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; Yağmurcukardeş, MehmetWhey 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 Green Synthesis of Nanostructured Bioactive Glass for Dental Applications(01. Izmir Institute of Technology, 2023) Tüncer, Melisa; Yücesoy, Deniz Tanıl; Öksel Karakuş, CeydaBioactive glass is a biomaterial commonly used in dental care products and bone tissue engineering applications due to its biocompatibility, bone-forming ability, and remineralization capability. Bioactive glasses form a hydroxyapatite-like layer on dentinal tubules by releasing calcium and phosphorus ions after interaction with saliva. Bioactive 45S5 glass traditionally synthesized by wet chemical methods which require high-temperature heating and the use of a strong acid catalyst, bringing into question of the possibility of introducing toxic acid residues into the final product. Therefore, there is a need to develop environmental-friendly bioactive glass synthesis methods or to modify existing ones in a way to uplift their environmental friendliness. To satisfy this need, we greenized the traditional sol-gel method by replacing the acid catalyst with an environment-friendly alternative and successfully used it for the synthesis of nanostructured 45S5 bioactive glass. First, physicochemical characterization of the synthesized bioactive glasses was performed. Then, the apatite formation capability of bioglasses were investigated in saliva. Next, the mineralization kinetics of bioglasses were tested in Ca/P buffer. In vitro toxicity tests were performed to assess the cytotoxic potential of the synthesized bioactive glass. All analyses were repeated for the traditional synthesis method for comparison purposes. The results confirmed that green synthesis is more advantageous in terms of bioactivity and functionality required for dental applications. Increasing the safety and functionality of bioglass at the same time during the production phase has critical importance for ensuring the sustainability of current applications as well as creating new uses in the biomedical fieldMaster Thesis A Real-Time 3d Scanner System Developed With Combined Usage of Active Triangulation and Time of Flight Sensors(01. Izmir Institute of Technology, 2023) Şi̇mşek, Burak; Gümüşteki̇n, ŞevketBu çalışma, aktif üçgenleme ve uçuş zamanı sensörü teknolojilerini birleştiren gerçek zamanlı bir 3 boyutlu tarayıcı sisteminin geliştirilmesini ve değerlendirilmesini sunmaktadır. Bu araştırmanın amacı, nesnelerin hassas 3 boyutlu modellerini yakalayabilen sağlam ve verimli bir sistem tasarlamaktır. Önerilen sistem, yapılandırılmış ışık desenlerinin hedefe yansıtılmasını ve yansıyan desenlerin bir kamera kullanılarak yakalanmasını içeren aktif üçgenlemeyi kullanır. Ek olarak, ışığın hedefe gidip geri gitmesi için geçen süreyi ölçen bir uçuş süresi (TOF) sensörü dahil edilerek derinlik bilgisinin elde edilmesi sağlanır. Sistemin uygulanması donanım bileşenlerinin, kalibrasyon prosedürlerinin ve yazılım algoritmalarının entegrasyonunu içerir. Donanım kurulumunda yüksek çözünürlüklü bir kamera, lazer projektörler ve bir TOF sensörü bulunur. Kamera, projektör ve TOF sensörü arasında doğru eşleşmeyi sağlamak için kalibrasyon teknikleri kullanılır. Elde edilen verileri işlemek ve tam bir 3 boyutlu model oluşturmak için nokta bulutu kaydı ve yüzey yeniden yapılandırması gibi çeşitli hesaplama algoritmaları kullanılır. Geliştirilen sistemin performans değerlendirmesi, farklı karmaşıklık düzeylerine sahip farklı nesneler üzerinde yapılan testleri içermektedir. Sonuçlar, sistemin ayrıntılı 3D modelleri gerçek zamanlı olarak yüksek doğruluk ve çözünürlükle yakalama yeteneğini göstermektedir. Sistemin ortam aydınlatması ve nesne yansıması gibi çevresel faktörlere karşı dayanıklı olduğu görülmektedir. Bu çalışmanın bulguları, gerçek zamanlı 3 boyutlu model edinimi için pratik ve etkili bir yaklaşım sunarak 3 boyutlu tarama alanına katkı sağlamaktadır. Geliştirilen sistemin hızlı ve hassas 3B tarama işleminden faydalabilecek tüm araştırma ve endüstri alanlarında uygulanma potansiyeli vardır.Master Thesis Utilization of Graphene and Mos2 for Volatile Organic Compound Sensor Applications(01. Izmir Institute of Technology, 2023) Duran, Tuna; Büyükçakır, Onur; Şahin, HasanThe novel 2D materials such as graphene and transition-metal dichalcogenides have already shown impressive volatile organic compound (VOC) gas monitoring performances as in sensitivity, limit of detection and response time. This thesis discusses the experimental-theoretical examination of optical, electronic and morphological properties of novel 2D materials and their utilization in VOC gas sensor field, by means of several characterization techniques and density functional theory (DFT). Aside from the basic familiarization with the experimental and theoretical methodology in Chapter 2, examination of the functionalization of exfoliated MoS2 using DDT (1-Dodecanethiol) in Chapter 3, which eventually led to a research paper. The DDT treatment is incorporated into the NMP (N-methyl pyrrolidone) exfoliation procedure, resulting in successful functionalization as confirmed by