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, University of Toledo, 2022, Chemistry

Molecular recognition between two or more molecular binding partners plays an essential role in many cellular processes and pathogen entry steps. It is widely accepted now that molecular recognition is mediated through non-covalent interactions (aka non-bonded interactions) like hydrogen bond (HB), salt bridge, π-system interactions like cation–π interaction, π–π stacking interaction, CH-π interaction, and XH-π interaction (X=N, S, O); and van der Waals interaction (VDW). In this dissertation, we have studied molecular recognition in three important biological systems, i.e., agonists/antagonists in G protein-coupled receptors, guanine in GTP-binding proteins, and spike proteins of novel coronavirus with the human ACE2 receptor. It is expected that the knowledge of molecular recognition in these selected proteins would help design of drugs targeting GPCRs and GTP-binding pockets, or design of neutralizing antibodies targeting the spike protein (RBD) of the novel coronavirus. In the first system, molecular recognition of ligands that binds to GPCRs, mainly A2A receptors, was studied. It has been reported that nearly 34% of FDA-approved drugs target GPCRs. Most drugs function as either an antagonist or an agonist of GPCRs. The molecular recognition of the ligands in A2A receptors represents a topic of great importance because of the significance of adenosine and cognate ligands in cellular physiology and the necessity to develop safe and effective medications for many pathophysiological issues. A total of 5 unique agonist-bound and 18 unique antagonist-bound complexes of adenosine A2A receptor were systematically studied. Interestingly, all agonists and antagonists feature a central heterocycle that is capable of hydrogen bonding and π-system interactions. For each complex, the interaction modes between an agonist/antagonist and its interacting residues were examined to identify all the non-covalent interactions necessary for molecular recognition. The interact (open full item for complete abstract)

Committee: Xiche Hu (Committee Chair); Song-Tao Liu (Committee Member); Ajith Karunarathne (Committee Member); Timothy Mueser (Committee Member) Subjects: Chemistry

Master of Science in Chemical Engineering, Cleveland State University, 2022, Washkewicz College of Engineering

Organic semiconductors have advantages over their inorganic counterparts including low cost, flexibility, and eco-friendliness. While organic semiconductors have interesting uses in devices such as solar cells, photovoltaic cells, and even flexible electronics, they are not competitive with inorganics due to their lower conductivity. One reason for this lower conductivity is due to their amorphous structure, making it difficult for electrons to tunnel from one adjacent molecule to the next. A possible method to increase the conductivity of organic semiconductors is crystallization via self-assembly. This work computationally examines the self-organization of an organic semiconductor, pentacene, on a simple and structurally similar surface, graphene. Ab initio calculations were used to determine the ground-state energy of a single pentacene molecule on a graphene sheet at various orientations, where the pentacene molecule is incrementally translated in the x and y directions at multiple angles. These energies are used to create potential energy maps of the system relative to the minima. This allows us to predict how pentacene organizes on graphene due to molecule-substrate interactions. The results in this study identify multiple configurations with relative energies less than that of room temperature, 27.8% of all considered. Additionally, 7.8% have a relative energy within 12.5 meV. Room temperature, 25 meV, is used as a comparative value to show how close (or far away) energy configurations are to each other. However, as it is more difficult for a molecule to thermally diffuse across a surface as all atoms would need to move in a uniform manner, a smaller energy range (12.5 meV) is also evaluated. These results demonstrate a need for an additional driving force (i.e., molecule-molecule interactions) for the self-organization of pentacene on graphene and provides a more complete understanding of the pentacene-graphene system.

Committee: Jessica Bickel (Advisor); Chelsea Monty-Bromer (Committee Member); Nolan Holland (Committee Chair) Subjects: Chemical Engineering; Materials Science; Physics

Doctor of Philosophy (PhD), Ohio University, 2022, Physics and Astronomy (Arts and Sciences)

