Graduate School of Engineering and Science
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Item Open Access Fabrication of mesoporous nickel oxide based thin film electrodes and their electrochemical properties(2025-01) Katırcı, Assel AmirzhanovaIn this thesis, robust electroactive mesoporous Ni1-xMnxO thin-film electrodes were synthesized on FTO and graphite rod substrates. Molten salt-assisted self-assembly (MASA) synthesis method was employed to produce uniform thin films. The synthesis started with preparing ethanol solutions, containing various molar ratios of [Mn(H2O)4](NO3)2 and [Ni(H2O)6](NO3)2 (between 1.0 to 0.1 Ni(II)/Mn(II) ratio ) and surfactants (C12H25(OCH2CH2)10OH, C12E10 and C16H33N(CH3)3Br, CTAB). Then, these solutions are coated over conductive substrates to obtain the salt-surfactant lyotropic liquid crystalline (LLC) mesophase. The thin mesophase is calcined in order to produce mesoporous Ni1-xMnxO thin-films on the FTO or graphite. The thin-films form solid solutions with the x value of up to 0.7. The Ni1-xMnxO thin-films transform to NiMnO3, Mn3O4, and Mn2O3 phases at increased Mn ratios and annealing temperatures. The films are mesoporous and were confirmed by N2 adsorption-desorption analysis and typical type IV isotherms characteristic for mesoporous materials. Pore sizes varied from 2.8 to 17.6 nm from Ni-rich to Mn-rich oxides. The surface area reaches to 211 m2/g in Ni0.9Mn1O, while the pure NiO has a BET surface area of 164 m2/g at 350 oC calcination temperature. The FTO and graphite-coated electrodes (FTO-Ni1-xMnxO and G-Ni1-xMnxO) display high charge capacities, but the FTO coated electrodes are unstable and undergo to degradation over extended time of usage. In the first few CV cycles of the FTO-based electrodes, they show an increased capacity, however, decline in further cycles. On the other hand, graphite-based electrodes show better stability and high charge capacity. Origin for increasing charge capacity with cycling is attributed to a transformation of the metal oxides to metal hydroxides. Thus, the electrochemical CV cycling of both pure NiO and Ni1-xMnxO electrodes results in a structural change into a NiO(core)/Ni(OH)2(shell) or Ni1-xMnxO(core)/Ni(OH)2(shell) configurations. The shell thickness is ranged from 2.0 nm (pure NiO) to 1.1 nm (Ni0.9Mn0.1O) at 350°C. Moreover, the shell thicknesses and charge capacities are affected by the pore-wall thicknesses, which increases with increasing annealing temperature. Despite these changes, the manganese addition improves the stability of the electrodes, but there is no improvements on the overpotential on oxygen evolution reaction (OER). Moreover, the annealing temperature reduces the charge capacity, whereas the OER performance remains the same. By using the same MASA method, m-NiO-SiO2 electrodes were synthesized using [Ni(H2O)6](NO3)2 and tetramethyl orthosilicate (TMOS) with CTAB and C12E10 surfactants at different Ni to TMOS ratios. Silica acts as hard template support for NiO, and the film is formed in good quality with bimodal pore size distribution. The sample pore size that was observed is 2.6 nm, which originates from the m-SiO2 domains. The second pore system had also mesopores; the average pore size is 15 nm, calcined at 350 oC. That property helps better infiltration of electrolytes, which is advantageous during electrochemistry. During electrochemical analysis, silica is etched out in basic electrolyte. These electrodes, prepared on graphite substrate have specific surface area of around 130 m2/g. The electrodes show an overpotential 381 mV in the CP experiment at 10 mA/cm2 current density.Item Open Access Aerospace metamaterials and functional coatings(2025-01) Astarlıoğlu, Aziz TanerOptically transparent and electrically conductive thin-film coatings are widely used to functionalize surfaces of various high-technology platforms, including mobile phones, displays, detectors, and LEDs. Their integration into aviation transparencies, such as canopies, windshields, and windows, is widely known and used for de-icing purposes. However, there are limited reports or information available about using such thin-film coatings for electromagnetic interference (EMI) shielding, low observability (LO), and solar irradiation protection features. This thesis aims to study and demonstrate optically transparent aviation structures possessing the properties of EMI shielding, LO features, and solar radiation protection altogether. To this end, in this thesis, we specifically addressed the problem of achieving high EMI shielding and solar protection, which require high electrical conductivity, resulting in a trade-off reducing the optical quality and LO performance. Transparent engineering polymers are widely used in structural parts in aviation thanks to their enhanced mechanical performance. However, good-quality films require high-temperature processes, which is not applicable to transparent aviation structures. Therefore, the architecture of layered films can be applied to meet the requirements of well-featured aviation transparencies. For these purposes, in the thesis we also designed monolithic and laminated aviation transparencies with surface modification based on stratified films and their patterned ones using numerical and experimental methods. We developed numerical approaches for the design of aircraft