optical, morphological, and theoretical analysis. Raman spectroscopy showed the formation of graphitic species on MoS2 sheets, with decreased sulfur-vacant sites as the DDT ratio increased. STEM and AFM data confirmed the presence of graphitic quantum dots (GQDs) on MoS2 nanosheets, while PL intensities demonstrated significant improvements in photoluminescent properties. This study enhances our understanding of surface and edge chemistry in exfoliated MoS2 and expands the possibilities for broader applications of MoS2 and GQD particles. Moreover, the attention was drawn to the investigation of the contrasting responses of graphene gas sensors fabricated using different synthesis methods, in the submitted paper explained in Chapter 4. Exfoliated graphene sensors decrease in current when exposed to methanol, while CVD graphene sensors increase in current. The differences in edge site population and electrical properties contribute to these responses. The study provided theoretical and experimental findings for an understanding of the reasons behind the inverse sensor responses of CVD and exfoliated graphene on an atomic scale.Master Thesis Investigation of Electronic, Vibrational, Mechanic and Chemicalproperties of 2d-Dlhc Cui Crystal(01. Izmir Institute of Technology, 2023) Demirok, Ali Cem; Büyükçakır, Onur; Şahin, HasanThe branch of material science and nanotechnology has recently seen the emergence of a remarkable class of materials known as 2D materials. These materials have unusual features and behaviours because of their special two-dimensional structure that separates them apart from bulk materials. One of the characteristics of 2D materials are related to their capacity to handle large mechanical deformation without fracture. Since the discovery of graphene, researchers have discovered and created an extensive range of additional 2D materials with a variety of chemical compositions and topologies. These materials can be used for energy storage, sensing, catalysis and biomedical applications. In this thesis, electronic, vibrational, mechanic and chemical properties of singlelayer CuI were investigated by using density functional theory (DFT) based first-principles calculations. It is shown that the CuI structure crystallizes in a hexagonal lattice by energy and geometry optimizations. The vibrational properties of the material were examined by phonon and Raman calculations and the structure found to be dynamically stable and there were four Raman active modes. The electronic band dispersions and corresponding density of states showed that the single-layer CuI crystal has semiconductor nature with direct band gap. Strain calculations were performed to examine the mechanical strength of the CuI crystal. Effect of biaxial strain on the electronic band structure of CuI crystal was investigated in the range of 5% and the direct band gap behaviour did not change. Biaxial and uniaxial strain calculations have shown that it is resistant to high stresses.Master Thesis Enhancement of Xylanase Activity in Xylooligosaccharide Production From Lignocellulosic Biomass(01. Izmir Institute of Technology, 2023) Şen, Şevval; Büyükkileci, Ali OğuzXylo-oligosaccharides (XOS) with prebiotic properties are obtained through xylan hydrolysis. Previously organosolv was found to be an effective pretreatment for XOS production from corncob. However, this process suffered from low XOS yields because of the limited hydrolysis of xylan in the pretreated biomass. This study was designed to test some approaches toward increasing the efficiency of xylanases on the organosolv-treated corncob. The two commercial enzymes (Shearzyme 500L and Veron 191S) used in this study showed a synergistic effect yielding higher XOS compared to single enzyme application. Partial removal of acetyl groups on the xylan in organosolv-treated corncobs enhanced XOS production significantly. The solid loading above 10% decreased XOS yield as it resulted in a highly viscous slurry that may have limited heat and mass transfer. Fed-batch addition of enzyme and biomass did not play a role in the improvement of hydrolysis. In sequential batch mode, the residual enzyme activity from the previous batch could release more XOS from the fresh biomass, though the yield was low. Addition of fresh enzymes to the previous hydrolysate together with biomass provided a more concentrated XOS solution (15.4 g/l) after the second batch. The addition of surfactants into the hydrolysis media to prevent enzyme binding to lignin did not improve XOS production. This study showed that organosolv could be considered an effective treatment for XOS production from corncob and the enzymatic hydrolysis could be improved by optimizing the conditions.Master Thesis Development of a Functional Snack(01. Izmir Institute of Technology, 2023) Maşa, Zeynep Tuğba; Korel, Figen; Sezgin, EfeNowadays, with the increasing animal food prices, many people in our country are malnourished because they cannot get the necessary protein in their bodies. Additionally, with the Corona virus, which entered our lives in 2019, many people had to struggle with various mental disorders. Although