Despite the long standing history of the research, production, and application of amorphous and glassy materials, generating good quality models still remains a challenge. The challenge arises from the inherent lack of the long range order, characteristic of crystals, in amorphous materials. Researchers have developed various techniques to create models of amorphous materials ranging from random Monte Carlo to classical molecular dynamics and from ab initio to the most recent machine-learned methods. In this dissertation, we apply force enhanced atomic refinement (FEAR) whereby experimental information from diffraction measurements are used jointly with ab initio density functional theory (DFT) based energy minimization to produce models of various amorphous materials that agree with diffraction data and are a suitable energy minimum of the chosen interatomic potential functions. By generating models of metal oxides and chalcogenides, we show that this method is broadly applicable to amorphous material if the experimental diffraction data is available. We used this to study the annealing induced changes in the structure of ZrO2-Ta2O5, a potential candidate for mirror coatings for the Laser Interferometer Gravitational-wave Observatory (LIGO) interferometer mirrors. We find that annealing increases the fraction of corner-shared metal-oxygen polyhedra in this material. Motivated by interest in carbonaceous materials, we studied the graphitization of carbon at temperatures near 3000 K. For the first time, we accurately simulate the process of graphitization and the mechanisms of layering. We have seen that individual layers of amorphous graphite are topologically disordered with some pentagon and heptagon carbon rings and have studied the effects of this disorder on charge density distribution, electronic density of states, and electronic conduction. The study of carbonaceous materials was extended to study the reactivity of carbon surfaces to diff (open full item for complete abstract)

Committee: David Drabold (Advisor); Eric Stinaff (Committee Member); Gang Chen (Committee Member); Jason Trembly (Committee Member) Subjects: Physics

Master of Science in Materials Science and Engineering (MSMSE), Wright State University, 2021, Materials Science and Engineering

Methylammonium lead triiodide (MAPbI3) has garnered attention due to their high solar cell efficiencies and low cost to manufacture, but commercialization is not yet possible owing to poor environmental stability. Thus, researchers seek ways which optimize the performance of the MAPbI3 solar cell by modifying the architecture and through interfacial engineering of the charge transport layers. Difficulties in understanding these devices arise from ion migration, charge separation and recombination, and metastable, thermally active precessions of the methylammonium (MA) moiety in the lead iodide framework. In this work, focus is given to the perovskite and an adsorbed monolayer, 2,3,4,5,6-pentafluorothiophenol (C6F5SH), which has demonstrated to increase environmental stability and solar cell efficiency when placed at the perovskite/hole transport layer interface. Utilizing a first principles approach, the interface of MAPbI3 and C6F5SH is explored using various metastable methylammonium orientations to understand the relative stability, electronic properties, bandgap, and infer impact on solar cell performance.

Committee: Amir A. Farajian Ph.D. (Advisor); Hong Huang Ph.D. (Committee Member); Raghavan Srinivasan Ph.D., P.E. (Committee Member) Subjects: Materials Science

Doctor of Philosophy, The Ohio State University, 2021, Materials Science and Engineering

From long-hauling vehicles operating in marine environments to reusable rockets aiming to take civilization beyond earth, from oil and gas pipelines transporting fossil fuels to offshore wind turbines and solar panels generating renewable energy, from chemical refinery operations to long-term storage of nuclear waste in underground cannisters, corrosion is one of the common denominators that play a critical role in the operational safety and performance limitations of the respective industries. Practicing corrosion control to minimize material degradation to within a desired safety threshold and a well-understood controllable margin that can be readily managed relies on mechanistic understanding of the science behind corrosion and the application of that scientific understanding to engineer solutions. Through decades of experimental investigations, empirical knowledge has accumulated, corrosion mechanisms proposed, and mitigation strategies practiced by the corrosion scientists and engineers. In the era of Integrated Computational Materials Engineering, the emergence of the first principles approach, as formulated in the density functional theory, provides an atomic level “virtual microscope” for probing corrosion mechanisms that occur at the interfaces that terminate materials and initiate interactions with environment. Applying DFT to investigate corrosion science presents unique challenges and opportunities. A multi-physics framework must be developed to systematically address these challenges. The frameworks proposed in this thesis require the electronic work functions and the species adsorption energies as inputs, which are readily computable in the state-of-the-art DFT code. The purpose of the framework is to bridge the electrochemical properties of alloys at the interface to the macroscale observable parameters measured in a laboratory setting. Two classes of alloys will serve as the framework testing ground: precipitation hardened aluminum alloys; and Ni (open full item for complete abstract)

