Item EmbargoComputational analysis of 3D genome organization and its effect on nuclear morphology and mechanics(Bilkent University, 2023-10) Attar, Ali Göktuğ; Erbaş, AykutSeveral 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. Item EmbargoRe-education of tumor-associated macrophages VIA TLR7/8 agonist-encapsulated liposomes(Bilkent University, 2023-09) Tabel, Eylül; Ortaç, BülendCancer 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. Item EmbargoQuantum dot-polymer interactions in contact electrification of common polymers(Bilkent University, 2023-08) Kaya, Görkem Eylül; Baytekin, BilgeContact 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. Item Open AccessSynthetic regulatory sequence designs for mRNA vaccines(Bilkent University, 2023-08) Hınçer, Ahmet; Şeker, Urartu Özgür ŞafakmRNA-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. Item EmbargoThermal management in high-power laser diodes by waveguide design(Bilkent University, 2023-08) Sünnetçioğlu, Ali Kaan; Demir, AbdullahSemiconductor 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. Item Open AccessSolution-processed/evaporation-based light-emitting diodes of face-down/edge-up oriented colloidal quantum wells(Bilkent University, 2023-08) Bozkaya, İklim; Demir, Hilmi VolkanColloidal 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. Item EmbargoHybrid biosensing systems for the detection of biomolecules and disease biomarkers(Bilkent University, 2023-08) Aslan, Yusuf; İnci, FatihOptical 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. Item EmbargoMolecular investigation of polyelectrolyte hydrogel under mechanical deformation(Bilkent University, 2023-07) Rafique, Muzaffar; Erbaş, AykutPolyelectrolyte 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. Item EmbargoSynthesis of nanoparticles by laser ablation in liquid method and optical applications(Bilkent University, 2023-08) Taylan, Umut; Ortaç, BülendPulsed 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. Item EmbargoFabrication and characterization of negative curvature hollow core polymer optical fibers for near-infrared light guidance(Bilkent University, 2023-07) Rahman, Mahmudur; Durgun, EnginPolymer 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. Item Open AccessMechanical and chemical properties of nanoparticle-coated E-glass fibers for composites applications(Bilkent University, 2023-07) Ahmed, Md Kawsar; Durgun, EnginGlass 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. Item Open AccessMonolayer-thick light-sensitive nanocrystal skins of oriented colloidal quantum wells(Bilkent University, 2023-05) Bozkaya, Taylan; Demir, Hilmi VolkanColloidal quantum wells (CQWs), a two-dimensional member of semiconductor nanocrystals, featuring very tight vertical quantum confinement, possess giant oscillator strengths. Also, CQWs exhibit remarkably large absorption cross-sections, thanks to their oscillator strengths combined with their laterally large geometries. Additionally, as a powerful tool of fabrication, CQWs lend themselves to be conveniently self-assembled into monolayer-thick films in a single orientation of our choice: either face-down (lying down on their large lateral surfaces and side by side leaving no large gap between them similar to a mosaic pattern) or edge-up (standing up on their thin edges and facing each other in a very dense superstructure formation of repeating chains). In this thesis, to make use of the attractive absorption properties of CQWs and leverage on our ability to construct their orientation-controlled self-assemblies, we show the first account of monolayer-thick light-sensitive nanocrystal skins (LS-NS) that employ self-oriented CQWs as their active absorptive layer. These CQW LS-NS devices operate on the principle of strong optical absorption of the monolayered assembly of CQWs and the subsequent photogenerated potential build-up across their strongly capacitive thin device for sensing in the visible to ultraviolet. Such oriented CQWs in the LS-NS device architecture yield profoundly reduced surface roughness in their monolayer-thick films, essential to high device performance. Here, specifically, we developed and demonstrated two groups of LS-NS devices: one group consisting of all face-down oriented CQWs and the other, of all edge-up ones. We systematically studied their photocharging effect, spectral sensitivity and decay times. We observed in all LS-NS devices that the spectral sensitivity complies with the first (heavy-hole) and second (light hole) excitonic peaks of the absorption of the CQWs. We also found that, as the excitation power is increased, the peak photovoltage readout increases while the sensitivity decreases. The photocharging effect