Graduate Program in Materials Science and Nanotechnology - Master's degree

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https://hdl.handle.net/11693/13949

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Longevity and circadian rhythm in Caenorhabditis elegans: the impact of lithium chloride
(Bilkent University, 2024-06) Temirci, Elif Sena
Lithium chloride (LiCl) is a popular treatment for various neurological disorders, especially bipolar disorders. While its complete mechanism of action remains partially elucidated, LiCl has been found to support new memory formation by triggering the construction of new neurons, reducing senescence, and regulating the circadian rhythm, particularly in bipolar patients, where it counteracts their abnormally fast biological clock. The circadian rhythm is vital in determining efficiency, understanding energy consumption, and biochemical balance for all organisms. This rhythm includes regulating body functions by the day/night cycle. Caenorhabditis elegans (C. elegans) is one of the most robust organisms for modeling circadian rhythm, although it lives in the soil. Therefore, by employing C. elegans as a model system, valuable insights could be gained for these complex processes. This study aims to elucidate the complex relationship between LiCl, circadian rhythms, and longevity, as disruptions in these pathways are implicated in neurodegenerative diseases and age-related cognitive and motor decline. In this project, white light was employed to manipulate the circadian rhythm in C. elegans, with one group additionally receiving LiCl treatment in addition to light exposure. The study focused on longevity, response to environmental factors, and circadian rhythm. To elucidate the effect on longevity, lifespan measurements showed that LiCl treatment extended the lifespan of C. elegans under both light and dark conditions, with a shorter lifespan observed in the light. Additionally, when comparing the effect of specific developmental time points, the signs of aging appeared later in the dark compared to the light. The differential gene expression of longevity genes suggested that LiCl treatment could impact gene expression, particularly the age-1 gene, but not the daf-16 gene. Furthermore, the response to environmental changes was examined imilarly and it was observed that C. elegans responded to the circadian rhythm disruption caused by light and LiCl administration. In conclusion, this study suggests that LiCl treatment has the potential to mitigate the adverse effects of circadian rhythm disruptions and reverse the aging process of C. elegans.
Open Access
Photophysics of interlayer excitons in TMDC heterobilayers
(2024-05) Durmuş, Mehmet Atıf
Since the first isolation of graphene (a single sheet of graphite) in 2004 and the remarkable discoveries achieved in the following years, there has been an ongoing growth in studies and interest in two-dimensional (2D) materials and their heterostructures. With the constant discovery of new 2D materials over time, their range of material properties has expanded significantly as well, opening up a greater variety of applications and corresponding theoretical and experimental research inquiries for their implementation. The majority of them are classified as layered van der Waals (vdW) materials, and the development of different transfer techniques has made it possible to fabricate vdW heterostructures, which introduced exciting possibilities for the development of quantum technologies. The unique characteristics of the constituent layers, in conjunction with the high carrier mobility characteristic of 2D materials, provide a wealth of opportunities for the development of devices with remarkable properties for various applications. Interest in semiconducting transition metal dichalcogenides (TMDCs) among other 2D materials has grown significantly owing to their exceptional optical, mechanical, and electrical properties, particularly as they exhibit direct bandgaps in atomic layer thicknesses (i.e., monolayers). The vdW heterostructures of monolayer TMDCs have been growing in popularity among researchers over the last decade since they typically exhibit staggered type-II band alignment, which promotes ultra-fast charge transfer between the constituent layers, in turn, leading to the formation of strongly Coulomb-bound electron-hole pairs (i.e., interlayer excitons, IXs) located in different layers. The emission characteristics of the IXs can be regulated by varying the twist angle between the constituent layers of the heterostructures, and a superlattice of single-photon quantum emitters of IXs through their localization to periodic quantum dot-like Moiré potentials can be achieved. The main focus of this dissertation is investigating and understanding the photophysics of IXs of hBN-encapsulated WSe2-MoSe2 heterobilayers, which will allow one to grasp the importance and capabilities they hold for the development of quantum applications. The heterobilayer samples used in this study were fabricated by first isolating the 2D layers using the micromechanical exfoliation method and then vertically stacking them via the dry transfer technique. Low-temperature photoluminescence (PL) spectroscopy methods have been performed on the IX species of the fabricated heterobilayers, including magneto-PL, excitation pump power-dependent PL, temperature-dependent PL, and time-resolved PL (TRPL). Finally, first-order correlation g(1)(τ) measurements in the time domain were performed using a home-built free-space Michelson interferometer. Our results on the effect of Moiré-localization of IXs demonstrate that the well-protection of the localized emitters can lead to prolonged dephasing times (T2 ~ 730 fs). Remarkably, we have also successfully shown the presence of coherent coupling for the first time between the two spin states (spin-singlet and spin-triplet) of IXs of hBN-encapsulated WSe2-MoSe2 heterobilayers by utilizing the quantum beat interferometry in the time domain with resulting dephasing times up to T2 ~ 400 fs. Our results on the dephasing characteristics of IXs can provide important insights into the future of exciton-based device development in quantum photonic and valleytronic applications.
Embargo
Facile synthesis of bimetallic nanoparticles with diverse nanostructures using metal acetylacetonates
(Bilkent University, 2024-01) Sayma, Dalya M. F.
