Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Protein-enzyme reaction followed by vibrational spectroscopy and dft (density functional theory) characterization(01. Izmir Institute of Technology, 2023) Öztoprak, Nazlı; Güler, Günnur; Öztoprak, Nazlı; Yağmurcukardeş, Mehmet; Güler, Günnur; Yağmurcukardeş, Mehmet; 04.04. Department of Photonics; 01. Izmir Institute of Technology; 04.05. Department of Pyhsics; 04. Faculty of ScienceWhey proteins are crucial for many functions of the human body. Determining the structural properties of the protein with the enzymatic hydrolysis makes it possible to improve food quality, identify allergens and better understand food poisoning. In this study, the structural alterations of β-Lactoglobulin (model whey protein) were investigated during proteolysis. Trypsin was used as a model enzyme. Digestion of β-LG by trypsin at different concentrations were measured by Fourier transform infrared (FTIR) spectroscopy as well as by Raman spectroscopy to identify the degradation of the protein and to verify the enzymatic reactions results at various temperatures in real time. Afterwards, the advanced analysis techniques, two-dimensional correlation spectroscopy (2DCOS) and curve-fitting analysis, were applied. In addition, the experimental measurements were supplemented with DFT simulations. Based on the FTIR spectroscopy results, the most notable changes take place in the amide I (1600-1700 cm-1) and in the amide II (1480-1580 cm-1) regions. FTIR spectroscopic results revealed that the structural elements of β-LG broken down and degraded during the enzymatic digestion. Moreover, the carboxylate groups (COO-) gives rise in the infrared range (1605-1580 cm-1) as released products. Raman spectroscopic results demonstrate that β-LG loses its secondary structure and the product is formed around 1425 cm-1 arising from the carboxylate groups (COO-) due to the digestion. DFT results show that the Raman spectrum of single unit arginine and lysine residues can be predicted by DFT method. Furthermore, DFT calculations give the rise at 1683 cm-1 and 3540 cm-1 caused by C-N vibrations and N-H vibrations arising from the amino groups (NH2+), respectively.Master Thesis Quantitative Phase Analysis in Lensless Digital Inline Holographic Microscopy(01. Izmir Institute of Technology, 2021) Tekin, Hüseyin Cumhur; Varlıklı, Canan; Tekin, Hüseyin Cumhur; Varlıklı, Canan; 03.01. Department of Bioengineering; 04.04. Department of Photonics; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of TechnologyComputational imaging modalities replace the bulky, complex, and expensive optical components of traditional imaging procedures with numerical reconstruction steps. Digital holographic microscopy is one of the most prominent ones with the possibility of obtaining quantitative phase information by measuring the phase shift change caused by the refractive index of objects. In the lensless digital holographic microscopy system, a pinhole and a light-emitting diode are sufficient to create a holographic pattern on the camera sensor. Here, the optimization of a digital lensless inline holographic microscopy setup was performed to obtain optimal phase value. Also, to retrieve the lost phase information during the recording step, the numerical solution was performed with the single and multi-shot phase retrieval methods. Then, human breast adenocarcinoma (MDA-MB-231) and human myeloid leukemia (U937) cells were analyzed to obtain phase shift, perimeter, and circularity values. These parameters were used to obtain a quantitative differentiation model to replace the traditional labeling or visual confirmation steps with a direct analysis manner. The analysis of respective cells with the classification, object detection, and conditional generative adversarial models can be used directly with pre-trained weights to lessen the computational workloads. With this study, the quantitative analysis with lensless holographic microscopy setup was shown to be a label-free differentiation mechanism to separate cancer cells from monocytes cells which could be used for the early diagnosis of cancer. Also, the proposed method has the potential to be used to identify other cells with links to the diagnosis of different diseases.Master Thesis Identification of Single-Layer Crystalline Structures Through Their Electronic and Optical Properties(01. Izmir Institute of Technology, 2021) Sözen, Yiğit; Şahin, Hasan; Şahin, Hasan; Balcı, Sinan; 01. Izmir Institute of Technology; 04.04. Department of Photonics; 04. Faculty of ScienceA large number of two-dimensional (2D) van der Waals type materials have become a focus of interest in many scientific fields, ever since the thinnest carbon compound, graphene, takes to the stage with its exceptional electronic properties. The outstanding electronic behavior resulting from quantum size effects requires an investigation of the electronic and optical features of materials at the atomic scale. The understanding of such properties of matter within the framework of the theoretical approaches is the first step to shed light on the discovery of electronic and optoelectronic devices including brand new features. This thesis discusses the identification of electronic and optical properties of several types of atomically thin crystals, consisting of 2D and lead-free perovskite structures, by means of density functional theory (DFT). In the first study, primarily, the strong interaction mechanism between Ge atom and single-layer GaAs was studied starting from single atom adsorption to detached germanene layer formation. Following that dynamically stable metallic structures