, which is a step toward enabling the real-time measurement of mechanical forces applied to proteins. These hybrid devices hold promise for studying protein mechanics, folding, and interactions at the nanoscale, with potential applications in biomedical research, for (open full item for complete abstract)

Committee: Marcos Sotomayor (Advisor); Carlos Castro (Advisor) Subjects: Biophysics

Doctor of Philosophy, The Ohio State University, 2024, Chemistry

Investigating dielectric behavior in inhomogeneous systems remains an open question, despite significant progress with homogeneous systems like the continuum. This work shifts the paradigm, interpreting dielectric behavior through a molecular picture instead of a continuum one. Our investigation focuses on water's dielectric behavior near a spherical ion—a model widely applicable to biological processes and electrokinetics. We demonstrate that the total bound charge near an ion is identical for both continuum and molecular systems. While polarization charge density is confined to an infinitely thin layer in continuum systems, it distributes within a finite range near the ion in molecular systems. We derive the formulations of dielectric properties in terms of polarization charge density compatible with both continuum and molecular solvents. Furthermore, we critically discuss a theoretical approach to interfacial dielectric constant that was recently proposed and underscore the necessity of appropriate treatment of dielectric properties under periodic boundary conditions. Building on dielectric behavior, we explore ion solvation through molecular dynamics simulations. We propose a theoretical methodology for correcting the finite size effect inherent in the periodic boundary condition, without employing Ewald summation. This correction leads to a free energy value and the corresponding Born radius for an infinite system aligning with existing literatures. Through simulations and our methodology, we provide a physical interpretation of the Born radius in molecular systems. We unveil unique overcompensations from alternating charge layers near the ion, which converge to the Born radius further from the ion. It has been observed that the Born radius in molecular systems is smaller than the radius where solvent molecules begin to appear. To interpret this smaller Born radius, we utilize a simple model for cumulative bound charge, where (open full item for complete abstract)

Committee: Sherwin Singer (Advisor); Alexander Sokolov (Committee Member); Steffen Lindert (Committee Member) Subjects: Chemistry; Physical Chemistry

Doctor of Philosophy, The Ohio State University, 2024, Chemical Engineering

Polymers have gained attention for their use as solid electrolytes in lithium-ion batteries due to their high energy density and enhanced safety. To increase cation conductivity in solid-state polymer electrolytes, particularly at room temperature, a range of polymer systems have been explored extensively in recent years. Understanding the ion behavior in polymer systems at the molecular level is essential. Generic coarse-grained bead-spring models are widely used to describe polymeric systems in molecular dynamics simulations, which have demonstrated qualitative consistency with a variety of structural and dynamic results from experiments. When ions are present, additional model features are needed to account for their longer-ranged interactions with each other (typically through Coulomb interactions within a uniform dielectric constant background) and for their interactions with polarizable polymers. For example, using additional pairwise potentials or embedding the classic Drude oscillator to achieve polarizable modeling. One objective of this research is to study the ion behavior across various polymer systems by employing a pairwise solvation potential. Additionally, this study aims to develop the Drude oscillator integrated model in coarse-grained polymer simulations to study ion-containing polymer electrolytes. We first studied the single-ion block copolymers, which are gaining interest as potential electrolytes with high cation transference numbers. Because anions are tethered to the polymer chains, the cation transference number, which is the fractional contribution of cation conductivity to overall ion conductivity, is unity in the limit that transport of the polymer chains is negligible. Such a high transference number is of interest in reaching a high charging rate and avoiding concentration polarization that is possible in salt-doped systems. However, tethered anions may decrease polymer and cation dynamics and thus reduce cation conduction. To (open full item for complete abstract)

Committee: Lisa Hall (Advisor); Xiaoguang (William) Wang (Committee Member); Isamu Kusaka (Committee Member) Subjects: Chemical Engineering

