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Öğe A microwave-powered continuous fluidic system for polymer nanocomposite manufacturing: A proof-of-concept study(Royal Society of Chemistry, 2022) Torabfam, Milad; Nejatpour, Mona; Fidan, Tuçe; Kurt, Hasan; Yüce, Meral; Bayazıt, Mustafa KemalContinuous manufacturing of pure nanocrystals with a narrow size distribution in a polymer matrix is very challenging, although it is highly crucial to get their full potential for advanced applications. A long-lasting nanocomposite (NC) manufacturing challenge is, for the first time, overcome by a microwave-powered fluidic system (MWFS). The effect of microwave power (MWP), flow rate, and the concentration of the reagents are systematically studied. The nylon-6 NC bearing evenly distributed silver nanoparticles (AgNPs) with a mean size of similar to 2.59 +/- 0.639 nm is manufactured continuously in similar to 2 min at similar to 50-55 degrees C using a green solvent, formic acid. The AgNP size becomes smaller when increasing the polymer concentration gradually. Small NPs with a narrow size distribution are produced at high MWP (40 W), but large ones with a broad size distribution at low MWP (10 W). The nylon-6 crystallinity is NP size-dependent, and the gamma-phase (pseudo-hexagonal crystal) is dominant in the presence of small NPs as against the large counterparts. Given the small-sized AgNPs in the MWF-manufactured NCs, the antibacterial activity tests with Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa show superior activity compared to that of the large AgNP-bearing (similar to 50 nm) NCs produced in a conventional heating fluidic system. The proposed MWFS can manufacture other added-value NCs continuously.Öğe Aptamer and nanomaterial based FRET biosensors: a review on recent advances (2014–2019)(Springer, 2019) Pehlivan, Zeki Semih; Torabfam, Milad; Kurt, Hasan; Ow-Yang, Cleva; Hildebrandt, Niko; Yüce, MeralFluorescence resonance energy transfer, one of the most powerful phenomena for elucidating molecular interactions, has been extensively utilized as a biosensing tool to provide accurate information at the nanoscale. Numerous aptamer- and nanomaterial-based FRET bioassays has been developed for detection of a large variety of molecules. Affinity probes are widely used in biosensors, in which aptamers have emerged as advantageous biorecognition elements, due to their chemical and structural stability. Similarly, optically active nanomaterials offer significant advantages over conventional organic dyes, such as superior photophysical properties, large surface-to-volume ratios, photostability, and longer shelf life. In this report (with 175 references), the use of aptamer-modified nanomaterials as FRET couples is reviewed: quantum dots, upconverting nanoparticles, graphene, reduced graphene oxide, gold nanoparticles, molybdenum disulfide, graphene quantum dots, carbon dots, and metal-organic frameworks. Tabulated summaries provide the reader with useful information on the current state of research in the field.Öğe Characterization of biological molecule–loaded nanostructures using circular dichroism and fourier transform infrared spectroscopy(Taylor and Francis, 2021) Parlar, Ayhan; Kulabhusan, Prabir Kumar; Kurt, Hasan; Gürel, Büşra; Torabfam, Milad; Özata, Başak; Yüce, MeralDrug-loaded nanoparticles have many advantages in drug administration, which is an essential step for the impact of the drugs and their mechanism of action. Circular dichroism (CD) is a spectroscopy technique that measures the absorbance difference between right-circularly polarized light and left-circularly polarized light. Of several analytical techniques available, Fourier transform infrared spectroscopy is a powerful and widely employed technique explicitly for identifying chemical species. The peaks in the IR spectrum of a sample represent the molecular vibrations of the molecules present in the sample, signifying the various chemical bonds and functional groups. Various types of nanoparticles are being utilized for drug delivery applications because of their advantages such as controlled drug release, protection of the therapeutic payload, improved bioavailability, and targeted delivery. The discovery of novel nanoparticles and their application to the diagnosis and treatment of diseases have received considerable attention during the past decades.