Doktora Tezleri

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Heat and mass transfer characteristics of adsorbents in heat pump and refrigerator
(01. Izmir Institute of Technology, 2023-01) Gündoğan, Şefika Çağla; Çakıcıoğlu Özkan, Seher Fehime
Due to increasing drought, pandemic and climate crisis in recent years, researchers have increased their studies on environmentally friendly energy use. Although there are technological developments in the production of energy from renewable energy sources, the storage of this produced energy is still a problem that awaits a solution. At this point, adsorption heat pumps with high primary energy efficiency come to the fore as a developing technology and attract the attention of researchers. However, low heat transfer properties in the adsorbent bed reduce the performance of adsorption heat pumps and limit their applications. The aim of this thesis was to improve the performance of the adsorption heat pump by increasing the effective thermal conductivity within the adsorbent bed. Two methods have been employed to enhance the effective thermal conductivity. In the first method, which was unconsolidated adsorbent bed design, it was aimed to increase the thermal conductivity of the bed with metal additives with a continuous structure. In the second method, which is known as consolidated bed design, the effective thermal conductivity of zeolite 13X was tried to be enhance with a high conductive material, reduced graphene oxide. In the experimental studies, it was observed that the thermal conductivity increased from 0.12 W/m.K to 0.28 W/m.K in unconsolidated bed design by means of fin-shaped metal additive. In consolidated adsorbent bed design, the effective thermal conductivity of the Graphene/Zeolite 13X (1 wt% Graphene) was determined as 0.1613 W/m.K. In theoretical studies, the effect of thermal conductivity in the temperature, pressure and adsorbate concentration was investigated. The indirect and direct effects of effective thermal conductivity on specific cooling/heating power (SCP/SHP) and coefficient of performance (COP) values were examined. Although the effect of thermal conductivity on COP was ignored in most of the studies in the literature, it was observed that COP increased from 0.01 to 0.10 when thermal conductivity increased from 0.12 W/m.K to 1 W/m.K.
A survey on spatial effects of newcomer entrepreneurs in rural Urla
(01. Izmir Institute of Technology, 2022-12) Güçü, İlker; Çıkış, Şeniz
Today, new production forms of rural space, which receive immigration and meet the entrepreneurial activities created by this population change, constitute the main aim of study. Thesis focuses on the mutual influence of rural space and rural entrepreneurship in terms of the architecture discipline. The main source of rural livelihood is agricultural production and animal husbandry from past to present. As a result of these migrations, the main livelihoods in the rural area are changing, developing and renewing. Rural architectural space is also in a process of change in line with these activities. In addition, what entrepreneurs understand from the countryside and their reflections gain importance in the transformed space. Based on the migration stories and spatial preferences of individuals who migrated from urban areas to rural, the study deals with thirty-four entrepreneurs and their enterprises located in the rural areas of Urla district of İzmir. Semi-structured interviews were conducted to measure the spatial context of enterprises located on Urla Wine Route and feeding this route. The spatial contexts of enterprises were grouped through the themes that emerged as a result of the analysis. As a result of the analyzes, it has been seen that the site plan, clousure movements, orientation and building form are the most used parameters in architectural design by newcomers. It is aimed that the study will contribute to the literature as it allows the rural entrepreneurship and ispatial context, which has been examined at an upper scale so far, to be evaluated at the scale of architectural space
Exactly solvable Burgers type equations with variable coefficients and moving boundary conditions
(01. Izmir Institute of Technology, 2022-12) Bozacı, Aylin; Atılgan Büyükaşık, Şirin
In this thesis, firstly, a generalized diffusion type equation is considered. A family of analytical solutions to an initial value problem on the whole line for this equation is obtained in terms of solutions to the characteristic ordinary differential equation and the standard heat model by using Wei-Norman Lie algebraic approach for finding the evolution operator of the associated diffusion type equation. Then, initial-boundary value problems on half-line and an initial-boundary value problem with moving boundary for this equation are studied. It is shown that if the boundary propagates according to an associated classical equation of motion determined by the time-dependent parameters, then the analytical solution is obtained in terms of the heat problem on the half-line. For this, a non-linear Riccati type dynamical system, that simultaneously determines the solution of the diffusion type problem and the moving boundary is solved by a linearization procedure. The mean position of the solutions, the influence of the moving boundaries and the variable parameters are examined by constructing exactly solvable models. Then, an initial value problem for a generalized Burgers type equation on whole real line is discussed. By using Cole-Hopf linearization and solution of the corresponding generalized linear diffusion type equation, a family of analytical solution is obtained in terms of solutions to the characteristic equation and the standard heat or Burgers model. Exactly solvable models are constructed and the influence of the variable coefficients are examined. Later, an initial-boundary value problem for the generalized Burgers type equation with Dirichlet boundary condition defined on the half-line is studied. Finally, an initial-boundary value problem for the generalized Burgers type equations with Dirichlet boundary condition imposed at a moving boundary is considered. The analytical solution is obtained in terms of solution to characteristic equation and the standard heat or Burgers model, if the moving boundary propagates according to an associated classical equation of motion. In order to show certain aspects of the general results, some exactly solvable models are introduced and solutions corresponding to different types of initial and homogeneous/inhomogeneous boundary conditions are discussed by examining the influence of the moving boundaries.