transparencies, including both the optical and electromagnetic requirements and validated our results. We successfully conducted experimental studies for uniform large-area thin-film coatings onto aviation transparencies. The results revealed that EMI shielding and solar control performance were achieved with minimal optical losses for planar structures. LO requirement was incorporated into prototypes built on curved or laminated transparent structures instead of monolithic ones to sustain optical, solar protection, and EMI shielding performance to a possible extent. We showed that the low observability performance of such patterned structures, the metamaterials, is enhanced in terms of bandwidth and attenuation compared to the planar thin-film-coated monolithic counterparts. These multi-functional thin-film coatings are essential in aviation, especially for high-performance 5th-generation fighter jets and other civil applications. This thesis paves the way for thin-film-coated transparent aviation structure designs across different domains, including visible, infrared, and microwaves, to enable their multi-functionality at large scales. The experimental large-area coating method guides the coating of a large and complex area to remove the limitation of metamaterial applications at the industrial level. We believe that our findings in this thesis will help to replace traditional planar thin film coatings with metamaterials at the industry scale, aiming to outperform traditional counterparts.Item Open Access Generation of transgenic flies to uncover the role of the intrinsically disordered regions in transcriptional regulation using Drosophila melanogaster transcription factor Bicoid(2025-01) Akdoğan, DilanMulticellular organisms develop from a single cell into a complex organism. Their development is strictly controlled by transcription factors that control the gene expression in a context-dependent manner, so that each gene is expressed at the right time and place. The specificity of transcription factors is determined mainly by their DNA-binding domains; however, their activity and interaction with DNA, proteins, and small molecules are modified by the effector domains (EDs). The EDs are generally low-complexity regions with high flexibility, often intrinsically disordered. Intrinsically disordered regions (IDRs), with their flexible and adaptable nature, help navigate protein activity in a context-dependent manner. The maternal morphogen Bicoid is a transcription factor responsible for the anterior development of Drosophila melanogaster embryos that regulates the expression of hundreds of genes responsible for Drosophila segmentation. It is absolutely required for embryo development and its absence results in the replacement of anterior structures by posterior ones. It consists of a 60 amino acid long structured homeodomain (HD) flanked by IDRs on both amino- and carboxyl termini. Through full Bicoid and HD swap experiments between D.melanogaster, Lucilia sericata, and Calliphora vicina, we found disordered EDs are required for Bicoid's full developmental functions. We used the Drosophila genetic manipulation tool recombinase-mediated cassette exchange to generate Bicoid ED mutant flies. We aim to elucidate the role of IDRs in regulating the activity of Bicoid via phenotypical and molecular analyses.Item Embargo Spider orb web, investigating structural features and using biomimicry for lattice design(2024-12) Yavuz, KoraySpider orb web has evolved to fulfil multiple roles, such as catching prey and acting as a sensing tool. For orb-weavers, the web must stop and retain prey, which can fly into it with considerable momentum. Considering orb weaver spiders are mostly blind, the web must also transmit accurate information about the prey’s location. There are many web features aiding these roles; some are known, and some are waiting to be shed light on. Considering these two cases, there are also two parts in this thesis, the first part is about a particular web-building behaviour of spiders and how it affects the signal transmittance, and the other is about creating a new lattice design for energy absorption utilizing some of the known structural characteristics of the spider web. The first part of this study is about designing a new lattice (SW) for energy absorption inspired by the structure of spider webs. Spider orb web comprises four structural elements: anchor, frame, radial, and spiral threads. The first three are the main components that provide structural integrity. These components have a hierarchical nature; the anchors bind to the environment and are generally thickest, while radii form the innermost part with the thinnest threads. The frames make up the connection between the anchor and radii; thus, there is no direct connection between them, and they generally have a thickness value between the radii and anchor threads. These features help the spider orb web to be a resilient, efficient structure for energy absorption, so using the same properties, a 3D lattice was designed for energy absorption. This design is then optimized for improved Energy Absorption Efficiency(EAE) and Energy Absorption(EA) value. The second part is about web-building behaviour that seems counterintuitive, heavier spiders increase the pretension of the threads as they get heavier, which diminishes the ability