Öğe Characterization of Fc?RIa (CD64) as a ligand molecule for site-specific IgG1 capture: A side-by-side comparison with protein a(American Chemical Society, 2022) Çapkın, Eda; Kurt, Hasan; Gürel, Büşra; Bıçak, Dilan; Akgün Baş, Sibel; Dağlıkoca, Duygu Emine; Yüce, MeralFc ?receptors (Fc?Rs) are one of the structures that can initiate effector function for monoclonal antibodies. Fc?RIa has the highest affinity toward IgG1-type monoclonal antibodies among all Fc?Rs. In this study, a comprehensive characterization was performed for Fc?RIa as a potential affinity ligand for IgG1-type monoclonal antibody binding. The binding interactions were assessed with the SPR technique using different immobilization techniques such as EDC-NHS coupling, streptavidin-biotin interaction, and His-tagged Fc?RIa capture. The His-tagged Fc?RIa capture was the most convenient method based on assay repeatability. Next, a crude IgG1 sample and its fractions with different monomer contents obtained from protein A affinity chromatography were used to evaluate Fc?RIa protein in terms of monoclonal antibody binding capacity. The samples were also compared with a protein A-immobilized chip (a frequently used affinity ligand) for IgG1 binding responses. The antibody binding capacity of the protein A-immobilized chip surface was significantly better than that of the Fc?RIa-immobilized chip surface due to its 5 Ig binding domains. The antibody binding responses changed similarly with protein A depending on the monomer content of the sample. Finally, a different configuration was used to assess the binding affinity of free Fc?Rs (Fc?RIa, Fc?RIIa, and Fc?RIIIa) to three different immobilized IgGs by immobilizing protein L to the chip surface. Unlike previous immobilization techniques tested where the Fc?RIa was utilized as a ligand, nonimmobilized or free Fc?RIa resulted in a significantly higher antibody binding response than free protein A. In this configuration, kinetics data of Fc?RI revealed that the association rate (ka 50-80 × 105 M-1 s-1) increased in comparison to His capture method (1.9-2.4 × 105 M-1 s-1). In addition, the dissociation rate (kd 10-5 s-1) seemed slower over the His capture method (10-4 s-1) and provided stability on the chip surface during the dissociation phase. The KD values for Fc?RIa were found in the picomolar range (2.1-10.33 pM from steady-state affinity analysis and 37.5-46.2 pM from kinetic analysis) for IgG1-type antibodies. Fc?RIa possesses comparable ligand potential as well as protein A. Even though the protein A-immobilized surface bound more antibodies than the Fc?RIa-captured surface, Fc?RIa presented a significant antibody binding capacity in protein L configuration. The results suggest Fc?RIa protein as a potential ligand for site-oriented immobilization of IgG1-type monoclonal antibodies, and it needs further performance investigation on different surfaces and interfaces for applications such as sensing and antibody purification.Öğe Enhancing enzymatic properties of endoglucanase i enzyme from trichoderma reesei via swapping from cellobiohydrolase i enzyme(MDPI, 2019) Yenenler, Aslı; Kurt, Hasan; Sezerman, Osman UğurUtilizing plant-based materials as a biofuel source is an increasingly popular attempt to redesign the global energy cycle. This endeavour underlines the potential of cellulase enzymes for green energy production and requires the structural and functional engineering of natural enzymes to enhance their utilization. In this work, we aimed to engineer enzymatic and functional properties of Endoglucanase I (EGI) by swapping the Ala43-Gly83 region of Cellobiohydrolase I (CBHI) from Trichoderma reesei. Herein, we report the enhanced enzymatic activity and improved thermal stability of the engineered enzyme, called EGI_swapped, compared to EGI. The difference in the enzymatic activity profile of EGI_swapped and the EGI enzymes became more pronounced upon increasing metal-ion concentrations in the reaction media. Notably, the engineered enzyme retained a considerable level of enzymatic activity after thermal incubation for 90 min at 70 degrees C while EGI completely lost its enzymatic activity. Circular Dichroism spectroscopy studies revealed distinctive conformational and thermal susceptibility differences between EGI_swapped and EGI enzymes, confirming the improved structural integrity of the swapped enzyme. This study highlights the importance of swapping the metal-ion coordination region in the engineering of EGI enzyme for enhanced structural and thermal stability.