Phd Degree / Doktora
Permanent URI for this collectionhttps://hdl.handle.net/11147/2869
Browse
395 results
Search Results
Now showing 1 - 10 of 395
Doctoral Thesis Investigation of the Effects of Ketogenic Diet Therapy in a Mouse Model of Gm2 Gangliosidosis(01. Izmir Institute of Technology, 2024) İnci, Orhan Kerim; Seyrantepe, VolkanGM2 gangliosidosis is an autosomal recessive lysosomal storage disorder in which GM2 ganglioside is accumulated, especially in the brain. GM2 gangliosidosis is divided into three different variants: Tay Sachs (B-variant or type I), Sandhoff (O-variant or type 2), and GM2AP deficiency (AB-variant). Accumulation of the GM2 ganglioside in brain causes disease pathology as neurodegeneration and neuroinflammation. Our lab first displayed the novel GM2 gangliosidosis type-I mouse model (Hexa-/-Neu3-/-). Compared to control, this model could survive a maximum of five-months due to severe pathologies, neurodegeneration, and neuroinflammation. The ketogenic diet is high-fat and low-carbohydrate/protein diet that triggers burning fat instead of carbohydrates. The ketogenic diet is used comprehensively in neurodegenerative disorders such as Sandhoff, Alzheimer’s, and Parkinson’s to regulate inflammation, neurodegeneration, and autophagy. In addition, elevation of CCL2 expression in Hexa-/-Neu3-/- mice resulted in increased amounts of active microglia and astrocytes. Therefore, the CCL2/CCR2 signaling inhibitor of propagermanium was used in addition to ketogenic diet. Thus, reducing neuroinflammation is aimed to be more effective as a combined therapy. In my Ph.D. thesis, expression and protein levels of autophagy and inflammation-associated genes were analyzed in the mouse brain to exhibit whether beneficial effects on autophagic flux and neuroinflammation are found after the ketogenic diet and propagermanium treatment. The pathology of the GM2 gangliosidosis mouse type-I brain was illustrated by thin-layer chromatography and immunofluorescence staining to display whether the ketogenic diet affects the ganglioside metabolism. Briefly, ketogenic diet therapy and its anti-inflammatory and neuroprotective effects were explored in the GM2 gangliosidosis mouse model.Doctoral Thesis Potential of Lactic Acid Bacteria To Produce Functional Fermented Whey With Putative Antihypertensive Properties : Enrichment Ofangiotensin–i Converting Enzyme (ace)– Inhibitory Peptides and Gamma–aminobutyric Acid (gaba)(Izmir Institute of Technology, 2023) Ağırbaşlı, Zeynep; Harsa, Hayri̇ye Şebnem; Sezgi̇n, EfeBu tez Laktik Asit Bakterileri koleksiyonunun (LAB) antihipertansif yetenek potensiyallerinin değerlendirilmesine ve fermente peynir altı suyu içecek bazlarının geliştirişmesine odaklanmıştır. Bu amaçla, 400 adetten fazla LAB proteolitik aktiviteleri açısından farklı yağsız süt ortamlarında taranmıştır. LAB'lar arasında 39 adedi yüksek proteolitik olarak tespit edilmiştir. Fermente sütleri üretmek için suşlar seçilmiştir, 34 en yüksek ACE inhibitor aktiviteli LAB'dan 13 tanesi Lactobacillus brevis D9 and Lactococcus lactis ssp. lactis C24 ile ikili kültürlü fermente peynir altı suyu bazı oluşturmak üzere kullanılmıştır. Fermente sütlerdeki proteolitik aktivite ve ACE inhibitor aktivite of 4.11-1.8 mg/L Lösin ve %49–86 aktivite olarak sırasıyla tespit edilmiştir. İkili kültür fermente peynier altı suyu bazlarında ACE inhibitör aktiviteler %80-97 aralığında bulunmuştur. Seçilen 11 LAB'ın fermentasyon surasındaki proteolitik aktiviteleri HPLC ve SDS-PAGE analizi ile peynir altı suyu proteinlerinin degredasyon profilleri ile değerlendirilmiştir. 300 LAB arasından modifiye sıvı besiyerinde 37 veya 42 C'de 48 saat inkübasyon sonrası 33 suş GABA üretim kapasitesi gösterdiği ince tabaka kromatografisi (TLC) ile gözlemlenmiştir. Fermente whey içeceği bazı feliştirmek için 10 LAB türü, örneğin Lactiplantibacillus plantarum, Latilactobacillus curvatus and Levilactobacillus brevis, modifiye sıvı besiyerinde 50–367 mg/L konsantrasyonlarında verim göstermesi nedeniyle seçilmiştir. Buna göre, fermente peynir altı suyu bazlarında 24 saat 37 °C sonrası GABA konsantrasyonları 11–21mg/L aralığında hesaplanmıştır.Doctoral Thesis An Inquiry Into Architectural Space in Computational Design Practice(Izmir Institute of Technology, 2023) Öztürk, Kadi̇r; Doğan, Fehmi̇; Kasalı, AltuğÇağdaş mimari uygulama ve araştırmalarında başat temalardan biri olan sayısal tasarım, mekana ilişkin düşünme biçimimizde köklü değişikliklere yol açmıştır. Sayısal tasarım uygulamaları, mimarlık üretiminde giderek daha