was further observed as the excitation was turned off. Finally, using the edge-up orientation, we identified a profound peak photovoltage signal enhancement. These findings of the thesis indicate that the proposed LS-NS devices of the orientation-controlled CQW monolayers hold great promise for applications in photos-sensing facades over larger surfaces. Item EmbargoIntegration of chips by flip-chip bonding techniques(Bilkent University, 2023-05) Öztürk, Mehmet Halit; Yılmaz, MehmetIntegration and packaging of MEMS devices are necessary for designing operational, independent and mobile products. Flip-chip bonding (FCB) has been recognized as an important technology to meet some of the integration and pack-aging needs. To assemble a probe for photoacoustic imaging (PAI), integration of ASIC chips with a CMUT chip and integration of the CMUT chip with a PCB is required, where various FCB techniques may be employed for integration. Thermo-sonic FCB was the most suitable for the ASIC-CMUT integration. Gold stud bumps (GSBs) were used for the TSFCB. Therefore, the fabrication of GSBs was optimized for 25.4 µm and 17.5 µm diameter gold wires. Also, to flatten the top surface of the GSBs and to level the height of the GSBs, a novel displacement-controlled coining (DCC) process is developed. The height and bonding surface area of the GSBs can be tailored for flip-chip bonding (FCB) processes. Furthermore, using the lumped-capacitance modeling approach, a heat energy transfer based, experimentally validated analytical model is developed for the thermo-sonic flip-chip bonding process (TSFCB). The developed analytical model is used to estimate TSFCB process parameters for ASIC-CMUT FCB integration. Successful TSFCB process trials are completed in this study at a wide range of process temperatures (Tprocess) of 24 °C, 25 °C, 40 °C, 150 °C, and 375 °C. Two ASIC chips are successfully integrated with a CMUT chip via the TSFCB. Another FCB process combines stacked GSBs and isotropic conductive adhesive (ICA) material optimized for the integration of CMUT-PCB. Surface-mount device (SMD) and a through-hole component of the PCB are soldered and fabrication of the integrated electronic systems of the probe is completed. Finally, the design and fabrication of the probe are presented. The probe is assembled using integrated electronic systems for PAI imaging. Item Open AccessFabrication of polarization-maintaining optical fiber with ultra-low bending-dependent polarization extinction ratio deterioration(Bilkent University, 2023-02) Akçimen, Samet; Ortaç, BülendPolarization-Maintaining Optical Fiber (PM) is a unique-designed fiber that pre-serves and utilizes the polarization state of the light transmission that is launched into it. With this aspect, our biaxial PM fiber is adequate for different applications, including interferometers, fiber optic gyroscopes (FOGs), telecommunication, and all-PM fiber lasers by maintaining single polarized light transmission against the environmental perturbation. A biaxial PM fiber, which was found to possess high polarization extinction ratio (PER) values over 30 dB among two orthogonal axes, is composed of the unique geometry that is the combination of elliptical core and Panda-type PM fibers. Even under environmental temperature conditions, from -55 °C to +85 °C, the PER values were obtained to be maintained. During the bending dependent PER measurements, it was observed that the PER values at relatively small diameters from 12 mm to 5 mm were not altered compared to the biaxial PM fibers not bent. PER deterioration was determined as 0.5%. We measured the group beat lengths which were 1.40 mm for one axes and 1.45 mm for the other at 1550 nm to confirm the biaxial PM property. The optical loss of the biaxial PM fiber was measured with an optical time-domain reflectometer (OTDR) and the loss was found to be below 1.5 dB/km for over 3 km of fiber length. Along two polarized axes, the mode field diameter (MFD) and the numerical aperture (NA) values were also determined. This novel PM fiber addresses a need for the Panda and elliptical core type (PM) fibers which are essential for integrated fiber based sensors and instruments, such as fiber optic gyroscopes. Item Open AccessGlycosylated conjugated oligomer and chlorophyll based nanoparticles for photodynamic therapy(Bilkent University, 2023-01) Oduncu, Ezgi; Tuncel, DönüşNanomaterial-based therapeutic agents are drawing a lot of attention because numerous capabilities, including drugs, targeting groups, and photoactive units, can be combined on one platform to treat infectious diseases and cancer. In this regard, two different nanomaterials and their nanomedicine applications were