we have left behind the pandemic period, negative emotional states such as depression and unhappiness are still observed in many people today. In this direction, vegetables rich in protein were investigated and used in developing functional snacks. In this study, vegetable chips dough was prepared with 40% pea flour content 15, 17.5, 20, 22.5, and 25% radish, 20, 22.5, 25, 27.5, and 30% zucchini, and 10, 12.5, 15, 17.5, and 20% pumpkin seeds. Each vegetable chip mix was cooked at 50°C, 55°C, and 60°C with the aid of a tray dryer. The proximate analyses (moisture, ash, fat and protein), chemical analyses (antioxidant activity and total phenolic content), physical analyses (color and texture) and sensory analysis were carried out. Mixture design was created with the help of MINITAB 16.0 (Minitab Inc., State College, PA, USA) program, the results of the analyses were evaluated statistically. Based on the design, it was decided to bake thirteen different mixtures at three different temperatures and to perform all the analyzes mentioned above. As a result of the evaluation of all analyses results, the optimized sample was determined as the vegetable chips sample with 40% pea flour, 22.5% zucchini, 25% radish, and 12.5% pumpkin seeds baked at 60°C. The vegetable chips, with this mixture, were baked at 50°C, 55°C and 60°C in the a tray dryer, and in addition to all analyses, sensory analysis and antioxidant activity analysis for all samples baked at 50°C, 55°C and 60°C were conducted. The sample baked at 60°C was the most liked sample.Master Thesis Implementation of a Real-Time Teleoperation System for the Control of a Robotic Squid(01. Izmir Institute of Technology, 2023) Cezayirli, Hasan; Dede, Mehmet İsmet CanTeleoperation is defined as the remote control of a robotic system from an operational environment. Teleoperation of soft robots has been a growing research topic in recent years and there are still areas awaiting further studies. In this study, a real-time teleoperation system has been implemented for a robotic squid with four soft arms, to be used in underwater operations. The teleoperation system consists of dissimilar master-slave system kinematics, with multiple master systems and multiple slave systems. An operator utilizes two haptic devices for the manipulation of the four soft robot arms. Haptic feedback is incorporated into the system for ease of use. The slave system within the implemented teleoperation system is simulated using hardware-in-the-loop simulation. For this purpose, communication protocols from the real system are employed. In other words, the applied teleoperation system is integrated within the hardware-in-the-loop simulation of the real system. Experiments were conducted to validate that the implemented system is a real-time system and to evaluate the ease of use of the system from the operator's perspective. Additionally, experiments were expanded to measure the impact of haptic feedback on the performance of the operator. The experimental results indicate that the system is a real-time system and haptic feedback improves the system's ease of use.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 Molecular Investigation of P. Aeruginosa in the Presence of 4-Hba(01. Izmir Institute of Technology, 2023) Ekenel, Nil Hazal; Soyer Dönmez, FerdaThe escalating threat to human health posed by bacterial pathogens is increasingly attributed to the growing prevalence and distribution of antibiotic-resistant bacteria. In response to antibiotics, microorganisms have developed resistance mechanisms to elude and survive the impacts of these drugs. Phenolic acids have emerged as potent candidates in the battle against bacterial infections due to their unique property of not inducing resistance. This study focuses explicitly on 4-hydroxybenzoic acid (4-HBA), a type of phenolic acid, as an effective antimicrobial agent. Proteomics research has become an indispensable tool in the fight against antimicrobial resistance. Pseudomonas aeruginosa, a bacterium capable of existing in both planktonic and biofilm states and known to cause numerous human diseases, is of particular significance in this context. Furthermore, the study explores the molecular aspects of P. aeruginosa when exposed to 4-HBA through proteomic analysis, revealing a significant impact on protein biosynthesis as a predominantly affected function. Additionally, P. aeruginosa, the study investigates the effects of phenolic acid and antibiotic-loaded bone cements on Methicillin-sensitive Staphylococcus aureus, Methicillin-resistant Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecium, and P. aeruginosa. Remarkably, 20 percent inhibition rate is achieved after 48 hours of treatment. Moreover, the study examines biofilm produced by P. aeruginosa in the presence of 4-HBA, utilizing both the Crystal Violet assay and Scanning Electron Microscopy. Significantly, the biofilm formation is observed to be disrupted by these methodologies. Overall, this study underscores the effectiveness of 4-HBA as antimicrobial compound against diverse range of pathogens, as demonstrated through both phenotypic and proteomic approaches.