of the web to stop and retain prey. To investigate this behaviour, a spider web model with controllable pretension is needed; thus, a pretension-adjusting algorithm has been developed. A realistic spider web model was created using non-linear material properties to describe the mechanical behaviour of the spider silk and web pretension values seen in nature. Using this model, different scenarios with changing spider weight and web pretension were simulated using a numerical method based on Solid Mechanics. Our results show that this behaviour is likely related to the signal transmittance on the spider web. Spider web evolved to withstand damaging environmental factors such as wind and rainfall while preserving its functionality for trapping prey. Understanding spider web structure could lead us to improve engineering designs by implementing similar resiliency. This thesis presents a study investigating spider webs and a biomimicking application inspired by spider web structure. So, while the two areas are different in the sense that one is closer to biology while the other is to mechanical engineering, they serve the same purpose: understanding how this structure, spider orb-web, functions and how we can take ideas from it.Item Open Access Leveraging file significance in bus factor estimation(2025-01) Haratian, VahidSoftware projects often face developer turnover for various reasons. Since develop-ers are key sources of knowledge in these projects, their absence inevitably leads to some degree of knowledge loss. The Bus Factor (BF) is a metric used to assess the impact of this knowledge loss on a project’s continuity. Traditionally, BF is defined as the smallest group of developers whose departure would result in a loss of more than half of the project’s knowledge. Current state-of-the-art methods calculate developers’ knowledge based on the number of files they have authored, using data from version control systems (VCS). However, numerous studies have highlighted that not all files in software projects hold the same level of significance. In this study, we investigate the impact of weighting files based on their significance on the performance of two widely used BF estimators. Significance scores are calculated using five established graph metrics derived from the project’s De-pendency Graph: PageRank, In-/Out-/All-Degree, and Betweenness Centralities. Additionally, we introduce BFSig, a prototype implementing our approach. Lastly, we present a new dataset featuring BF scores reported by software practitioners from five prominent GitHub repositories. Our findings show that BFSig surpasses the baseline methods, achieving up to an 18% reduction in Normalized Mean Absolute Error (NMAE). Additionally, BFSig reduces False Negatives by 18%when identifying potential risks linked to low BF. Furthermore, our respondents validated BFSig’s versatility, highlighting its capability to evaluate the BF of individual project subfolders. In conclusion, we believe that when estimating BF from authorship, software components of greater significance should be given higher weight.Item Embargo Elucidation of the role of IKK-related kinases in ulcerative colitis(2025-01) Borucu, ÜmranUlcerative colitis is an inflammatory disease of the colon resulting from the imbalance of the inflammatory mechanisms. Its onset and development depend on multiple factors, which are not yet fully uncovered. Understanding the factors involved in the pathophysiology of ulcerative colitis is important for the management of the disease. IKK-related kinases are involved in numerous pathways in cellular signaling. They play significant roles in the modulation of the inflammatory responses. In this study, we investigated the roles played by IKK-related kinases in ulcerative colitis. We generated DSS-induced colitis mouse models in acute and chronic phases. We treated these mice with a dual IKK-related kinase inhibitor, Amlexanox, to understand the role played by these kinases on the onset and development of the condition. Moreover, we performed biochemical analyses on the samples to gain molecular insights. We observed an increased inflammatory response both phenotypically and biochemically upon inhibition of IKK-related kinases.Item Embargo Do visual cortices in the blind activate to language processing demands?(2024-12) Varol, Ayşe BetülThe fate of the occipital cortices in the blind has been of considerable interest in neuroscience to investigate whether and how much brain regions change with experience. Neuroimaging shows that the occipital cortices in the blind are activated during all kinds of non-visual tasks. In our previous study, we recently showed that all visual regions become MD regions and activate in response to any kind of control demand in the blind. Therefore, we hypothesized that the activation of the deprived visual cortex in language tasks in the literature is related to high cognitive control demand rather than language processing. This means that if V1 is involved in cognitive control demand, then it should not be activated in the passive listening task. Therefore, the study investigates whether the primary visual cortex (V1) in blind subjects participates in cognitive functions, particularly language processing, during a passive listening task with minimal cognitive control demand. Using fMRI, we compared whole brain