Öğe Exploiting stokes and anti-stokes type emission profiles of aptamer-functionalized luminescent nanoprobes for multiplex sensing applications(Wiley-VCH Verlag Gmbh, 2018) Yüce, Meral; Kurt, Hasan; Hussain, Babar; Ow-Yang, Cleva W.; Budak, HikmetMultiplex biosensing of four types of bacterial food pathogens in one pot is described. Stokes and anti-Stokes type photoluminescence (PL) of two quantum dots (QD) and two upconverting nanoparticles (UCNP) were utilised for realisation of the multiplex detection. The biosensing system was composed of aptamer-functionalized QD and UCNP nanoprobes that were conjugated with partially complementary DNA-modified magnetic beads for separation. PL signals of the conjugates were collected before and after incubation with target pathogens in one pot through the sequential excitations at 335nm for QD probes and 980nm for UCNP probes. The limit of detection values achieved were 28, 15, 12 and 25 cfu center dot mL(-1) for Listeria monocytogenes, Staphylococcus aureus, Salmonella typhimurium and Pseudomonas aeruginosa, respectively. Efforts for extending the multiplex detection up to five pathogens were also presented even though the PL signal cross-talk of a third QD nanoprobe hindered the detection. This work empowers co-deployment of QDs and UCNPs and paves the way for future studies in multiplex sensing, labelling, and bioimaging fields.Öğe Field-dependent charge collection model for thin film organic photovoltaics(Bingöl Üniversitesi, 2020) Kurt, HasanIn this study, a unified charge collection model is developed using an optical cavity dependent charge carrier generation and non-uniform built-in electric field distribution within a bulk heterojunction photovoltaic device. The charge collection model relies on the experimental inputs related to the charge carrier dynamics such as mobilities of charge carriers, recombination lifetime, and junction width of charge carrier species. Optical cavity modes and field strength were calculated using the experimental variable angle ellipsometry analysis of individual components of the devices. In order to evaluate the model, ambient processed PCDTBT:PC71BM based conventional and inverted derive architectures were utilized to underline the effect of unintentional doping and distinct optical cavity modes. The simulated external quantum efficiency and shortcircuit current density profiles from the model were compared to the experimental results with differing active layers thicknesses and device architectures. The proposed charge collection model presented a high degree of correlation with the experimental results and underlined its validity for further application on other types of organic photovoltaic devices.Öğe Functionalized graphitic carbon nitrides for environmental and sensing applications(Wiley, 2021) Fidan, Tuçe; Torabfam, Milad; Saleem, Qandeel; Wang, Chao; Kurt, Hasan; Yüce, Meral; Tang, Junwang; Bayazıt, Mustafa KemalGraphitic carbon nitride (g-C3N4) is a metal-free semiconductor that has been widely regarded as a promising candidate for sustainable energy production or storage. In recent years, g-C3N4 has become the center of attention by virtue of its impressive properties, such as being inexpensive, easily fabricable, nontoxic, highly stable, and environment friendly. Herein, the recent research developments related to g-C3N4 are outlined, which sheds light on its future prospective. Various synthetic methods and their impact on the properties of g-C3N4 are detailed, along with discussion on frequently used characterization methods. Different approaches for g-C3N4 surface functionalization, mainly categorized under covalent and noncovalent strategies, are outlined. Moreover, the processing methods of g-C3N4, such as g-C3N4-based thin films, hierarchical, and hybrid structures, are explored. Next, compared with the extensively studied energy-related applications of the modified g-C(3)N(4)s, relatively less-examined areas, such as environmental and sensing, are presented. By highlighting the strong potential of these materials and the existing research gaps, new researchers are encouraged to produce functional g-C3N4-based materials using diverse surface modification and processing routes.Öğe How to make nanobiosensors: Surface modification and characterisation of nanomaterials for biosensing applications(Royal Society of Chemistry, 2017) Yüce, Meral; Kurt, HasanThis report aims to provide the audience with a guideline for construction and characterisation of nanobiosensors that are based on widely used affinity probes including antibodies and aptamers and nanomaterials such as carbon-based nanomaterials, plasmonic nanomaterials and luminescent nanomaterials. The affinity probes and major methodologies that have been extensively used to make nanobiosensors, such as thiol-metal interactions, avidin-biotin interaction, p-interactions and EDC-NHS chemistry, were described with the most recent examples from the literature. Characterisation techniques that have been practised to validate nanoparticle surface modification with antibodies and aptamers, including gel electrophoresis, ultraviolet-visible spectrophotometry, dynamic light scattering and circular dichroism were described with examples. This report mainly covers the reports published between 2014 and 2017.