Committee: Christopher Taylor (Advisor); Gerald Frankel (Advisor); Narasi Sridhar (Committee Member) Subjects: Chemistry; Condensed Matter Physics; Materials Science

Doctor of Philosophy, The Ohio State University, 2021, Chemistry

The computational bottleneck of applying quantum chemistry methods has always been a significant obstacle to calculating the properties of condensed-phase systems. In this work we present accurate, scalable methods that push the dynamic range of ground- and excited-state quantum chemistry into the condensed-phase. First, we introduce an extension of symmetry-adapted perturbation theory that includes nonadditive (many-atom) dispersion effects that are essential in the description of large systems. Application of this approach to the study of π-π interactions has revealed that the dominant paradigm (based on low-order electrostatic multipoles) for understanding π-stacking is fundamentally flawed. We propose a reformulation of the electrostatic model of aromatic π-π interactions that is based on van der Waals forces, instead. Our work with π-stacking is exemplary of the utility that symmetry-adapted perturbation theory with many-body dispersion (SAPT+MBD) has as an interpretive tool, and our results suggest that it will be extremely useful in characterizing intermolecular interactions at the nanoscale. In the second part of this work, we introduce several efficient methods for solution-phase photochemistry. Contributions of this work include the implementation of a vibrational exciton model, a new root-homing algorithm based on level shifting, and introducing natural charge-transfer orbitals to combat spurious states in solution-phase time-dependent density functional theory (TDDFT). The vibrational exciton model is extremely scalable, and we use it to investigate the infrared spectrum of >200 surfactant molecules at the air/water interface. Our results have lead to insights into the nature of signal depletion in one-dimensional infrared spectra of self-aggregating molecules at interfaces. Our root-homing algorithm is robust to variational collapse, and shows promise in finding orbital-optimized excited states when the density of states becomes large. Lastly, our na (open full item for complete abstract)

Committee: John Herbert (Advisor); Heather Allen (Committee Member); Sherwin Singer (Committee Member); Barbara Ryden (Committee Member) Subjects: Physical Chemistry

Master of Science in Materials Science and Engineering (MSMSE), Wright State University, 2020, Materials Science and Engineering

Hybrid organic-inorganic perovskite solar cell is an emerging technology which has shown the fastest advancement in power conversion efficiency within a few years since introduction, thus making it one of the clean energy breakthroughs. These cells are based on thin-film technology which makes them suitable to manufacture using low-cost solution processing methods. As these types of cells are easily tunable with the selection of different materials, interfacial engineering is an important approach to increasing their efficiency. One of the main hurdles in this regard is the loss caused by the recombination of separated charges. An approach to tackle these issues is to incorporate organic monolayers between the charge (electron/hole) transport layers and the perovskite active layer. Such interface engineering has experimentally shown to improve the overall efficiency and stability of the cell. The current research focuses on the study of TiO2/HOOC-Ph-SH interface in order to understand the improved efficiency. Using ab initio quantum mechanical approach, we investigate the monolayer (HOOC-Ph-SH) adsorption onto the TiO2 surface to determine structural and electronic properties of the interface and discuss the connection of the results to solar cell performance.

Committee: Amit A. Farajian Ph.D. (Advisor); Raghavan Srinivasan Ph.D., P.E. (Committee Member); James A. Menart Ph.D. (Committee Member) Subjects: Chemistry; Materials Science; Physics; Quantum Physics

Doctor of Philosophy (PhD), Ohio University, 2020, Physics and Astronomy (Arts and Sciences)

