LEE- Nano Bilim ve Nano Mühendislik Lisansüstü Programı

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http://hdl.handle.net/11527/19415

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Design and simulation of a microfluidic biochip for optic detection with derivatized microbeads and the biochemistry of learning

(Fen Bilimleri Enstitüsü, 2020) Tüysüz, Tuğçe ; Alptürk, Onur ; Uludağ, Yıldız ; 630291 ; Nano Bilim ve Nano Mühendislik

Microfluidic systems are an important technology suitable for a wide range of applications due to their rapid response capabilities, low cost and, small amounts of sample need. Microfluidics tries to overcome difficulties in conventional assays in medical diagnosis. The combination of biosensors and microfluidic chips increases the analytical capability to extend the scope of possible applications. In this thesis, two types of microfluidic modeling were designed for biomedical applications. The first design is a bead derivatized sensor in a microfluidic chip to detect biomarkers. The second model is designed to observe the effect of α-syn protein which constitutes the communication of two nerve cells through channels in the microfluidic system and the long term potentiation. In Project 1, Integrated affinity sensors within microfluidic platforms show great interest in life environmental and science analytical science applications. They are generally placed in the base of a fluidic flow channel on which an analyte solution is passed. The analyte detection on the sensor depends on the event of a recognition-binding, most generally antigen-antibody, for which the recognition molecules are attached to the surface of the sensor for the analyte. The analyte -recognition molecule complex is detected on the sensor. The integration of bead-based immunoaffinity assays in microfluidic chips has recently become an area of interest for many researchers. Integrated affinity sensors inside of the microfluidic structures have many advantages which are low-cost, rapid, highly specific detection and sensitivity. In this study, the microfluidic system has been designed with different substrate patterns in the continuous flow of phosphate-buffered saline (PBS), and microbeads were examined. Functionalized microbeads have been used as biomolecules to enhance the affinity of biomarkers and for high sensitivity. Microchannel was patterned with square pyramid well array, conic well array, triangle pyramid array, and the each microbeads made of polystyrene were placed into the each microwell; PS beads were simulated with different flow rates. Initially, PBS was utilized to simulate blood serum, and PS nanoparticles, functionalized and fluorescently labeled nanoparticles that allow detection of biomarkers, were simulated for examination by fluorescence microscopy. As a result of three different geometric well chip patterns and three different bead size simulations, it was determined that the shape of the well should be conical and the bead size should be 150 µm. The lowest cross-section flow rate of the fluid sent from the inlet of the channel with a flow rate of 300 µl was determined in conical design. This indicates that there will be more interaction with the surface compared to other patterned arrays. In Project 2, The purpose of this project is to create a biosynthetic neuron-on-a-chip to reproduce the activity of neuronal function. Neurons are the main important units of the nervous system and brain. The target of neurons is to receive sensory input from the outside world and send motor commands to the muscles. They are also responsible for converting and transmitting electrical signals in every step that takes place in this cycle. Neurons communicate with electrochemical signals. Therefore, electrical and chemical events must occur together for the communication of two neuron cells. It transmits a neuron signal through the axons to the dendrites of other neurons to which it connects via the axons called synapses. Long Term Potentialization is a process in which synaptic connections between neurons are strengthened by frequent activation. LTP is thought to change the brain in response to experience, thereby providing a mechanism underlying learning and memory. In the process of learning, nerve cells, the basic computing units of any nervous system, are thought to exhibit digital and analog properties. Alpha-synuclein(α-syn) proteins are of high importance to sustaining LTP in the brain. In this thesis, the most suitable platform for communication between two yeast cells and the passage of α-syn proteins through channels is optimized and designed. It refers to nerve cells in the computer environment by yeast cells in the simulation program. A channel that enables the communication of two yeast cells was designed and these yeast cells were placed in the traps located at the entrances of the channels. The activating agent was sent to produce α-syn of yeast cells in the A channel. Αlpha-synuclein protein, which is synthesized from yeast cells in the A channel, has passed through the channel and attached to the NDMA receptor in the other yeast cell in the B channel. Then, LTP was provided by activating the α-syn protein bound to the NDMA receptor in a balanced manner with Ca^+ions. Irregularity in the ratio of protein Ca^+ and α-syn prevents the formation of long term potentiation and causes Parkinson's disease. Optimization studies were carried out in microfluidic chip design. The number of channels along with the microfluidic chip, the width of chamber A and B, the width of the communication channel, the distance between communication channels, the length of yeast cells chamber, the length of yeast cells communication channel, the inlet-outlet radius of chamber A and B were determined. As a result of these determinations, it was observed how each parameter affects diffusion. The greater diffusion indicates that the amount of α-syn protein passes more from chamber A to chamber B. It was also observed that some parameters started diffusion earlier. Therefore, it enabled more yeast cells to interact. Computer modeling and simulation were applied as a very useful tool for improvements in the design of microfluidic chip geometry, as well as for the optimization of the technological and functional parameters. In this thesis, COMSOL Multiphysics, which is the most used in microfluidic systems, is used in two projects for microfluidic chip design and simulations within the designed chip.
Development of antibacterial coatings on titanium based biomaterials