Investigating molecular mechanisms underlying resistance to notch inhibitors in breast and ovarian cancer
(2022-11) Telli, Kübra; Yalçın Özuysal, Özden
Breast and ovarian cancers remain highly malignant among women with more than 11% overall of incidence rates worldwide. Traditional treatment strategies including chemotherapy, radiotherapy and hormone therapies continues to be successful yet for the long-term, cancer recurrence and drug resistance remains to be the main issue. In addition to the altering common cell fate regulations, cancer cells modify signaling pathways to overcome cytotoxicity. Notch signalling pathway is a conserved ligand-receptor pathway that necessarily plays role in survival homeostasis, yet it is dysregulated in various cancers. Currently, novel treatment strategies are targeting this pathway through Gamma Secretase Inhibitors (GSI) DAPT, R04929097 and MK0752 that are use both as a single agent and in combinations with Docetaxel or Cisplatin. The clinical success of these inhibitors requires further examination of potential intrinsic or acquired resistance profiles. In this study, we generated breast cancer cells (MDA-MB-231 and MCF-7) resistant to DAPT or R04929097 and ovarian cancer cells (IGROV-1, BG-1, SKOV-3 and A2780) resistant to MK0752 by gradual treatments of increasing doses based on drugs’ IC50 values. Morphological changes, growth rates, migration alterations, mRNA expressions of Notch pathway components and epithelial mesenchymal transition markers, 3D setups for acidosis responses and protein expressions for c-myc and oxidative stress response markers were analyzed. Furthermore, proteomic analysis was carried out with the ovarian cancer cell line IGROV-1. The response of the cells to different drug treatments and dysregulated protein families exposed in resistance mechanisms behind DAPT, R04929097 and MK0752 for both breast and ovarian cancer cells are reported. Overall, this study reveals possible resistance mechanisms against GSIs and emphasizes potential targets through well-known hallmarks of cancer drug resistance.
Utilization of endophytic fungi and their enzymes for transformation to obtain bioactive compounds
(01. Izmir Institute of Technology, 2022-12) Küçüksolak, Melis; Bedir, Erdal; Sağ, Duygu
Biotransformation is a chemical reaction performed by biological systems or their components to modify molecules and has many applications in the pharmaceutical industry. In our previous project, biotransformation studies were carried out on Astragalus cycloartanes using endophytic fungi isolated from the tissues of Astragalus species, and the effects of the metabolites on telomerase activation were investigated. Among the isolated endophytic fungi, Alternaria eureka and Camarosporium laburnicola were identified as potent biocatalysts in developing molecule libraries and producing potent telomerase activators. This thesis aims to demonstrate the potential use of endophytic fungi in the production of bioactive metabolites. In the first part, biotransformation studies were performed on cyclocephagenol, a novel cycloartane-type sapogenin with tetrahydropyran unit, using Alternaria eureka and Camarosporium laburnicola, and twenty-eight new metabolites were obtained. According to the results of bioactivity studies, Alternaria eureka and Camarosporium laburnicola were found to be responsible for producing potent neuroprotective agents and potent telomerase activators, respectively. In parallel, biotransformation conditions were statistically optimized to afford potential telomerase activators, discovered in our previous studies (E-CG-01, E-AG-01 and E-AG-02). For this, nine parameters were screened by Plackett-Burman Design, and three significant parameters were optimized using Central Composite Design. As a result, production yields were increased by 1.95-fold for E-CG-01, 70-fold for E-AG-01, and 19-fold for E-AG-02. In the last part, the partial purification and characterization of alcohol dehydrogenase, Baeyer-Villiger monooxygenase, and lactone hydrolase enzymes, which were catalyzing the modifications in the production of telomerase activators, from Camarosporium laburnicola were performed.