baskın hale gelse de mekan hakkında düşünme ve hayal etme biçimimizdeki yansımalarına yönelik derinlemesine çalışmalar hala gerekmektedir. Bu araştırma, sayısal tasarım uygulamaları ile birlikte mekanı kavramsallaştırma biçimimizde yaşanan değişiklikleri sorgulayarak modern mekan anlayışımıza ilişkin nelerin korunduğunu, uyarlandığını veya ihmal edildiğini tartışır. Sunulan çalışma ile sayısal tasarım araçlarını kullanan deneyimli uygulayıcılarla gerçekleştirilen görüşmeler üzerinden mekanla ilgili kavramsallaştırmaların farklı boyutlarının anlaşılması amaçlanmaktadır. Görüşmelerden elde edilen veriler nitel tematik inceleme yöntemiyle analiz edilmiştir. Bu araştırma iki ana soru etrafında şekillenmektedir. Hesaplamalı tasarım pratiğinde mimari mekan nasıl hayal edilir? Prosedürlerin kesin, tanımlayıcı ve kurala dayalı olduğu hesaplamalı tasarım yaklaşımlarında mimari mekan çok katmanlı, tanımlanması ve ifade edilmesi zor bir kavram olarak nasıl ele alınır? Mimari kelime dağarcığına aktarılan sayısal terminoloji, tasarımcıların sadece sözlü ifadelerine değil, aynı zamanda mimari mekan hakkındaki düşüncelerine de hakim olmaktadır. Sayısal tasarım araçlarının, tasarımcıların göz önünde bulundurdukları parametrelerin yanı sıra mekanı hayal ederken onların düşünme biçimleri üzerinde de etkisi olduğu tartışılmaktadır. Buradaki varsayım, birden fazla katman ve anlam barındıran bir kavram olarak mekanın hesaplanabilir değişkenlerinin yanında hesaplanamaz yönleri de olduğu ve sayısal tasarım pratiğinin bu iki yönü nasıl ele aldığını araştırmanın keşfetmeye değer olduğudur. Sayısal düşünce, mekanın ölçülebilir yönlerini düşünmek ve temsil etmek için uygun bir ortam sağlarken, mekanın tarif edilemez ve belirsiz yönleri de hesaplanabilir olanın sınırlarını ortaya çıkarabilir. Mekan kavramının sayısal tasarım teknolojileriyle nasıl yeniden düşünüldüğüne ilişkin bulgular irdelenmeye değerdir.Doctoral Thesis Evaluation of Different Urban Transformation Strategies Through Effectiveness Indicators in Earthquake-Prone Areas(Izmir Institute of Technology, 2023) Bozkurt, Uğur; Veli̇beyoğlu, KorayTürkiye gibi gelişmekte olan ülkelerde afet riski altındaki alanların kentsel dayanıklılığını artırmak için öncelikle fiziksel yapının afet risklerini azaltırken sürdürülebilir kalkınmayı sağlamak gerekmektedir. Bu bağlamda Fiziksel, Ekonomik, Sosyal, Çevresel, Yasal ve Kurumsal, Planlama ve Tasarım ile Teknolojik gibi birçok kategoride önemli sorunlar bulunmaktadır. Ancak bu tez kapsamında, kentsel dönüşüm stratejilerinin belirlenmesinde yaşanan karar verme sorununa odaklanılmıştır. Bu bağlamda amaç, afet riskli alanlarda kentsel dönüşümden sorumlu kurumların kullanabileceği Çok Kriterli Karar Verme Yöntemlerine dayalı bir karar verme modeli geliştirmek ve modelin çalışma sürecine ilişkin bir pilot çalışma gerçekleştirmektir. Bu amaçla, literatürde, mevzuatta ve kentsel dönüşüm pratiğinde yer alan üç yüz adet gösterge/kriter ile tez kapsamında belirlenen beş adet kentsel dönüşüm sürecine [(1) Bütüncül Kentsel Dönüşüm ve Uygulama Modeli, (2) Bütüncül Kentsel Dönüşüm ve Parçalar Halinde Uygulama Modeli, (3) Parçacıl Kentsel Dönüşüm ve Uygulama Modeli, (4) Önemli Yatırımların Mevcut Yapıya Eklenmesi Modeli, (5) Parsel Bazlı Kentsel Dönüşüm Modeli] ilişkin karar alternatifi tipolojisi kullanılarak bu araştırma sonuçları test edilmiştir. Bu değerlendirme için kurumlarla anket çalışması yapılarak gösterge sayısı azaltılmış ve Aktepe-Emrez Mahalleleri Kentsel Dönüşüm Projesi kapsamında bir vaka çalışması yapılarak anketin analizinin sonrasında kritik göstergeler olarak belirlenen yirmi adet gösterge ilgili birimlerin yetkilileri ile test edilmiş ve sonuçlar değerlendirilmiştir. Microsoft Excel Programı üzerinde geliştirilen kriter ağırlıklarının belirlenmesine dayalı DEMATEL ve ENTROPI yöntemleri ile karar alternatiflerinin sıralanmasına dayalı PROMETHEE ve COPRAS yöntemleri kullanılarak geliştirilen INTEMUS yönteminin, kentsel dönüşümden sorumlu kurumlar tarafından uygulanabilecek bir karar verme yöntemi olarak kullanılması amaçlanmaktadır.Doctoral Thesis Modulation of terahertz waves by VO2 based metamaterials(01. Izmir Institute of Technology, 2023) Noori, Aileen; Aygün Özyüzer, GülnurTerahertz (THz) waves, being a form of electromagnetic radiation have frequen-cies ranging from 0.1 THz to 10 THz. Due to the lack of suitable radiation sources and detectors, this region is not well known. Interaction with THz waves becomes more effective by introducing the metamaterials (MM) and metasurfaces (MS) (3D and 