(Lisansüstü Eğitim Enstitüsü, 2022) Aydoğan, Dilek Teker ; Çimenoğlu, Hüseyin ; 723039 ; Nanobilim ve Nanomühendislik

Since the average human life is getting longer, research on long-lasting and biocompatible biomaterials has become more common. A biomaterial is a material that can replace any damaged tissue or organ and therefore, it is in continuous interaction with body fluids. There are various biomaterials for different application areas. The main issues to be considered are the mechanical properties, design, and biocompatibility of the developed biomaterial. Metal and metal alloys are the most frequently preferred biomaterials and they have been used as hip, knee, and dental implants for many years. These biomaterials are also expected to show superiour biocompatibility, corrosion and wear resistance, along with non-toxicity. Especially the long-term stability of orthopedic and dental implants depends on the bonding properties at the implant-bone interface and being free of any post-operative infections due to the implant features. Titanium and titanium alloys stand out among other metallic implant materials (such as stainless steel and cobalt-chromium alloys) with their excellent mechanical properties, biocompatibility, low densitiy, high corrosion and wear resistance. The most important feature that separates titanium from the other metals is the natural oxide film layer on its surface. Even though, this stable, dense, and continuous layer provides corrosion resistance and biocompatibility to the material, but, its ability to bond to bone is quite weak. In addition, due to the toxic effect caused by alloying elements that can be released from some titanium alloys (such as Ti6Al4V), titanium alloys may fail in long-term implant applications. For this reason, numerous surface treatment methods are used to enhanced the surface features of titanium and its alloys. Micro-arc oxidation (MAO), also called plasma electrolytic oxidation, is a convenient technic that is used to produce ceramic coatings on titanium, aluminum, magnesium, and their alloys. With this method, it is possible to get thick, porous, firmly attached ceramic coatings on the surface of titanium and its alloys. In addition to these, antibacterial oxide coatings can also be obtained by adding appropriate antibacterial agents into the electrolyte used during the process. The ability to coat materials with complex shapes, using environmentally friendly chemicals, and being a cost-effective process are the prominent advantages of this method. In the scope of this study, the formation of bioactive and antibacterial oxide coatings on the surface of titanium and its alloys was carried out via MAO process. In the first chapter of the thesis, it was aimed to produce multi-layer bioactive and antibacterial coatings on the commercially pure titanium (grade 4 quality, Cp-Ti) surface, which is frequently preferred in biomedical applications, by applying the MAO process. For this purpose, samples were subjected to a base electrolyte (which is containing calcium acetate hydrate (Ca(CH3COO)2.H2O) and disodium hydrogen phosphate (Na2HPO4)) during the MAO process. To obtain antibacterial properties on the coating surface silver acetate (AgC2H3O2) was added into the base electrolyte (the amount of silver (Ag) on the coating was measured as 4.6 wt.%). After the MAO process, a multi-layered oxide coating consisting of TiO2 (dense rutile-anatase phases) on the inner layer, and biocompatible compounds such as hydroxyapatite (HA) and calcium titanate (CaTiO3) just above oxide layer was obtained. It was observed that MAO treated samples in the base electrolyte formed biomimetic apatite structure faster in the simulated body fluid (SBF), as well as showed higher antibacterial activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) bacteria. It has been determined that the addition of AgC2H3O2 to the base electrolyte increased the antibacterial activity of the samples without sacrificing bioactivity. In the second chapter of the thesis, optimization of AgC2H3O2 amount which had been added into the base electrolyte was studied in order to avoid toxic effect of Ag without sacrificing the antibacterial effect. The MAO process has been conducted in the base electrolyte containing Na2HP04 and Ca(CH3COO)2.H2O and AgC2H3O2 was added at different concentrations. Samples treated with an electrolyte containing 0.005 mol/L AgC2H3O2 concentration showed poor antibacterial activity against S. aureus bacteria, while samples treated with the electrolyte containing 0.001 and 0.002 mol/L Ag concentrations was determined strong antibacterial activity. Based on these results, considering the possible toxic effect of Ag, 0.001 mol/L AgC2H3O2 concentration into the base electrolyte is sufficient for MAO process. It was determined that used optimum AgC2H3O2 concentration into the base electrolyte