The first complete ab initio leading-order effective interactions for protons or neutrons on light spin-0 nuclei are presented. The technological advances leading to this result are described in detail starting with the nonlocal momentum distributions created from No Core Shell Model (NCSM) reduced matrix elements. The effective potential is calculated using the leading-order of the multiple scattering approach with the NN amplitudes expressed in terms of Wolfenstein amplitudes. In order for the effective interaction to be ab initio, the complete NN interaction enters both the reaction as well as the structure calculation on equal footing. Elastic scattering amplitudes for this work are mostly limited 100 to 200 MeV projectile kinetic energy to be consistent with a leading-order calculation. This work for the first time takes into account the spin of the struck target nucleon in a realistic calculation. Elastic scattering observables for closed-shell nuclei 4He and 16O are given along with a comparison to previous assumptions that neglect the spin of the struck nucleon. The same observables for open-shell nuclei 12C, 6He, and 8He are presented with the same comparison. It is found that the difference between a complete ab initio calculation and one that neglects the spin of the struck nucleon is small for nuclei that have equal numbers of protons and neutrons. For nuclei with N , Z, the effect of the spin from the struck nucleon is energy dependent and significant at lower energies. The quality of the first leading-order ab initio effective interaction calculation to predict scattering observables is found to be good for the studied range of energies and nuclei and for the NN interaction chosen for this work.

Committee: Charlotte Elster (Committee Chair); Daniel Phillips (Committee Member); Zach Meisel (Committee Member); Gabriela Popa (Committee Member); Klaus Himmeldirk (Committee Member) Subjects: Physics

Doctor of Philosophy (Ph.D.), University of Dayton, 2019, Biology

Pathways involved during regeneration/restoration of missing body parts are conserved throughout animal kingdom, but only few animals like newts have a remarkable ability to repeatedly regenerate/restore missing organs/tissues throughout its lifespan. It remains to be determined if such an exceptional ability of the newt is attributed to strategic regulation of evolutionarily conserved pathways by genes that newt may have evolved. Previously, using a de novo assembly of the newt transcriptome combined with proteomic validation, our group identified a novel family of 5 protein members expressed in adult tissues during regeneration in Notophthalmus viridescens (Red-spotted newt). The presence of a putative signal peptide suggests that all these proteins are secretory in nature. Here we employed iterative threading assembly refinement (I-TASSER) server to generate a three-dimensional structures of these novel newt proteins and predicted their function. The data suggest that these proteins could act as ion transporters, and be involved in redox reactions. To investigate downstream events (signaling pathways) that can be modulated by newt genes, and due to absence of transgenic approaches in N. Viridescens, and conservation of genetic machinery across species, we generated transgenic Drosophila melanogaster in which these genes were misexpressed using GAL4/UAS binary system. Expression of more than 2700 transcripts were compared between these 5 newly identified newt genes. Genes involved in the developmental process, cell cycle, apoptosis, and immune response are among those that are highly enriched. Wingless (Wg) / Wnt was one of the important evolutionarily conserved pathways that was reported to be differentially regulated. To validate the RNA Seq. data, expression of six highly regulated genes (Pka-C1, hsp70Bb, PGRP-SB2, CG12224, Syp, Unc-115b ) were verified using real time Quantitative Polymerase Chain Reaction (RT-qPCR). Wg signaling pathway is one (open full item for complete abstract)

Committee: Amit Singh (Advisor); Katia Del Rio-Tsonis (Committee Member); Madhuri Kango-Singh (Committee Member); Mark Nielsen (Committee Member); Pothitos Pitychoutis (Committee Member) Subjects: Bioinformatics; Biology; Biomedical Engineering; Biophysics; Cellular Biology; Developmental Biology

Master of Science (MS), Wright State University, 2017, Chemistry

This research contains four different research projects, the first an educational project introducing hydrogen bromide and deuterium bromide (HBr/DBr) and carbon monoxide (CO) as viable options for infrared vibration-rotation spectroscopy at 0.125 cm-1 or 0.5 cm-1 resolution in the teaching laboratory. The second project involved determining the spectral shifts of lanthanide fibers for diode-pumped alkali laser (DPAL) applications. Spectral shifts of lanthanides were determined using UV-VIS-NIR absorbance spectroscopy and laser-induced fluorescence (LIF). The third project entailed computing Ar* atomic energy levels and the potential energy curves of Ar*+He laser systems arising from 3p54s1 and 3p54p1 Ar* electronic configurations using ab initio theory. The final project of this research determined rate coefficients and the equilibrium constant of the formation of nitrosyl bromide (BrNO) using relaxation kinetics. Integrated solution of the relaxation rate equation and third-order integrated rate law methodologies produced final values of kf = 1.50(6) x 10-5 torr-2s-1, kr = 5.8(8) x 10-5 torr-1s-1, and Keq = 0.26(3) torr-1, agreeing with literature within uncertainty.