re-ported. Firstly, red-emitting glycosylated conjugated oligomer (COL) nanopar-ticle was prepared and hybrid conjugation with gold nanoparticles was prepared by the nanoprecipitation method in order to examine photothermal applications. Due to their authentic electronic and optical characteristics, showing high sin-glet oxygen production ability, enabling control of the sizes of nanoparticles by acetyl groups in the side chains, enhancing their stability, and improving cell permeability via the hydrophobic effect they are promoting photosensitizers for photodynamic therapy. Secondly, chlorophyll, a natural photo absorbent, was ex-tracted from spinach leaves, and chlorophyll nanoparticles were prepared by nano-precipitation method because of their promoting properties which are high bio-compatibility, low production cost, and natural reductive chemical atmosphere, containing plenty of hydrogen atoms and being environmentally friendly. Then, hybrid conjugation with gold nanoparticles was prepared to investigate photother-mal therapy application. Both of the nanoparticles showed a high generation ability of reactive oxygen species (ROS) even at low light intensities and short exposure times which makes nanoparticles an ideal photosensitizer. From the antibacterial experiment, when Gram-negative (Escherichia coli, E. coli) bacteria were incubated with chlorophyll-based nanoparticles, a reduction up to 2.8-log and 2.33-log in colony-forming units (CFUs) was obtained under light irradiation for Chl-Au and Chl nanoparticles, respectively. Also, these nanoparticles showed minimal dark cytotoxicity (0.32-log and 0.15-log). On the other hand, conjugated oligomer-based nanoparticles precipitated in bacterial suspension and were un-able to pass across the cell wall of bacteria which was proved by SEM images and 4 mm and 5 mm inhibition zone were recorded for COL and COL-Au nanopar-ticles which are highly lower than ampicillin (7 mm). Along with these results, it is deduced that conjugated oligomer nanoparticles are not proper for antibac-terial photodynamic applications although the interaction between the bacterial cell wall and nanoparticle was promoted with gold conjugation. For anticancer photodynamic therapy applications, MCF-7 breast cancer cells were treated with these nanoparticles in the dark and under white light illumination for 20 min-utes, and the decline in cell viability was recorded at 50 %, 60 %, and 58 %, 72 %reduction for Chl, Chl-Au, and COL, Chl-Au nanoparticles, respectively. Also, they demonstrated dark cytotoxicity with the increment of concentration. Ad-ditionally, they also demonstrated the capacity for cellular imaging due to their inherent fluorescent properties, which might be used for image-guided PDT ap-plications. Along with this, the cytotoxicity results were supported by displaying the cellular uptake of nanoparticles and their surrounding the nucleus of breast cancer cells. Item Open AccessExplorations on optomechanical devices for energy sink applications(Bilkent University, 2023-01) Lee, ChulHyeong; Hanay, Mehmet SelimResonance energy dissipation mechanism has been gaining importance in the interest of sensing applications. As such, the capacity for precise and fast measurement of the transient phase of motion has been desirable. The development of optomechanics in recent years has enabled such a fast scheme. Here a design, setup, and measurement of a silicon nitride optomechanical system is explored. Fundamental parameters of the design are investigated with simulation analysis. Grating structures, waveguides, and resonator parameters are explored. A series of optical resonance responses are observed, and the resonance characteristics are analyzed for optomechanical devices of combinations of design parameters. Measurements on devices of different nanomechanical beam modulation schemes are performed. To translate the technique from the optical to microwave domain, an integration of a split ring resonator (SRR) cavity and NEMS device is explored. Mode simulation of the modified cavity design is done. A technique of alignment of EBL to an existing pattern on an insulating surface is optimized. The studied designs leave possibilities for applications in real-time mass sensing and fundamental studies on energy dissipation mechanisms. Item Open AccessColloidal doping of thick nanoplatelets(Bilkent University, 2022-12) Ahmad, Muhammad; Demir, Hilmi VolkanSemiconductor nanoplatelets (NPLs) make an interesting group of nanocrystals with unique optical properties as a result of their quasi 2-dimensional (2D) electronic structure. Such emerging fascinating optical features of NPLs include high absorption cross-section, narrow emission linewidths, and