caused 1.14% Ag on the oxide coating surface after MAO process. Cell culture experiments were performed using SAOS-2 (a human primary osteogenic sarcoma cell line) to understand the effect of the amount of silver measured from the coating surface on the cell. As a result, it was observed that the amount of Ag determined in the oxide coating did not prevent cell growth however retarted it and also showed high antibacterial efficiency against S. aureus bacteria. In the third chapter of the thesis, after determining the optimum amount of AgC2H3O2 concentration in the base electrolyte containing Ca(CH3COO)2.H2O and Na2HPO4 in the previous section, the biological properties of the oxide coating formed in the MAO process using Ti6Al4V alloy were investigated by biofilm formation and cell culture experiments. After adding 0.001 mol/L AgC2H3O2 to the base electrolyte during the MAO process, it was determined that there was 0.76 wt.% Ag on the oxide coating surface. It was observed that the alloying elements in the Ti6Al4V alloy effect the structure of the oxide coating formed by the MAO process conditions. The low amount of Ag measured from the coating surface was explained by the precipitation of Ag particles mostly around the pores of the thick TiO2 layer, and the formation of a thick HA layer on it. The presence of Ag particles between TiO2 and HA layer effected Ag release behavior in simulated body fluid (SBF). Compared with Ag-free coatings, the presence of 0.76 wt. % Ag in oxide coatings exhibited antibacterial activity to some extent against Streptococcus mutans (S. mutans) bacteria and did not adversely effect the proliferation of SAOS-2 cells. However, in order to obtain enhanced antibacterial efficiency, higher amount of silver must be incorporated into the MAO coating. In the fourth chapter of the thesis, the structural features, Ag release behavior and bioactivity of HT treated oxide layer with different amounts of Ag nanoparticles formed via MAO process on Ti6Al7Nb alloy have been investigated. While MAO process was applied in the base electrolyte (containing (Ca(CH3COO)2.H2O) and (Na2HPO4)) with and without the addition of AgC2H3O2 to obtain oxide layer, HT treatment was performed in an alkaline solution (pH = 11) at 230 ºC to improve bioactivity. After the MAO process, HA structure with a low degree of crystallinity and TiO2 layer containing rutile and anatase structures was formed on the surface. Nano-sized Ag particles were detected on the coatings formed over Ag incorporated oxide coatings. Moreover, higher AgC2H3O2 concentration in the base electrolyte caused a higher number of Ag nano-particles in the MAO coating. Afterwards, application of the HT treatment fabricated an 1-2 m thick exterior surface layer that is composed of nano-rod TiO2 and hexagonal HA crystal morphologies on oxide surface and increased degree of HA crystallinity. When samples treated with MAO and MAO+HT are compared, it was observed that HT treatment not only accelerated biomimetic apatite accumulation on Ti6Al7Nb alloy but it also eliminated the negative effect of Ag, which delayed the apatite formation on the MAO coatings. In addition, unlike the oxide coatings formed with MAO, HT treatment considerably reduced the amount of Ag released from the oxide coating into the SBF solution. As a result, thick, microporous and multi-layered oxide coatings containing bioactive components have been successfully produced on the surface of titanium and its alloys, which are frequently prefered in implant applications. Generally, various additives such as ions or particles can be introduced into the electrolyte to fabricate antibacterial oxide coatings with biocampatible properties via MAO process. Within the scope of the thesis, studies have shown that oxide coatings which were fabricated using different amount of Ag agent in the base electrolyte exhibited antibacterial efficiency on bacterial cultures and bioactive components support the bioactivity. Especially in obtaining antibacterial coatings, the importance of Ag agent amount in the base electrolyte has been demonstrated by antibacterial tests. In addition to the MAO process, when MAO process is combined with HT treatment, it is possible to fabricate highly bioactive surfaces without obtaining multi-layered coatings on the substrates. Moreover, Ag agent has been introduced into the oxide coating to give antibacterial properties to the surface. The Ag agents and their amounts is still one of the biggest concerns for health. In the future studies, the living body applications (in vivo) will guide the evaluation and development of short and long term effects of TiO2 based bioactive and antibacterial coatings fabricated with MAO process and HT treatment.
Development of interlayer based thin-film nanofibrous composite membranes adjusted by functionalized carbon nanotubes for effectual water purification