Öğe Microwave-promoted continuous flow synthesis of thermoplastic polyurethane-silver nanocomposites and their antimicrobial performance(Royal Society of Chemistry, 2022) Saleem, Qandeel; Torabfam, Milad; Kurt, Hasan; Yüce, Meral; Bayazıt, Mustafa KemalThermoplastic polyurethane-silver nanocomposites (PU-Ag NCs) have considerable potential in many medical applications due to their superior mechanical and antimicrobial properties. Herein, a microwave-promoted flow system is successfully employed for continuous in situ manufacturing of PU NCs having spherical silver nanoparticles (AgNPs) without any reducing agent at similar to 40 degrees C in approximately 4 minutes. The main experimental parameters, including microwave power, metal salt concentration, polymer concentration, and flow rate, are optimised for the reproducible synthesis of AgNPs (similar to 5 nm) in the PU matrix, characterised by HRTEM-EDS and DLS analysis. XRD patterns indicate an increase in PU crystallinity with decreased particle size. Conventional heating flow synthesis at similar to 50 degrees C or microwave-batch synthesis (MWB) at similar to 44 and similar to 50 degrees C is ineffective in preparing AgNPs, and only large AgNPs (>100 nm) are synthesised at 70 degrees C in the MWB reactor. PU-Ag NC films bearing small AgNPs (similar to 5 nm) exhibit superior antibacterial activity (>97%) against Escherichia coli, Pseudomonas aeruginosa, and Staphylococcus aureus compared to large NPs (similar to 218 nm). The proposed method may manufacture other metal-polymer matrix composites.Öğe Microwave-promoted continuous flow systems in nanoparticle synthesis-A perspective(American Chemical Society, 2021) Saleem, Qandeel; Torabfam, Milad; Fidan, Tuçe; Kurt, Hasan; Yüce, Meral; Clarke, Nigel; Bayazıt, Mustafa KemalMicrowave-promoted continuous flow systems have emerged as a game-changer in nanoparticle synthesis. Owing to the excellent compatibility between fast, sustainable microwave heating and one-step, efficient flow chemistry, this promising technology is meant to enhance the synthetic abilities of nanoscientists. This Perspective aims to present a panoramic view of the state of the art in this field. Additionally, the effect of various microwave and flow parameters on the properties of nanoparticles is discussed along with a comparative glance at the features that make flow reactors more practical and sustainable than their batch counterparts. The overview has also analyzed various microwave continuous flow reactors available in the literature, with an acute emphasis on the nanosynthesis route and design features. Moreover, a discussion on the numerical modeling of microwave flow systems has been made a part of this perspective to reiterate its significance and encourage research in this domain. The Perspective also briefly comments on existing challenges and future prospects of this technology.Öğe Nanoplasmonic biosensors: Theory, structure, design, and review of recent applications(Elsevier, 2021) Kurt, Hasan; Pishva, Parsa; Pehlivan, Zeki Semih; Arsoy, Elif Gül; Saleem, Qandeel; Bayaz, Mustafa Kemal; Yüce, MeralNanoplasmonic biosensing shows an immense potential to satisfy the needs of the global health industry -low-cost, fast, and portable automated systems; highly sensitive and real-time detection; multiplexing and miniaturization. In this review, we presented the theory of nanoplasmonic biosensing for popular detection schemes -SPR, LSPR, and EOT -and underline the consideration for nanostructure design, material selection, and their effects on refractometric sensing performance. Later, we covered the bottom-up and top-down nanofabrication methods for nanoplasmonic biosensors. Subsequently, we reviewed the recent examples of nanoplasmonic biosensors over a wide range of clinically relevant analytes in the diagnosis and prognosis of a wide range of diseases and conditions such as biomarker proteins, infectious bacteria, viral agents. Finally, we discussed the challenges of nanoplasmonic biosensing toward clinical translation and proposed strategic avenues to be competitive against current clinical detection methods. Hopefully, nanoplasmonic biosensing can realize its potential through successful demonstrations of clinical translation in the upcoming years.