of Janus and alloy type GaGeAs crystals are discovered by performing one-sided and alternated decoration of GaAs single-layer with Ge atoms, respectively. %The Raman spectroscopy is found to be applicable for phase detection as the theoretically calculated Raman spectra of each polytype exhibit distinctive signals. In the second study, bulk and dynamically stable ultra-thin structures of lead-free CsMnCl$_3$ are discussed. According to total energy and electronic band structure calculations, bulk, bilayer, and single-layer structures of CsMnCl$_3$ are robust antiferromagnetic insulators. In third and fourth chapters are devoted to the identification of different stacking types of GaP/GaSe heterobilayers, and two different hexagonal phases of single-layer Germanium Oxide by means of electronic and optical characterization tools, respectively. In these studies, for the purpose of providing an accurate solution for the prediction of absorption, reflectance, and transmission spectra of materials, excitonic effects are considered by employing Bethe-Salpeter formalism following the $G_0W_0$ approximation. Wide range of atomically thin crystal structures studied within the framework of this thesis are verified to be promising candidates for the development of future nano-sized electronic and optoelectronic device applications thanks to their attractive electronic and optical properties arising from strong quantum confinement effects.Master Thesis Design and Fabrication of a Wearable, Flexible Pulse Oximeter(01. Izmir Institute of Technology, 2020) Aydın, Ahmed; Tekin, Hüseyin Cumhur; Tekin, Hüseyin Cumhur; 01. Izmir Institute of Technology; 03.01. Department of Bioengineering; 03. Faculty of EngineeringOxygen is vital for the healthy functioning of tissues and organs. For this reason, it is indispensable to monitor the oxygen saturation of the human body during daily activities in order to improve the quality of life, in the detection and tracking of respiratory diseases. Pulse Oximeter is an electro-optic device that non-invasively measures peripheral oxygen saturation and provides information about how well oxygen diffuses the tissues. Conventional devices are not suitable for daily use due to their bulky structure and designs that restrict movement. With this thesis, the design and production of a flexible reflectance type Pulse Oximeter device that is conformally adapt to measurement suite, can be used all day long and is intended for continuous measurement has been realized.Master Thesis Emission Characteristics of a Solution Processed, Single Layer White Organic Light Emitting Diode(01. Izmir Institute of Technology, 2020) Varlıklı, Canan; Varlıklı, Canan; Gültekin, Burak; 04.04. Department of Photonics; 04. Faculty of Science; 01. Izmir Institute of TechnologyWhite organic light emitting diodes (WOLEDs) are getting more attention day by day because of their some superior properties like viewing angle, refresh rate, flexibility, easy production process and consequently relatively cost-effective natures. Within the scope of this thesis, WOLED has been prepared and characterized by using the single emitter layer prepared by solution process method. In the emission layer, the host material is used for both obtaining the blue region of the visible spectrum and for efficient energy transfer to the green and orange-red guest material. Poly(N-vinylcarbazole) (PVK): 2-(4-Biphenylyl)-5-phenyl-1,3,4-oxadiazole (PBD) or 1,3-bis[(4-tert-butylphenyl)-1,3,4-oxadiazolyl] phenylene (OXD-7) matrices are used as host for orange-red emitting material of N,N'-bis(2-ethylhexyl)perylene-3,4,9,10-dicarboxylic diimide (PDI) and green emitting material of perylene-3,4,9,10-tetracarboxy tetrabutylester (PTE). Electron and hole mobility, L-V-J characteristics and morphologies of two different host matrix of PVK:PBD and PVK:OXD-7 were examined. As a result of these evaluations, the appropriate host was determined as PVK:PBD. Host:PTE and Host:PDI emission characteristics were examined and exciplex, electroplex formations were detected. After, Host:PTE:PDI configuration were discussed and high white light properties of optimized WOLED are displayed CIE 1931 coordinates (x, y) of (0.34, 0.36), correlated colour temperature of 4916 K and CRI of 96. Finally, lethal time 70 of the latest devices was examined.Master Thesis Graphene-Like Materials for Electronic Applications(01. Izmir Institute of Technology, 2020) Balcı, Sinan; Şahin, Hasan; Şahin, Hasan; Balcı, Sinan; 04.04. Department of Photonics; 04. Faculty of Science; 01. Izmir Institute of TechnologyTwo-dimensional (2D) materials have gained vast interest in nanotechnology since these materials exhibit extraordinary properties due to electron confinement. Starting with graphene, many other 2D materials with characteristics of metals, semiconductors, insulators, and their magnetic analogues have been studied over the years. Insulators show importance as dielectric layers. Low dimensional metallic materials are used in electrical conduction. Ultra-thin semiconductors have variety of potential applications due to their characteristic band gap. Magnetic analogues of low dimensional materials are used in spintronics, offering high frequency, controllable switching. In addition, defects in these materials alter their physical properties and the concept can be adopted in order to use in different practices. Therefore it is important to study array of such materials and consider the alteration in their lattice theoretically and experimentally. In this thesis, first-principles calculations are used to predict insulating calcium halide single-layers are predicted, determine