(Graduate School, 2022-01-20) Arabi, Seyedehnegar ; Gökoğlu Zeytuncu, Bihter ; 513191019 ; Nano Science and Nano Engineering ; Nano Bilim ve Nano Mühendislik

Drinkable water supply is one of the fundamental human prerequisites all over the world. Due to the population expansion, the changes in the global climate, and water degradation, The requirement for freshwater increases with time around the world. Based on the reported calculations, except for 2.5% of existence global water, which is classified in the potable water range for humans, 70% of the remaining freshwater (FW) is frozen. Due to recent reports, more than 700 million people worldwide have not been accessed clean water. Ascribed to the severe FW demands, which have been observed in some developing countries and sub-Saharan African countries, the water treatment technologies must be enforced in these overwhelmed countries. Nanoscience and nanotechnology are other novel solutions to water treatment technology problems. Ascribed to nanomaterials properties, including high aspect ratio, reactivity, adjustable pore volume, hydrophilic, hydrophobic, and electrostatic interactions, they have been utilized in numerous types of applications. Multiple types of batteries, optics, fuel cells, sensors, electrics, thermoelectric devices, pharmaceuticals, and cosmetics are some industries that have used nanomaterials to improve their products. Moreover, nanotechnology has been performed in economically unconventional water sources, resolving contaminant-free water for humans, and suggesting many solutions to alleviate needs with regard to reducing scarcity or removing contamination. For example, there are filters that remove pesticides from drinking water using nanochemistry. At the same time, due to the multidisciplinary feature of membrane technology and essential advantages of membrane science technology, such as being clean energy, the ability of energy-saving, high-quality products, and system versatility, it has been applied in multiple applications. The power of membrane technology to replace other purification systems, including distillation and ion exchange systems, has been distinguished as other membrane technology's benefits. Furthermore, because of the forward osmosis (FO) and nanofiltration (NF), membranes' excellent features such as energy conversion, low-cost procedure, and high water recovery ability have received much more attention in wastewater treatment, water purification, and brackish water desalination over the last decade. The electrospinning device generally consists of a high voltage power supply, a supply unit, and a grounded collector. The feed solution is sent to the feed end by a pump. An electric field is created by a high-voltage power supply connected to the supply terminal. As the applied voltage increases, the electrical forces overcome the viscoelastic forces of the solution at the feed end. After a critical voltage, a jet formation is observed at the supply end. The bubbler solution diffuses in the electrical field and accumulates randomly on the collecting plate in microscopic diameter fibers. The solvent in the solution evaporates before or after the fibers are collected in the container. Among the factors affecting the nanofiber production by electrospinning method are the type of polymer to be obtained, conductivity and dielectric properties, the solvent used, the viscosity of the feed solution, the distance between the feed unit and the collector, the feed rate (flow rate), the voltage used. More than 100 polymers can be electrospinning, and the most preferred among these polymers in nanofiber membrane construction are; polyacrylonitrile (PAN), poly(ethylene oxide) (PEO), polystyrene (PS), Nylon-6, poly(vinyl alcohol) (PVA), poly(ε-caprolactone) (PCL) and polycarbonate. PVA is a water-soluble, non-toxic, and biocompatible polyhydroxy polymer with high chemical resistance and thermal stability among these polymers. It is known that PVA easily interacts with other organic and inorganic materials. However, PVA's applications are limited due to its hydrophilic nature. Therefore, it must be modified to minimize dissolution, mainly used in aqueous applications such as filtration and adsorption. Chemical crosslinking of PVA nanofibers with dialdehydes, dicarboxylic acids, or dianhydride is advantageous in becoming insoluble in all solvents and increasing their thermal and chemical properties. Polymeric thin-film composites are essential types of compounds applied in various practical applications, including surface coatings and modifications, adsorption and immobilization, membrane technologies, and low surface energy interfaces. Also, the inherent internal concentration polarization (ICP), which causes osmotic driving force's decline, is another major problem of conventional TFC membranes which has been challenged for several years. Moreover, biological fouling is another disadvantage that limits the conventional TFC membranes' performance in multiple usages. Due to the biological fouling of TFC type membranes, microorganisms and micropollutants, which require reproduction, easily stick to the membrane's surface and cause a significant reduction of FO membranes' stability and durability. In order to break the trade-off between permeability and selectivity of TFC membranes and obtain membranes with balanced permeability and rejection performance and excellent durability, triple-layered thin film composite (TFC) forward osmosis (FO) membranes fabricated by introducing an interlayer on the porous electrospun membranes before interfacial polymerization (IP) procedure. Introducing an interlayer on the electrospun substrate overcomes the conventional TFC membranes' limitations and causes synthesizing controlled polyamide (PA) layer and improving the IP process. Carbon nanotubes (CNTs), cellulose nanocrystal, and cadmium hydroxide nano-strands are some of the nanomaterials that have been introduced as an interlayer in TFC types of membranes. The adopted interlayers develop the barrier selective layer's structure and control the IP procedure. Due to the CNT's ideal characteristics, such as large specific surface area (SSA) and excellent mechanical stability, CNTs are distinguished as superior nanomaterials that have been performed as interlayers in TFC membranes. Triple-layered TFC membranes with CNT interlayer enhance the PA layer formation with defect-free and ultrathin structure and promote the membrane's permeation ability, even rejecting monovalent and divalent ions. The membranes were utilized in this research are thin-film nanofibrous composite membranes with hydrolyzed multi-walled carbon nanotubes (MWCNTs) as an interlayer. First of all, MWCNTs had been acid-treated in the presence of sulfuric (H2SO4) and nitric (HNO3) acids. Secondly, the different amounts of hydrolyzed MWCNTs were dispersed in the distilled water using ultrasonication and then introduced as an interlayer onto the porous polyacrylonitrile (PAN) electrospun membranes by vacuum filtration procedure. Finally, TFC membranes were prepared to utilize the IP procedure. In this study, MPD and TMC solutions had been performed as aqueous and organic phases to begin the IP proceeding. The prepared membranes had been tested in dead-end filtration systems to investigate the membranes' performance in salt rejections. Also, these interlayer-based TFC membranes had been applied in the dye removal from industrial wastewaters and compared to the conventional TFC type of membranes in their filtration performance.
Development of microfluidic based single cell capturing systems for early detection of diseases

(Fen Bilimleri Enstitüsü, 2020) Altınağaç, Emre ; Kızıl, Hüseyin ; 650348 ; Nanobilim ve Nanomühendislik Ana Bilim Dalı

