Master Degree / Yüksek Lisans Tezleri
Permanent URI for this collectionhttps://hdl.handle.net/11147/3008
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Master Thesis Centrifugal microfluidic-based platforms for in vitro diagnostics(01. Izmir Institute of Technology, 2024) Koç, Sadık; Tekin, Hüseyin Cumhurİn vitro tanı (IVD) yöntemleri, tanı koymak için kullanılan tüm araçları kapsarlar ve erken teşhis sağladıkları için büyük önem taşırlar. IVD'lerin gelişimi, hücreler arası iletişimi sağlayan eksozomların, özellikle hastalıkların erken teşhisinde biyomarker olarak kullanılmasına olanak tanımıştır. Geleneksel IVD'ler altın standart olarak kabul edilmesine rağmen, genellikle yüksek maliyetli ve zaman alıcıdır. Bu zorlukların üstesinden gelmek için IVD'lerin mikroakışkan sistemler kullanılarak hasta başı sistemlerine uyarlanması gerekmektedir. Bu bağlamda, polimetil metakrilat (PMMA) bazlı bir mikroakışkan çip üzerinde eksozomları izole etmek ve zenginleştirmek için yeni bir mikroakışkan üretim yöntemi geliştirilmiştir. Bu yöntemde, saf aseton hem yüzey iyileştirici hem de yapıştırıcı olarak kullanılmış, PMMA kanallarındaki yüzey pürüzlülüğü ve opaklık sorunlarını ortadan kaldırarak yüzeyin kendini onarmasını ve şeffaf hale gelmesini sağlamıştır. Elde edilen çipler, yalnızca daha dayanıklı olmakla kalmayıp, aynı zamanda uygun maliyetli ve kolay üretilebilir niteliktedir. Bu yöntem, nanoparçacık ve eksozom izolasyonu için kapalı bir kanal içeren santrifüjlü mikroakışkan bir çip üretmek için başarıyla uygulanmıştır. Çip, 9000 rpm (9418 g) hızında standart bir masaüstü santrifüjde 200 nm parçacıkları 20 dakikada, 100 nm parçacıkları 30 dakikada ve 50 nm parçacıkları 60 dakikada izole etmeyi başarmıştır. Özellikle, eksozomlar, belirteç kullanmadan, hücre ortamından bir saat içinde izole edilmiştir. Bu yenilikçi santrifüj tabanlı mikroakışkan platform, farklı IVD uygulamaları için umut vaat etmektedir.Master Thesis Effect of Gold Nanorod Properties on Lspr Response(01. Izmir Institute of Technology, 2023) Kılıç, Şebnem; Bulmuş Zareie, Esma Volga; Tekin, Hüseyin CumhurOptical qualities make gold nanorods (GNRs) excellent for plasmonic biosensors. Localized surface plasmon resonance (LSPR) phenomenon which occurs on GNR surfaces enables the creation of highly sensitive biosensors. The physical properties such as aspect ratio and size are directly related to the LSPR response of GNRs. The aim of this study is to investigate the impact of the aspect ratio (AR) and the interparticle distance on the localized surface plasmon resonance (LSPR) response of GNRs decorated glass sensor chips. For this aim, GNRs were first synthesized using a seed-mediated growth method. The effect of AgNO3 concentration on the AR of GNRs was investigated. It was observed that increasing AgNO3 concentration resulted in GNRs with higher AR and a red shift in the longitudinal plasmon peak wavelength. GNRs with an AR of 4, 6 and 8 were successfully synthesized. Next, the effect of the stabilizer molecule type and molecular weight on the distribution of GNRs on the silanized glass surface was investigated. It was found that the APTES modified glass surfaces cannot be coated with CTAB stabilized GNRs. Using GNRs stabilized with PEG5K resulted in a more homogeneous distribution of GNRs on the glass surface with respect to GNRs stabilized with PEG2K. The interparticle distance between GNRs on the glass surface was successfully controlled by simply concentrating or diluting the GNR solution used for coating the glass surfaces. It was observed that the LSPR peak shifts decreased upon binding of analytes as the interparticle distance between GNRs decreased in the studied range. On the other hand, as the AR decreased, the LSPR response of the GNRs shifted blue. The results presented in this thesis may contribute to future research to improve the potential of LSPR-based biosensors for diverse biomedical and diagnostic applications.Master Thesis Development of an Advanced Lspr-Based Biosensor Chip for Rapid Detection of Border Disease Virus(01. Izmir Institute of Technology, 2023) Alakbarov, Abdullah; Bulmuş Zareie, Esma Volga; Tekin, Hüseyin CumhurThe Border Disease Virus (BDV) is responsible for causing fetal deathly infection, leading to annual occurrences of affected farms. BDV, along with other pestiviruses such as classical swine fever virus (CSFV) and bovine viral diarrhea virus (BVDV), are known to cause major losses in stock farming. These losses can result in reproductive failure, expensive inspections, and other impacts on livestock health. The current detection methods of BDV include various techniques such as RT-PCR, ELISA, VNT, and immunofluorescence assays. These methods, although reliable, may require specialized equipment, time-consuming procedures, and laboratory facilities, making them less suitable for rapid on-site detection. Hence, it is imperative to employ diverse methodologies for detection of BDV. LSPR-based biosensors are a subset of plasmonic biosensors that exhibit numerous advantages for diverse applications. LSPR-based biosensors are particularly