WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Borax-Doped Fe2O3 and CeO2 Nanoparticles Regulate Dose-Dependently Inflammation, the Cell Cycle, and Migration in LPS-Activated THP-1 Cells(Wiley-VCH Verlag GmbH, 2026-03) Sulak, Mine; Ceylan Ekiz, Yağmur; Şen, Alaattin; Acar, Büşra; Çelik Turgut, Gurbet; Aktaş Pepe, NihanThis study examined the biological effects of borax-doped Fe2O3 and CeO2 nanoparticles (NPs) on lipopolysaccharide (LPS)-activated THP-1 cells. The morphology and composition of the nanocomposites were confirmed via scanning electron microscopy (SEM) and energy-dispersive x-ray spectroscopy (EDX). Cell viability (resazurin and crystal violet assays), apoptosis/necrosis (annexin V/propidium iodide [PI]), cell cycle (flow cytometry), migration (scratch assay), and inflammatory response (Iba1 immunofluorescence staining, inducible nitric oxide synthase [iNOS] activity, and RT-PCR) were evaluated. The particle sizes ranged from 21.34 to 33.47 nm (Fe2O3-B-NPs) and 31.07 to 36.62 nm (CeO2-B-NPs). The IC10 and IC50 dose ranges were defined for each nanocomposite and applied across different cell lines to evaluate dose-dependent biological effects. Fe2O3-B-NPs altered cell cycle progression, increasing the number of S phase cells. Both nanocomposites promoted migration at low doses but inhibited it at high doses. CeO2-B-NPs reduced Iba1 levels, whereas Fe2O3-B-NPs increased inflammatory marker levels at higher concentrations. CeO2-B-NPs suppressed TNF-alpha and IL-1 beta gene expression at the IC50 dose, while both nanocomposites reduced iNOS activity. These results indicate that the dose-dependent effects of nanocomposites should be carefully evaluated.Article Citation - WoS: 1Citation - Scopus: 1Ultra-Durable Information-Encoded Anti-Counterfeiting Self-Assembled Nanocrystal Labels(Wiley-VCH Verlag GmbH, 2025-11-28) Haddadifam, Taha; Shabani, Farzan; Kalay, Mustafa; Khaligh, Aisan; Mutlugun, Evren; Onses, Mustafa Serdar; Demir, Hilmi VolkanForgery, a serious universal problem, is causing huge economic losses every year. Against forgery, information-encoded labelling systems have attracted significant attention for a diverse range of anti-counterfeiting applications. Here, cost-effective and ultra-durable nanocrystal-based labels are proposed and demonstrated in which information can be encoded as physically unclonable functions (PUFs) of hardware-oriented security systems. The fabrication method of the PUFs is based on the self-assembly of colloidal quantum wells (CQWs) and generation of unclonable features within their pattern at a liquid-liquid interface. These CQW PUFs are analyzed with well-known statistical tests, which show a uniqueness level of 0.5060 +/- 0.0323 and prove their randomness. In addition, a feature-matching algorithm is used to authenticate these information-encoded CQW PUFs. For the safety of the semiconductor chips, a CQW PUF is attached to the surface of the chip to protect against hardware cyber-attacks. Eventually, fabricated labels are examined against high temperatures and moisture environments. The fabricated CQW label is durable for a period of 150 days it is tested, demonstrating ultra-high stability of the label. High stability and durability, cost-effectiveness, and high encoding capacity make these proposed nanocrystal labels extremely attractive for large-scale commercialization.Article Toward the Design of New Α-Carboline Derivatives Against Anaplastic Lymphoma Kinase (Alk): A Comprehensive in Silico Approach(Wiley-VCH Verlag GmbH, 2025-11) Sari, Ceyhun; Akcok, IsmailAfter the first description of anaplastic lymphoma kinase (ALK) in an anaplastic large cell lymphoma cell line as a nucleophosmin (NPM) fusion partner, ALK and its various fusion partners have been implicated in numerous cancers such as non-small cell lung cancer (NSCLC), anaplastic large cell lymphoma (ALCL), neuroblastoma, and rhabdomyosarcoma. In the last decade, several compounds targeting ALK have been developed and approved by the Food and Drug Administration (FDA). Despite the advances of generations of ALK inhibitors, a recent study highlighted that around half of the ALK-positive NSCLC patients will go through disease progression in response to first-line alectinib, which is a second-generation ALK inhibitor. In this study, we aimed to propose a novel alpha-carboline compound targeting the ALK tyrosine kinase domain to be used against various types of cancer in which ALK fusion proteins may be involved. In this regard, we designed more than 200 alpha-carboline derivatives and investigated their binding properties against ALK tyrosine kinase by using in silico protocols consisting of molecular docking studies, molecular dynamics simulations, MM/PBSA binding free energy calculation, and essential dynamics analysis. Considering the obtained results, we developed two promising candidates, compounds 208 & 209 with -9.05 and -9.80 binding energies, respectively, which demonstrated improved binding profiles over the course of a 300 ns simulation.Article Citation - WoS: 6Citation - Scopus: 7Therapeutic Potential of Nitrogen-Substituted Oleanolic Acid Derivatives in Neuroinflammatory and Cytokine Pathways: Insights From Cell-Based and Computational Models(Wiley-VCH Verlag GmbH, 2025-04-22) Turgut, Gurbet Celik; Pepe, Nihan Aktas; Ekiz, Yagmur Ceylan; Senol, Halil; Sen, AlaattinThis study was conducted to investigate the mechanism of the potential and anti-inflammatory properties of nitrogen-substituted oleanolic acid derivatives