Phd Degree / Doktora
Permanent URI for this collectionhttps://hdl.handle.net/11147/2869
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Doctoral Thesis Fabrication of carbonnanomaterial-polymer composite microelectrodes for electrochemical sensors(01. Izmir Institute of Technology, 2024) Önder, Ahmet; Yıldız, Ümit HakanDüşük hacimli numunelerde iyonların tespiti, küçük boyutları, yüksek hareketlilikleri ve hızlı difüzyonları nedeniyle önemli zorluklar sunar. Potansiyometrik iyon seçici elektrotlar (ISE'ler), maliyet etkinlikleri, kullanım kolaylıkları ve minyatürleştirme potansiyelleri nedeniyle iyon tespiti için güvenilir bir yöntem olarak ortaya çıkmıştır ve bu da onları mikroakışkan uygulamalar için uygun hale getirmiştir. Tezin ilk bölümünde, katı kontak malzemeleri olarak kimyasal buhar biriktirme yoluyla doğrudan cam elyafı (GF) üzerinde büyütülen radyal olarak hizalanmış karbon nanotüpler (RACNT) kullanılarak mikroelektrotların (r-ISE) üretimi açıklanmaktadır. Bir arayüz malzemesi olarak RACNT-GF ile üretilen r-ISE, 7.5×10⁻⁶ M'lik bir tayin limiti (LOD) ve 1.0×10⁻⁵ ila 1.0×10⁻¹ M arasında doğrusal bir yanıt sergilemiştir. RACNT-GF kullanımı, grafit gibi geleneksel katı kontak malzemelere kıyasla LOD'yi ve seçiciliği önemli ölçüde iyileştirmiştir. RACNT-GF'nin yüksek yüzey alanı ve mekanik dayanıklılığı, elektrotun performansını artırmış ve sınırlı mikroakışkan ortamlarda bile kararlı ve tekrarlanabilir potansiyometrik tepkiler sağlamıştır. Tezin ikinci bölümünde, nitrat iyonları için sentetik bir iyonofor olarak moleküler kafese sistematik bir yaklaşım araştırılmaktadır. Kafes moleküllerinin moleküler yapısını ve dolayısıyla boyutlarını değiştirerek, konak-kafes molekülleri ile misafir-NO3- iyonları arasındaki etkileşimi ayarlamayı amaçlamıştır. Altı sentetik moleküler kafes iyonoforu, nitrat seçici bağlanma yetenekleri açısından değerlendirilmiştir. Optimize edilmiş KAFES iyonoforuna dayalı ISE, yüksek bir belirleme katsayısı (R² = 0.9971), -53.1 ± 1.4 mV/on kat ve nitrat tespiti için 7.5×10⁻⁶ M LOD ile 1.0×10⁻⁵ ila 1.×0.10⁻¹ M arasında doğrusal bir yanıt göstermiştir. Tezin son bölümünde, yüzey baskılı elektrot ile iyon tespitinde damla buharlaşmasının duyarlılığa etkisi incelenmiştir. Sonuçlar, 1.0×10⁻⁵ M'den düşük iyon konsantrasyonlarının doğrusal yanıt vermediğini ve damla buharlaşma yönteminin tercih edilmediğini ortaya koymuştur.Doctoral Thesis Synthesis and Characterization of Near-Infrared (nir) Emissive Conjugated Polymer Dots for Tumoroid Imaging(01. Izmir Institute of Technology, 2024) Karabacak, Soner; Yıldız, Ümit HakanThis thesis describes the synthesis and characterization of near-infrared (NIR) emissive conjugated polymers and their polymer dots (Pdots). The Pdots were exploited to image the tumor cells and tumor spheroids. The penetration behavior of NIR emissive Pdots was characterized in five different tumor spheroid models. Three different polymerization techniques were tried to synthesize the NIR emissive polymers, namely oxidative, direct arylation, and Stille polymerization. The obtained NIR emissive polymers underwent structural and optical characterization. P1 was chosen as a model polymer to obtain Pdots from NIR emissive polymers for imaging tumoroids. Pdot preparation includes using ultrasonic emulsification to modify nonionic D-A-D type alkoxy thiophene-benzobisthiadiazole-based conjugated polymers (P1) with amphiphilic cetyltrimethylammonium bromide (CTAB). The technique yields Pdots with a significant positive surface charge of +56.5 mV ± 9.5 and an average hydrodynamic radius of 12 nm. Optical characterization reveals that these Pdots were found as emissive in the NIR region, with a maximum wavelength of 860 nm. These Pdots possess colloidal and optical properties that make them appropriate for use as fluorescence emissive probes in bioimaging applications. The advantageous use of positively charged Pdots has been proven in diffusion-limited settings such as tissues, specifically in certain tumor spheroid models produced from the tumoroid cell lines. After the fluorescence imaging analysis, the Pdots' emission intensity profile indicates that they have high penetration capability into the tumoroid models' center parts. The results show that Pdots with a single-chain donor-acceptor polymer structure that has been cationized with CTAB can penetrate through dense materials over about 1 μm. This provides valuable insights into the progression of targeted theranostic strategies in cancer therapy.Doctoral Thesis Two Dimensional Material Based Field Effect Transistor for Biosensing Applications(01. Izmir Institute of Technology, 2023) İnanç, Dilce; Yıldız, Ümit Hakan; Çelebi, CemThis thesis presents research on the use of two-dimensional material graphene as an area-effective transistor and its application in biological fields. The formation of wrinkled and flat structures on the surface of a single-layer graphene area-effective transistor, epitaxially grown for determining the bio-membrane dynamics of graphene, was examined using two different methods of deposition (thermal evaporation and pulsed electron accumulation) of a silicon dioxide (SiO2) layer. The investigation aimed to evaluate the pH and lipid bilayer formation performance of both wrinkled and flat GFETs. Increased sensitivity was determined through electrical measurements, as the oxide layer becomes thinner due to the existence of wrinkles, thus providing electrostatic coating on graphene. A sensor platform of chemiresistor type was developed for the differential determination of volatile organic compounds (VOCs) by synthesizing single-layer, bilayer, and multilayer graphene, enabling the analysis of ethanol (EtOH) and methanol (MetOH). Sensors produced using three different graphene morphologies demonstrated differential MeOH-EtOH responses attributed