and region of interest (ROI) activations in blind, and sighted participants across multiple areas, including occipital, language, and multiple demand (MD) regions. Results revealed no significant activation in V1 across all groups during the passive listening task, suggesting task-dependent limitations in the integration of V1 into higher-order cognitive processes rather than language. Furthermore, no significant differences in language or MD area activity were observed between blind and sighted participants. These findings challenge previous evidence on the occipital cortex becoming a language region in the blind and emphasize the importance of task complexity in modulating such interpretation. All of these suggest that blind occipital regions primarily become MD regions, and their activation during language tasks is limited to those that require domain-general cognitive control.Item Embargo Laser micro drilling of de Laval nozzles using a hybrid hexapod system(2024-12) Bakan, AykutIn recent years, miniaturization, one of the most intensely focused topics in science and technology, has enabled the use of macroscale engineered components at the microscale. Although components at this scale are extremely small, they can exhibit complex geometries. Therefore, precise manufacturing setups are required for their production or for processing existing ones. An example of such components is micro de Laval nozzles, which are used in the propulsion systems of micro-satellites. In this thesis, a novel method is presented for the production of micro de Laval nozzles, in addition to a method that enables drilling on freeform surfaces using a nanosecond laser and performing angled drillings on planar surfaces, all facilitated by a hybrid hexapod. The effects of parameters such as laser power, laser frequency, scan speed, number of loops, and rotation speed on the geometry and morphology of the nozzle were investigated for the method developed for micro de Laval nozzles. Experimental results demonstrated that critical geometric parameters for micro de Laval nozzles, such as throat diameter, outlet diameter, and outlet half angle, meet the requirements specified in the literature. The findings suggest that the developed method has the potential to provide a single-step, cost-effective solution for fabricating micro de Laval nozzles. In the future, efforts will focus on minimizing the sidewall roughness of the produced nozzles and automating the method for practical applications.Item Open Access Plastic degradation using genetically engineered microorganisms(2025-01) Polat, Cem DirseThe usage of PET plastics in daily life have excessively increased in the last decade. The increased usage of PET is accompanied with the massive amount of PET waste accumulating rapidly. Environmental pollution caused by this waste has reached a critical point with pollutants being found even in the most remote parts of the world. Causing massive damage to ecosystems and even human health, PET plastic waste needs to be handled urgently. Although there are ongoing PET recycling and treatment efforts, the current methods in use are insufficient. The techniques currently used are either costly, leave a significant carbon footprint or are lacking in their ability to recycle microplastics. However, with the discovery of microorganisms which have the ability of degrading PET, biodegradation of PET products has emerged as a promising green alternative. In this thesis we designed bacterial tools to utilize the PET hydrolyzing enzyme, PETase. For this purpose, living bacterial platforms were engineered. The first system employed E. coli as the host to display PETase on the cellular surface. With PETase molecules anchored on its surface, aiding in the stability and the activity of the enzyme, the system will be a useful tool for PET degradation. For the surface display system, the Ag43 autotransporter protein is used. The system was cloned, and expression was analyzed using immunocytochemistry labeling. The activity of the system was analyzed with chromatography and mass spectrometry. The second system proposed uses E. coli once again as a workhorse for PETase secretion, creating a simple yet effective tool for the bioremediation of PET. For secretion of the enzyme, the disruption of Braun’s lipoprotein to create a leaky outer membrane is exploited. The system was cloned, and the cloning was verified. Also, the activity of native PETase was analyzed with HPLC and mass spectrometry. With this analysis, the PET degrading activity of PETase was confirmed.Item Embargo Distributed waveguide design for reducing thermal load in semiconductor high power lasers(2025-01) Saadi, Osama AadilSemiconductor lasers lead laser technology due to their high efficiency, compact size, and cost-effectiveness. Among these, GaAs-based laser diodes (LDs) are the most efficient light sources, but are still constrained by self-heating, which elevates internal temperatures and degrades performance, output power, and de-vice lifetime. Traditionally, increasing the cavity length has mitigated this issue by improving thermal conductivity, facilitated by advances in epitaxial growth, design, and device packaging. However, the cavity lengths of high-power GaAs LDs are now limited to approximately 5 mm, beyond which the output power declines because of intrinsic physical