reduced Auger recombination, making them a superior choice compared to conventional semiconductor nanocrystals for optoelectronic applications. Doping of these materials with transition metals, such as silver and copper, provides great opportunities to modify and tune the electronic structure of these NPLs for various devices including light-emitting diodes and luminescent solar concentrators. Such doping with transition metals allows for manipulation of the photoluminescence from these NPLs, control of the recombination processes of the photogenerated carriers in these NPLs, and observation of the giant Zeeman effect as a result of exchange interactions between the dopants and carriers in these NPLs. Previously, CdSe NPLs have been doped with copper and silver only up to vertical thickness of 5 monolayers (ML). However, doping of thicker NPLs has not been possible to date. In this thesis work, we successfully doped thick CdSe NPLs having 7 ML in thickness with silver and copper using partial cation exchange to obtain large Stokes-shifted emission in the near-infrared (NIR) region. Here, the effect of precursor ratio and reaction temperature were systematically studied to tune the resulting emission. For both copper and silver dopants, we successfully quenched fully the band-edge emission, and purely dopantinduced emission was obtained. We also co-doped these NPLs with silver and copper, and we successfully obtained both copper- and silver-induced emissions from these NPLs. We further grew the CdZnS shell on 7 ML CdSe core by hot injection method and doped the resulting CdSe/CdZnS core/shell NPLs with silver and copper to push their emission further towards longer wavelengths in the NIR region. These thick doped-NPLs with large Stokes shift and emission in the NIR region present a promising platform for light-emitting and -harvesting applications. Item Open AccessMicrofluidic chip-based systems for monitoring cancer therapy(Bilkent University, 2022-12) Yılmaz, Eylül Gülşen; İnci, FatihIn tumor microenvironment, cancer cells are exposed to a range of fluid shear stresses (FSS); yet, current in vitro three-dimensional (3D) models have limitations to investigate the impact of biophysical stimuli on cancer mechanism and chemoresistance in a dynamic manner. In the past few decades, vital demand for exploring biological significance of mechanical forces has led to the development of several innovative approaches. One of these approaches is the integration of microfluidic systems into cancer studies. The use of microfluidic chips has garnered increasing attention since they offer ease-of-manipulation, high-throughput, less material/reagent consumption, and low-cost. On the other hand, the researches have stated explicitly that tumor-derived extracellular vesicles (EVs) regulate local and systemic milieu to drive the development and spread of cancer through nano- and micron-sized vesicles they carry. In this thesis, breast cancer cells (MCF-7) have been utilized as a model cancer system, and accordingly, they are cultivated through SF-coated microfluidic systems in order to mimic tumor microenvironment, exhibiting a more dynamic condition. Simultaneously, traditional static culture of MCF-7 cells is also performed as a control group in order to understand the impact of flow conditions. The effects of FSS on gene expression—in particular, EpCAM and CK-18 genes, which are highly expressed in MCF-7 cells— have been examined at the end of cell culturing process. In addition, cancer cells developing any resistance to anti-cancer drugs on the course of FSS have been investigated. In this regard, the cells are treated with either doxorubicin or docetaxel (anti-cancer drugs) in the cases of dynamic (microfluidic system) and static (tissue culture flask) culture conditions. Multi-Drug Resistance 1 (MDR-1) and Breast Cancer Resistance Protein (BCRP) gene expression levels have been assessed once anti-cancer treatment has been finalized. The final step of this study relies on the isolation and analysis of EVs from both static and dynamic conditions with the presence and absence of anti-cancer drug treatment. The utility of EVs has been evaluated deliberately as biomarkers for real-time monitoring of treatment efficacy. Item Open AccessChalcogenide integrated hollow-core optical fibers for infrared light guidance(Bilkent University, 2022-12) Khan, Asfandyar; Demir, AbdullahThe low-loss light transmission and broad bandwidth of hollow-core negative curvature fibers (NCFs) have a variety of applications in infrared (IR) light guidance, such as chemical detection, biomedical surgery, and laser delivery. Although silica is a material of choice for light guidance in the visible and