Probabilistic finite element model updating and damage detection of structures by using Bayesian statistics
(01. Izmir Institute of Technology, 2022-12) Ceylan, Hasan; Turan, Gürsoy
Finite element (FE) model updating is extensively employed in many applications of various engineering branches for damage detection purposes. An FE model is expected to reflect the properties of actual structures. However, it is almost impossible for an FE model to carry the properties of the real-life structure. As a result, differences exist between analytical models and actual structures. The aim of model updating is to minimize these differences as much as possible. In model updating procedures, there are inevitable uncertainties due to inevitable measurement noise and modelling errors. Therefore, model updating and damage detection process should be performed in a probabilistic way instead of a deterministic one. To this end, Bayesian model updating methods have gained much attention in the literature to account for the uncertainties of the parameters to be updated. Among these methods, those that use the concept of system modes have gained much more attention since it enables researchers to account for modelling error uncertainties and to avoid mode matching problem. For those methods, discrepancies between system modes and measured modes are considered and system modes are updated to obtain those that best fit the measured modes. Further, system modes are connected to the FE model via eigenvalue equations. In this study, a two-stage Bayesian model updating method which utilizes the concept of system modes has been firstly reformulated to compare three different assumptions on the modelling error variance of eigenvalue equations. Results reveal that the Bayesian model updating formulations that use the system modes concept give unreasonably too small posterior uncertainties for the updated parameters. This makes the probabilistic approach questionable since getting such small uncertainties may almost be equivalent to a deterministic approach. To increase the posterior uncertainty levels to more reasonable levels, a two-stage sensitivity-based Bayesian model updating methodology is proposed in this study. The results show that the proposed method successfully improves the updating results and increases the posterior uncertainties to more realistic levels.
Development of conducting polymer-based fluorescence on/off biosensor for biomolecule analysis
(01. Izmir Institute of Technology, 2022-11) Arslantaş, Duygu; Arslan Yıldız, Ahu
Sensitive and selective detection of biomolecules and cells is essential for early diagnosis of diseases, prognosis monitoring, and effective therapy. This thesis aimed to develop a novel fluorescence ‘‘turn-on/off’’ biosensor for biomolecules and cells detection. In this study, cationic polythiophene derivative poly(1,4-dimethyl-1-(3-((4- methylthiophen-3-yl)oxy)propyl)piperazin-1-ium bromide) (PT–Pip) was used as an efficient fluorescence transduction element to discriminate proteins, mammalian cells, and amino acids for the first time. Initially, pH–dependent spectroscopic characterization of the PT–Pip was performed to monitor the conformational and optical changes. The pH sensitivity of the PT–Pip was demonstrated for the first time. Afterwards, the fluorescence ‘‘turn–off’’ phenomena were investigated in detail using citrate–capped gold nanoparticles as an efficient fluorescence quencher. Further, the interaction of target analytes such as proteins, mammalian cells, and amino acids with pre–quenched non–covalent PT–Pip–AuNP complexes was examined. Disruption of the binding equilibrium between PT–Pip and AuNP by analytes resulted in the selective displacement of PT–Pip, which generated signal output as a fluorescence ‘‘turn–on’’ mode. Consequently, for the sensitive detection of biomolecules and cells, chemical tongue sensor arrays were developed utilizing differential sensing approaches. PCA was used for the statistical evaluation of the multi–dimentional fluorescence response patterns. As a result, unique fingerprints were rapidly obtained by the direct sensing of proteins, ratiometric sensing of mammalian cells, and indirect sensing of amino acids. The combination of a differential sensing strategy with an appropriate multivariate statistical technique enabled the selective and sensitive detection and identification of proteins, mammalian cells, and amino acids.