Bimetallic nanoparticles (NPs) have become a fundamental subject in the field of nanoscience and inorganic chemistry. Owing to the fascinating optical and catalytic properties that rise from their synergetic effect, plasmonic-catalytic bimetallic NPs, in particular, are employed in a myriad of applications such as catalysis, sensing and photocatalysis. Optical properties of plasmonic NPs such as gold or silver NPs are based on the localized surface plasmon resonance (LSPR) in the visible spectral range. Plasmonic NPs enhance the localization of electromagnetic fields, converting light to hot carriers or heat that can be used to drive chemical reactions. On the other hand, catalytic metals, which have d-bands close to the Fermi-level, make strong binding to reactants and lower the activation energy of chemical reactions. The properties of plasmonic-catalytic bimetallic NPs such as efficiency or product selectivity in the chemical reaction do not only rely on factors like size and composition of metal NPs, but more importantly, on the types of nanostructures formed. Herein, several nanostructures were synthesized by developing a facile approach using metal acetylacetonates. The synthesized NPs include bare silver NPs, bare palladium NPs, Pd@Ag core-shell NPs, Pd@Ag nanowires, Ag-Pd alloyed core-satellite NPs, Ag-Pt alloyed nano-stars and concave nano-cubes, and trimetallic AgPdPt NPs. In this study, it was found that the temperature, composition of metal components, and amount of capping and reducing agents play a key role in the synthesis of different types of bimetallic NPs. This study is important in the field of nanochemistry as it provides a novel synthesis method for generating plasmonic-catalytic bimetallic NPs.
Embargo
Diet-induced changes in mouse cells in vitro and in vivo zebrafish models of angiogenesis
(Bilkent University, 2024-01) Yıldız, Selvin
Cardiovascular disorders rank as the primary cause of global mortality. Being overweight or obese impacts the pathogenesis of cardiovascular disease, resulting in an imbalance in endothelial function, cell growth, and inflammatory activation. Disruption of these factors resulting from endothelial cell dysfunction serves as both an outcome and a catalyst for vascular disease processes. Endothelial cells (ECs) are a natural barrier between circulating blood and vessel components. They also play critical roles in multiple physiological and pathophysiological processes, such as angiogenesis, vascular permeability, and inflammation. Amelioration of endothelial dysfunction may be attained by weight loss; however, complementary in vitro and in vivo studies are needed to establish the effects of weight loss on endothelial function and angiogenesis. This study developed an in vitro model to understand better the diet-induced changes in angiogenesis for mouse endothelial cells. In addition, a novel in vivo model of diet-induced vascular changes and its potential reversal with a return to regular diet in a zebrafish model was also studied. In vitro studies showed that a serum from mice fed a high-fat diet (HFD) might lead to proliferation of endothelial cells, yet weight loss did not compensate for prior stress induced by HFD. In vivo, studies in adult zebrafish showed that egg yolk-based high-fat diet might affect cytological architecture in the adult fish liver. Switching to a normal diet could effectively reverse these changes. Moreover, a caudal fin inter-ray vascularization assay was developed and used to test whether vessel sprouting was affected by different diets. Overfeeding resulted in a higher number of vessels, yet future studies with higher sample sizes are needed. Similarly, the expressions of several angiogenesis-related genes, which were quantified using cDNAs from the whole larvae and adult caudal fin treated with different diets, showed significant changes in vcam in larvae and cdh5 in adult fin by diet. However, further experiments are needed due to high individual variability and low sample size. The findings herein show that in vitro mouse endothelial cells and zebrafish larvae and adults could be used as valuable models for studies involving reversal/weight loss of high fat or overfeeding dietary regimes. Furthermore, the caudal fin vascularization assay in Tg(fli1:eGFP) Casper fish could be a promising preclinical model for testing the effects of different diets on angiogenesis and endothelial dysfunction.
Embargo
Metal oxide nanoparticle coatings for enhanced mechanical and chemical properties of glass fibers
(Bilkent University, 2024-01) Kurucu, Arda
Glass fibers are one of the most used reinforcement fibers in composites. They have highly demanded properties such as good mechanical properties, impact resistance, high strength-to-weight ratio, and cost-efficiency. Glass fiber composites are utilized in many fields such as aerospace, automotive, and maritime. Glass fibers are one of the components in the composite structure aside from the resin matrix and their properties heavily affect the overall properties of the composite material. By improving the properties of glass fiber reinforcement, composite performance can also be improved. Industrial-scale fabrication of glass fiber re-quires the construction of a certain glass-type exclusive factory. This study aims to have an alternative solution to meet the strength demands of industry with a relatively simple modification to the production process of E-glass fibers. In this study, the mechanical, chemical, and dielectric properties of glass fibers are altered via metal oxide nanoparticle coating. A thin layer of ZnO coating is applied onto the E-glass fibers via the dip coating method. Through spectroscopic and SEM characterization, the presence of ZnO coating is confirmed, and the effect of this coating on mechanical properties is investigated through micromechanical analysis. ZnO coating proved to increase the tensile strength of E-glass fibers by 14.67%. In addition to mechanical improvements, the ZnO nanoparticles proved to be effective in corrosion resistance. Their corrosion-resistant properties are investigated using an acidic environment. Coated fibers are then used to manufacture a glass fiber felt composite to investigate the effect of nanoparticles on signal transmittance properties of glass fiber composites. In addition to the modification of common E-glass fibers, a novel pure silica fiber fabrication method for advanced aerospace composite applications is developed. Principles of optical fiber production are utilized to fabricate structural high-purity fiber with unconventional fuel gas heating sources. This study aims to obtain know-how and knowledge on the production of pure silica fiber. To fabricate the pure silica fiber, a novel custom fabrication setup is designed and manufactured. This setup includes a custom heating system, a custom capstan tractor, and a custom feeding system.