It is known that cancer cells in the bloodstream are quite low compared to other cells in the blood. Microfluidic based systems have been studied for diagnosis, follow-up of the disease and new drug tests to be performed on this disease. A microfluidic based system with two successive regions for separation and analysis has been developed. In the first region, the target cell type is differentiated from a complex mixture containing multiple cells by dielectrophoresis, which allows an insulating particle to be polarized under an electric field. Since different cell types can be polarized at different rates under the same electric field, this method allows the separation of the cells from each other under suitable conditions. In this study, a microfluidic system consists of two consecutive regions, namely the separation and analysis regions are demonstrated. In the first region, the target cell type is separated by dielectrophoresis from a complex cell mixture. The target cells collected in the first region are continuously transferred to the second region and are captured in a single cell array formation at the hydrodynamic capture stations placed on the measuring electrodes. Impedance analysis was performed to establish a platform for detection and drug screening. While both regions were integrated on a single chip in the final device, each region were examined separately during our study. The results of impedance analysis obtained from different cells based on different medium conductivities with a frequency range of 0.1kHz – 500kHz are presented here. We recorded impedance measurements at stations where cells were individually captured before and after cell entrapment. Experimental results are divided into cases where the conductivity of the medium is higher and lower than the cell conductance. Overall magnitude of impedance shift is significantly higher when the medium conductivity is lower than the cell conductance. When all results are evaluated, it can be seen that depending on the target cell type, an optimum medium conductivity and frequency range can be selected so as to obtain the measurement result with the highest sensitivity. A microfluidic cell culture platform, named as organ-on-a-chip in the literature, has been increasingly studied over the last few years to mimic tissue and organ-level physiology, containing a membrane with a continuous and porous structure inhabited by living cells, and with microfluidic channels to mimic the mechanical effects and to supply the necessary nutrients. These platforms create tissue and organ environments that are not possible with traditional 2D or 3D culture systems, and enable real time imaging and analysis of biochemical, genetic and metabolic activities of living cells. In this project, present fabrication techniques of microfluidic devices are used for the fabrication of organ-on-a-chip platforms. The tissue structure was imitated by coating a single-layer cell on the upper and lower sides of the membrane in the structures of the renal chip tubules and lung alveoli on organ-on-a-chip platforms. The cell viability was characterized by MTT test and the cell viability was maintained by providing oxygen, carbon dioxide and nutrient exchange under incubation conditions by means of nutrient medium flow provided into the upper and lower channels, and the barrier property of the cell tissue was measured by electrical resistance (TEER) measurements. The viability of the renal tubules cultured in the microfluidic system between 0-48 hours was recorded by MTT assay. TEER results showed that the tight-junctions of cell tissue were different under static and dynamic conditions in the kidney-on-chip systems. The results obtained by MTT test to measure cell viability were in agreement with TEER and the viability of kidney cells was higher in 48 hours under dynamic conditions compared to static conditions. With the successful culturing of two different cell types under static conditions in lung-on-chip systems, their viability and cell barrier resistance values were recorded by TEER measurement for 0-48 hours. The results obtained by MTT test and TEER measurements showed that lung cells under shear stress and mechanical stress had higher viability than cells under static conditions.
Fabrication of nanostructured metal oxide materials and their use in energy and environmental applications

( 2020) Çalışır, Mehmet Durmuş ; Kılıç, Ali ; 634370 ; Nanobilim ve Nanomühendislik Ana Bilim Dalı