Development and use of contactless magnetic manipulation methodologies for the formation of 3D cardiac models
(01. Izmir Institute of Technology, 2022-12) Önbaş, Rabia; Arslan Yıldız, Ahu
In this thesis, two contactless magnetic manipulation methodologies were introduced, which are magnetic levitation (MagLev) and biopatterning techniques. The optimization steps of both techniques were completed with NIH/3T3 mouse fibroblast cells. Later, 3D cardiac models were developed using H9c2 rat cardiomyocytes. For the MagLev technique, tunable 3D spheroids were obtained with changing initial cell seeding number, gadobutrol concentrations, and culturing time. For the biopatterning approach, a new bio-ink formulation, which comprises alginate, magnetic nanoparticles, and cells, was developed. Further, biopatterned cellular structures were fabricated in different shapes such as discs, rings, and rectangles under an external magnetic field. Later, characterization was done successfully via immunostaining of collagen I, F-actin, and DAPI. Moreover, cardiac-specific markers; cardiac troponin T and MYH6 were analyzed for both 3D cardiac spheroids and patterned 3D cardiac structures. Finally, doxorubicin was applied to evaluate the drug responses. IC50 values were calculated as 14.7 μM and 8.1 μM for 3D cardiac spheroids and 3D cellular structures respectively, while standard 2D cell culture was 3.5 μM which indicated 3D cardiac models were more resistant to drug exposure. In the last part of thesis, patterned 3D cardiac structures were fabricated using co-cultured hiPSC-derived cardiomyocytes and cardiac fibroblast cells via biopatterning methodology. Characterization was carried out successfully by immunostaining of α-actinin, collagen I, Cx-43, Troponin T, and DAPI. Taken together, to fabricate 3D cell culture models, MagLev and biopatterning-based contactless manipulation methodologies may be good alternatives to conventional 2D cell culture methods for tissue engineering applications, especially for drug screening.
Transformation of 19th century İzmir's harbor zone and its urban fabric via morphological approach
(01. Izmir Institute of Technology, 2022-12) Gelişkan, Nil Nadire; Çıkış, Şeniz
İzmir, which has a considerable place among the Mediterranean port cities of the 19th century, is not only similar to other Mediterranean port cities due to its trade dynamics, but also differs with the diversity and political development of the actors who have a say in commerce. After the industrial revolution, the hierarchical structure in world trade is reshaped with the expansion of the market area of trade. While industrial countries are at the top of the pyramid, the peripherical countries, whose economy is based on agriculture, are at the lower levels. The position that distinguishes the Ottoman Empire from the others is that it is the scene of the endless competition between industrialized European countries that will start from the 18th century and continue until the 21st century. İzmir is one of the plateaus of this competition. The city, which was considered the second capital center of the empire after Istanbul, especially in the 19th century, continues to be one of the most important ports. In this period, architectural and urban design-scale arrangements and innovations were made in İzmir by the Ottoman government and on a local scale, but especially the initiatives of western countries had a significant impact on the morphology of the city. In this context, the morphological transformation of the city of Izmir in the 19th century, the location of Izmir in local, regional and global networks and its relations with which urban interventions will be evaluated through maps, drawings and documents related to railway and transportation, especially from the Ottoman archive records of the Presidency of State Archives dated after 1850. In this study, in addition to the previous Izmir narratives, the transformation and structuring of the parcels to be used for the Kordon region and mega transportation projects, which will serve especially the industry channels, will be studied at a lower scale. It is within the scope of the study to focus on how the urban fabric of İzmir harbor zone was transformed in the light of the historical and economic breaks experienced by the empire in this period, and to seek a new conceptual port reading for the 19th century İzmir.
Studies toward the synthesis of novel 1,4-oxazepan-5-one and coumarin derivatives
(01. Izmir Institute of Technology, 2022-12) Akbaş, Tuğçe; Çağır, Ali
In this study it is aimed to synthesize potential novel MDM2 inhibitor which has 1,4-oxazepan-5-one skeleton. For this purpose (R)-(4-chlorophenyl)glycine was used as a starting material. Reduction of that with LiAlH4 and the protection of amine by Trt group was performed. After oxidation to aldehyde, direct or stepwise installation of glutaconic to the structure by either Michael type addition or coupling with amine by using HATU was quite problematic and all attempts were failed toward the preparation of this skeleton. Besides, synthesis of 1,4-oxazepan-5-one was also tried starting from chiral aminoalcohol and protected 5-hydroxy-2-pentanoic acid in two steps, first coupling then oxa-Michael addition. However this did not work well too. It seems that presence of activated methylene group might be the main problem in the addition of glutaconic acid reactions. In the second part of this thesis it was aimed to synthesize the 1,2,3-triazole substituted coumarin in order to investigate the potential antiproliferative properties of these over cancer cells. Acetylsalicilic acid was used as starting material in these syntheses. That was transformed 4-acetylene substituted coumarin derivatives as key intermediates then their transformations to corresponding final products was performed by click chemistry.