constraints. This work presents a new type of waveguide design, called distributed waveguide (DWG), that overcomes conventional cavity-length limitations. The DWG integrates lasing and secondary sections along the waveguide, which are electrically isolated to control current injection, yet optically connected for efficient beam transport. The laser section is electrically pumped to generate output, while the secondary section operates near-threshold to dissipate heat effectively. Extending the cavity length from 4 to 8 mm, DWG LDs exhibit significantly improved thermal management with favorable device characteristics. Experimental results, corroborated by numerical analysis, demonstrate that DWGs achieve approximately 1.8× lower junction temperature change while delivering high output power. Additionally, the DWG platform and its fabrication process are fully com-patible with standard semiconductor laser manufacturing techniques, ensuring industrial adoption. This work provides clear evidence that innovative waveguide designs can effectively mitigate self-heating, promising enhanced performance, output power, and reliability in semiconductor lasers.Item Embargo Interpretable holistic manipulation strategies in household environments for task and motion planning(2025-01) Yenicesu, Arda SarpInterpretable Responsibility Sharing (IRS) introduces a novel heuristic for Task and Motion Planning (TAMP), leveraging holistic manipulation strategies to enhance planning efficiency and interpretability in household environments. By systematically incorporating auxiliary objects such as trays and pitchers—common in human-constructed spaces—IRS simplifies and optimizes task execution. The heuristic is based on the concept of Responsibility Sharing (RS), where auxiliary objects share task responsibilities with robotic agents, dividing complex tasks into manageable sub-problems. This division not only mirrors human usage patterns but also aids robots in navigating and manipulating within human-designed spaces more effectively. By integrating Optimized Rule Synthesis (ORS) for decision-making, IRS ensures that the use of auxiliary objects is both strategic and context-aware, enhancing the interpretability and effectiveness of robotic planning. Experiments across diverse household tasks, including serving, pouring, and handover, demonstrate that IRS significantly outperforms traditional methods, reducing effort in task execution and improving decision-making. This approach aligns with human-inspired strategies while offering a scalable framework adaptable to the dynamic complexities of household environments.Item Open Access Development of a combination vaccine against N. Meningitidis and SARS-CoV-2 and analysis of MIS-C plasma and extracellular vesicles in relation to disease severity in pediatric patients(2024-12) Yıldırım, Tuğçe CanavarNeisseria meningitidis is the causative agent of invasive meningococcal disease (IMD). Serogroup B remains the leading cause of IMD, representing 62% of documented serogroup cases overall, and is the most prevalent across all age groups under 65. In Türkiye, Serogroups B and W are responsible for most cases, accounting for over 75%. IMD has a case fatality rate of 10%, and 10% to 20% of survivors experience lifelong, disabling complications. Coronavirus disease 2019 (COVID-19), caused by the highly contagious SARS-CoV-2 virus, has had a devastating impact globally, leading to over 7 million deaths. It has become the most significant global health crisis since the influenza pandemic in 1918. Since the introduction of the first COVID-19 vaccine in the U.S., it is estimated that over 18 million hospitalizations and 3 million deaths have been prevented. Like flu vaccines, COVID-19 vaccines are expected to be introduced seasonally. In this thesis, we aim to develop a combination vaccine for populations where the prevalence of both COVID-19 and meningitis presents significant health risks. Our previous data indicated that our OMV-based bivalent vaccine, targeting B and W serogroups of Neisseria meningitidis, generates a broader humoral response and exhibits strong bactericidal activity. Similarly, our lab has developed a virus-like particle-based SARS-CoV-2 vaccine incorporating all four virus structural proteins, eliciting both humoral and cell-mediated immunity. Herein, we combined these two platforms and assessed their respective protective potencies in mice. Data revealed that combining the OMV and VLP vaccines with Alum adjuvant produced the most robust anti-meningococcal and anti-SARS-CoV-2 responses. The second part of the study focused on uncovering the immune parameters present in the plasma of MIS-C patients and investigating the role of extracellular vesicles in influencing disease severity. The data revealed that plasma from MIS-C patients contained significantly elevated levels of proinflammatory cytokines, including TNF-α, IFN-γ, IL-6, and IL-17. We also investigated the pathological role of extracellular vesicles (EVs) in MIS-C. Our findings showed that patient-derived EVs induced significantly higher levels of IRF9 in the THP1-dual reporter cell line. Contrary to our expectations, however, we did not observe EV-specific NF-κB induction in the THP1 cells.Item Embargo Efficient neural network processing via model compression and low-power functional units(2024-12) Karakuloğlu, Ali