Matching Items (108)
Description
Precise modulation of gene expression is essential for proper tissue and cell-specific differentiation and function. Multiple distinct post-transcriptional regulatory mechanisms, such as miRNA (microRNA)-based regulation and alternative polyadenylation (APA), are an intrinsic part of this modulation and orchestrate intricate pathways to achieve and maintain balanced gene expression.MiRNA-based regulation and APA function through sequence motifs located in the 3’ Untranslated Region (3’UTR) of mRNA transcripts. MiRNAs are short (~22 nt) non-coding RNA molecules that bind target sequences within the 3’UTR of an mRNA transcript, inhibiting its translation or promoting its degradation. APA occurs during RNA transcription termination and leads to the preparation of mature mRNAs with different 3’UTR lengths, allowing shorter 3’UTRs to bypass miRNA regulation.
In addition to these two post-transcriptional forms of regulation, co-transcriptional mechanisms such as alternative RNA splicing, which produces distinct gene products from a precursor mRNA, are also important in controlling gene expression.
While miRNA-based regulation, APA, and alternative RNA splicing are important regulatory mechanisms, there is a lack of comprehensive understanding of how they interact and communicate with each other. This thesis studies these three forms of gene regulation in the nematode C. elegans, with the goal of extracting rules and mechanisms used by each of them in development to establish and maintain somatic tissue identity.
After isolating miRNA targets in multiple C. elegans somatic tissues, it was found that miRNAs can modulate the abundance of hnRNPs and SR proteins, which are known to control alternative RNA splicing in a dosage-dependent manner.To identify tissue-specific miRNAs, a nuclear fluorescent cell sorting (FACS)-based methodology named Nuc-Seq, was developed to isolate and sequence tissue-specific miRNAs from body muscle tissue. Nuc-Seq identified 2,848 muscle-specific protein-coding genes and 16 body muscle-specific miRNAs. This data was used to develop a high-quality body muscle-specific miRNA-APA Interactome which allows studies in regulatory processes in detail.
Taken together, this work highlights some of the complexity of pre- and post-transcriptional gene regulation and sheds light on how miRNA-based regulation, APA, and alternative RNA splicing are interconnected and are responsible for the establishment and maintenance of tissue identity.
ContributorsSchorr, Anna L (Author) / Mangone, Marco (Thesis advisor) / Harris, Robin (Committee member) / Sharma, Shalini (Committee member) / Varsani, Arvind (Committee member) / Arizona State University (Publisher)
Created2023
Description
Metal-Oxide-Semiconductor (MOS) is essential to modern VLSI devices. In the past decades, a wealth of literature has been created to understand the impact of the radiation-induced charges on the devices, i.e., the creation of electron-hole pairs in the oxide layer which is the most sensitive part of MOS structure to the radiation effect. In this work, both MOS and MNOS devices were fabricated at ASU NanoFab to study the total ionizing dose effect using capacitance-voltage (C-V) electrical characterization by observing the direction and amounts of the shift in C-V curves and electron holography observation to directly image the charge buildup at the irradiated oxide film of the oxide-only MOS device.C-V measurements revealed the C-V curves shifted to the left after irradiation (with a positive bias applied) because of the net positive charges trapped at the oxide layer for the oxide-only sample. On the other hand, for nitride/oxide samples with positive biased during irradiation, the C-V curve shifted to the right due to the net negative charges trapped at the oxide layer. It was also observed that the C-V curve has less shift in voltage for MNOS than MOS devices after irradiation due to the less charge buildup after irradiation.
Off-axis electron holography was performed to map the charge distribution across the MOSCAP sample. Compared with both pre-and post-irradiated samples, a larger potential drop at the Si/SiO2 was noticed in post-irradiation samples, which indicates the presence of greater amounts of positive charges that buildup the Si/SiO2 interface after the TID exposure.
TCAD modeling was used to extract the density of charges accumulated near the SiO2/Si and SiO2/ Metal interface by matching the simulation results to the potential data from holography. The increase of near-interface positive charges in post-irradiated samples is consistent with the C-V results.