well-suited for the production of compact, practical devices for rapid, on-site detection of analytes. The aim of this study is to design and fabricate a biosensor chip utilizing LSPR technology for potential BDV detection. For this aim, glass surfaces were functionalized with gold nanorods modified with a BDV-specific primer sequence, complementary single-strand DNA sequence of 19 bases, and fabricated with PMMA microchannels. Different concentrations of target BDV-DNAsequence ranging from 0.01 pM to 100 nM were exposed to the channels, and the LSPR response was quantified using a Vis-NIR spectrometer. The limit of quantification of the biosensor chips was determined to be 10 pM, while the limit of detection was found to be less than or equal to 1 pM. The sensitivity of the biosensor chips was calculated to be 0.0567 nm/RIU. The dynamic range of the biochips lies between 10 pM to 100 pM.Master Thesis Design and Fabrication of a Wearable, Flexible Pulse Oximeter(01. Izmir Institute of Technology, 2020) Aydın, Ahmed; Tekin, Hüseyin CumhurOxygen 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 Manufacturing and Characterization of Perovskite Thin Films Using Novel Methods(Izmir Institute of Technology, 2020) Bıyıklı, Ozan; Sarı, Emre; Tekin, Hüseyin CumhurPerovskite photovoltaics is a promising technology due to its low-cost fabrication and high efficiency. Since their first demonstration in 2009, efficiencies of perovskite solar cells (PSCs) increased unprecedently fast from 3.81% to 25.2% in 10 years. The most common method for the deposition of the absorber layer of the perovskite solar cells is the spin-coating method, which is not a scalable method, and this method is an obstacle to their commercialization. Efficiencies obtained with scalable methods are currently lower than that of the spin-coating method. In this thesis, among the scalable deposition methods, a novel ultrasonic spray-coating was used by adding antisolvent vapor to the system. The antisolvent quenching technique, that is commonly used to improve the crystalline quality of the film by spin-coating was successfully adapted for ultrasonic spray coating. The interaction between diethyl ether (DE) vapor, which is used as an antisolvent, and MAPb(I(3-x)Brx)3 precursor solution (where the solvent is DMF:DMSO, 4:1) was utilized to improve the crystalline quality of the perovskite film. As a result of this interaction, the intermediate phase was observed. The transition to the intermediate phase is supported by data from characterization methods such as optical microscopy, scanning electron microscopy (SEM), X-Ray diffraction (XRD), and current-voltage measurement. Furthermore, n-i-p devices with the FTO/c-TiO2/m-TiO2/MAPb(I(1-x)Brx)3/Spiro-OMeTAD architecture were produced with different antisolvent vapors and their efficiencies was compared. It was observed that devices using DE vapor reach higher efficiencies than devices without any antisolvent vapor.Master Thesis Detection of Febrile Illness and Its Monitoring Using Iot Technology(Izmir Institute of Technology, 2019) Tamur Kaya, Gamze; Tekin, Hüseyin Cumhur; Özuysal, MustafaMeasuring and monitoring body temperature has importance for disease diagnosis. It could also help following the course of the disease. Extensive number of body temperature monitoring applications are designed and developed. These applications could be named as healthcare applications aiming to provide convenience to the users. The Internet of Things technology is popular in healthcare applications by offering remote and real-time monitoring. In this project, a telemedicine platform facilitating the diagnosis and monitoring of febrile illnesses is designed. A user-friendly platform is implemented using software components. Message Queuing Telemetry Transport (MQTT), which is a communication protocol, is used for the communication between devices and monitoring system. A broker is used to transmit measured body temperature data from a device to the cloud server. The performance of the broker is evaluated with thousands of generated data packets. It is showed that the platform can handle data requests with a high throughput, i.e, up to 40000 packets/s. The monitoring system is designed as an interactive user interface. For this purpose, Telegram is adapted to the requirements of the platform by using an open-source library of Telegram BOT API. Hence, a user is able to access the measurement results and also control the measurements using instant messaging via Telegram interface. Moreover, this proposed platform could eliminate the use of separate healthcare applications for different diseases by using just a single instant messaging program for all different applications.Master Thesis Development of a Cell Sorting Platform Based on Magnetic Levitation Principle(Izmir Institute of Technology, 2019) Yılmaz, Esra; Tekin, Hüseyin Cumhur; Özçivici, EnginCirculating Tumor Cells (CTCs) play a vital role in cancer diagnosis, prognosis and personalized medicine. However, CTCs are extremely rare in blood (i.e., down to 1- 100 CTC per 1 mL human