PhD, University of Cincinnati, 2024, Arts and Sciences: Chemistry

The cytoskeleton, a key feature of the cell, acts as scaffolding that is responsible for maintaining the cell shape as well as forming a highway system for intra-cellular transportation. Thus, the cell must maintain strict regulation of its cytoskeleton to undergo deliberate change. Microtubules, an essential biopolymer of the cytoskeleton, are routinely severed by specific AAA (ATPases Associated with cellular Activities) nanomachines. Severing is required for a variety of significant cellular functions including, but not limited to, cellular division and neurogenesis. Changes to microtubules themselves, their various regulatory processes, and these proteins would have far reaching, serious implications on the viability and health of the cell and its organism. The microtubule severing enzymes are katanin, spastin, and fidgetin. Recent structural studies have solved hexameric structures for katanin and spastin in the presence of cofactors indicating they operate via a global conformational change induced by ATP hydrolysis. Simulations were previously used to study the functional states of both severing enzymes where it was identified that in long time-scales, at least one conformation will disassemble in the absence of cofactors. To further understand this observed disassembly process and the influence of the cofactors, a similar study of the resulting lower order oligomers was designed in part one. Through machine learning and in-house developed analyses, we recognized significant allosteric shifts due to the presence of ligands and neighboring protomers. During this study we also identified a particular region of katanin that is highly correlated with ligand binding from the helical bundle domain (HBD). We developed StELa, an in-house clustering algorithm, to characterize observed structural changes from simulation which identified a specific local conformational change due to ligand binding. In part two, this method was compared with other available algor (open full item for complete abstract)

Committee: Ruxandra Dima Ph.D. (Committee Chair); Ryan White Ph.D. (Committee Member); Anna Gudmundsdottir Ph.D. (Committee Member) Subjects: Chemistry

Doctor of Philosophy, The Ohio State University, 2024, Chemistry

Molecular docking and molecular dynamics simulations are two commonly used computational techniques for the in silico evaluation of receptor-ligand binding and characterization of biomacromolecules. This work presents two independent projects to elucidate the molecular interactions in different prospective protein targets and provide physical insights into structure-based drug design. The focus of the first part is the “interacts-with-Spt6” protein (IWS1), a eukaryotic transcription elongation factor present in the RNAP II polymerase (RNAP II) complexes. IWS1 is gaining increasing attention as recent works revealed its collaborative actions with many formerly identified transcription factors of known regulatory effects and its direct interaction with the catalytic alpha subunit of RNAP II (RPB1). However, having about 70% of residues in human IWS1 being intrinsically disordered, its structure and function are not fully understood. Motivated by the recently discovered connection between IWS1 and liposarcoma (LPS), a cancer that can grow and spread aggressively, we initiated the effort of finding drug molecules targeting IWS1 to suppress transcriptional activities in cancer cells. To begin with, we analyzed the supermolecular arrangement, the protein interactions within the structured core, and the potential interactions with chromatin in the intrinsically disordered region of hIWS1 based on various recent studies of the structures and biological functions of IWS1. We then identified a potential binding pocket on IWS1's interface with Spt6 for a drug molecule to act as a competitive inhibitor that downregulates the transcriptional activity of RNAP II by diminishing the association of IWS1/Spt6. Next, we designed and performed a series of molecular docking calculations. Among the top-ranked compounds from the virtual screening of FDA-approved drugs, Ketotifen and Desloratadine were selected for experimental validation and were shown to reduce the association of IWS (open full item for complete abstract)

Committee: Christopher Hadad (Advisor); Rafael Bruschweiler (Committee Member); Alexander Sokolov (Committee Member) Subjects: Chemistry

PhD, University of Cincinnati, 2023, Arts and Sciences: Chemistry

The intricate dynamics of molecular systems are pivotal to understanding numerous biological processes and have significant implications in biomedical research. This thesis presents a compre- hensive study of the behaviors of various molecular systems through molecular dynamics (MD) simulations, corroborated by empirical evidence from cutting-edge experimental techniques. The first part of the study investigates Sodium Dodecyl Sulfate (SDS), revealing the relaxation behaviors of SDS molecules through MD simulations. The congruence between the simulation results and empirical data from Nuclear Magnetic Resonance (NMR) experiments validates the simulation ap- proach, suggesting the potential for combined MD and NMR studies to explore molecule dynamics akin to SDS with high reliability. The thesis also delves into the complex functionality of the molecular chaperone ClpB, which is integral to protein disaggregation. By integrating single-molecule F ¨orster Resonance Energy Transfer (FRET) experiments with computational predictions from MD simulations, the research advances understanding of ClpB's conformational mechanics. Crucially, the optimization of MD force field parameters, informed by experimental data, enhances the accuracy of the protein dynam- ics representation. This optimized model captures the nuances of ClpB activity, providing a refined tool for examining protein disaggregation and signaling a leap forward in predictive simulations that could be applicable across the spectrum of protein dynamics research. Lastly, the thesis explores the role of the disaggregase nanomachine Hsp104 in protein home- ostasis through targeted MD simulations. The research elucidates a dual pathway in the mechanical unfolding of substrate proteins, exemplified by the green fluorescent protein (GFP), and underscores the influence of protein orientation on unfolding pathways. These insights into Hsp104's substrate (open full item for complete abstract)