Effects of electromagnetic fields on the performance of molecular communications
(01. Izmir Institute of Technology, 2022-12) Taşçı, Aslı; Atakan, Barış
This thesis analyzes molecular communication (MC) systems’ performance under electromagnetic fields. The aim of the thesis is to model and study molecular behavior under electromagnetic fields (EMF). The thesis starts with the theoretical explanation of classic electromagnetism. The directional and thermal changes are the main effects of EMF on particles. The directional effects of EMF are studied with regard to electromagnetic forces. The applied electromagnetic forces are presented for different types of particles. The effect of EMF on magnetically susceptible particles is analyzed in particular. Furthermore, molecular movement is analyzed by considering four fundamental forces on diffusing molecules under EMF. The energy transfer between EMF and particles is studied to understand the thermal effects of EMF. AnMCscheme that transmits information with magnetically susceptible molecules is studied in the second part of the thesis. The molecular type and the configuration of EMF are studied to understand the effect of EMF on the diffusion rate. The effects of magnetic field gradient (MFG) and concentration gradient magnetic force (CGMF) are analyzed to model the change in the diffusion rate and concentration of magnetically susceptible molecules. The last part of the thesis focuses on molecular dynamics under EMF. The effect of thermal changes on the molecular reaction rate and binding kinetics is modeled with reaction-diffusion systems. The specific reaction rate constant is analyzed to determine the effect of temperature change caused by the EMF. The movement of molecules is modeled by Langevin’s diffusion model. The probability distribution functions of the molecule’s velocity and displacement are studied to understand and model the molecular behavior under EMF. Moreover, the mean-squared displacement is employed to analyze the diffusion type under EMF.
An agent based model for exploring the effects of overconfidence on the winner's curse in construction projects
(01. Izmir Institute of Technology, 2022-12) Aldemir, Bora; Kale, Serdar
As a result of errors in cost estimation, the winning companies in competitive environments such as bids, auctions, etc. fail to achieve the anticipated profit or even incur losses. This phenomenon is labelled as the “winner’s curse.” Diverse causes led to the occurrence of this circumstance. Until recently, technical errors were thought to cause most construction estimation errors. Behavioral economics has shown that certain biases in individual decision-making can also contribute to these undesirable situations. Overconfidence is common. This illusion is when a person thinks they are better at making decisions than they really are. The agent-based modeling method was used to examine this bias. This method investigates the system pattern created by heterogeneous individuals with independent macro-level behavior. In this study, individuals can be considered as construction companies. The prevalent pattern in the sector is the phenomenon of the winner's curse. However, focusing solely on the overconfidence effect may not yield meaningful results. Risk aversion is regarded as a protective behavior against the negative effects of the overconfidence. There may also be a correlation between the number of bidders and the winner's curse. This study demonstrates that the phenomenon of the winner's curse exists in all dimensions of the overconfidence effect. When the number of bidders is small, overconfidence behavior has little impact on the winner's curse, but when the number of bidders is medium or large, the winner's curse increases slightly as the overconfidence effect decreases. Risk aversion does not provide any protection against the winner's curse phenomenon.
Lead-free ferroelectric ceramics for energy storage and electrocaloric cooling applications
(01. Izmir Institute of Technology, 2022-12) Karakaya, Merve; Adem, Umut
This thesis study consists of five main chapters that include an introduction about the principles and applications of ferroelectrics and four chapters on different lead-free ferroelectric ceramic systems developed for the energy storage and electrocaloric cooling applications. In the first chapter, the principles of ferroelectricity and dielectric, piezoelectric and pyroelectric properties of ferroelectrics are introduced followed by the applications considered in this thesis: Electrocaloric cooling and capacitive energy storage. In the second chapter, the effects of bismuth lithium titanate incorporation into sodium bismuth titanate-barium titanate systems on the energy storage properties have been discussed. In addition, it has been calculated that these compositions have improved energy storage properties close to the high values obtained in the literature. In the third chapter, the effect of two different manganese precursors on the probability of defect dipole formation, ferroelectric aging and resulting manganese valences of ceramics were investigated by manganese doping on barium strontium titanate base ceramics. In addition, their electrocaloric properties were investigated by indirect method. In the fourth chapter, electrocaloric properties of barium titanate - sodium bismuth titanate systems has been investigated. The increase in tetragonality by sodium bismuth titanate incorporation has been verified by Rietveld refinement and those compositions were shown to be suitable for electrocaloric applications. In the fifth chapter, a sodium bismuth titanate - potasium bismuth titanate composition which is in morphotropic phase boundary, was synthesized by templated grain growth method, and the effect of orientation on the electrocaloric effect was investigated by direct and indirect measurements.