Committee: David Dolson Ph.D. (Advisor); Rachel Aga Ph.D. (Committee Chair); Amit Sharma Ph.D. (Committee Member); Paul Seybold Ph.D. (Committee Member) Subjects: Atmospheric Chemistry; Chemistry; Physical Chemistry; Science Education

Doctor of Philosophy, The Ohio State University, 2016, Materials Science and Engineering

High-temperature alloys in general and superalloys in particular are crucial for manufacturing gas turbines for aircraft and power generators. Among the superalloy family, the Ni-based superalloys are the most frequently used due to their excellent strength-to-weight ratio. Their strength results from their ordered intermetallic phases (precipitates), which are relatively stable at elevated temperatures. The major deformation processes of Ni-based and Co-based superalloys are precipitate shearing and Orowan looping. The key to developing physics-based models of creep and yield strength of aircraft engine components is to understand the two deformation mechanisms mentioned above. Recent discoveries of novel dislocation structures and stacking-fault configurations in deformed superalloys implied that the traditional anti-phase boundary (APB)-type, yield-strength model is unable to explain the shearing mechanisms of the gamma” phase in 718-type (Ni-based) superalloys. While the onset of plastic deformation is still related to the formation of highly-energetic stacking faults, the physics-based yield strength prediction requires that the novel dislocation structure and the correct intermediate stacking-fault be considered in the mathematical expressions. In order to obtain the dependence of deformation mechanisms on a material's chemical composition, the relationship between the generalized-stacking-fault (GSF) surface and its chemical composition must be understood. For some deformation scenarios in which one precipitate phase and one mechanism are dominant (e.g., Orowan looping), their use in industry requires a fast-acting model that can capture the features of the deformation (e.g., the volume fraction of the sheared matrix) and reduces lost time by not repeating fine-scale simulations. The objective of this thesis was to develop a multi-scale, physics-based simulation approach that can be used to optimize existing superalloys and to accelerate the design of new (open full item for complete abstract)

Committee: Yunzhi Wang (Advisor); Michael Mills (Committee Member); Stephen Niezgoda (Committee Member) Subjects: Materials Science

Doctor of Philosophy, The Ohio State University, 2016, Chemistry

We discuss the development and application of a number of fragmentation methods focused on understanding of intermolecular interactions in different systems. The advantage of fragmentation methods is to avoid the exponential growth of required computational power for the most advanced and accurate quantum chemistry theories which preclude the application in systems with large number of atoms and molecules. In those fragmentation methods, the full chemical system is partitioned into different subsystems, circumventing the exponential scaling computational cost. How this partitioning is performed and applied appropriately is the principal emphasis of this work. One of the fragmentation methods developed by our group, called extended XSAPT, combines an efficient, iterative, monomer-based approach to computing many-body polarization interactions with a two-body version of symmetry-adapted perturbation theory (SAPT). The result is an efficient method for computing accurate intermolecular interaction energies in large non-covalent assemblies such as molecular and ionic clusters, supramolecular complexes, clathrates, or DNA--drug complexes. As in traditional SAPT, the XSAPT energy is decomposable into physically-meaningful components. Dispersion interactions are problematic in traditional low-order SAPT, and the empirical atom-atom dispersion potentials are introduced here in an attempt to improve this situation. Comparison to high-level ab initio benchmarks for biologically-related dimers, water clusters, halide--water clusters, supremolecular complexes, methane clathrate hydrates, and a DNA intercalation complex illustrate both the accuracy of XSAPT-based methods as well as their limitations. The computational cost of XSAPT scales as third to fifth order with respect to monomer size, depending upon the particular version that is employed, but the accuracy is typically superior to alternative ab initio methods with similar scaling. Moreover, the monomer-based nature of (open full item for complete abstract)

Committee: John Herbert (Advisor); Sherwin Singer (Committee Member); Marcos Sotomayor (Committee Member) Subjects: Chemistry; Physical Chemistry

Doctor of Philosophy (Ph.D.), Bowling Green State University, 2015, Photochemical Sciences