Öğe Non-destructive covalent surface alkylation of graphitic carbon nitride for enhanced photocatalytic dye degradation in water(Elsevier B.V., 2024) Arat, Refik; Fidan, Tuçe; Yüce, Meral; Kurt, Hasan; Bayazıt, Mustafa KemalGraphitic carbon nitride (g-CN) is a promising material for various applications due to its unique electronic, optical, and photocatalytic properties, tunable by surface modifications. Herein, a novel and straightforward approach to the covalent addition of low molecular weight polyethylene glycol (PEG550) to g-CNs surface following non-destructive chemistry benefiting from simultaneous activation of hydroxyl and free-amine surface groups by a weak base, potassium carbonate, is for the first time described. The resulting g-CN-PEG550 exhibits almost two-fold enhanced water solubility due to 1 PEG550 chain addition for every ? 128 g-CN atoms, detected by thermogravimetric analysis. Complementary X-ray photoelectron spectroscopy elemental analysis of the isolated g-CN-PEG550 displays an increased C?O chemical environment attributed to the covalent addition of carbon- and oxygen-rich PEG550 to the g-CN surface. The g-CN-PEG550 photocatalyst performs 2.5-fold better in degrading rhodamine B due to its enhanced light absorption, improved water-dispersibility, and the efficient separation of photogenerated electron-hole pairs compared to the as-prepared g-CN. The study underscores the potential use of covalently PEGylated oxygen-rich g-CNs in photocatalytic applications.Öğe Oxide glass formers extending persistent luminescence in Eu and Dy co-doped strontium aluminates(Elsevier B.V., 2023) Coşgun Ergene, Arzu; Khabbaz Abkenar, Sirous; Şenol Güngör, Ayça; Günay, Ece; Kurt, Hasan; Topçu, Gökhan; Ow-Yang, Cleva W.Recent work has shown that the incorporation of electrically charged, non-bridging oxygen (NBO) species into Eu and Dy co-doped Sr4Al14O25 (S4A7ED) crystal structure, in the form of BØ2O?, induces the clustering of divalent Eu and trivalent Dy, which is manifested as persistent luminescence (PersiL). Because other ceramic compounds exhibiting persistent luminescence also contain Si, P, and Zr, we evaluated other oxide glass forming cations—Si, P, Zr and V—for extending PersiL in S4A7ED. To understand the structural changes that these cations imparted to the atomic arrangements inside the S4A7ED crystal structure, we applied FTIR and micro-Raman spectroscopy to analyze the impact of charged NBOs. Raman shifts were revealed in Si-doped S4A7ED exhibiting PersiL at 1077 cm?1, corresponding to vibrations involving SiO4 tetrahedra with 2 bridging oxygens (BOs) and 2 NBOs and at 1107 cm?1, corresponding to vibrations involving SiO4 tetrahedra with 3 BOs and 1 NBOs. Raman shifts were also observed in P-doped S4A7ED exhibiting PersiL at 1070 cm?1, corresponding to PO4 tetrahedra with 1 BO and 3 NBOs, and at 700 cm?1, corresponding to PO4 tetrahedra with 2 BOs and 2 NBOs. These results suggest that PersiL extension in S4A7ED compounds, Pechini-processed with oxides of Si, P, Zr, and V, is correlated to structural changes from the incorporation of polyanions with NBOs, although the presence of a BO in the cation polyhedra is also essential.Öğe Plasmonic biosensor design and alternative plasmonic materials(İstanbul Medipol Üniversitesi, Fen Bilimleri Enstitüsü, 2022) Saatçioğlu, Erhan; Kurt, Hasan; Yüce, MeralLight-matter interaction is the one of the most important and studied topic in time dependent quantum mechanic especially for description of spectroscopy. Light matter interaction can be described in two ways. First one is classic way which explains as ligh-matter interactions are the outcome of the charged particles interaction with oscillating electromagnetic field. Second one is quantum mechanically which explain as coupling of quantum states of the matter with light fields. This thesis focuses on a field of light matter interactions called Plasmonics. Plasmonics can be described as manipulation of light at certain frequencies along different interfaces such as metal-dielectric, metal-insulator in nanometric scale. These interactions are investigated with different technologies like surface plasmon resonances, localized surface plasmon resonances, extraordinary optical transmission, and surface lattice resonance. These four technologies have their own advantages and disadvantages which makes them suitable for different applications. In the field plasmonics mostly used materials are gold and silver due to their high DC conductivities and small ohmic losses. Nevertheless, optical frequencies requires