Compliant control of robotic co-workers in surgical applications
(01. Izmir Institute of Technology, 2023-01) Ayit, Orhan; Dede, Mehmet İsmet Can
In recent years, robots have taken place in surgical operations due to their advantages over humans, such as power, endurance, dexterity, and accuracy. Because of the lack of abilities, such as decision-making, adaptability, and creativity, human surgeons supervise the robots. The robots share the operation places with humans, called co-worker robots. Robots have the power to harm their environment; therefore, robots can generate dangerous situations for surgeons and patients. To deal with the issues, this dissertation aims to design active compliant control algorithms such as impedance control, admittance control, and hybrid position/force control to achieve safe interaction forces in surgical operations by considering the performance. The surgical co-worker robot’s type, actuation system, robot dynamics, and environment dynamics are important factors for designing the active compliant controller. Besides these, stability and robustness for safety, and agility and human effort for performance are considered for designing the controller. This dissertation takes into account three interaction scenarios encountered in surgical operations. In these scenarios, it is expected from the co-worker robot that it adapts to the sudden change in its environment dynamics. For instance, safe interaction is desired when the robot interacts with the stiff and soft tissues. To handle the issue, a switching control methodology is presented where the predefined control parameters are switched according to their environments. The methodology is implemented in a novel co-worker robot named NeuRoboScope, designed to assist the endoscopic pituitary gland surgery with the support of The Scientific and Technological Research Council of Turkey (TUBITAK). Moreover, active compliant control algorithms require a motion control algorithm as a low-level controller. In this dissertation, the computed torque method and independent joint controllers with gravity compensation are used as motion control algorithms. The computed torque method requires the dynamic model of the robot. Due to that, the dissertation proposes a simplified dynamic model with a correction coefficient for computational efficiency. ARM Cortex M4 processor runs the computed torque method with the proposed dynamic modeling method at 500 Hz. Also, this dissertation presents an independent joint controller which uses the simplified gravity matrix as a feedforward term for compensating the NeuRoboScope’s gravitational effect. The experimental results of both controllers are discussed in this dissertation.
Physiologic effects of the golden thistle (Scolymus hispanicus L.) hydromethanolic extracts: Outcomes of phytochemical health benefits
(01. Izmir Institute of Technology, 2022-12) Özel Taşcı, Cansu; Güleç, Şükrü; Büyükkileci, Ali Oğuz
This dissertation aimed to screen the beneficial health effects of a hydromethanolic extract (GTE) obtained from the golden thistle (S. hispanicus L.) on different health conditions, including type 2 diabetes, inflammation, cancer, and wound healing. First, 1 mg/mL GTE resulted in 6.94% chlorogenic acid (CGA) bioavailability with (1.82±0.07)x10-6 cm/s apparent permeability on differentiated CaCo-2 cells. Then, 1 mg/mL GTE prompted 39.4-42.6% less glucose efflux and 49-66% less GLUT2 mRNA expressions on CaCo-2 cells. In the systemic inflammation model, pre-treatments of 50-500 μg/mL GTE reduced some inflammatory markers after 0.5 μg/mL lipopolysaccharide (LPS) inflammation induction for 12 h on RAW 264.7 cells. Reductions in 30-53%, 32-45% and 16-36% ranges for nitric oxide, tumor necrosis factor-α, and interleukin-6 (IL-6) were determined, respectively. Additionally, same GTE concentrations were pre-treated with the CaCo-2 cells in the colonic inflammation model. 15.5-19.5% and 8.7-17.3% less IL-6 and IL-8 cytokine releases were detected from CaCo-2 cells, respectively. The wound healing model of 3T3-L1 mouse fibroblasts revealed that 40-80 μg/mL root bark extract resulted in enhanced wound closures with significant differences in the cell cycle distributions. As the most significant result, G2 phase distributions were 1.8% and 12.5% in the negative and positive control samples, respectively. The root bark extract treatments of 10, 40, and 80 μg/mL resulted in 6.6%, 7.1%, and 9.1% in increasing concentrations. Finally, 4 mg/mL GTE application to CaCo-2 human adenocarcinoma cells caused 78.4% reduced cell viability, a cell cycle arrest, and increased early and late apoptotic properties. Overall results suggest that S. hispanicus L. has functional molecules that influence cellular regulations and have potential beneficial health effects.