A molecular level understanding of photodynamics in condensed media is one of the recent challenges to chemical physics. This is because of the intrinsic complexity of liquid-phase photophysical and photochemical singularities arising from competing intra- and intermolecular processes. Such processes often take place on a timescale of a few femtoseconds (10-15 s) to several tens of picoseconds (10-12 s). In this work, the model photochemical processes used to investigate ultrafast photo-induced reaction dynamics in solution. The model compounds are non-metal/metal polyhalogenated small molecules. The gas-phase photochemistry of these small molecules is thoroughly examined, which also enables to establish the connection between liquid and gas phase dynamics. Furthermore, contrary to the scrupulously investigated di- and triatomic molecular systems, more vibrational degrees of freedom are accessible both for the model parent molecules, nascent polyatomic radical species, and isomer photoproducts. Therefore, a detailed mapping of the photochemical reaction paths of these molecular systems can possibly reveal different couplings between the reactive modes and other dark states in a far-from-equilibrium situation. The complexity of the encountered ultrafast events requires the utilization of several experimental and computational approaches. Results of femtosecond transient absorption, picosecond transient resonance Raman, excited state ab initio calculations are discussed in this context.

Committee: Alexander Tarnovsky Dr. (Advisor); Haowen Xi Dr. (Other); Marshall Wilson Dr. (Committee Chair); Alexey Zayak Dr. (Committee Chair) Subjects: Chemistry; Physical Chemistry

Doctor of Philosophy (PhD), Wright State University, 2014, Engineering PhD

Novel silicene-based nanomaterials are designed and characterized by first principle computer simulations to assess the effects of adsorptions and defects on stability, electronic, and thermal properties. To explore quantum thermal transport in nanostructures a general purpose code based on Green's function formalism is developed. Specifically, we explore the energetics, temperature dependent dynamics, phonon frequencies, and electronic structure associated with lithium chemisorption on silicene. Our results predict the stability of completely lithiated silicene sheets (silicel) in which lithium atoms adsorb on the atom-down sites on both sides of the silicene sheet. Upon complete lithiation, the band structure of silicene is transformed from a zero-gap semiconductor to a 0.368 eV bandgap semiconductor. This new, uniquely stable, two-atom-thick, semiconductor material could be of interest for nanoscale electronic devices. We further explore the electronic tunability of silicene through molecular adsorption of CO, CO2, O2, N2, and H2O on nanoribbons for potential gas sensor applications. We find that quantum conduction is detectibly modified by weak chemisorption of a single CO molecule on a pristine silicene nanoribbon. Moderate binding energies provide an optimal mix of high detectability and recoverability. With Ag contacts attached to a ~ 1 nm silicene nanoribbon, the interface states mask the conductance modulations caused by CO adsorption, emphasizing length effects for sensor applications. The effects of atmospheric gases: nitrogen, oxygen, carbon dioxide, and water, as well as CO adsorption density and edge-dangling bond defects, on sensor functionality are also investigated. Our results reveal pristine silicene nanoribbons as a promising new sensing material with single molecule resolution. Next, the thermal conductance of silicene nanoribbons with and without defects is explored by Non-Equilibrium Green's function method as implemented in our Th (open full item for complete abstract)

Committee: Amir Farajian Ph.D. (Advisor); Khalid Lafdi Ph.D. (Committee Member); Sharmila Mukhopadhyay Ph.D. (Committee Member); Ajit Roy Ph.D. (Committee Member); H. Daniel Young Ph.D. (Committee Member) Subjects: Materials Science; Nanoscience; Nanotechnology

Master of Computer Science, Miami University, 2014, Computational Science and Engineering

De novo repeat discovery is increasingly important due to the growth rate of new genomic data. Library-based programs such as RepeatMasker effectively expand known families of repeats, but discovering new families is difficult due to their inexact nature. Tools relying on self-alignment (e.g RECON), become prohibitively time-consuming with large sequences, while text-indexing methods, such as the Suffix Array or FM-Index, are poorly suited for the wildcard searches needed to account for single base mismatches. We present a tool, RAIDER, that uses spaced seeds in the spirit of PatternHunter to identify inexact repeats with wildcard matching. RAIDER's speed allows extensive parameter tuning, processing Human Chromosome 22 in approximately 1 minute (as compared to 39 minutes for RepeatScout or longer for RECON). RAIDER shows great promise in terms of both sensitivity and specificity, with results comparable to RepeatScout, and much potential for improvement with unexplored spaced-seed patterns.