Committee: George Stan Ph.D. (Committee Chair); Stephen Fox Ph.D. (Committee Member); Ryan White Ph.D. (Committee Member); Pietro Strobbia Ph.D. (Committee Member); Allison Talley Edwards Ph.D. (Committee Member); In-Kwon Kim Ph.D. (Committee Member) Subjects: Chemistry

Doctor of Philosophy, Case Western Reserve University, 2024, Pharmacology

Dynamin superfamily proteins (DSPs) are present in all organisms, mediating critical membrane remodeling events throughout the cell. Despite the decades of structural and functional studies across the superfamily, no structure has been determined of a DSP demonstrating the conformational changes required to transition from a cytosolic, solution state to a helical assembly. This gap in knowledge limits the field's understanding of the mechanisms required for regulation and functional assembly into membrane remodeling complexes. Dynamin-related protein 1 (Drp1) is the master regulator of outer membrane fission for mitochondria. Proper mitochondrial dynamics is essential for cellular health, and an imbalance in this cycle has been implicated in many diseases, from heart failure to prion-related neurodegeneration. Drp1 has been identified as a potential therapeutic target; however, the underlying mechanisms governing its regulation are largely unclear. Drp1 exists predominantly as a mixture of dimers and tetramers in solution, but the specific interactions that stabilize these solution forms and prevent the assembly of larger complexes are not known. Using cryo-EM, we have observed significant conformational rearrangements in native solution structures for both dimer and tetramer states when compared to existing DSP crystal structures. Additionally, we have identified a helical lattice which demonstrates unique GTPase domain assembly between adjacent filaments, providing insight into the mechanisms of constriction. Finally, we studied the impact of terminal tags on the structure and function of Drp1 and identified a newly appreciated intrinsically disordered region of regulation. Together, these observations provide insight into regulatory interactions that stabilize oligomer states and mediate the activation of assembly into a functional fission machinery.

Committee: Jason Mears (Advisor); Edward Yu (Committee Chair); Marcin Golczak (Committee Member); Rajesh Ramachandran (Committee Member); Beata Jastrzebska (Committee Member) Subjects: Biology; Biophysics; Molecular Biology; Pharmacology

Master of Science (M.S.), University of Dayton, 2023, Chemistry

Rare earth elements are found in relative ubiquity within the earth's crust and have a multitude of application to both everyday life and military defense. On the periodic table, rare earth elements consist of all 15 lanthanides, along with scandium and yttrium. These elements have a wide variety of application, spanning from private and public sector applications, all the way to military defense, thus making them highly desirable metals for eventual utilization. Current methods of rare earth element extraction and purification involve environmentally harmful processes, leading to North America's decision to not mine for rare earth elements within its territories. This decision has created a distinct lack of self-sufficiency in rare earth element production, currently resulting in a complete reliance of rare earth element imports from other countries, namely China. Due to the current processes of rare earth element extraction and purification posing large detriment to environmental stability along with a decrease in U.S. autonomy, determination of new, safer routes of rare earth element processing is of utmost priority. Specific proteins are known to bind metal ions, which has provided the scientific foundation for a protein-based extraction and purification method targeting rare earth elements. Previous research has identified a protein which is known to bind lanthanides, providing a high potential prospect for the solution to this problem. The protein of interest, named lanmodulin (LanM), contains four regions, denoted as EF hands, with three of which being involved in lanthanide binding. Building upon the previously mentioned solution is a thioredoxin protein found in the extremophile Pyrococcus furiosus. P. furiosus thioredoxin has shown the ability to stably accept newly introduced peptide sequences within its native amino acid sequence. The area of insertion possesses closely located cysteine residues which show p (open full item for complete abstract)