blood) and hard to isolate because of the heterogeneity of CTCs in biomarker expression. The current CTC separation techniques use numerous differences between cells such as size, electric charges, density and expression of cell surface markers. However, these techniques have many limitations in terms of manual sample preparation steps, inconsistent results caused by low specificity and efficiency, and increased cost. Hence, there is no standard method for isolating CTCs yet. With this study, it was aimed to fill the gap in CTC isolation by proposing a new method based on magnetic levitation principle, which has recently been demonstrated as a highly acceptable method for biological characterization of cells and monitoring of their cellular events. Short while ago, magnetic levitation technology has been used to measure cell densities at single-cell level. By using this technology, unique differences in levitation height and so in density have been identified between cancer cells and blood cells. In this study, we have been developed a new label-free microfluidic cell sorter that is based on the principles of magnetic levitation. After successfully completing this master thesis, this device can be used for rapid, low cost and label-free in-vitro diagnosis of cancer by sorting CTCs from whole blood in a high-throughput manner. The sorted cells might further be collected for downstream analysis for personalized and precision medicineMaster Thesis Fabrication of Microfluidic Devices Via 3d Printer(Izmir Institute of Technology, 2019) Keçili, Seren; Tekin, Hüseyin Cumhur; Bulmuş, VolgaThe purpose of this thesis is to provide easy and rapid prototyping of microfluidic devices using 3D printing technology that overcomes disadvantages of traditional fabrication techniques and also enhanced optical transparency of 3D-printed microfluidic devices fabricated using new bonding strategies. For performance analysis of 3D printer, microfluidic channels and molds having different shape and dimensions were designed and fabricated. After the fabrication process, designed and fabricated channel dimensions were compared. Structures having at least having 50 μm feature were printed successfully. For enhancing transparency of fabricated 3D structures, two different fabrication techniques were developed. In these techniques, 3D structures were bonded on glass substrates with poly (dimethylsiloxane) (PDMS) and Formlabs Clear Resin interlayers. After 3D-printed structures were put on interlayers coated glass slides, they were either remained on coated slides or transferred on new slides. Bonding between 3D structures and glass slides were provided with UV exposure for resin and with elevated temperature for PDMS interlayers. Bonding strength of fabricated channels was investigated for different thicknesses of PDMS and resin interlayers. The bright-field and fluorescence imaging properties of these channels were also analyzed. Proposed fabrication technique showed 2-fold improved bonding strength and comparable bright-field and fluorescence imaging capability with respect to traditional plasma activated PDMS-glass bonding. Furthermore, protein modified glass substrates can be integrated in 3D-printed channels using the presented fabrication technique without disturbing protein functionality. Finally, in order to design a 3D-printed micropump having membranes that can be activated with compressed air, membrane deformation was characterized with different dimension.Master Thesis Development of a Fluidic Platform for Automated Analysis of Heavy Metals(Izmir Institute of Technology, 2019) Gülmez, Yekta; Tekin, Hüseyin Cumhur; Bulmuş, VolgaHeavy metals are part of Earth’s crust and the significant problem is accumulation of them in the ground waters. They have harmful results to body even they are at low concentration. Arsenic is one of the heavy metals which cause serious health problems such as; cancer, diabetes etc. Most of the developing countries are lack of detecting arsenic amount into drinking water. Therefore, especially in Bangladesh 1 out of 100 people die due to arsenic related cancer. According to World Health Organization, the maximum arsenic concentration in the drinking water must be 10 μg/L but the concentration amount reaches 50 μg/L or more at the developing countries. However, existing methods cannot detect arsenic at this range or the ones that can detect arsenic at the standard have so high prices that developing countries cannot afford. Therefore, the aim of this project is to develop a device for arsenic detection. In this thesis, a microfluidic chip was developed, and gold nanoparticles was used to detect arsenic in samples using absorbance spectroscopy. The detection principle was designed based absorption of arsenic and then gold on thiol-modified surfaces. The different concentration of arsenic samples was injected into microfluidic chip and 1.3 mg/L arsenic concentration could be detected. Then, syringe pump was added to the system and flow applied. As a result, the developed microfluidic chip is able to detect arsenic at 2.2 μg/L.