Innovative food applications of novel multifunctional active edible gel fillings and coatings
(01. Izmir Institute of Technology, 2022-12) Barış Kavur, Pelin; Yemenicioğlu, Ahmet
This thesis organized as two chapters aimed to develop and test multifunctional novel gel filling and coating. In Chapter 1, the thesis focuses on developing antimicrobial and antibrowning gelatin based gel filling to produce safe caramel apples. For this purpose, water holding capacity and mechanical stability of gelatin (GEL) gels were improved by the incorporation of soy proteins (SP) and inulin (IN), respectively. The water activity (aw) of gels was also reduced to < 0.9 by the addition of sucrose (SUC). The apples were cored and the void cores were filled with GEL-SP-IN-SUC blend gel solution containing synergetic antimicrobials, nisin and lysozyme, and antibrowning agent ascorbic acid (each at 1% in gel). Candy sticks were then placed into gel-filled void cores, and apples were kept at 4oC for 20 h for gelation of filling before caramel dipcoating. The caramel apples with antimicrobial GEL-SP-IN-SUC filling showed 2.4 – 2.9 D lower Listeria count than traditional caramel apples during 7-day cold storage. The active blend gel-filling also prevented discoloration of apple core. In Chapter 2, the thesis focuses on controlling postharvest sprouting and microbial risks associated with shallot bulbs by active chitosan based coating loaded with eugenol (EUG). The sustained release of EUG was achieved by applying ultrasonic homogenization (US) to prepare a composite of chitosan (CHI) with chickpea proteins (CP) (CHI:CP ratio of films = 2). The CHI-CPEUG coating successfully reduced the sprouting and inhibited the inoculated E. coli and L. innocua in shallot bulbs by 2.3 log and 1.7 log, respectively.
Molecular genetic analyses in Origanum (Lamiaceae) taxa in Türkiye
(01. Izmir Institute of Technology, 2022-12) Taşcıoğlu, Tülin; Frary, Anne
Medicinal and aromatic plants (MAPs) belonging to the genus, Origanum L. (Lamiaceae), are called “oregano”. They are economically important and beneficial for trade, medicine, food, cosmetics, and ornamental purposes with their bioactive compound diversity and richness. Although Türkiye is the gene center for generation, speciation, and diversification of oregano throughout the world, their uncontrolled consumption and other factors threaten their status. According to Ietswaart (1980), there are ten morphological sections in the genus. Of these, 25 taxa (including 13 endemics) and 13 hybrids from eight sections grow naturally in Türkiye. The cross-pollinating and gynodioecious nature of oreganos makes their taxonomic classification difficult. In this dissertation, molecular markers (EST-SSRs and SRAPs) were used to assess the complex evolutionary relationships in a herbarium and the Turkish national AARI Gene Bank collection. Cross hybridization due to high gene flow was found to be the main source of genetic diversity within both collections. In both collections, the highest gene flow was observed between two sections, ANA and BRE, with diecious flowers which supports their frequent hybridization when compared to gynodioecious oreganos in nature. The Aegean and Mediterranean regions had the highest gene flow among all regions, while five province pairs had the highest gene flow among all provinces. In conclusion, molecular markers were shown to be a useful tool for examinations of genetic diversity and evolution in oregano.