Committee: Kevin Hinkle (Committee Chair); Rajiv Berry (Committee Chair); Justin Biffinger (Committee Chair) Subjects: Chemical Engineering; Chemistry; Computer Science; Molecular Chemistry; Molecular Physics; Molecules

Doctor of Philosophy, Case Western Reserve University, 2023, Pharmacology

Mitochondria form dynamic networks and need to maintain a delicate balance between fission and fusion to satisfy the cell's energetic and metabolic requirements. Fission is necessary to ensure mitochondria are properly distributed throughout the cell and to remove damaged mitochondrial components. The dysregulation of mitochondrial dynamics resulting in either an abnormally fragmented or interconnected mitochondrial network is associated with a variety of pathologies. Mutations in dynamin-related protein 1 (Drp1), the master regulator of mitochondrial fission, have been identified in patients presenting with severe neurological defects. Patient-derived fibroblasts exhibit hyperfused mitochondria, indicating mitochondrial dysregulation. Thus, these clinically relevant mutations impair Drp1 function, but the mechanism by which these mutations disrupt mitochondrial fission was undetermined. To address this lack of knowledge, the overarching objective of this research was to elucidate the specific Drp1 functional defects that are caused by these disease-associated mutations to better understand the relationship between impaired Drp1 function and disease. Drp1 self-assembles around the outer mitochondrial membrane (OMM) and, subsequently, hydrolyzes GTP which provides the mechanical force required to cleave apart the mitochondrion. The recruitment of Drp1 to the OMM is mediated in part by lipid interactions. A mitochondria-specific lipid, cardiolipin, promotes Drp1 self-assembly, enhances its GTPase activity, and is believed to facilitate membrane constriction. Disease-associated mutations in Drp1 are predominantly located within the GTPase and middle domains, which mediate its capabilities for hydrolysis and self-assembly, respectively. We have employed an ensemble of biochemical and EM-based techniques to investigate the impact of these mutations on the self-assembly, lipid recognition, and enzymatic capabilities of Drp1. Ultimately, we have shown that even mutatio (open full item for complete abstract)

Committee: Jason Mears (Advisor); Marvin Nieman (Committee Chair); Phoebe Stewart (Committee Member); Danny Manor (Committee Member); Edward Yu (Committee Member) Subjects: Biochemistry; Biomedical Research; Biophysics; Molecular Biology

Doctor of Philosophy, The Ohio State University, 2023, Biophysics

Cadherins are a family of large transmembrane glycoproteins instrumental in facilitating organ formation during morphogenesis in vertebrates and invertebrates. At the cellular level, they are involved in adhesion, signaling, recognition, mechanotransduction, and motility. In the modern classification of the cadherin superfamily, classical cadherins with five extracellular cadherin (EC) repeats as well as clustered and non-clustered -protocadherins with six or seven EC repeats have been well-studied and their homophilic/heterophilic interactions with molecules on the same (cis) cell or opposite (trans) cells have been characterized. Complexity arises when the number of EC repeats increases with diverse Ca2+ coordination at linker regions between two consecutive EC repeats. In larger cadherins, such as cadherin-23 (CDH23), protocadherin-15 (PCDH15) and cadherin epithelial growth factor (EGF) Laminin-G (LAG or LamG) seven pass G-type receptor-1 (CELSR1), the structural flexibility afforded by different Ca2+ coordination plays determinant roles in their adhesion capacity during inner-ear mechanotransduction and planar cell polarity (PCP). CDH23 and PCDH15, each with 27 and 11 EC repeats, connect two adjacent hair- like protrusions known as stereocilia together atop of a hair cell, the primary mechanosensory cell in the inner ear. Through heterophilic interactions between their first two N-terminal EC repeats, CDH23 and PCDH15 form a filament known as the tip link. In response to sound, stereocilia undergo displacement and the tip link experiences tension, which opens the ion-conducting mechanotransduction channels on the tip-link's lower end to send signals to the brain. The heterophilic trans tetrameric complex formed by CDH23 and PCDH15, and the cis interactions along the length of PCDH15 have been well-studied in the past but full-length ectodomain structures and high-resolution structural models of complete CDH23 and PCHD15 ectodomain have not been resolved. H (open full item for complete abstract)