NecatWe present a framework that contributes neural network optimization through novel methods in pruning, quantization, and arithmetic unit design for resource-constrained devices to datacenters. The first component is a pruning method that employs an importance metric to measure and selectively eliminate less critical neurons and weights, achieving high compression rates up to 99.9% without sacrificing significant accuracy. This idea is improved by a novel pruning schedule that optimizes the balance between compression and model’s generalization capa-bility. Next, we introduce a quantization method that combines with pruning to improve hardware compatibility for floating point format, offering efficient model compression and fast computation and general usability. Finally, we propose a logarithmic arithmetic unit that designed as an energy-efficient alternative to conventional floating-point operations, providing precise and configurable processing without relying on bulky lookup tables. Extensive evaluations across different datasets and CUDA-based simulations and Verilog based hardware designs indicate that our approaches outperforms existing methods, making it a powerful solution for deploying artificial intelligence models more efficiently.Item Embargo Genetic and environmental contributions to psychotic-like experiences and working memory connectivity in Turkish adolescents and young adults : a twin study(2024-12) Çevik, Didenur ŞahinPsychosis lies on a continuum, with psychotic-like experiences (PLEs) observed in healthy populations to full-blown psychotic disorders such as schizophrenia. PLEs are relatively common during adolescence, with distress associated with these experiences playing an essential role in determining their clinical significance. Adolescence is a critical time period where the brain undergoes substantial functional reorganization and where psychotic disorders first manifest. One promising intermediate phenotype for psychosis is the working memory with both patients, their first-degree relatives showing disruptions in performance and functional connectivity (FC). The overall aim of this thesis was to investigate the relationship between PLEs and FC mechanisms. The first study investigated the relationship between PLEs and task-based FC during a working memory task in adolescents. Moreover, we aimed to decompose the genetic and environmental influences in PLEs and FC measures via twin modeling. Our findings revealed that altered connectivity in the inferior frontal gyrus was associated with in- creased frequency and distress of PLEs during adolescence. Importantly, distress associated with PLEs showed moderate heritability, while the frequency of PLEs was predominantly shaped by environmental factors. The FC measures were mainly influenced by unique environmental factors, highlighting the critical role of environmental exposures during adolescence. The second study investigated COVID-19 as an environmental risk factor for psychosis and examined the differences in FC between COVID-19 patients and healthy controls. Further, the effect of the frequency of PLEs and the inflammation markers on functional connectivity differences was studied. The results demonstrated that while COVID-19 patients showed hypoconnectivity in the sensorimotor, central executive, and language networks, they showed hyperconnectivity in the visual network compared to healthy controls. Furthermore, including positive PLEs as a covariate revealed that the COVID-19 group exhibited greater functional connectivity within the salience and central executive networks. The findings of this thesis highlight the importance of environmental risk factors that increase psychosis risk by altering the underlying functional brain mechanisms.Item Open Access Design and optimization of a sub-1dB noise figure low noise amplifier for magnetic resonance applications using CMOS technology(2024-12) Bal, Ayşe RanaLow Noise Amplifiers (LNAs) are crucial components in magnetic resonance imaging (MRI) receivers, primarily designed to amplify weak signals while minimizing the added noise. They have a special requirement of having an input impedance very close to a short-circuit. This requirement assures that there is no current in the MRI coil when the LNA is connected to the coil with a quarter-wave transmission line. By eliminating the current in the coil, the risk of coupling between coils also known as mutual coupling, within an array is reduced. This thesis explores designs of sub-1dB noise figure CMOS LNAs operating at 437 MHz and 477 MHz for 10.3 T and 10.5 T MRI systems, respectively, using variations of cascode amplifier structures while addressing the challenges and advancements in CMOS RF design. The first LNA designed for a singular 10.3 T MRI coil system demonstrates a power gain of 20.54 dB, a noise figure of 0.97 dB, an input return loss of −11.70 dB, and an IIP3 of −12.26 dBm with its fully modeled design. For a 10.5 T Array MRI system, one single-ended and one differential-ended LNA is designed. The single-ended demonstrates a power gain of 18.42 dB, a noise figure of 0.42 dB, an input return loss of −0.90 dB, an output return loss of −18.03 dB, and an IIP3 of −17.12 dBm, whereas the differential-ended demonstrates a power gain of 14.76 dB, a noise figure of 0.60 dB, an input return loss of −0.94 dB, an