Metal oxides are considered to be the most vital material class and they show unique chemical, physical and electronic properties when produced on the nanometer scale. In this context, metal oxide nanomaterials are of increasing importance in many industries and are used in applications such as sensors, medical technologies, energy, water treatment, and personal care products. In this thesis, the fabrication of nanostructured metal oxide materials and their use in energy and environmental applications which have strategic and vital importance are focused. The optimization of process parameters for the production of metal oxide nanostructures via industrial-scale production methods and application-oriented modifications of the properties of metal oxides via controlling their size and composition have been realized. Solar energy is an environmentally friendly technology that allows direct energy production from the sun. Perovskite solar cells (PSCs) have been studied intensively in the last decade and they constitute the energy leg of this thesis. In this context, the effects of metal oxide nanomaterials on perovskite cells performance were investigated. The performance of planar and mesostructured PSCs was compared, while all the experimental studies for the production of highly-efficient PSCs were given in detail. The mesoporous architecture allows the deposition of denser perovskite films than planar architecture due to the high porosity. Though higher efficiency was expected due to effective absorption of incoming light, XRD results showed that PbI2 - perovskite conversion in the mesoporous structure was more difficult. The average efficiency of the cells produced with mesoporous architecture was 15.07 %, which was just 0.9 % higher than the planar one. As can be deduced from the absorbance curves and IPCE analysis, this is because of the mesoporous structure showing more absorbance in the 400-600 nm wavelength range resulting in more photocurrent. However, due to the small difference in efficiency and fewer steps in the planar architecture, it was found more viable for industrial scale-up. Air pollution is one of the most critical environmental problems today, and filtration is one of the practical solutions to remove the pollutants, especially particulate matter within the air. However, exhaust gases might be at high temperatures and require high-temperature resistant filter materials. The use of ceramic-based, fibrous filter elements in filtration applications will enable the production of highly efficient filters with high-temperature stability. In this context, SiO2 nanofibrous mats were produced from sol-gel based solutions via centrifugal spinning (CS) and solution blowing (SB) methods. According to results, centrifugally spun SiO2 fibers were found more flexible where fibers have diameters between 1 and 1.5 microns. Solution blown silica fibrous mats consisted of thinner fibers but have denser bead and droplet defects. Besides, due to the fibrous mats obtained by SB had a dense-packed structure it showed more shrinkage during heat treatment. XRD results show that all fibers have an amorphous SiO2 structure after heat treatment at 600°C. According to the porosity analysis, the solution blown and centrifugally spun SiO2 samples had the lowest pore diameters of 5.2 and 10.5 microns, respectively. Moreover, the effects of SiO2 precursor solution concentration on spinnability in the CS method, the diameter of SiO2 fibers, and filtration efficiency were investigated. Contrary to expectations, the average diameter of the fibers has been found to decrease with increasing precursor concentration a result of reduced viscosity of the spinning solution. While all the produced fibers are incredibly flexible, the highest filtration efficiency (43.35 Pa pressure drop and 75% particle capture efficiency) was obtained from the sample that produced from 15 wt.% TEOS added solution. Due to excellent thermal stability and high mechanical performance of centrifugally spun SiO2 fibrous mats they have the potential as filter materials for hot air filtration applications. Photocatalyst-based purification techniques emerge as a solution for recovery of used water. While the studies focused on the development of photocatalyst material with visible light activity, there is also a need for the development of photocatalyst geometries that can be easily separated from treated water. Although nanoparticulate morphology offers high surface area, it is difficult to remove them from treated water. On the other hand, TiO2 is one of the most studied materials among the photocatalysts due to its high photocatalytic activity, photostability, chemical inertness, and low-cost. TiO2 fibers were fabricated via CS and subsequent calcination methods. The effects of precursor concentrations on fiber diameter, surface area, and photocatalytic activity were investigated. Results showed that the fiber diameter was increased from 0.65 to 1.2 µm with increasing precursor content. The calcined fibers consisted mainly of anatase and also a minor amount of rutile phases. PVP used as the carrier polymer for precursor solution also behaved as a nitrogen source for TiO2 fibers during calcination. The slight shift of peaks in XRD, the presence of nitrogen in XPS spectrum and EDX mapping, and the enhanced visible-light photocatalytic response were pieces of evidence for in-situ N-doped TiO2 NFs. Besides, nanoparticles (P25 NPs) were added into the spinning solution to increase the surface area by producing nanoparticle in nanofiber structure, and it was also used as a reference sample. According to the results of photocatalysis tests, the surface area is the dominant factor for photocatalysis under UV illumination and the optical bandgap is the critical factor for the tests performed under visible light illumination. Moreover, recycle analysis showed that fibrous photocatalysts were easily separated from the treated water. In this regard, the fibrous TiO2 was emphasized as the best visible-light photocatalyst, losing only 14% of its degradation performance after the 3rd use. The effect of Al and Li doping on the crystallinity, fiber diameter, optical bandgap, and photocatalytic activity of TiO2 fibers was investigated in the last part of this thesis. Al and Li doped N-TiO2 fibers were successfully produced via CS method and followed calcination. N- TiO2 showed a fiber diameter of 0.54 µm while Al- and Li-doped N- TiO2 had a diameter of 0.94 and 1.15 nm, respectively. While the crystal structure of N-TiO2 transformed from major anatase and minor rutile phases to the only anatase in the case of Al- and major rutile and minor anatase phases in the case of Li-doped N-TiO2. Additionally, band gap values were calculated as 3.00, 2.94, and 3.14 eV for N- TiO2, Li- and Al-doped N- TiO2, respectively. For the photocatalysis tests conducted under UV-light, the most efficient sample was the nanoparticulate TiO2 due to its high surface areas, while all-fibrous structures showed similar activities, which were nearly two times higher than the activity of nanoparticulate TiO2 under visible-light.
Formation and structural properties of water induced structures at graphene/mica and graphene/CrxO/glass interfaces

(Graduate School, 2021-10-08) Novruzov, Orkhan ; Gürlü, Oğuzhan ; 513171019 ; Nano Science and Nano Engineering ; Nano Bilim ve Nano Mühendislik