the effects of strain and V dopant in recently synthesized magnetic semiconducting VI3 single-layers, propose synthesis of magnetic, semiconducting manganese fluorides from manganese dichalcogenides, investigate the affects of defects and simulate scanning tunneling microscopy images in order to compare with experimental results, and finally to determine rather the detection of volatile organic compounds (VOC) such as methanol and ethanol by graphene-based sensors is feasible or not. Experiments are carried out to construct and further investigate the mechanism of VOC detection and working, highly sensitive alcohol sensors.Master Thesis Photophysical Characterization of Green and Blue Emitting Quantum Dots and Their Application in Qd-Leds(01. Izmir Institute of Technology, 2020) Özgüler, Şahika; Varlıklı, Canan; Varlıklı, Canan; 04.04. Department of Photonics; 04. Faculty of Science; 01. Izmir Institute of TechnologyQLED device construction and characterization studies were carried out in which QD nanoparticles synthesized within the scope of TÜBİTAK project no 115F616, and were used as emission layer. By examining the photo-physical and morphological properties of films prepared with the use of quantum dot (QD) nanoparticles, quantum dot light emitting diodes (QLEDs) which are one of the fields of molecular electronics, were applied as an emission layer using the spin coating technique from wet coating processes. The photo-physical and morphological characterizations of the solution and film phase of blue and green emitted QD nanoparticles were made. For the QDs, the concentration difference in the solution phase was characterized and its effects on film properties were investigated. It has been determined that the increase in concentration does not have a dramatic effect on photo-physical properties but seriously affects film thickness and surface roughness. In this case, performance of blue and green light emitting quantum dot diodes (QLED) prepared by the spin-coating technique, where each QD film is used as the emission layer, have been investigated.Master Thesis Flexible Transparent Conducting Electrodes Based on Silver Nanowire, Graphene, and Two-Dimensional Transition Metal Dichalgogenide(01. Izmir Institute of Technology, 2020) Balcı, Sinan; Balcı, Sinan; 04.04. Department of Photonics; 04. Faculty of Science; 01. Izmir Institute of TechnologyIn recent years, transparent conductive electrodes have attracted great interests owing to their critical applications in various optoelectronic devices, such as light emitting diodes, solar cells, liquid crystal displays, optical modulators, and touch screens. In this thesis, graphene-silver nanowires-transition metal dichalcogenide based hybrid transparent and conductive electrodes have been fabricated. In order to reach this goal; (1) single layer graphene on copper foil has been synthesized in large area in a CVD furnace, (2) ultrathin and very long silver nanowires have been synthesized by using wet chemistry methods, (3) MoS2 and WS2 single layer flakes and multilayer thin films have been synthesized in a CVD furnace, (4) electrodes of graphene, silver nanowires, and transition metal dichalcogenides have been fabricated on rigid and flexible substrates.Master Thesis A Comparative Study on the Photocatalytic Activity of Dye-Sensitized and Non-Sensitized Graphene Oxide-Ti̇o2 Composites Under Simulated and Direct Sunlight(01. Izmir Institute of Technology, 2019) İlhan, Hatice; Varlıklı, Canan; Demir, Mustafa Muammer; Varlıklı, Canan; Demir, Mustafa Muammer; 04.04. Department of Photonics; 03.09. Department of Materials Science and Engineering; 03. Faculty of Engineering; 04. Faculty of Science; 01. Izmir Institute of TechnologyAmine modified graphene oxide (mGO) and TiO2 composite was synthesized by low temperature hydrothermal method. Characterization of the synthesized material was carried out by using X-ray diffraction, X-ray photoelectron spectroscopy, and BET analysis techniques. The films of mGO:TiO2 and formerly synthesized TiO2, N-TiO2, GO-TiO2 and GO:N-TiO2 were fabricated by doctor blade method and employed as photocatalysts for the photodegradation of Rhodamine-B (RhB) dye under simulated (Xe lamb) and direct sun-light. P25 was also used as reference photocatalyst for all of the synthesized ones. Photodegradation of RhB was monitored by UV-Vis spectroscopy. Among all the catalysts, GO:N-TiO2, the composite of GO and N-doped TiO2, presented the best photocatalytic activity and although the activity of mGO:TiO2 was better than the activities of P25 and TiO2, it presented lower degradation rate constant even than that of the N-TiO2. It is proposed that increased abundance of C-C bonds and decreased number of oxygenated functional groups on mGO:TiO2, in addition to the morphological difference between GO (sheet like) and mGO (dot like) has great influence on their photocatalytic activities. Among the GO containing photocatalysts including mGO:TiO2, specific surface area (SSA) and number of RhB molecules per film volume were the lowest and particle size was the highest for mGO:TiO2. Although the number of RhB molecules per film volume was higher in mGO:TiO2 than that of the N-TiO2, it is thought that approximately 2 folds higher SSA of N-TiO2 allowed better photocatalytic performance. Additionally, the films were sensitized with PTE dye to obtain effective catalysts in visible region and reusability of the films were also tested. Degradation rate constants of all fabricated films have increased under both of the irradiation media and no significant change in rate constants were detected after the reusability tests.