ContributorsChang, Ching Tao (Author) / Barnaby, Hugh (Thesis advisor) / Holbert, Keith (Committee member) / Tongay, Sefaattin (Committee member) / Arizona State University (Publisher)
Created2023
Description
My thesis, Design of Hierarchically Porous Materials Containing Covalent Organic Frameworks, focuses on testing the validity of incorporating nanoporous organic materials into macroporous scaffolding to improve the functionality of covalent organic frameworks as materials for filtration applications. The macroporous scaffold was based off of a material recently described in literature and the bulk of the experimentation was focused on the effects of the necessary processing for the creation of the macroporous material on the structure of the covalent organic frameworks. The property primarily investigated was the Brunauer-Emmett-Teller surface area, as the applicability of the frameworks is largely determined by their nanoporous surface area.
ContributorsRidenour, Brian (Author) / Jin, Kailong (Thesis director) / Tongay, Sefaattin (Committee member) / Barrett, The Honors College (Contributor) / Materials Science and Engineering Program (Contributor)
Created2023-05
Description
The recent discoveries of 2D van der Waals (vdW) materials have led to the realization of 2D magnetic crystals. Previously debated and thought impossible, transition metal halides (TMH) have given rise to layer dependent magnetism. Using these TMH as a basis, an alloy composing of Fe1-xNixCl2 (where 0 ≤ x ≤ 1) was grown using chemical vapor transport. The intrigue for this alloy composition stems from the interest in spin canting and magnet moment behavior since NiCl2 has in-plane ferromagnetism whereas FeCl2 has out-of-plane ferromagnetism. While in its infancy, this project lays out a foundation to fully develop and characterize this TMH via cationic alloying. To study the magnetic properties of this alloy system, Vibrating Sample Magnetometry was employed extensively to measure the magnetism as a function of temperature as well as applied magnetic field. Future work with use a combination of X-Ray Diffraction, Raman, Scanning Electron Microscopy, and Energy-Dispersive X-Ray Spectroscopy Mapping to verify homogeneous alloying rather than phase separation. Additionally, ellipsometry will be used with Kramer-Kronig relations to extract the dielectric constant from Fe1-xNixCl2. This work lays the foundation for future, fruitful work to prepare this vdW cationic alloy for eventual device applications.
ContributorsPovilus, Blake (Author) / Tongay, Sefaattin (Thesis director) / Yang, Sui (Committee member) / Barrett, The Honors College (Contributor) / Materials Science and Engineering Program (Contributor)
Created2022-05
Description
Vanadium-dioxide-based devices show great switchability in their optical properties due to its dramatic thermochromic phase transition from insulator to metal, but generally have concerns due to its relatively high transition temperature at 68 °C. Doping the vanadium dioxide with tungsten has been shown to reduce its transition temperature at the cost lower optical property differences between its insulating and metallic phases. A recipe is developed through parametric experimentation to fabricate tungsten-doped vanadium dioxide consisting of a novel dual target co-sputtering deposition, a furnace oxidation process, and a post-oxidation annealing process. The transmittance spectra of the resulting films are measured via Fourier-transform infrared spectroscopy at different temperatures to confirm the lowered transition temperature and analyze their thermal-optical hysteresis behavior through the transition temperature range. Afterwards, the optical properties of undoped sputtered vanadium films are modeled and effective medium theory is used to explain the effect of tungsten dopants on the observed transmittance decrease of doped vanadium dioxide. The optical modeling is used to predict the performance of tungsten-doped vanadium dioxide devices, in particular a Fabry-Perot infrared emitter and a nanophotonic infrared transmission filter. Both devices show great promise in their optical properties despite a slight performance decrease from the tungsten doping. These results serve to illustrate the excellent performance of the co-sputtered tungsten-doped vanadium dioxide films.