2D, respectively), which are made up of artificially subwavelength compositions arranged in periodic arrays. MMs provide a unique control on the propagation of (EM) waves and their geometries determine their properties. Recently, coding MM has made it possible to regulate the far-field scattering pattern of EM waves. In other words, it is possible to shape the THz wavefront by changing the sequence of the coding unit cells into a 2D surface pattern. The reflection phase of the two types of unit cells in 1-bit coding MM is 0 and π. In this thesis, two different types of coding MMs were designed and fabricated. One type is hard-coded (metal-based), while the other is based on VO2 thin film. Both types of samples share a similar structure, which includes a sapphire substrate, a gold patch, a PET layer serving as a dielectric spacer, and a ground gold layer. However, there is an additional layer of VO2 beneath the gold patch and on top of the sapphire substrate in one of the fabricated MMs. The coding MM consists of two identical unit cells, with the only distinction being the size of the gold patch's side. This size determines whether the unit cell is considered as 0-bit or 1-bit. When the side size is 90 µm, the unit cell is 0-bit. On the other hand, when the side sizes are 60 µm and 70 µm (for different samples), the unit cell is 1-bit. Two different sets of hard-coded MM were fabricated. One set is composed of the 60-90 µm unit cells arranged in the form of checkerboard and stripe designs. The other set is made of 70-90 µm unit cells arranged in the form of checkerboard and stripe designs. The samples were measured with a custom-built setup and the THz full spectrum (0.50-0.75 THz) was obtained at each reflection angle. The results indicate that the checkerboard samples' reflection angle for each frequency has a good consistency with the calculations. Since the detector was obstructing the incoming beam, the measurable angle range begins at 23 degrees from normal incidence. This issue limits the ability to obtain the maximum scattering pattern of the strip design samples. At the final section of the thesis, the VO2-based MM, was fabricated and mea-sured. VO2 layer was used in this structure, due to its phase-changing characteristic. It undergoes a reversible transformation from an insulator to a metallic state at about 68◦C. The initial concept was to design and fabricate the MM just entirely out of 1-bit (60 µm) unit cells. After that, using a CW laser pump and a digital micromirror (DMD), convert this 1-bit into the 0-bit unit cell by modifying the conductivity of the VO2 layer of each individual unit cell. Using this idea, it was possible to develop a tunable digital MM. However, the CST simulation results demonstrated that the proposed MM is ineffective due to the significant amplitude difference between the 0 and 1-bit unit cells. Due to that, using the VO2-based unit cells (0 and 1-bit) the striped and checkerboarded pattern of MMs was designed and fabricated. The VO2 conductivity was modulated using a CW 915 nm laser beam. The measurement results show that VO2-based MM can be used for THz beam splitting at room temperature, and the scattering pattern weakens when the laser is illuminated over the sample, causing the VO2 layer to turn conductive. CST Studio Suite simulation software was used to determine the unit cells' geo-metrical dimensions, amplitudes, and phases. The analytical calculations were performed using MATLAB. The investigated MM has the potential to be used in THz communica-tions.Doctoral Thesis Fabrication and Characterization of Soi Based Photodetectors With Graphene Electrode(01. Izmir Institute of Technology, 2023) Yanılmaz, Alper; Çelebi, Cem; Balcı, SinanThis thesis presents the pioneering methods for the design, fabrication process, and performance evaluation of graphene (G) and n-type silicon (n-Si) based self-powered one dimensional (1D) and two dimensional (2D) photodetector arrays (PDAs) on a silicon on insulator (SOI) substrate. In the device structure, monolayer G is utilized as hole collecting transparent conductive electrode (TCE) and n-Si is used as light absorbing material, respectively. After analyzing the photo-response characteristics of single pixel G/n-Si diode on SOI, we fabricated G/n-Si based Schottky barrier 1D PDAs with common G electrode, separate G electrode and 2D PDA with individual G electrodes on linearly arrayed n-Si channels, respectively. Each G/n-Si diodes exhibited a clear rectifying Schottky character with low dark current