output return loss of −18.73 dB, and an IIP3 of −14.36 dBm both with their fully modeled designs. The differential amplifier also displays a significant improvement in PSRR, making it a good choice for array MRI applications.Item Open Access Designing post-disaster reconstruction: the role of architects in the recovery of Antakya in the wake of 2023 earthquakes(2024-12) Sezer, SuThis thesis analyses the recovery process of post-disaster Antakya, the actors, distribution of responsibilities, and ambiguities in decision-making mechanisms within the housing production models, and examines the role of architects through the concept of accountability. A mixed qualitative method was employed, with data collected through in-depth interviews and field observations. The design process in Antakya, claimed to be participatory but involving only architects, was observed to proceed through non-transparent verbal agreements with public authorities. This process prioritised construction speed over recovery efforts. Architects operated within a framework where the legal infrastructure was established through emergency decrees, disregarding zoning plans and urban planners. Despite being labelled as research-based, the process was far from participatory, advancing in a top-down manner. In this context, doxa refers to the common, unquestioned beliefs that architects used to legitimize the lack of accountability in their design processes. These doxas, frequently encountered in the propositions about Turkey's construction sector, bureaucracy, and society, facilitated the rapid production of standardised housing. However, this approach neglected long-term societal and urban resilience, local community participation and accountability. Consequently, this study highlights the necessity of scientific and participatory planning approaches, institutionalised practices, and strengthened legal frameworks to position architects as accountable actors in post-disaster reconstruction. Antakya illustrates the critical need for a more holistic approach to resilient cities.Item Open Access Optimized RF safety monitoring for cerebellar magnetic resonance imaging at 7T(2024-09) Mahmoudalilou, Elnaz MahmoudiThe primary objective of this thesis is to develop optimized RF safety assessment techniques for cerebellar imaging using 7T MRI systems, with a specific focus on Spinocerebellar Ataxias (SCAs). Due to the unavailability of detailed electro- magnetic simulation data from the manufacturer, this study focused on predicting the electromagnetic behavior of the Nova 8Tx/32Rx coil’S 8 pTx channels to en- sure accurate and safe imaging. Accurate prediction of the coil’s electromagnetic performance is essential for both RF safety and imaging quality, particularly in managing RF exposure and minimizing tissue heating. The approach involved replicating the electromagnetic fields of the Nova coil through simulations, validating these predictions against experimental measure- ments, and implementing an algorithm for calculating the temperature-based Virtual Observation Points (tVOPs) in future works for rapid RF safety assess- ments. While the initial simulations captured key aspects of the coil’s B1+ field distribution, discrepancies between predicted and experimental results revealed challenges, especially in random-phase shimming configurations. The limitations of using ideal current sources and the reduced dataset for optimization highlighted the need for more comprehensive data and realistic models. The findings underscore the importance of integrating empirical measurements with refined simulations to bridge the gap between theoretical models and real- world performance. Future work should focus on enhancing current source mod- els, mitigating noise and experimental inaccuracies, and expanding the applica- tion of these techniques to broader clinical scenarios. By addressing these chal- lenges, this research can contribute to improving both the safety and quality of high-field MRI, ultimately advancing its reliability for both clinical and research applications.Item Embargo Reconfigurable CNN accelerator design using dataflow analysis(2024-09) Kalay, AlperenDataflow reconfigurability plays a crucial role in Convolutional Neural Network (CNN) acceleration by determining the optimal dataflow pattern for convolution operations. Fully reconfigurable architectures provide versatility and high resource utilization by supporting multiple dataflow options, but this comes with increased design complexity and operational overhead. On the other hand, non-reconfigurable architectures, optimized for a single dataflow pattern, deliver high efficiency for specific tasks but lack adaptability. This thesis introduces a novel intermediate dataflow reconfigurable CNN accelerator that balances flexibility and efficiency by integrating key dataflow patterns, enhancing adaptability and performance across diverse CNN applications. Through a detailed analysis, key dataflows are identified, and a unique architectural unit is developed for dataflow selection, with an average of 0.15% excess latency compared to the optimal scenario. Our specialized systolic array architecture accommodates various kernel sizes, providing an additional layer of reconfigurability. Our architecture requires 39% less area and 35% less power than fully reconfigurable designs. Additionally, it