Committee: John Karro Phd. (Advisor); James Kiper Phd. (Committee Member); Chun Liang Phd. (Committee Member) Subjects: Bioinformatics; Computer Science

Doctor of Philosophy (PhD), Wright State University, 2013, Engineering PhD

We investigate detection mechanisms of real time sensors, based on ultra-thin (single and bi-atomic layer thick) and ultra-narrow (~1nm) graphene nanoribbons (GNRs), using first principle based theoretical methods. In the first part of this study we study the electronic and magnetic structures of bilayer graphene nanoribbons (BGNRs) beyond the conventional AA and AB stackings, by using density functional theory within both local density and generalized gradient approximations (LDA and GGA). Our results show that, irrespective of the method chosen, stacking arrangements other than the conventional ones are most stable, and result in significant modification of BGNRs characeristics. The most stable bilayer armchair and zigzag structures with a width of ~1 nm are semiconducting with band gaps of 0.04 and 0.05 eV, respectively. We show shift evolution of magnetic states and emergence of magnetization upon deformation in bilayer zigzag GNRs. Band gap dependence on shift can be used to design accurate nanosensors. In the second part of this study we study detection of CO and CO2 gas molecules by change in quantum conductance of armchair graphene nanoribbons (AGNR) with a width of ~1 nm. Quantum conductance modulations are calculated by using second-order Møller-Plesset (MP2) method and density functional theory (DFT) for geometry optimization and a hybrid approach for electronic structure calculations. We determine stable and metastable physisorption orientations of gas molecules with varying concentrations. Our MP2-calculated binding energies relate 8.33% and 16.33% surface coverages of CO and CO2, respectively, to 1.72×104 and 497 parts per million (ppm). With such concentrations molecules adsorption results in conductance characteristics shifts on the order of few meV. As the concentrations detected in experiments are much less, other mechanisms including substrate and/or carrier gas doping as well as adsorption on defects or electrodes may contribute towa (open full item for complete abstract)

Committee: Amir Farajian Ph.D. (Advisor); Raghavan Srinivasan Ph.D. (Committee Member); Henry Daniel Young Ph.D. (Committee Member); Yan Zhuang Ph.D. (Committee Member); Vikram Kuppa Ph.D. (Committee Member) Subjects: Engineering; Materials Science; Nanoscience; Nanotechnology

Doctor of Philosophy, The Ohio State University, 2013, Materials Science and Engineering

Advancement of nuclear power technology has led to the critical questions of detecting emission of harmful radiation and monitoring the exact amount of fissile material present. Thus, finding devices that allow precise detection and monitoring in even the harshest nuclear environment has become one of the key challenges in nuclear energy technology. The detector materials and device structure need to allow fast and accurate measurements at high temperatures as well as survive significant radiation and corrosive environments. While semiconductor based devices fulfill the measurement requirements, current materials (predominantly silicon) are prone to radiation damage and cease functioning at approximately 150 degrees Celsius. Silicon carbide has shown some remarkable properties which can potentially overcome these deficiencies. Among various polytypes of SiC, 4H-SiC exhibits the best electronic properties, possessing a measured electronic mobility of ~1000 cm2/V-s, high thermal conductivity, wide band gap and low leakage current. These properties make it an ideal candidate material for radiation detection applications. This dissertation aimed to develop a 4H-SiC based detector, and demonstrate its function for radiation detection in harsh conditions. This included the development of multi-scale computational modeling that can predict the long-term performance of the detectors in harsh nuclear environments. For this project, we targeted the extreme conditions found in pyroprocessing, a method used to reprocess spent nuclear fuel with potential importance for next-generation power plants. There, nuclear fuel is dissolved in molten salt at processing temperatures of at least 500 degrees Celsius in order to electroplate the radionuclides of interest. While especially the high temperatures limit many design choices for the device structure, we show that a Schottky diode made with 4H-SiC and nickel-based Schottky and ohmic contacts is capable of working at temperatures up (open full item for complete abstract)