near-IR spectra, transmission losses increase drastically in the mid-IR region; thus, other mid-IR transparent materials, such as chalcogenide glasses, are potentially preferred to guide the light. In this thesis, various cladding designs of arsenic trisulfide (As2S3) and arsenic triselenide (As2Se3) chalcogenide NCFs are numerically explored for low-loss transmission in the mid-IR region. A detailed numerical investigation in the optimization of As2S3 NCFs with tubular and elliptical cladding elements was performed, and a low-loss ellipse-nested tubular NCF design is proposed for mid-IR guidance. The effect on the transmission loss due to cladding elements of the proposed low-loss As2Se3 ellipse-nested tubular fiber design was investigated. Confinement and total loss of all fiber designs were numerically studied, and the single-mode light guidance performance of the proposed low-loss fiber design was explored. The bending loss performance of the fiber was analyzed in the targeted spectrum, and a dispersion control study was carried out to investigate the effect of the primary design parameters on the dispersion performance. A fabrication tolerance study was performed to investigate the effects of common fabrication issues on the proposed design’s guidance properties. In the second part of the thesis, NCFs with silica, chalcogenide, and chalcogenide-coated silica cladding elements were numerically investigated for low-loss near and mid-IR transmission. As2S3 coated silica NCF was compared to simple silica and simple As2S3 fiber to understand the effect of the As2S3 coating on the transmission loss of silica NCF. Fabrication of silica NCF through the stack-and-draw technique followed by micro-coating with As2S3 solution was performed to improve the transmission performance of the As2S3 coated silica glass-based NCF. Further modifications in the fabrication of the NCFs were realized for a thorough comparison with the numerical investigations. Item Open AccessPhotocurrent generation in low dimensional nanomaterials(Bilkent University, 2022-11) Razeghi, Mohammadali; Kasırga, Talip SerkanThis thesis focuses on crucial issue on the understanding the underlying mechanisms of photoresponse in low-dimensional nanomaterials. As the size goes down to the micro and nano level, fine features and induced inhomogeneities like strain, thickness variation, substrate, and junctions become influential in determining plausible effects that can explain and control the light-matter interactions in an optoelectronic device. To develop a better understanding of the fundamental physical characteristics of nanomaterials and optimize thermal and electrical transport in nanomaterial devices, microscopic investigation at a single crystal level is required. In this thesis, I investigated photocurrent generation in two extreme cases: metallic silver nanowire (Ag NW) and semiconducting multilayer molybdenum disulfide (MoS2) using scanning photocurrent microscopy (SPCM). SPCM provides spatial mapping of photoresponse along with corresponding reflected light intensity with a few hundred nanometer resolution. Two terminal devices of Ag and Ag network devices are made by drop-casting NW and placing indium as metal contacts. The SPCM maps show that the NW- NW junctions and NW-contacts interface locally enhance the plasmonic field and act as hot spots. The increased temperature at hot spots is enough to modulate the resistance and results in a photo-bolometric response under the bias voltage. To further enhance the photo-bolometric effect, we decorated the nanowires with plasmonic Ag nanoparticles. The nanoparticles increase the number of hot spots and strengthen light coupling into plasmons. We also attributed zero bias response to the photothermoelectric effect. The photocurrent is generated by the Seebeck coefficient difference caused by nanogaps and nonuniformities in the geometry along the Ag NW. The second part of this thesis describes photocurrent generation by substrate engineering of a few-layer MoS2. To partially suspend a crystal, a flake of MoS2 is exfoliated and then transferred on a substrate with rectangular or circular holes. We observed photocurrent generation from the junction of the supported and suspended parts. Substrate effects like induced doping play an essential role in determining the properties of two-dimensional materials. Our investigations show that the Seebeck coefficient of the suspended part is changed due to isolation from the substrate. The difference in the Seebeck coefficient of suspended and supported regions forms a thermoelectric junction. We also investigated the impact of carrier type and concentration on photocurrent generation by gating experiments.