another feature related to interband transition which occurs when an electron moves to fermi surface or empty conduction band. Also, nanofabrication of gold and silver have some challenges like morphological changes. These challenges and features of light make scientist to find new materials to use in plasmonics field. Metals like copper, aluminum, titanium, nickel, platinum also metal nitrides like titanium nitride, zirconium nitride are studied as candidates to replace gold and silver in the field of plasmonics. Inside these materials' aluminum, titanium nitride, hafnium nitride and zirconium nitride are chosen and studied to compare with gold and silver. Parameters used to compare these materials are surface sensitivity, thickness of the nanohole, radius of the nanohole, different substrates and period of the nanoholes. Nanoholes are constructed using simulation software for each of the material and each of the parameter. Simulations were made results are extracted and investigated via excel and Origin.Öğe Plasmonic enhancement in PTB7-Th:PC71BM organic photovoltaics(Elsevier B.V., 2022) Kurt, HasanOrganic photovoltaics struggles with limited exciton diffusion rate and low light absorption rates. The trade-off between these deficiencies limits the thickness of the active layer around 100–200 nm range. Plasmonic light management was introduced as one of the solutions to these problems in the last decade. The plasmonic metal nanostructures can manipulate light in subwavelength regime such as thin-film organic photovoltaics. In this work, we introduced a controllable and reproducible method to incorporate quasi-hexagonal arrays of Au nanostructure on the electron transport layer (ETL), which can directly facilitate light management in the active layer. The inverted PTB7-Th:PC71BM OPVs were selected as the model system, and Au nanostructure arrays were introduced in selected interfaces. In order to match the work function of Au nanostructures and the LUMO level of the PC71BM fullerene component of the bulk heterojunction, PEI was utilized to modify the work function of such surfaces. The plasmon-enhanced inverted OPV devices showed up to 22% higher power conversion efficiencies than reference devices. In order to elucidate the underlying reason for such high improvement, finite-difference time-domain simulations of whole OPV devices under AM1.5G solar illumination were performed. The results revealed up to 25 times higher local exciton generation rate in close proximity to the Au nanostructures and ETLs.Öğe Plasmonic selection of ssDNA aptamers against fibroblast growth factor receptor(American Chemical Society, 2019) Kurt, Hasan; Eyüpoğlu, Alp Ertunga; Sütlü, Tolga; Budak, Hikmet; Yüce, MeralIn this work, we describe the selection of ssDNA aptamers targeting fibroblast growth factor receptor binding protein 3 K650E, which has roles in cell division, growth, and differentiation through the kinase cascade. The selection process was based on the label-free, real-time monitoring of binding interactions by surface plasmon resonance, allowing for convenient manipulation of the selection rounds. Next generation sequencing data provided four major motif families from which nine individual sequences were selected based on their abundance levels. Electrophoretic mobility shift assays revealed binding of the selected aptamers to the target protein without significant interference from fibroblast growth factor receptor binding protein 2, indicating the selectivity of the aptamers. The dissociation constant at equilibrium for the best aptamer candidate, SU-3, was found to be (28.2 ± 19.6) × 10–9 M (n = 5) using a single-cycle kinetic analysis method. Advantages of the experimental setup and potential applications of the selected aptamers are discussed.Öğe Plasmonic titanium nitride nanohole arrays for refractometric sensing(American Chemical Society, 2023) Günaydın, Beyza Nur; Gülmez, Mert; Torabfam, Milad; Pehlivan, Zeki Semih; Tütüncüoğlu, Atacan; Kayalan, Cemre Irmak; Saatçioğlu, Erhan; Bayazıt, Mustafa Kemal; Yüce, Meral; Kurt, HasanGroup IVB metal nitrides have attracted great interest as alternative plasmonic materials. Among them, titanium nitride (TiN) stands out due to the ease of deposition and relative abundance of Ti compared to those of Zr and Hf metals. Even though they do not have Au or Ag-like plasmonic characteristics, they offer many advantages, from high mechanical stability to refractory behavior and complementary metal oxide semiconductor-compatible fabrication to tunable electrical/optical properties. In this study, we utilized reactive RF magnetron