and diode parameters were analyzed using the current-voltage measurement. Besides, all diodes demonstrated a clear photovoltaic activity under the light illumination and maximum responsivity at 660 nm peak wavelength. Each diode in PDA revealed similar device performances under self-powered mode in terms of an Ilight/Idark ratio up to 104, a responsivity of ~0.1 A/W and a response speed of ~1.3 μs at 660 nm wavelength. The optical crosstalk was extremely low between neighboring diodes and also it could be greatly minimized when G is used as separated electrode on arrayed Si up to ~0.10% (-60 dB) per array. Time dependent photocurrent spectroscopy measurements revealed an excellent photocurrent reversibility of both device types. In the diode structure, the homogeneity of the graphene film transferred on n-Si were examined by Raman mapping and correlated with the sensitivity of diode to incoming light. This thesis paves the way for the new generation of optoelectronic devices with various potential by integrating G and SOI technology to PDA devices with ease of fabrication.Doctoral Thesis Stability Analysis of Nonlinear Dynamical Systems With Lévy Typeperturbations(01. Izmir Institute of Technology, 2023) Tamcı, Ege; Batal, Ahmet; Savacı, Ferit AcarIn order to model the noise in power networks, generally, normal distribution is used. However, normal distribution is not convenient in modelling noise which has sudden peaks. Instead, combination of a continuous process and a jump processes is much more suitable. With this idea in mind, in this thesis, the stability and control of two equations used in modeling power grids is analyzed, under the assumption that they are exposed to Lévy process noise which includes jumps. These equations are the swing equation and the Kuramoto Model. The swing equation is used to model the single machine infinite bus system (SMIBS). Kuramoto Model is used when a large number of generators are considered as a network of coupled oscillators with their own natural frequencies. In our stability control study in the SMIBS, the noise in the system has sudden and finite changes is assumed and therefore should be modelled with a modified tempered α-stable process obtained by adding a finite jump condition on the tempered α-stable process when α < 1. The control functions depending on the mechanical power input and damping parameters are designed in order to make the system stable in probability and exponential stable at its equilibrium point. These theoretical results are supported by numerical studies. For Kuromato model, assuming that the power network consists of two layers, namely oscillator, and control layers and that is affected with a general Lévy process which has finite jumps, functions which provide the stability of phase and frequencies are obtained, depending on oscillator and coupling strengths. In the light of the numerical studies, the control of frequency and phase synchronization up to a certain noise intensity level can be evaluated, but it is not possible beyond that level is concluded.Doctoral Thesis Critical Spatial Standpoint on Neoliberal Urban Restructuring: a Case Study on Urban Restructuring Processes in Narlıdere, İzmir(01. Izmir Institute of Technology, 2023) Kılıçkaya, Ulaş Şansal; Arslan Avar, AdileThe thesis proposes a critical spatial approach to reveal the political, economic, and social dimensions of the urban development plans and projects (UDPs) in the context of neoliberal urban restructuring in Turkey. . It aims to enrich the theoretical and methodological foundations of critical urban studies and spatial planning, focusing on UDPs as a key neoliberal urban strategy. Despite extensive research on cities and their spaces, there is still a lack of critical understanding of the 'urban process', and of the actors and networks underlying these processes. The study tries to fill this gap by providing a critique of capitalism and its inherent uneven development, neoliberal political and economic restructuring, and neoliberal urban policy from a political economic perspective. The thesis concentrates on the neoliberal plans and projects produced by the state and capital as mechanisms to overcome capitalist crises. The thesis problem is to contribute to a critical urban theory that can explain and transform the socio-spatial processes in urban spaces, especially in light of the global expansion of 21st-century capitalism. The methodology used in the thesis is methodological pluralism, using various qualitative and quantitative