Committee: Marcos Sotomayor (Advisor) Subjects: Biochemistry; Biophysics

Doctor of Philosophy, The Ohio State University, 2023, Physics

When a molecule is ionized by an attosecond pulse, the cation is often left in a coherent superposition of excited states. These states will evolve according to their phase relationships and can periodically drive localized charge densities throughout the molecule solely due to the electron-electron interactions. These dynamics are known as charge migration and both their characterization and influence on the longer timescale charge transfer are openly pursued questions. In this dissertation we discuss two lab-based experimental techniques, high-harmonic spectroscopy and attosecond spectroscopy, which are ideal for charge migration characterization, and we use our experimental work on simpler dynamics as demonstrations. Our first experiment uses high-harmonic spectroscopy to resolve the cause of a minimum in the radiation emitted from high-harmonic generation in CO2. By measuring both the phase and amplitude of the radiation, we see that there are two sources of the minimum, a two-center interference and a multichannel interference, whose contribution depends on the driving wavelength. Using this information we are able to isolate the multichannel interference and resolve the evolution of the X and B-states of the CO2+ cation during propagation of the free electron in high-harmonic generation. Our second experiment uses an attosecond pulse train produced with high-harmonic generation to measure the ionization delay of the four highest ionization channels of CO2. We resolve a longstanding literature disagreement about the existence of a shape resonance in the C-ionization channel around 42 eV as we observe a delay excursion near the resonance not in the C-channel but in the A and B-channels. This confirms previous theories that interchannel couplings play an important role in CO2 ionization and that the shape resonance decays mostly through these adjacent channels. We then generally discuss how continuum state resonances could act as probes of (open full item for complete abstract)

Committee: Louis DiMauro (Advisor); Daniel Gauthier (Committee Member); Jay Gupta (Committee Member); Christopher Hirata (Committee Member) Subjects: Molecular Physics; Optics; Physics; Quantum Physics

Doctor of Philosophy (Ph.D.), Bowling Green State University, 2023, Photochemical Sciences

The very initial photoprocesses of relevant chromophores and organic molecular probes can provide important mechanistic insight into designing more robust and useful compounds for targeting in vivo applications, drug delivery, as well as an overall understanding of significant biological functions. Therefore, examining and comprehending these ultrafast processes is critical. In this dissertation, the elucidation of excited state dynamics of several molecular probes and organic systems is obtained from the results of multiple femtosecond transient absorption experiments. Chapters I and II detail the theoretical and experimental aspects, respectively, of this dissertation as fundamental and practical methods are addressed. The first chapter will cover laser spectroscopy and associated theories surrounding the technique relevant to the work discussed herein in general, while the second chapter will discuss specifics of experimental design and practices used for data analysis. The third chapter focuses on a photochromic system, trans-4,4'-azopyridine, capable of undergoing trans-cis isomerization upon irradiation and how similar and different this compound's dynamics are compared to trans-azobenzene and other azo dyes in general. An unusual trend in the quantum yield increasing upon exciting with higher excitation photon energies is linked to vibrational coherence observed for an in-plane bending mode. Chapter IV delves into a project on two polymethine cyanine dyes, which are utilized for deep tissue imaging due to their absorption and emission in the shortwave infrared region. The excited state dynamics in the fluorescent state and non-radiative relaxation mechanisms in this state, discovered to be competing photoisomerization and the energy gap law relaxation pathways, are analyzed and discussed. Finally, Chapter V describes work on a series of enaminones where the question of if and how excited state intramolecular proton transfer plays a role in the excited state m (open full item for complete abstract)

Committee: Alexander Tarnovsky Ph.D. (Committee Chair); Yuning Fu Ph.D. (Other); John Cable Ph.D. (Committee Member); Peter Lu Ph.D. (Committee Member) Subjects: Chemistry; Physical Chemistry