ContributorsChao, Jeremy (Author) / Wang, Liping (Thesis advisor) / Wang, Robert (Committee member) / Tongay, Sefaattin (Committee member) / Arizona State University (Publisher)
Created2022
Description
Most protein-coding mRNAs in eukaryotes must undergo a series of processing steps so they can be exported from the nucleus and translated into protein. Cleavage and polyadenylation are vital steps in this maturation process. Improper cleavage and polyadenylation results in variation in the 3′ UTR length of genes, which is a hallmark of various human diseases. Previous data have shown that the majority of 3’UTRs of mRNAs from the nematode Caenorhabditis elegans terminate at an adenosine nucleotide, and that mutating this adenosine disrupts the cleavage reaction. It is unclear if the adenosine is included in the mature mRNA transcript or if it is cleaved off. To address this question, we are developing a novel method called the Terminal Adenosine Methylation (TAM) assay which will allow us to precisely define whether the cleavage reaction takes place upstream or downstream of this terminal adenosine. The TAM Assay utilizes the ability of the methyltransferase domain (MTD) of the human methyltransferase METTL16 to methylate the terminal adenosine of a test mRNA transcript prior to the cleavage reaction in vivo. The presence or absence of methylation at the terminal adenosine will then be identified using direct RNA sequencing. This project focuses on 1) preparing the chimeric construct that positions the MTD on the mRNA cleavage site of a test mRNA transcript, and 2) testing the functionality of this construct in vitro and developing a transgenic C. elegans strain expressing it. The TAM assay has the potential to be a valuable tool for elucidating the role of the terminal adenosine in cleavage and polyadenylation.
ContributorsKeane, Sara (Author) / Mangone, Marco (Thesis director) / Lapinaite, Audrone (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of English (Contributor)
Created2023-05
Description
Rare-earth tritellurides (RTe3) are two-dimensional materials with unique quantum properties, ideal for investigating quantum phenomena and applications in supercapacitors, spintronics, and twistronics. This dissertation examines the electronic, magnetic, and phononic properties of the RTe3 family, exploring how these can be controlled using chemical pressure, cationic alloying, and external pressure.The impact of chemical pressure on RTe3 phononic properties was investigated through noninvasive micro-Raman spectroscopy, demonstrating the potential of optical measurements for determining charge density wave (CDW) transition temperatures. Cationic alloying studies showed seamless tuning of CDW transition temperatures by modifying lattice constants and revealed complex magnetism in alloyed RTe3 with multiple magnetic transitions.
A comprehensive external pressure study examined the influence of spacing between RTe3 layers on phononic and CDW properties across the RTe3 family. Comparisons between different RTe3 materials showed LaTe3, with the largest thermodynamic equilibrium interlayer spacing (smallest chemical pressure), has the most stable CDW phases at high pressures. Conversely, CDW phases in late RTe3 systems with larger internal chemical pressures were more easily suppressed by applied pressure.
The dissertation also investigated Schottky barrier realignment at RTe3/semiconductor interfaces induced by CDW transitions, revealing changes in Schottky barrier height and ideality factor around the CDW transition temperature. This indicates that chemical potential changes of RTe3 below the CDW transition temperature influence Schottky junction properties, enabling CDW state probing through interface property measurements.
A detailed experimental and theoretical analysis of the oxidation process of RTe3 compounds was performed, which revealed faster degradation in late RTe3 systems. Electronic property changes, like CDW transition temperature and chemical potential, are observed as degradation progresses. Quantum mechanical simulations suggested that degradation primarily results from strong oxidizing reactions with O2 molecules, while humidity (H2O) plays a negligible role unless Te vacancies exist.
Lastly, the dissertation establishes a large-area thin film deposition at relatively low temperatures using a soft sputtering technique. While focused on MoTe2 deposition, this technique may also apply to RTe3 thin film deposition.
Overall, this dissertation expands the understanding of the fundamental properties of RTe3 materials and lays the groundwork for potential device applications.