Embargo
A bacterial living therapeutics with engineered protein secretion circuits to eliminate breast cancer cells
(Bilkent University, 2024-01) Binte Shahid, Gozeel
Cancer therapy often faces limitations due to potential side effects, prompting scientific interest in bacteria-based living cancer treatments. Yet, the complete utilization of bacteria in therapeutic applications confronts engineering hurdles. This thesis focuses on introducing a novel bacterial mechanism specifically intended to target and eliminate breast cancer cells. Our innovative approach involves modifying Escherichia coli (E. coli) to secrete a Shiga toxin called HlyE, a pore-forming protein that binds to HER2 receptors found on breast cancer cells. This binding process is facilitated by a nanobody expressed on the bacterial surface through the Ag43 autotransporter protein system. Our research demonstrates the effective binding of the nanobody to HER2+ cells in laboratory conditions (in vitro). Utilizing the YebF secretion system, we successfully leverage the secretion of HlyE, leading to the eradication of the targeted cancer cells. These outcomes emphasize the significant potential of our engineered bacteria as an innovative and promising strategy for breast cancer treatment. This pioneering approach represents a groundbreaking development in the field of cancer therapeutics. By harnessing the unique properties of bacteria and utilizing advanced engineering techniques, we've succeeded in creating a targeted and potent system capable of attacking breast cancer cells specifically marked by the HER2 receptor. Our study lays a robust foundation for future exploration and development in the realm of bacterial-based cancer therapies, offering potential solutions to the challenges encountered in traditional cancer treatment methods.
Embargo
Batch-compatible microfabrication of CMUT array chips for photoacoustic imaging of tissue-like phantoms (Part-II)
(Bilkent University, 2024-01) Mahmood, Muhammad Rashid
In this thesis study, Capacitive Micromachined Ultrasound Transducer (CMUT) array chips are microfabricated with wafer-scale batch-compatible approaches as sensors for photoacoustic imaging (PAI) applications. Photoacoustic imaging (PAI) is a non-invasive medical imaging technology, free from X-ray radiation, that utilizes contrast data resulting from acoustic detection of optical stimulation to construct images. CMUT array devices are microelectromechanical systems (MEMS) devices that generate or detect acoustic or pressure waves within the ultrasonic frequency range. The CMUT devices function on the principle of vibrating parallel plate variable capacitors. Capacitance variations due to vibrating plate electrode create electrical current signals in CMUT cells, which are further processed to obtain meaningful results. In PAI, pulsed laser light is transmit-ted and absorbed by naturally occurring photo-absorber compounds or contrast agents in selective body-tissue or tissue-like materials. The laser pulses are con-verted into heat, resulting in thermoelastic expansion vibrations of the tissue or tissue-like materials (i.e., phantom material). These vibrations travel as pressure or acoustic waves through the tissue or tissue-like materials that may be detected by CMUT sensors. For the production of the CMUT array devices, borosilicate glass (Pyrex-7740) wafers were selected as transparent substrates. The bottom electrode and electrical insulation layer above the bottom electrode of the CMUT sensors are processed on the Pyrex substrates. Anodic wafer bonding is selected as one of the suitable CMUT gap formation and top electrode integration technologies. Clean and unprocessed SOI (silicon-on-insulator) wafers are used for the formation of the top electrode of the CMUT sensors. The silicon handle layer and buried oxide (SiO2) layer of the SOI wafer are removed in order to reveal the silicon device layer that is used as the vibrating top electrode for the CMUT sensors. Metallization stacks on the Silicon device layer have been deposited for electrical conductivity enhancement and wire bonding connections between CMUT top electrodes and printed circuit boards (PCBs). After the patterning of the vibrating top electrode layer, dicing saw processing is done to singulate the CMUT chips from 4-inch diameter wafers. Chip-scale sealing of the CMUT chips is done by conformal Parylene C deposition using UV-sensitive dicing tape as a manual mask to prevent the deposition of Paylene C on the electrical pad regions of the CMUT chips. After Parylene C deposition, UV-sensitive dicing tape is re-moved from chips to reveal the electrical connection pads. CMUT array devices are characterized by inspecting their capacitive gap height, measuring their resonance frequencies, and determining the integration process yield. The resonance frequency results obtained from impedance analyzer measurements of individual CMUT cells are around 5.7 MHz. Furthermore, change in the resonance frequency is clearly detectable when the applied DC bias voltage is increased during the small AC plus incremental DC excitation of CMUT cell membranes.