delivers an average of 33% better performance compared to non-reconfigurable architectures. In terms of efficiency, it provides a 7% increase over fully reconfigurable designs and outperforms non-reconfigurable options by up to 3.57X.Item Embargo Real time identification of cornering coefficients and ideal twin driving assistance(2024-08) Keleş, Ahmet FarukCornering coefficients play a crucial role in vehicles’ lateral and longitudinal dynamics. They depend on many factors, including environmental factors such as road conditions. In this study, a method that identifies cornering coefficients in real-time by utilizing deep neural networks is developed. Three different neural network architectures with two different datasets are compared for this identification. Results show that a fully connected network trained with time-varying cornering coefficients performs best. Compared to constant cornering coefficients, this method improves the lateral force estimation between 42.62-75.47 % in experiments conducted on a 1/8 scale four-wheel drive four-wheel steering vehicle. A control method that utilizes the identified cornering coefficients to cancel out the changes in cornering coefficient by utilizing 4 wheel drive 4 wheel steering system is developed. The control method utilizes a nonlinear model predictive controller. The control system uses the driver’s control inputs in an ideal front wheel drive front wheel steering twin of the vehicle with constant cornering coefficients set by the driver, to obtain reference velocities. The nonlinear model predictive controller can calculate the optimal control inputs for a 4-wheel drive, 4-wheel steering vehicle from these references. The simulation results show that this control method improves reference tracking by 85 % compared to a conventional configuration, i.e., a front wheel drive front wheel steering vehicle. The controller is tested on an experimental setting and found to be improving the results by 12.12 %. The reduction in improvement can be attributed to noise in measurements and delays in the control system.Item Open Access Investigating hyperlipidemia-driven organelle stress and neuroinflammation on the mouse cerebral cortex: insights into the intervention of perk pathway(2024-09) Kızıldağ, FulyaDeficits in the metabolism of lipids called hyperlipidemia have been linked to a higher risk of developing neurodegenerative diseases. Protein Kinase RNA-like Endoplasmic Reticulum Kinase (PERK) signaling is crucial in cellular homeostasis. Abnormalities in the PERK have been associated with neurodegeneration. Mitophagy and the PERK pathway emphasize how cellular stress responses are regulated to preserve cellular homeostasis and mitochondrial quality control. The activity of main mitophagy regulators, such as Parkin and PINK1 (PTEN-induced kinase 1), is regulated by the phosphorylation of eukaryotic initiation factor 2 alpha (eIF2α) by PERK. If lipid metabolism is at a high level, abnormalities in the mitochondria and endoplasmic stress (ER) emerge. During the ER stress activation, the PERK pathway is induced, and mitophagy is blocked, causing an enhancement in the neuroinflammation. The underlying molecular mechanism by which hyperlipidemia impacts the PERK pathway and mitophagy in the cerebral cortex, as well as the relationship between mitophagy and neuroinflammation, is not fully understood. In this study, Apoe-/- and C57BL/6 mice were given a chow or western diet to stimulate hyperlipidemia. Moreover, western diet-fed Apoe-/- mice were injected with PERK inhibitors, GSK2606414 and Trans-ISRIB, intraperitoneally for six weeks to suppress the PERK pathway. This study explores the effects of hyperlipidemia on the PERK pathway, inflammatory and mitophagy markers in the cerebral cortex of chow and western diet-fed C57BL/6 and Apoe-/- mice and investigates whether the inhibition of the PERK pathway can change the levels of inflammatory and mitochondrial markers in the cerebral cortex of hyperlipidemic mice subjects. mRNA and protein expression levels of mitophagy and inflammatory markers were assessed using the RT-qPCR and western blot, respectively. PERK pathway activation under hyperlipidemia conditions was not determined. Nevertheless, significant alterations in mitophagy markers and inflammation were detected in Apoe-/- mice apart from the diet. Furthermore, significant alterations were not seen in the PERK pathway markers; however, mitophagy was stimulated, and some inflammation markers were significantly decreased mildly at the cortical tissue of WD-fed Apoe-/- mice administrated with PERK pathway inhibitors, GSK2606414 and Trans-ISRIB. Besides, no statistically significant changes were observed in the transcript levels of the inflammatory markers. Taken together, hyperlipidemia did not cause the PERK pathway to be activated in the cerebral cortex of mice; nevertheless, it mildly altered inflammation and caused mild effects of the dysregulation of the mitochondria by hyperlipidemia independent from the PERK pathway. Furthermore, although the PERK pathway was not inhibited by the administration of PERK pathway inhibitors, mitophagy was induced, and inflammation was decreased mildly. Targeting the PERK pathway with GSK2606414 and Trans-ISRIB inhibitors from the cerebral cortex would not be a therapeutic approach for neurodegenerative diseases.