ContributorsYumigeta, Kentaro (Author) / Tongay, Sefaattin (Thesis advisor) / Ponce, Fernando (Committee member) / Drucker, Jeffery (Committee member) / Erten, Onur (Committee member) / Arizona State University (Publisher)
Created2023
Description
Janus Transition Metal Dichalcogenides (TMDs) are emerging 2D quantum materials with an asymmetric chalcogen configuration that induces an out-of-plane dipole moment. Their synthesis has been a limiting factor in exploring these systems' many-body physics and interactions. This dissertation examines the challenges associated with synthesis and charts the excitonic landscape of Janus crystals by proposing the development of the Selective Epitaxy and Atomic Replacement (SEAR) technique. SEAR utilizes ionized radical precursors to modify TMD monolayers into their Janus counterparts selectively. The synthesis is coupled with optical spectroscopy and monitored in real-time, enabling precise control of reaction kinetics and the structural evolution of Janus TMDs. The results demonstrate the synthesis of Janus TMDs at ambient temperatures, reducing defects and preserving the structural integrity with the hitherto best-reported exciton linewidth emission value, indicating ultra-high optical quality. Cryogenic optical spectroscopy (4K) coupled with a magnetic field on Janus monolayers has allowed the isolation of excitonic transitions and the identification of charged exciton complexes. Further study into macroscopic and microscopic defects reveals that structural asymmetry results in the spontaneous formation of 2D Janus Nanoscrolls from an in-plane strain. The chalcogen arrangement in these structures dictates two types of scrolling dynamics that form Archimedean or inverted C-scrolls. High-resolution scanning transmission electron microscopy of these superlattices shows a preferential orientation of scrolling and formation of Moiré patterns. These materials' thermodynamically favorable defect states are identified and shown to be optically active. The encapsulation of Janus TMDs with hexagonal Boron Nitride (h-BN) has allowed isolation defect transitions. DFT coupled with power-dependent PL spectroscopy at 4K shows the broad defect band to be a convolution of individual defect states with extremely narrow linewidth (2 meV) indicative of a two-state quantum system. The research presents a comprehensive synthesis approach with insights into the structural and morphological stability of 2D Janus layers, establishing a complete structure-property correlation of optical transitions and defect states, broadening the scope for practical applications in quantum information technologies.
ContributorsSayyad, Mohammed Yasir (Author) / Tongay, Sefaattin (Thesis advisor) / Esqueda, Ivan S (Committee member) / Zhuang, Houlong (Committee member) / Arizona State University (Publisher)
Created2024
Description
Recently, two-dimensional (2D) materials have emerged as a new class of materials with highly attractive electronic, optical, magnetic, and thermal properties. However, there exists a sub-category of 2D layers wherein constituent metal atoms are arranged in a way that they form weakly coupled chains confined in the 2D landscape. These weakly coupled chains extend along particular lattice directions and host highly attractive properties including high thermal conduction pathways, high-mobility carriers, and polarized excitons. In a sense, these materials offer a bridge between traditional one-dimensional (1D) materials (nanowires and nanotubes) and 2D layered systems. Therefore, they are often referred as pseudo-1D materials, and are anticipated to impact photonics and optoelectronics fields.
This dissertation focuses on the novel growth routes and fundamental investigation of the physical properties of pseudo-1D materials. Example systems are based on transition metal chalcogenide such as rhenium disulfide (ReS2), titanium trisulfide (TiS3), tantalum trisulfide (TaS3), and titanium-niobium trisulfide (Nb(1-x)TixS3) ternary alloys. Advanced growth, spectroscopy, and microscopy techniques with density functional theory (DFT) calculations have offered the opportunity to understand the properties of these materials both experimentally and theoretically. The first controllable growth of ReS2 flakes with well-defined domain architectures has been established by a state-of-art chemical vapor deposition (CVD) method. High-resolution electron microscopy has offered the very first investigation into the structural pseudo-1D nature of these materials at an atomic level such as the chain-like features, grain boundaries, and local defects.
Pressure-dependent Raman spectroscopy and DFT calculations have investigated the origin of the Raman vibrational modes in TiS3 and TaS3, and discovered the unusual pressure response and its effect on Raman anisotropy. Interestingly, the structural and vibrational anisotropy can be retained in the Nb(1-x)TixS3 alloy system with the presence of phase transition at a nominal Ti alloying limit. Results have offered valuable experimental and theoretical insights into the growth routes as well as the structural, optical, and vibrational properties of typical pseudo-1D layered systems. The overall findings hope to shield lights to the understanding of this entire class of materials and benefit the design of 2D electronics and optoelectronics.