Open Access
Multiphase flow displacement application of novel green nanoparticle synthesis in glycerol and reconfigurable nanoemulsions in reservoir-on-a-chip
(Bilkent University, 2024-01) Jahangir, Robab
Nanofluids and oil in water (O/W) nano/micro emulsions have been extensively investigated for their potential in multiphase displacement applications such as enhanced oil recovery (EOR). However, the potential of metal nanofluids and water-in-oil nanoemulsions (W/O) has not been readily studied and the under-lying mechanisms are yet to be investigated. Moreover, most nanofluids pose toxicity risks to reservoirs, and a high polydispersity index of conventionally syn-thesized nanofluids adversely impacts displacement efficiencies. Hence, in this study, we synthesized two injection fluids including, a novel green nanofluid comprising of ultra-small silver nanoparticles (NPs) in glycerol and reconfigurable nanoemulsions to investigate their impact on displacement efficiencies. We have carried out the synthesis of green nanofluid comprising silver NPs in a customized microfluidic (Mf) chip, with 18 omega-shaped micromixers, by using glycerol as a promising green solvent and reducing agent at various concentrations (10-80 %), and simultaneous comparison of the results from batch synthesis. Interestingly, the experimental findings depicted that by varying different parameters, the spherical silver nanoparticles with an average ultra-small particle diameter of < 2nm were obtained at all glycerol concentrations (10-80 %) and variables, as compared to batch synthesis (giving a yield of 10-fold larger particles). The synthesis was then confirmed by Dynamic Light scattering (DLS), UV-visible spectroscopy, and Tunnelling Electron Microscope (TEM). Subsequently, the dis-placement efficiencies were then investigated in a reservoir-on-a-chip platform (filled with fluorescence-doped oil) for real-time visualization, quantification and pore-scale investigation. The measurement data for green nanofluid revealed the wettability alteration and IFT reduction with the increase in viscosity and size of NPs. No significant effect of the IFT on sweep efficiencies was observed, however, the contact angle of the injection fluids shifted from an oil-wet state (101◦-113◦) towards an intermediate wettability state (90◦-97◦) over 2 minutes. A shift to-wards intermediate wettability in a short time indicated the influence of AgNPs in displacing oil ganglia by structural disjoining pressure. It was reported that a critical glycerol viscosity (30 %) was essential to increase the sweep efficiency by 5 % in microfluidics-synthesized nanofluid (1.7 nm) and by 8 % in benchtop synthesized nanofluid (3.3 nm). Finally, the NPs-surfactant assemblies between SiO2 and Poly[dimethylsiloxane-co-(3-aminopropyl)methylsiloxane] copolymer were in-vestigated for the synthesis of reconfigurable nanoemulsions. The buckling phenomena was confirmed between pH 5 and 6 and nanoemulsions were synthesized with 3 different Oil: NPs concentrations i.e., 80:20, 70:30 and 60:40 at pH 3, 5, 6, and 8 (pH 3 and 8 taken as control groups). The sweep efficiency gradually increased in the order of 60:40 < 70:30 < 80:20, with the highest sweep efficiency obtained in the case of 80:20 nanoemulsions at pH 5, pH 6 and pH 5 in case of 70:30 nanoemulsions respectively, due to the displacement of oil because of formation of wedge film and in-situ emulsification.
Embargo
Scalable fabrication of nanomaterial integrated polymer fibers as self-powered sensors
(2023-12) Hasan, Md Mehdi
Wearable electronics have great potential to revolutionize healthcare by enabling real-time data acquisition and transfer. Textiles, a ubiquitous part of our daily lives, get exposed to a vast amount of biomarkers to provide information on health status and the onset of diseases without compromising comfort. Self-powered sensors have gained interest as these devices do not require any external power to operate but rather can harvest energy to operate the low-power elec-tronics. However, textile-based sensor fabrication requires complex multi-step fabrication protocols. In this study, a one-step fabrication of functional fibers for self-powered sensing using thermal drawing process was investigated. Inte-gration of 2D nanomaterials have significantly improved the performance of the fluoropolymer (PVDF) based triboelectric and piezoelectric fibers. 2D nanoma-terials enhance the output predominantly by the combined effect of interfacial polarization and microcapacitor formation. MXene-PVDF nanocomposite fiber shows β phase increases consistently up to 44% upon 5 wt% MXene addition. The triboelectric fiber demonstrates the capability to harvest energy and biomotion monitoring such as gait analysis. The structural design of MoS2-PVDF piezoelec-tric fiber ensures efficient stress transfer to the piezoelectric domain. Moreover, MoS2 addition increases up to 3 wt% with β phase amount 50% and decreases upon higher MoS2 addition. The Piezoelectric fiber demonstrates the ability to detect physiological signals such as pulse and respiration. The sensors can wirelessly transmit data to store and analyze using a microcontroller unit. The demonstration of large-scale fabrication of the self-powered fiber sensors shows the prospect of the technology as industrially translatable for developing smart clothing.
Open Access
Computational analysis of 3D genome organization and its effect on nuclear morphology and mechanics
(Bilkent University, 2023-10) Attar, Ali Göktuğ
Several disorders, including progeria, cancer, and Emery-Dreifuss muscular dystrophy, share abnormalities in eukaryotic cells' nuclear structure and mechanics. One of the contributors to nuclear morphology and mechanics is the chromatin filling the 10-micron elastic nucleus. The polymer physics principles behind the relationship between chromatin and nuclear morphology and its mechanics need to be clarified. To elucidate this relationship between chromatin and polymer and nuclear morphology and mechanics, we concentrate on chromatin phase separation utilizing a coarse-grained polymer model encapsulated in an elastic shell. Our approach can capture the conventional and inverted nucleus organization while allowing nuclear deformability. Heterochromatin can be one of the key determinants of the nuclear shape by revealed by examining heterochromatin heterochromatin interactions, as well as the interaction between chromatin and lamina inspecting through the biologically relevant volume fractions. The simulations showed that the heterochromatin-nuclear shell interactions influence the variation in the nuclear shape fluctuations, thus leading to nuclear deformations. The interplay between heterochromatin-heterochromatin interactions and its interaction with the nuclear shell plays a role in phase separation and nuclear shape fluctuations. Higher heterochromatin concentration resulted in abnormal morphology in lower volume fraction, in contrast to some experiments suggesting the opposite trend. The volume fraction exhibits a suppressing effect on the nuclear shape fluctuations in all examinations of heterochromatin interactions. Additionally, the tethering and crosslinking of the heterochromatin provide a chromatin-based stiffness to the nuclear shell revealed by force-strain relationships. Altogether, our results imply that chromatin, mainly heterochromatin, considerably contributes to nuclear morphology and mechanics.