Dinect and interior inverse generalized impedance problems for the modified Helmholtz equation
(01. Izmir Institute of Technology, 2022-11) Özdemir, Gazi; Ivanyshyn Yaman, Olha; Yılmaz, Oğuz
Our research is motivated by the classical inverse scattering problem to reconstruct impedance functions. This problem is ill-posed and nonlinear. This problem can be solved by Newton-type iterative and regularization methods. In the first part, we suggest numerical methods for resolving the generalized impedance boundary value problem for the modified Helmholtz equation. We follow some strategies to solve it. The strategies of the first method are founded on the idea that the problem can be reduced to the boundary integral equation with a hyper-singular kernel. While the strategy of the second approach makes use of the concept of numerical differentiation, the first approach treats the hyper singular integral operator by splitting off the singularity. We also show the convergence of the first method in the Sobolev sense and the solvability of the boundary integral equation. We give numerical examples which show exponential convergence for analytical data. In the second part of this work, we take into account the inverse scattering problem of reconstructing the cavity’s surface impedance from sources and measurements positioned on a curve within it. For the approximate solution of an ill-posed and nonlinear problem, we propose a direct and hybrid method which is a Newton-type method based on a boundary integral equation approach for the boundary value problem for the modified Helmholtz equation. As a consequence of this, the numerical algorithm combines the benefits of direct and iterative schemes and has the same level of accuracy as a Newton-type method while not requiring an initial guess. The results are confirmed by numerical examples which show that the numerical method is feasible and effective.
Development of sensor systems for food quality monitoring
(01. Izmir Institute of Technology, 2022-12) Büyüktaş, Duygu; Farris, Stefano; Korel, Figen
The main objective of this thesis is to fabricate electrochemical sensors for the detection of 2,4-diaminotoluene (2,4 TDA), 2,6-diaminotoluene (2,6 TDA), and 4,4´-methylene diphenyl diamine (MDA), possibly carcinogenic primary aromatic amines (PAAs) that poses a serious health risk because they can transfer from multilayer food packages including adhesives based on aromatic polyurethane (PU) systems, to the food. The thesis is based on the following three chapters: (1) Development of a nano-modified glassy carbon electrode for the determination of 2,6-diaminotoluene (2) A screen-printed electrode modified with gold nanoparticles/cellulose nanocrystals for electrochemical detection of 4,4´-methylene diphenyl diamine (3) Development of a nano-modified screen-printed electrode for the determination of 2,4-diaminotoluene. In this work, full electrochemical characterization of the nano-modified electrodes was carried out, and the electrochemical properties were described. Migration tests were also conducted to modified sensors in order to investigate their potential application in real food systems. The results of this work clearly showed that modified electrochemical sensors allow reliable quantification of the most important primary aromatic amines migrating from packaging materials to food and can be used as an alternative to the commonly used conventional analytical techniques for the detection of these toxic compounds.
Biological nano silica reinforced polymeric composites
(01. Izmir Institute of Technology, 2022-12) Ülker, Sevkan; Güden, Mustafa
The present thesis study focused on processing nano-silica powders of varying sizes and crystallinities through heat treatment (900–1200 °C), hydrofluoric acid leaching (1–7 N), and ball milling (1 h, 500 rpm) of natural diatom frustules. As-received frustules was composed of amorphous silica (88%) and quartz. The partially ordered crystalline low-quartz and/or precursor to low-cristobalite started to form at ~900 °C. As the heat treatment temperature increased, the crystallinity of the frustules increased from 9.3% at 25 °C to 46% at 1200 °C. Applying a ball milling reduced the mean particle sizes of the as-received and heat-treated frustules from 15.6–13.7 μm to 7.2-6.7 μm, respectively. Acid leaching of the as-received and heat-treated frustules resulted in a further increase in the crystallinity. Furthermore, ball milling applied after an acid leaching was very effective in reducing the particle size of the as-received and heat-treated frustules. The mean particle size of the acid-leached frustules decreased to 774-547 nm with a crystallinity varying between 12 and 48% after ball milling. A partially dissolved amorphous phase was observed in between crystalline silica grains after acid leaching, which resulted in a rapid fracture/separation of the frustules in ball milling. The prepared nano-silica powders were further used as a filler in an epoxy matrix. The tensile strength, fracture strain, and modulus of epoxy increased with increasing the volume percent of nano-silica up to 2%. The increase in the yield strength and elastic modulus was about 50% and 30% with the addition of 2 vol% frustules, respectively. The rule of mixtures showed a very good agreement with the experimental elastic modulus values and a numerical model of the tensile test in LS-DYNA agreed well with the experimental tensile stress-strain behavior. The microscopic observations showed the presence of nano-silica powder, proving an efficient load transfer from matrix to powders on the fracture surfaces, confirming a strong interface between silica powders and matrix.

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