This dissertation focuses on the novel growth routes and fundamental investigation of the physical properties of pseudo-1D materials. Example systems are based on transition metal chalcogenide such as rhenium disulfide (ReS2), titanium trisulfide (TiS3), tantalum trisulfide (TaS3), and titanium-niobium trisulfide (Nb(1-x)TixS3) ternary alloys. Advanced growth, spectroscopy, and microscopy techniques with density functional theory (DFT) calculations have offered the opportunity to understand the properties of these materials both experimentally and theoretically. The first controllable growth of ReS2 flakes with well-defined domain architectures has been established by a state-of-art chemical vapor deposition (CVD) method. High-resolution electron microscopy has offered the very first investigation into the structural pseudo-1D nature of these materials at an atomic level such as the chain-like features, grain boundaries, and local defects.
Pressure-dependent Raman spectroscopy and DFT calculations have investigated the origin of the Raman vibrational modes in TiS3 and TaS3, and discovered the unusual pressure response and its effect on Raman anisotropy. Interestingly, the structural and vibrational anisotropy can be retained in the Nb(1-x)TixS3 alloy system with the presence of phase transition at a nominal Ti alloying limit. Results have offered valuable experimental and theoretical insights into the growth routes as well as the structural, optical, and vibrational properties of typical pseudo-1D layered systems. The overall findings hope to shield lights to the understanding of this entire class of materials and benefit the design of 2D electronics and optoelectronics.
ContributorsWu, Kedi (Author) / Tongay, Sefaattin (Thesis advisor) / Zhuang, Houlong (Committee member) / Green, Matthew (Committee member) / Arizona State University (Publisher)
Created2018
Description
There has been a surge in two-dimensional (2D) materials field since the discovery of graphene in 2004. Recently, a new class of layered atomically thin materials that exhibit in-plane structural anisotropy, such as black phosphorous, transition metal trichalcogenides and rhenium dichalcogenides (ReS2), have attracted great attention. The reduced symmetry in these novel 2D materials gives rise to highly anisotropic physical properties that enable unique applications in next-gen electronics and optoelectronics. For example, higher carrier mobility along one preferential crystal direction for anisotropic field effect transistors and anisotropic photon absorption for polarization-sensitive photodetectors.
This dissertation endeavors to address two key challenges towards practical application of anisotropic materials. One is the scalable production of high quality 2D anisotropic thin films, and the other is the controllability over anisotropy present in synthesized crystals. The investigation is focused primarily on rhenium disulfide because of its chemical similarity to conventional 2D transition metal dichalcogenides and yet anisotropic nature. Carefully designed vapor phase deposition has been demonstrated effective for batch synthesis of high quality ReS2 monolayer. Heteroepitaxial growth proves to be a feasible route for controlling anisotropic directions. Scanning/transmission electron microscopy and angle-resolved Raman spectroscopy have been extensively applied to reveal the structure-property relationship in synthesized 2D anisotropic layers and their heterostructures.
This dissertation endeavors to address two key challenges towards practical application of anisotropic materials. One is the scalable production of high quality 2D anisotropic thin films, and the other is the controllability over anisotropy present in synthesized crystals. The investigation is focused primarily on rhenium disulfide because of its chemical similarity to conventional 2D transition metal dichalcogenides and yet anisotropic nature. Carefully designed vapor phase deposition has been demonstrated effective for batch synthesis of high quality ReS2 monolayer. Heteroepitaxial growth proves to be a feasible route for controlling anisotropic directions. Scanning/transmission electron microscopy and angle-resolved Raman spectroscopy have been extensively applied to reveal the structure-property relationship in synthesized 2D anisotropic layers and their heterostructures.
ContributorsChen, Bin, 1968- (Author) / Tongay, Sefaattin (Thesis advisor) / Bertoni, Mariana (Committee member) / Chang, Lan-Yun (Committee member) / Arizona State University (Publisher)
Created2018