Open Access
Re-education of tumor-associated macrophages VIA TLR7/8 agonist-encapsulated liposomes
(Bilkent University, 2023-09) Tabel, Eylül
Cancer is an extremely complicated disease, and even though there have been years of effort in science to understand and find a cure, it still is one of the most terminal conditions. Lately, it is more clearly understood that the intricate wiring of the tumor microenvironment is more determinative than the intrinsic cancerous nature of tumor cells, for both disease prognosis and treatment efficiency. This environment bears many types of non-cancerous cells; such as endothelial cells, fibroblasts, and immune cells; all of which become heavily influenced by the cancer cells through their wiring of the cancer-helping niche. As proved by the success of a cancer staging approach, that utilizes a quantification of the infiltration of cytotoxic T cell populations, and which often offers a more effective staging system than traditional TNM staging for cancer, the low immunogenicity of the tumor microenvironment has been a new focus of target for kinds of therapies, including cytotoxic and immunesystem stimulation approaches One such approach is targeting tumor-associated macrophages, which are highly specialized immune cells in the tumor microenvironment responsible for many biological functions such as proliferation of cancer cells, enhancement of cancer stemness, metastasis, and a low immunogenic profile around the environment. Amongst many strategies against these cells that have extraordinary polarization and switch-of-function capabilities, polarizing them back to a tumor-fighting polarization via stimulatory molecules have yielded promising results, with the biggest obstacle of induction of a systemic immune response. Here, we have utilized liposomal encapsulation of a Toll-Like Receptor 7/8 agonist called resiquimod, in order to re-educate THP-1 macrophages that transformed into tumor-associated macrophages, back to an opposite state where they could no longer be allies of cancer cells. We have characterized the liposomes by size and morphology, and obtained a 200nm size. After we showed that this size ensured selective phagocytosis by macrophages; we loaded resiquimod molecules inside the liposomes through remote loading, with a loading efficiency of 96%. Tumorassociated macrophages that were obtained by HT-29-conditioned media incubation of THP-1 cells were characterized for their polarization state, and were re-educated with resiquimod-encapsulating liposomes. The efficiency of re-education was assessed by the reversal of tumor-associated polarization’s impact on HT-29 cells in proliferation in standard cell culture by coverage assay and in spheroid culture, cell viability by flow cytometry, metastatic capabilities by wound-healing assay, and stemness by immunocytochemistry for CD133. Overall, with a limitation of variety of tests to assess biological functions of the reeducation, we have obtained promising results for an immunotherapeutic approach of re-educating tumor-associated macrophages in colorectal cancer.
Open Access
Quantum dot-polymer interactions in contact electrification of common polymers
(Bilkent University, 2023-08) Kaya, Görkem Eylül
Contact electrification or static charging occurs when we rub or contact insulator surfaces. This contact leads to the development of electrical charges, and accumulation of these charges may lead to uncontrolled electrostatic discharging (ESD), causing accidents, e.g., powder explosions, and economic losses in the industry. Conversely, contact charges can contribute to many application fields, such as recently developed triboelectric nanogenerators for harvesting mechanical energy. Therefore, it is crucial to control contact charges by knowing the mechanisms of contact electrification in dept. However, despite centuries of research, there are still many debates and unknowns in contact charging of polymers since it has many complex events such as electron, ion and material transfer between the surfaces. In this thesis, we studied the contact electrification of common polymers doped with quantum dots (QDs). Surface engineering of polymers at the nanoscale can open doors for new applications and give insights into contact electrification. In the first part of the thesis, we investigated the mitigation mechanisms of contact charges by doping CdSxSe1−x and CdSxSe1−x/ZnSe QDs into PDMS polymer. We tested the interaction of QDs with the polymer based on the different locations of charge carriers (electrons and holes) via a band-gap engineering approach. In the following sections of the thesis, we studied the contact charge generation in the QD-polymer composites, initially by testing the effect of ligand exchange treatment on QDs by pyridine treatment of QDs capped with oleic acid. Then, the effect of different polymer matrices was tested by doping QDs into polyethylene, polystyrene, and polymethyl methacrylate. In the last section of the thesis, nitrogen-doped carbon dots - a more biocompatible and environmentally friendly additive compared to inorganic QDs - were doped into polyvinyl alcohol to study contact charge generation. QDs and QD-doped polymers were characterized by UV-VIS spectroscopy, photoluminescence, time-resolved fluorescence, atomic force microscopy, transmission electron microscopy, and X-ray diffractometry. It was demonstrated that QDs can be used to stabilize or destabilize the contact charges on the surfaces, and this effect can be further manipulated by UV light illumination. This first-time display of the light-tunability of static charges in common polymers might help prevent excessive accumulation of charges on them or enhance the static charge stability on demand. Finally, we believe our results can be beneficial to enlighten the physical interactions of QDs with common polymers at the nanoscale and may be used to design straightforwardly-accessible materials having advanced electronic properties.