to the differential intercalation phenomenon in multilayer graphene morphologies when compared to ethanol. For the detection of VOCs such as acetone, ethanol, and hexane in human breath, a polymer nanofiber/multi-walled carbon nanotube or poly (3,4-ethylenedioxythiophene)/gold (Au) and iron oxide (Fe) hybrid bioelectronic interface was developed. Sensitivity studies were conducted by applying pure VOCs at different concentrations to the sensor platforms, and the behavior of the sensor platforms against interfering elements was evaluated by recharacterizing them under CO2 and humidity conditions. Considering the responses of MWCNT-PLLCL-Fe-based sensors to acetone, ethanol, and hexane, the tendency of water molecules to adhere to the Fe surface was shown to decrease water condensation on the conductive layer compared to other sensor configurations, indicating that the humidity effect was minimized in MWCNT-PLLCL-Fe-based sensors.Doctoral Thesis Characterization of Conjugated Polyelectrolytes for Nucleic Acid Sensing, Gene Delivery and Imaging(01. Izmir Institute of Technology, 2022) Yücel, Müge; Yıldız, Ümit Hakan; Yıldız, Ümit HakanIn this thesis, cationic derivatives of poly(3-alkylmethoxythiophene) (PT) which are a class of conjugated polyelectrolytes (CPE), have been synthesized. PT has been polymerized via FeCl3 oxidative polymerization, were treated in a set of solvents to elaborate coil conformation of polymer chain in different physicochemical environment. Spectroscopic and scattering techniques have ascertained that ethylene glycol is a good solvent for PT regarding Flory-Huggins theory. The smaller interaction parameter of PT with respect to ethylene glycol than water drives a thermodynamically driven ultra-small particle (Pdot) formation in aqueous phase by a rapid nanophase separation between PTrich ethylene glycol and PT-poor water phase. All CPEs have been then employed to prepare single polymer chain polymer dots (Pdot) by “nanophase separation” method. As a next step, Pdots have been characterized in terms of optical and colloidal properties that they possess in the backbone conformations altered by solvation effect. Regarding their colloidal characteristic, translocation of Pdot into cancerous cells was analyzed compared to healthy cells by 2D cell culture and co-culture studies. It has reported that Pdots have ability to penetrate through nuclear envelope in hepatocellular carcinoma whereas accumulate around nucleus of healthy liver cells in cytoplasm. Additionally, Pdots were studied in breast cancer cell lines to understand the behavior of Pdot staining in 2D cell culture of invasive and non-invasive breast cancer types. The findings suggest that Pdots are prone to penetrate into the invasive cancerous cells attributed to the greater deformations on nucleus membrane of triple negative breast cancer cells. In a next application, the enhanced photophysical property of PT exhibited in ethylene glycol media allows PT to be utilized as a fluorescent probe for determination of single nucleotide polymorphism by a non-amplification-based protocol. Fluorescence emission at specific wavelengths resulted from very distinct conformations of PT chain is the key elements for the SNP detection assay. The evaluation of optical data obtained from the probe with principal component analysis proves the separation of healthy individuals from patients with an overall 96% accuracy.Doctoral Thesis Preparation of Nanostructured Interface by Polymer Grafting on Various Solid Substrates for Biosensor Applications(Izmir Institute of Technology, 2021) Özenler, Sezer; Yıldız, Ümit HakanThis thesis presents the utilization, various applications, and characterization of the soft material-based coating formed on the gold surface with varying thickness and chemical properties resulting from the isocyanate-gold interaction. Theoretical calculations regarding the interaction of isocyanate with the gold surface revealed the character of the bond formed and the orientation of the functional groups on the surface. Results by X-ray photoelectron spectroscopy showed the tendency to shift to the high energy at N 1s and C 1s binding energies in the gold-interacting isocyanate group. In the next steps, the isocyanate-activated gold substrate was subjected to sequential incubation of 1,4-butanediol/hexamethylene diisocyanate, and thin-film formation was achieved by surface assisted (SurfAst) urethane polymerization. It was revealed with three different applications that a nano-porous polyurethane (PU) structure was formed on the gold substrate and could be postmodified by using SurfAst polymerization method. In the first application, modification with polyethylene glycol (PEG) was provided to obtain antifouling properties. The PEG-terminated PU structure on the gold surface was shown to reduce protein adhesion by approximately ten-fold. In the second application, SurfAst was applied on the 11-mercaptodecanoic acid incubated surface and grafting onto the poly (N-allyl-N-methyl-N-(3-((4-methylthiophen-3-yl)oxy)propyl) prop-2-en-1-aminium surface was characterized. As a result of PT grafting, PT nanowires with an average height of 100 nm, a width of 250 nm, and a length of 7 μm were obtained on the gold surface. In the last application, a soft nanogel was obtained by a reactive layer-layer (rLBL) coating method using the aza-Michael addition reaction of branched polyethyleneimine and polyester on the isocyanate functional surface. The mechanical and electrical permeability and coating properties of the nanogel layer were assessed. In conclusion, the high potential of isocyanate in surface activation has been demonstrated theoretically and experimentally. Effective modification of gold surfaces by polymer grafting with the SurfAst method and rLBL coating techniques has been achieved.