research techniques to critically analyze the socio spatial processes of neoliberal urban restructuring.. It argues that UDPs are driven by the logic of profit and land rent, and that they exclude the participation and the rights of the poor and marginalized inhabitants. It seeks to critically elaborate on issues such as gentrification, dispossession, displacement, segregation, and polarization in the spaces of UDPs, instrumentalized as a mechanism of neoliberal urban restructuring processes in NarlıdereDoctoral Thesis Bose-Einstein Condensation and Black Holes in Dark Matter and Dark Energy(01. Izmir Institute of Technology, 2023) Gültekin, Kemal; Erdem, RecaiThe main aim of this study is to reveal curved space and particle physics effects on the formation of Bose-Einstein condensate scalar fields in cosmology and around a black hole. Cosmological scalar fields for dark energy and dark matter may be considered as a result of Bose-Einstein condensation. In this regard, our main attention will be devoted to Bose-Einstein condensates in curved space. By considering the dynamics of a scalar Bose-Einstein condensation at a microscopic level, we first study the initial phase of the formation of condensation in cosmology. To this end, we initially introduce an effective Minkowski space formulation that enables considering only the effect of particle physics processes, excluding the effect of gravitational particle production and enabling us to see cosmological evolution more easily. Then, by using this formulation, we study a model with a trilinear coupling that induces the processes. After considering the phase evolution of the produced particles, we find that they evolve towards the formation of a Bose-Einstein condensate if some specific conditions are satisfied. In principle, the effective Minkowski space formulation introduced in this study can be applied to particle physics processes in any sufficiently smooth spacetime. In this regard, we also analyse if a condensate scalar field is realized in the spacetime around a Reissner - Nordstrøm black hole. We find that the produced particles of particle physics processes are localized in a region around the black hole and have a tendency toward condensation if the emerged particles are much heavier than ingoing particles. We also find that such a configuration is phenomenologically viable only if the scalars and the black hole have dark electric charges. Finally, we consider gravitational collapse around Schwarzschild black holes and form a first step towards a study in future about the effects of gravitational collapse on Bose-Einstein condensation.Doctoral Thesis Advanced Material Characterization and Modeling the Foreign Body Impact Damage Initiation and Progression of a Laminated Carbon Composite(01. Izmir Institute of Technology, 2023) Bayhan, Mesut; Taşdemirci, Alper; Güden, MustafaThe coupon level composite sample tests and the accompanying numerical models were carried out to predict the response of woven carbon fiber composite structures against impact. The numerical models of the coupon-level tests were implemented in LSDYNA software using the MAT_162 and MAT_58 composite material models. The results obtained by both quasi-static and dynamic tests were used to determine their constants. In addition to the tests that were used for the determination and calibration of the material model parameters, separate tests and their models were performed for the validation, including punch shear tests and low-velocity impact tests. It could be said that the material models examined were considered comprehensive and precise as the experimental results were well predicted by the numerical models. Also, the rate sensitivity of the woven carbon composite in the in-plane and thickness directions was investigated experimentally and numerically. In the tests, the DIC method was employed in the determination of the displacement and strain of the specimen. Based on the results obtained, it was concluded that the in-plane tensile properties are rate insensitive. Besides, the simulations of the component level tests, such as bird strike and drone impact, were established to investigate the damage initiation and propagation within the composite. It was found that the drone impact results in more severe damage compared to the bird impact. It is worth noting that the development of such precise composite material models to simulate dynamic loadings will definitely shorten the time between the beginning of designing and the component testing.