Open Access
Synthetic regulatory sequence designs for mRNA vaccines
(Bilkent University, 2023-08) Hınçer, Ahmet
mRNA-based therapeutics have demonstrated significant potential for enhancing human health across various applications. Notably, mRNA vaccines, a prominent subset of this therapeutic approach, showcased their efficacy during the COVID-19 pandemic by safeguarding billions of lives. Despite their success, the full scope of mRNA vaccines in addressing diverse health concerns, such as cancer, remains constrained by existing limitations in tunability and targetability. A deeper exploration of mRNA vaccine regulation is inevitable to harness their complete capabilities. This thesis centers on comprehending and manipulating two pivotal regulatory domains within the mRNA molecule itself: the coding sequence and the 5’ untranslated region (UTR). Regarding the coding sequence, we engineered an mRNA vaccine candidate featuring a combined antigen coding region for SARS-CoV-2 to elicit a dual immune response against the virus. Our findings underscore that the resultant antigen exhibited interactions with distinct antibodies generated throughout the natural course of infection. This interaction profile potentially signifies a dual immune activity for enduring protection. Therefore, we practiced the essential stages of mRNA molecule manipulation requisite for an effective vaccine candidate. In parallel, we devised an innovative methodology for constructing synthetic 5’ UTR libraries tailored for selective expression within cancer cells. Collectively, this thesis advances our grasp of mRNA vaccine regulation and design. Considering the needs of the current state of mRNA vaccines, this heightened control over mRNA molecules promises novel avenues for addressing a spectrum of diseases.
Open Access
Thermal management in high-power laser diodes by waveguide design
(Bilkent University, 2023-08) Sünnetçioğlu, Ali Kaan
Semiconductor edge-emitting laser diodes (LDs) are known for their high efficiencies but face challenges in managing self-heating at high operating currents and output powers. The excessive heat density experienced by LDs can lead to critical temperature levels, resulting in catastrophic optical damage (COD) and device failure. Understanding the root cause of COD is crucial for enhancing their reliability and operating output power. This thesis investigates the self-heating mechanism in LDs and introduces novel waveguide designs for thermal management. Initially, we experimentally analyzed LDs with varying waveguide widths to uncover the cause of their failure mechanism. Narrower waveguide LDs achieved higher output power densities but maintained lower internal and facet temperatures. The thermal simulation results showed that narrower waveguide LDs exhibit improved three-dimensional heat dissipation, reducing internal and facet temperatures. The results clarified the fundamental reasons behind the superior reliability of narrower waveguide LDs. Next, we designed and fabricated LDs with two different types of waveguides for their thermal management. The first design introduced a two-section waveguide, which moved the laser section heating away from the facet by positioning a window section near the output facet that is pumped to transparency. This approach reduced facet temperature below the laser internal temperature and eliminated the catastrophic optical mirror damage (COMD) failure. The second design, a distributed waveguide (DWG), increased the lateral heat-dissipation area with passive sections between the laser sections. This method achieved LD cooling by effectively dissipating self-heating and reducing the facet temperature. These findings provide valuable guidance for thermal management to realize LDs with significantly improved reliability and lifetime.
Open Access
Solution-processed/evaporation-based light-emitting diodes of face-down/edge-up oriented colloidal quantum wells
(Bilkent University, 2023-08) Bozkaya, İklim
Colloidal quantum wells (CQWs) have emerged as a quasi-two-dimensional class of semiconductor nanocrystals with the critical structural properties of being both atomically flat and vertically ultrathin. In these CQWs with atomically accurate thickness control, their extremely strong and precise one-dimensional quantum confinement, defined by few nanometers in sub-nm precision, gives rise to well-controlled anisotropic emission. The emission characteristics are composed by the contributions of transition dipole moments (TDMs), which are by their nature highly anisotropic in CQWs. In-plane TDMs lying in the lateral plane and out-of-plane TDMs along the vertical direction, taken with respect to the plane of a CQW, contribute to the emission characteristics proportionally. These features of CQWs make them highly attractive for use in light-emitting diodes (LEDs). In this thesis, to this end, in LEDs constructed either using all-solution based processing or evaporation, we show face-down and edge-up oriented self-assemblies of CdSe/Cd0.25Zn0.75S core/hot-injection shell (HIS) grown CQWs, along with their Fourier analyses using back focal plane (BFP) imaging. Results show that the out-of-plane TDM distribution for all-face-down oriented CQW film is suppressed 4.1 times, with its in-plane TDM distribution reaching 92%. Thanks to the strong contribution from the in-plane TDMs, the corresponding angularly resolved distribution of luminescence exhibits a highly directional intensity profile for the film of face-down CQWs placed lying on a substrate. Used as an electroluminescent layer, all-face-down oriented CQWs enable extraordinarily large external quantum efficiency (EQE) increased by almost 2 folds compared to that of randomly-oriented CQWs, with EQE reaching 18.1% in the case of face-down orientation, a record high level for solution-processed CQW LEDs. Moreover, in this thesis work, for the edge-up oriented self-assemblies of CQWs creating superstructures in chain, we investigated the distribution of TDMs and discovered length of the chain formation of such stacked CQWs plays an essential role. Extending CQW chains from 50 to 500 nm in length, on average in the film, the out-of-plane TDMs in the long-chained edge-up CQWs placed standing on a substrate is increased 3.5 times in comparison to those of the short-chained edge-up CQWs. The contribution of out-of-plane TDMs in directional emission is also improved via inducing longer chains. In the light of the results of Fourier image analysis, being used as the electroluminescent layer of evaporated LEDs in inverted architecture, all-edge-up oriented CQWs enable 50% enhancement in luminance levels compared to that of randomly-oriented CQWs. Additionally, in comparison to the face-down oriented CQWs used as the electrically driven emissive layer in the same device structure of LEDs, the edge-up oriented CQWs exhibit 60% improvement in charge injection. Such strongly orientation-dependent behavior of CQW layered structures, as exploited in this thesis, encourages further systematic studies on their ensemble optical emission characteristics in both solution-processed and evaporation-based LEDs and promises great potential for LED and other optoelectronic device applications.