Water behavior at interfaces has great importance. Especially molecularly thin layer water or nanoconfined water. Nanoconfined water properties are different from bulk ones. Studying nanoconfined water properties have fundamental importance in biology, material science, nanofluidics, tribology, and corrosion. Nanoconfiment materials are carbon nanotubes and layered two-dimensional materials or Van der Waals crystals. In this thesis, we studied water interaction behavior with graphene/water/CrxOy/glass and graphene/mica systems. For this purpose, we needed the following devices: Optic microscope with the isolated system, PVD system, graphene heater, and materials like CVD-grown graphene, muscovite mica, soda-lime glass, and chromium granulates. Firstly, we started with graphene/water/CrxOy/glass system. We did thermal evaporation of chromium using PVD system that was assembled in our laboratory. As a substrate, we used soda lime microscope slide glass(INTROLAB). Chromium thin-film on glass samples was produced. The thickness of thin-film chromium was varied. We transferred CVD-grown graphene onto chromium thin-film glass with the wet transfer method, then annealed it in a tube furnace around 450°C degrees under atmospheric ambient conditions for approximately 40 minutes. As soon as annealing finished we quickly transferred produced sample into a container full of silica gels to preserve from environmental humidity. We reduced humidity within enclosed boxes in which an Optical light microscope stayed for study samples under controlled humidification. We took optic data before, during, and after the humidification process. Secondly, our second system for research was graphene/water/mica. Again as in the graphene/water/CrxOy/glass system, we used CVD-grown graphene and V2grade muscovite mica(Ted Pella). Using scotch tape we cleavage mica several times then CVD-grown graphene was transferred onto it using the wet transfer method. We preserve graphene/mica samples in a container full of silica gels. We studied them with two methods: First under the optic microscope in the isolated box and second using the graphene heater. We reduced humidity to 9% in the isolated box using silica. In the case of the graphene heater, we managed to heat up nearly 200°C. We observed fractal in graphene/CrxOy/glass system but due to non-homogeneous deposition of chromium fractal formation was inconsistent. In case of graphene/mica system observation of de/rewetting process was not possible even though we reduce humidity. The graphene heater was functional, the reason that we couldn't use it was a poorer resolution of the graphene/mica system. Otherwise, observation de/rewetting graphene/water/mica with the optic microscope is challenging.
Mixed-anion photochromic yttrium oxyhydride and gadolinium oxyhydride: Research and applications

(Graduate School, 2021-02-04) Baba, Elbruz Murat ; Zayim, Esra ; Karazhanov, Smagul ; 513152002 ; Nano Science and Nano Engineering ; Nano Bilim ve Nano Mühendislik

are-earth metal oxides and hydrides are the focal point in literature, promising various high demand solutions in industry and everyday life. Recently, a multi-functional, multi-anion material class called "rare-earth metal oxyhydrides" were shown to be synthesized as a thin film under ambient temperatures with photochromic properties. Oxyhydrides present high level of flexibility for material development through various combination possibilities having multi-anions. The newly realized possibility of ambient temperature thin film synthesis possibility of rare-earth metal oxyhydrides attracted high attention from literature but, there is little to no data is available in conventional databases for rare-earth oxyhydrides. Combination of the oxyhydrides being an under-developed class of materials and the promise of presenting important solutions for a high demanding era we live in, oxyhydrides is an excellent topic to research. In 2011, the synthesis of yttrium hydride thin film in room temperature with wide-spectrum transparency using only one step deposition process was shown. Originally, this research started to search for an alternative material for solar cells but, evolved into another dimension when the material was realized to be a highly responsive photochromic material that can modulate in wide spectrum. The material attracted high attention from literature and initially named as "oxygen containing yttrium hydride". However, it was later found through synchrotron measurements that this material is belong to the emerging class of materials; rare-earth metal oxyhydrides. When exposed to air, yttrium dihydride (YH2) and gadolinium dihydride (GdH2) films turn into insulating and transparent yttrium oxyhydride (YHO) and gadolinium oxyhydride (GdHO), respectively. Oxidation in air, hence bandgap, can be controlled by deposition parameters. MHO (M; rare-earth metal) photodarkens when illuminated with light of adequate energy and intensity, recovers (bleaching) when stored in dark. Photochromic rare-earth metal oxyhydride knowledge and know-how was established around synthesis method, band-gap engineering, optical properties, anion sites in the lattice etc. but the photochromic mechanism and environmental effects either yet to be understood or never even investigated before the present thesis work has been started. Also, yttrium was the only rare-earth element that was shown to have photochromic properties and investigated. Especially the knowledge gap over the interaction of photochromic oxyhydrides with the environment, prevented the realization into a product that sought heavily in industry. Therefore, in the present PhD thesis the interactions of the photochromic rare-earth metal oxyhydride thin films with the environment were first and foremost investigated. This endeavor resulted with solutions that enabled product development. Furthermore, contribution to the knowledge of photochromic rare-earth metal oxyhydrides by developing and studying at least one more rare-earth element next to the yttrium was also targeted. The studies showed that photochromic rare-earth metal oxyhydride thin films interacts with environment heavily. Additionally, we have published one article in Physical Review Materials that tries to shine a light to the understanding of the rare-earth metal oxyhydride photochromic mechanism, related to the environmental interaction: "Light-induced breathing in photochromic yttrium oxyhydrides". The studies showed that during the photodarkening/bleaching cycle of yttrium oxyhydride, material releases/intakes oxygen following lattice contraction/expansion, respectively. We coined the term, breathing, after the accordion-like structural process of yttrium oxyhydride based on oxidation. The article was selected as an editor selection and featured in Physics magazine. Based on these studies, stable IGUs which has been long sought since 2016 was able to be manufactured. Another contribution for the explanation of the photochromic mechanism of yttrium oxyhydride thin films published in Physica Status Solidi Rapid Research Letters with the title of "Temperature-dependent photochromic performance of yttrium oxyhydride thin films". In this article, we have presented the photochromic kinetics of yttrium oxyhydride thin films studied between 5-250K and presented a new approach which would enable new questions. The second part of the PhD thesis plan was contributing to the knowledge of photochromic rare-earth metal oxyhydrides by at least one another rare-earth element. Gadolinium was selected as a member of the rare-earth elements for study for having similar chemical properties and widely accepted by the nuclear industry for large neutron capture diameter. In the span of a year, the production know-how and knowledge related to gadolinium oxyhydride thin films were elevated also. One article was published in the journal Molecules that shows the post-deposition oxidation is related with the preferential lattice orientation which controlled by the deposition parameters: "Preferential Orientation of Photochromic Gadolinium Oxyhydride Films". Additionally, another article based on the environmental interaction of gadolinium oxyhydride thin films will be submitted in an international journal in 2020. Environmental effect on rare-earth metal oxyhydrides was investigated further by systematic study of yttrium oxyhydride thin films under atmospheres with varying relative humidity levels. Correlation between the relative humidity levels and photochromic kinetics was observed and microstructure formation that causes the delamination was shown. One article based on the results is under progress and planned to be submitted in 2021. In the last part, applications developed during this thesis based on yttrium and gadolinium oxyhydride thin films were presented. First, photochromic kinetics of stable IGUs based on yttrium oxyhydride were presented. However, the properties photochromic rare-earth metal oxyhydrides present is much wider than only window applications as a result of their multi-anion nature. Lastly, photocatalytic properties of photochromic gadolinium oxyhydrides were also shown.
Synthesis of folate receptor 1 targeted dye-conjugated peptides for use in positron emission tomography imaging systems