sputtering to deposit plasmonic TiN thin films. The flow rate and ratio of Ar/N2 and oxygen scavenging methods were optimized to improve the plasmonic performance of TiN thin films. The stoichiometry and structure of the TiN thin films were thoroughly investigated to assess the viability of the optimized operation procedures. To assess the plasmonic performance of TiN thin films, periodic nanohole arrays were perforated on TiN thin films by using electron beam lithography and reactive ion etching methods. The resulting TiN periodic nanohole array with varying periods was investigated by using a custom microspectroscopy setup for both reflection and transmission characteristics in various media to underline the efficacy of TiN for refractometric sensing.Öğe SELEX against whole-cell bacteria resulted in lipopolysaccharide binding aptamers(Elsevier B.V., 2022) Yılmaz, Deniz; Muslu, Tuğdem; Parlar, Ayhan; Kurt, Hasan; Yüce, MeralNucleic acid aptamers are target-specific oligonucleotides selected from combinatorial libraries through an iterative in vitro screening process known as Systemic Evolution of Ligands by Exponential Enrichment (SELEX). In this report, the selection of bacteria differentiating ssDNA aptamer candidates from a combinatorial library through the whole-cell SELEX method was performed. The enriched SELEX pool was sequenced using Illumina Next-Generation Sequencing (NGS) technology and analyzed for the most abundant sequences using CLC Genomics Workbench. The sequencing data resulted in several oligonucleotide families from which three individual sequences were chosen per SELEX based on the copy numbers. The binding performance of the selected aptamers was assessed by flow cytometry and fluorescence spectroscopy, and the binding constants were estimated using binding saturation curves. Varying results were obtained from two independent SELEX procedures where the SELEX against the model gram-negative bacterium Escherichia coli provided more selective sequences while the SELEX library used against gram-positive bacterium Listeria monocytogenes did not evolve as expected. The sequences that emerged from E. coli SELEX were shown to bind Lipopolysaccharide residues (LPS) and inhibit LPS-induced macrophage polarization. Thus, it can be said that, performed whole-cell SELEX could be resulted as the selection of aptamers which can bind LPS and inhibit LPS induced inflammation response and thus can be candidates for the inhibition of bacterial infections. In future studies, the selected aptamer sequences could be structurally and chemically modified and exploited as potential diagnostic tools and therapeutic agents as LPS antagonists.Öğe Soft segment length controls morphology of poly(ethylene oxide) based segmented poly(urethane-urea) copolymers in a binary solvent(Elsevier Science Bv., 2017) Avaz, Senem; Oğuz, Oğuzhan; Kurt, Hasan; Menceloğlu, Yusuf Ziya; Atılgan, CananIt is known that morphology and structure-property behavior of poly(ethylene oxide) (PEO) based poly (urethane-urea) copolymers are affected by soft segment (SS) chain length. Here, a multi-scale computational study is carried out to determine the origins of this behavior, supported by atomic force microscopy (AFM) imaging. First, single PEO chains of varying lengths are comparatively examined by molecular dynamics and dissipative particle dynamics (DPD) simulations in THF: DMF solvent mixture to verify that the coarse graining strategy is applicable to the system at hand. In the second step, hard segment (HS) beads are attached to PEO chains to study their effect on the overall morphology. We find that the critical chain length of PEO plays a key role on the structure-property behavior of these copolymers. Density fields obtained from DPD calculations reveal a stable channel formation by SS beads in the copolymers if their length is below a threshold value. HS-SS interactions drive this behavior by promoting phase mixing. The role of the binary solvent is essential as the channel-like structures are not stable in the pure solvents. In contrast, for chains having long enough PEO segments, spontaneous clustering of the PEO units controls morphology development. This behavior gives rise to the formation of globular SS clusters surrounded by HS units. The dual solvent acts as a lubricant, with THF preferring the PEO clusters. Results obtained from DPD studies are corroborated by AFM images obtained for the corresponding copolymers. The strategy employed lays the foundations for developing systems having novel morphologies and macroscopic-properties using designs based on HS-SS cooligomers.