Embargo
Hybrid biosensing systems for the detection of biomolecules and disease biomarkers
(Bilkent University, 2023-08) Aslan, Yusuf
Optical metasurfaces are configurations of artificially structured surfaces designed to obtain unusual electromagnetic properties. The ability to manipulate a confined electromagnetic field enables metasurfaces to be utilized as optical point-of-care (POC) biosensors for the detection of low concentrations of biomarkers. Moreover, the integration of fluorescent molecules and plasmonic metasurfaces is utilized to enhance both plasmonic and fluorescent signals; however, the nanoscale distance and spectral overlap between the fluorescent emitter and plasmonic metasurface are crucial for the separation of the fluorescence-coupled plasmonic radiation and non-radiative induced plasmon surface entrapment. In this study, fluorescently labeled (FITC) proteins are integrated over a plasmonic metasurface via three different surface modifications for obtaining a hybrid biosensing system that boosts the device’s plasmonic sensitivity and lowers the detection limit. The metasurface is fabricated via physical vapor deposition of titanium (10 nm), silver (30 nm), and gold (15 nm), respectively over polycarbonate nanograting substrates of optical disks (DVDs). Additionally, the surface modifications are arranged via short-distance, medium-distance, and long-distance modifications for fluorescently labeled molecule binding. After the evaluations, the highest plasmonic wavelength shift over the FITC labeled protein binding is obtained from the medium-distance modification with ~4.4 times signal enhancement over the short-distance modification. The medium-distance modification is further combined with an immunoassay for the detection of Alzheimer’s disease. Consequently, this study paves the way for designing new arrangements on a metasurface to couple with fluorescence molecules while enhancing the analytical performance of the plasmonic biosensor.
Open Access
Molecular investigation of polyelectrolyte hydrogel under mechanical deformation
(Bilkent University, 2023-07) Rafique, Muzaffar
Polyelectrolyte hydrogels are fascinating materials that can produce electromechanical responses when they are electrically or mechanically deformed. However, the accurate molecular origins of such phenomenon are still unknown, even though it is often ascribed to the change in condensation of counterion levels or alteration of ionic conditions in the pervaded volume of the hydrogel. We used all-atom molecular dynamics (MD) simulations to investigate this behavior by utilizing a polyacrylic acid (PAA) hydrogel immersed in an explicit polar solvent as our model system. In the atomistic MD simulation, we investigated the swelling behavior of polyelectrolyte hydrogels, traditionally computed through the equilibrium of chemical potential and pressure between the system and reservoir. However, we discovered that achieving the equilibrium swelling state was non-trivial, as faster relaxation of the simulation box resulted in lower swelling ratios, while slower relaxation led to larger swelling ratios. To address this challenge, we employed theoretical calculations with a Gaussian state as the reference to estimate the hydrogel’s swelling ratio effectively. In our computational study, we investigated the response of PAA polyelectrolyte hydrogel from weak to highly swollen (i.e., between 60 to 90% solvent content) when subjected to uniaxial mechanical compression and extension. Our primary aim is to compute the condensed counterions at different deformations at the microscopic level. We found out that condensation of counterion shows highly non-monotonic behavior when they are mechanically deformed, with an overall increase in total counterion condensation when the PAA hydrogel is uniaxially compressed or stretched. However, this effect diminishes for weakly swollen gel because a large fraction of counterions are already condensed on the polyelectrolyte polymer. Upon closer examination, we found that counterion condensation increases along the stretched chains in the hydrogel. on the one hand, this increase reaches to maximum value for certain deformation ratios after that, we see a decline in the condensation of counterions when the hydrogel chains are stretched further. On the other hand, we see a very minimal increase in condensation when the hydrogel is compressed, and chains are collapsed state. We also analyzed the single polyelectrolyte chains, which also displayed a qualitatively similar response. This observation gives us insight that polymer chain conformations affect the distribution of counterions in the gel. We further investigated the counterion condensation behavior for polyelectrolyte solutions at their critical concentration level. However, we don’t see any deformation-dependent counterion condensation. This suggests the importance of hydrogel topology, which constrains the polyelectrolyte chain ends and leads to the observed behavior. These extensive molecular dynamics simulations shed light on the interesting and heterogeneous behavior of counterion condensation when the hydrogel is deformed, showing a rich electrostatic response behavior. These findings contribute significantly to the understanding of the underlying behavior of mechanically deformed polyelectrolyte hydrogels.