(Graduate School, 2022-01-26) Cin, Derya ; Alptürk, Onur ; Yılmaz, Özgür ; 513191022 ; Nanoscience and Nanoengineering ; Nano Bilim ve Nano Mühendislik

Nowadays, it is tried to find solutions for human beings to have a long and high-quality life, increase the number of studies in the field of health, and detect diseases that become difficult to treat with their progress. Cancer is one of the first causes of death statistics in official records in the world and Turkey. It is known that the diagnosis of cancer is difficult and takes time, and the number of cases continues to increase rapidly day by day. Because of the metabolism change in cancer cells, the cells continue to grow and divide instead of dying. Cancer factors; inherited mutations can be internal, such as hormones, or acquired environmental, such as carcinogens, radiation, infectious organisms, and lifestyle. By imaging the changes caused by cancer in cells, information about the stage of cancer can be obtained. Cancer researchers want to detect cells where cancers develop, identify biomarkers of cancers early, and create treatment plans for cancer. Proteins produced by tumor cells can be used as biomarkers to evaluate disease processes. Molecular imaging (MI) aims to combine patient and disease-specific molecular information and is an interdisciplinary area covering a wide range of sciences when is used in the diagnosis and treatment of diverse disease genres. For this purpose, targeted cell-specific chemical biomolecules are delivered to the organism by labeled radioactive isotopes. The imaging method to be utilized varies specifically according to the disease state. Positron emission tomography (PET), which has become more advanced with the integration of scanners such as computerized tomography (CT) used in the imaging of cancer, is one of the several imaging methods widely used in the diagnosis of cancer today. Since radioisotope imaging agents are required for imaging in PET devices, studies for their development are increasing day by day. Peptides are used as ligands/agents in imaging cancer imaging, thanks to their properties such as high selectivity and high affinity, ease of synthesis and chemical stability, quick removal from blood, and low immunogenicity/safety for cell surface proteins. Due to the metabolic rate of cancer cells, more folic acid is produced in these cells than in normal healthy body cells, and this uncontrolled increase has led to its use in cancer imaging studies. Peptide-based imaging agents are used for molecular imaging by binding to target cancer receptors such as Folate Receptor 1 (FOLR1) of tumor cells. Molecules that can bind to the FOLR1 receptor with high sensitivity and affinity were synthesized by the Solid Phase Peptide Synthesis (SPPS) method. The peptides KWGFR, KLWWN, KFLSW, KWIAG, KWSYW, KGWRN, and KSYFA were selected from the peptide library and successfully synthesized. Reversed-Phase High-Performance Liquid Chromatography (RP-HPLC) was used to purify the peptides and Liquid Chromatography-Mass Spectrometry (LC-MS) was utilized for peptide characterization. Finally, the imaging agent will be obtained by conjugating the peptide-based signaling agent labeled with the 68Ga isotope.

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