Committee: Wolfgang Windl (Advisor); Thomas E. Blue (Committee Member); Roberto Myers (Committee Member); Siddharth Rajan (Committee Member); Yu-Ping Chin (Other) Subjects: Materials Science

PhD, University of Cincinnati, 2009, Engineering : Electrical Engineering

Binary AsxS1-x glasses are studied in modulated-DSC, Raman scattering, IR reflectance and molar volume experiments over a wide range (8% < x < 41%) of compositions. Calorimetric experiments reveal a reversibility window, which permits fixing the three elastic phases; flexible at x < 22.5%, intermediate in the 22.5% < x < 29.5% range, and stressed-rigid at x > 29.5%. Raman vibrational density of states supported by first principles cluster calculations show features of both pyramidal (PYR) [As(S1/2)3] and quasi-tetrahedral (QT) [S=As(S1/2)3] local structures. The QT unit concentrations maximize in the intermediate phase (IP) and both PYR and QT local structures contribute to the width of the IP. The IP centroid in the sulfides is shifted to lower As content x than in corresponding selenides, a feature identified with excess chalcogen partially segregating from the backbone in the sulfides, but forming part of the backbone in selenides. These ideas are corroborated by the proportionately larger free volumes of sulfides than selenides, and the absence of chemical bond strength scaling of Tg's between As-sulfides and As-selenides. Low-frequency Raman modes (Boson modes) increase in scattering strength linearly as As content decreases from x = 20% to 8%, with a slope that is close to the floppy mode fraction in flexible glasses predicted by rigidity theory, showing that floppy modes contribute to the excess vibrations observed at low frequency, the Boson modes. Long term aging, extending from months to several years, is studied on several families of chalcogenide glasses including the Ge-Se, As-Se, Ge-P-Se and Ge-As-Se systems. Our results show all samples display sub-Tg endotherms typically 10°C to 70°C below Tg in glassy networks possessing a mean coordination number r in the 2.25 < r < 2.45 range. Special attention is given to the As-Se binary and XRD, m-DSC and Raman scattering experiments are undertaken. Two sets of AsxSe1-x samples aged for 8 years were compared, s (open full item for complete abstract)

Committee: Punit Boolchand PhD (Advisor); Marc Cahay PhD (Committee Member); Bernard Goodman PhD (Committee Member); Peter Kosel PhD (Committee Member); Darl McDaniel PhD (Committee Member) Subjects: Electrical Engineering; Materials Science; Physics

Doctor of Philosophy, The Ohio State University, 2011, Chemistry

Construction of accurate potential energy (PE) surfaces for molecular systems is one of the primary tasks performed by theoretical physical chemists. Once in hand, these PE functions can be used to study the dynamics and spectroscopies, as well as the structures and properties of molecular systems. This study focuses on approximating many-body electronic induction in order to improve the accuracy of existing potentials and improve the efficiency of {em{ab initio}} methods in order to allow “on-the-fly” energy and force evaluations in dynamical calculations. The majority of the work reported here focuses on the solvated electron. We initiate a study aimed at understanding the effects of explicitly including the (ultrafast) electron--solvent electronic induction, or polarization. We construct a single electron potential in which the coarse grained electronic degrees of freedom of the solvent are treated self-consistently along with the electronic wave function. Predictions of the binding energy of an excess electron in water clusters obtained using this potential compare well to {em{ab initio}} electronic structure theories. Subsequently, this potential was used to investigate the behavior of the excess electron in liquid water. The explicit treatment of induction appears to have a minimal impact on the structure and solvation dynamics of the excess electron (in the ground state) but does have a large impact on the vertical detachment energy and the optical absorption spectrum. In these latter cases there is an abrupt change in the charge distribution of the excess electron. In such cases the electronic response from the solvent can be large and should be taken into account. The electronic response of the solvent occurs on the time scale of electronic excitation. This introduces technical complications when solving for orthogonal eigenstates of this system since the model Hamiltonian is state dependent. We describe a simple meth (open full item for complete abstract)

Committee: John Herbert (Advisor); Sherwin Singer (Committee Member); Anne McCoy (Committee Member) Subjects: Chemistry; Physical Chemistry; Physics