Open Access
Synthesis of nanoparticles by laser ablation in liquid method and optical applications
(Bilkent University, 2023-08) Taylan, Umut
Pulsed laser ablation in liquids (PLAL) method is a fast, green, and straightforward method that can be used to synthesize pure nanoparticles free of ligands, capping agents, and waste products. Several types of nanoparticles such as metals, oxides, alloys, semiconductors, composite and compound nanoparticles with spherical or complex morphologies can be synthesized with PLAL method. In this thesis, AuCu nanoparticles for photovoltaic application, AgCu nanoparticles for tunable optical properties, CuS/Cu1.8S nanoparticles for photothermal and photoacoustic application, and (Y0.83Yb0.16Er0.01)2O3 nanoparticles for upconversion photoluminescence application are synthesized. The synthesized AuCu nanoparticles are used in organic solar cells and enhanced the photocurrent production, proven by the 21.4% increase in the power conversion efficiency. AgCu nanoparticles show composition and laser fragmentation dependent tunable surface plasmon resonance between 420 nm – 580 nm, giving 160 nm tunability. These nanoparticles also show complex morphologies with Janus nanoparticle and core-shell type configurations. Copper sulphide nanoparticles show a broad absorbance in the NIR region with absorbance peak at 1183 nm. Nanoparticles with 1 mg/mL concentration show a 52.2 °C temperature increase in 3 minutes of 3.23 W/cm2 1080 nm CW laser irradiation. Photoacoustic imaging experiments where copper sulphide nanoparticles are utilized show a significant contrast enhancement compared to ultrasonic imaging at 1 cm depth. The upconversion nanoparticles show an intense red emission at 651 nm from 980 nm laser irradiation and lowered green emission compared to the target material which shows nanoparticles produce more heat compared to the target which can be useful for photoluminescence – photothermal applications.
Open Access
Fabrication and characterization of negative curvature hollow core polymer optical fibers for near-infrared light guidance
(Bilkent University, 2023-07) Rahman, Mahmudur
Polymer optical fibers (POFs) have attracted significant attention for their short-distance data transmission, industrial automation, and chemical and biological sensing applications. The low cost, lightweight, flexibility, accessibility, and ease of material processing features of the polymers make them superior to their silica counterparts. Moreover, compared to conventional POFs, hollow core polymer optical fibers (HCPOFs) exhibit light guidance through the air, significantly reducing material absorption loss in the near-infrared (NIR) region. Structuring the cladding part with the appropriate fiber material can further modify the light-guiding properties of HCPOF with low transmission loss in NIR. Several methods have already been employed for the successful fabrication of POFs, but the possibility of fabricating intricate geometry-based HCPOFs with these approaches and optimization of fabrication methods are yet to be resolved. This study explored the stack and draw technique and fused deposition modeling (3D printing) approaches to find the fabrication feasibility of long-length and intricate geometry-based negative curvature-based HCMPOFs with two different polymeric materials. A detailed investigation was carried out on the modified thermal drawing process to achieve well-structured HCMPOFs directly drawn at high tension from the fabricated preforms. Moreover, during the thermal drawing, expansion and contraction of the core and cladding part of the fibers were frequently observed. Inflation of the cladding tubes during the fiber drawing was required to preserve the designed structure in the fibers. This was achieved by applying gas pressurization inside the fibers in both preforms made by the stack and draw technique and 3D printing. Optical characterization is performed using Supercontinuum (SC) Laser in the 600 − 1700 nm wavelength range. Differences in the transmission spectra between core and cladding structures significantly prove the light-guiding prop-erties of the proposed HCMPOFs. The transmission losses of the HCMPOFs were measured using Optical Spectrum Analyzer (OSA), and were found to average 49.26 dB/m for stack and draw-based fabricated six-tube HCMPOF and 16 dB/m for 3D printed six-pointed star cladding-based HCMPOF. Further investigation is carried out on bend-induced loss against the mechanical effects of the 3D printed intricate geometry-based HCMPOF at different bending angles. The lower transmission loss with a low bend-induced loss against the mechanical effects of HCMPOFs explicitly shows the potential of using HCMPOFs as an alternative to conventional polymer optical fibers for visible and infrared light guidance.
Open Access
Mechanical and chemical properties of nanoparticle-coated E-glass fibers for composites applications
(Bilkent University, 2023-07) Ahmed, Md Kawsar
Glass fibers are the most extensively employed reinforcement materials in the fiber-reinforced composites field owing to their superior mechanical properties with cost-effectiveness. The mechanical and chemical properties of the composites are greatly dependent upon the reinforcement materials. In order to enhance the performance of composites, it is necessary to improve the mechanical property of the reinforcement materials, i.e., glass fibers. In this thesis, the mechanical and chemical properties of E-glass fibers were investigated via the incorporation of metal oxide nanoparticles. As part of this process, E-glass fibers were dip-coated with nanoparticle solutions using titania (TiO2), silica (SiO2), and zirconia (ZrO2) nanoparticles. Microscopic and spectroscopic analysis proved the presence of nanoparticles on the surface of the fibers. Tensile tests were conducted on bare and nanoparticle-coated fibers to see the effect of coating and the concentration of nanoparticles over the fiber’s surface. Weibull statistical analysis was carried out on bare and coated fibers to see the effect of stress on the probability of failures of the E-glass fibers. A fractographic study was also carried out on E-glass fibers to see the effect of tensile strength on the mirror region of the fracture surface. Additionally, chemical analysis was also carried out to see the resistivity of the fibers in a highly alkaline environment. The results suggest that glass fibers coated with TiO2 nanoparticles improved the tensile strength of fibers up to 11.7% by providing a lower probability of failure. On the other hand, coating with SiO2 nanoparticles had a slightly negative impact on the strength of fibers due to the lower quality of coating, leading to a decrease in the tensile strength and an increase in the probability of failure. Moreover, ZrO2 nanoparticles were found effective in providing resistance against the corrosion to the glass fibers in an alkaline environment for up to 4 days of dwelling. Nanoparticle-coated E-glass fibers are expected to improve the mechanical and chemical properties of glass fiber-reinforced composites for various industrial applications in the future.