that can be used to treat neuroinflammatory diseases. Nitrogen-containing oleanolic acid derivatives have been evaluated for their anti-neuroinflammatory effects in vitro in neuronal and monocytic cell lines at nontoxic doses, and the production of cytokines (TNF-alpha, IL-6 and IL-17), the inflammatory enzyme induced nitric oxide synthase (iNOS) and NF-kappa B signalling under LPS-stimulated conditions, and the expression of genes associated with Alzheimer's disease have been assessed. In addition, molecular docking and molecular dynamics simulation assessments are conducted in silico. Key protein markers of neurodegenerative diseases, especially Alzheimer's disease and neuroinflammation, TAU protein levels, and microglial activation, as well as ionised calcium-binding adaptor protein-1 (IBA1) levels, were significantly reduced with the addition of oleanolic acid derivatives. LPS-induced NF-kappa B luciferase reporter activity and iNOS activity were significantly inhibited, approaching the levels in uninduced controls. The mRNA expression of proinflammatory cytokines critical for neuroinflammation, such as TNF-alpha, NF-kappa B, IL-6 and IL-17, was reduced twofold to sevenfold. Furthermore, the molecular docking and MD simulation analyses revealed potential interactions with the TNF-alpha and NF-kappa B proteins. These findings underscore the potential of oleanolic acid derivatives, particularly compound 16, as candidates for further development as therapeutic agents for neurodegenerative diseases associated with chronic inflammation.Article Citation - WoS: 23Citation - Scopus: 21Tattoo-Like Multi-Color Physically Unclonable Functions(Wiley-VCH Verlag GmbH, 2023-12-07) Kiremitler, N. Burak; Esidir, Abidin; Drake, Gryphon A.; Yazici, Ahmet Faruk; Sahin, Furkan; Torun, Ilker; Onses, M. SerdarAdvanced anti-counterfeiting and authentication approaches are in urgent need of the rapidly digitizing society. Physically unclonable functions (PUFs) attract significant attention as a new-generation security primitive. The challenge is design and generation of multi-color PUFs that can be universally applicable to objects of varied composition, geometry, and rigidity. Herein, tattoo-like multi-color fluorescent PUFs are proposed and demonstrated. Multi-channel optical responses are created by electrospraying of polymers that contain semiconductor nanocrystals with precisely defined photoluminescence. The universality of this approach enables the use of dot and dot-in-rod geometries with unique optical characteristics. The fabricated multi-color PUFs are then transferred to a target object by using a temporary tattoo approach. Digitized keys generated from the red, green and blue fluorescence channels facilitate large encoding capacity and rapid authentication. Feature matching algorithms complement the authentication by direct image comparison, effectively alleviating constraints associated with imaging conditions. The strategy that paves the way for the development of practical, cost-effective, and secure anticounterfeiting systems is presented. Tattoo-like multi-color encoding layers based on random processing of semiconductor nanocrystals of varied composition and geometry are reported. Additive deposition via chaotic electrospraying enables randomness and multiplexing, whereas the tattoo approach provides substrate independence.imageArticle Citation - WoS: 1Citation - Scopus: 1Stochastic Orientational Encoding via Hydrogen Bonding Driven Assembly of Woven-Like Molecular Physically Unclonable Functions(Wiley-VCH Verlag GmbH, 2025-07-02) Kayaci, Nilgun; Kiremitler, Nuri Burak; Deneme, Ibrahim; Kalay, Mustafa; Ozbasaran, Aleyna; Zorlu, Yunus; Usta, HakanThe prevention of counterfeiting and the assurance of object authenticity require stochastic encoding schemes based on physically unclonable functions (PUFs). There is an urgent need for exceptionally large encoding capacities and multi-level responses within a molecularly defined, single-material system. Herein, a novel stochastic orientational encoding approach is demonstrated using a facile ambient-atmosphere solution processing of a molecular thin film based on the rod-shaped oligo(p-phenyleneethynylene) (OPE) pi-architecture. The nanoscopic film, derived from the small molecule 2EHO-CF3PyPE with donor, acceptor, and pi-spacer building units, is designed for energetically favorable uniaxial molecular assembly and crystal growth via directional multiple hydrogen-bonding motifs at the molecular termini and short C & horbar;H<middle dot><middle dot><middle dot>pi contacts at the center. A facile solvent vapor annealing induces concurrent dewetting and microscopic 1D random crystallization, yielding a woven-textured random features. Using convolutional neural networks, the rich variations in microcrystal domain properties and stochastic encoding of 1D crystal orientations generate artificial coloration, achieving an encoding capacity reaching (6.5 x 10(4))(2752 x 2208). The results demonstrate an effective strategy for achieving ultrahigh encoding capacities in a thin film composed of a single-material. This approach enables low-cost, solution-processed fabrication for mass production and broad adoption, while opening new opportunities to explore molecular-PUFs through structural design and engineering noncovalent interactions.Article Citation - WoS: 10Citation - Scopus: 11Recent Advances in CsPbX3 (X = Cl, Br, I) Perovskite NCs@Glass: Structures, Characterizations, and Applications(Wiley-VCH Verlag GmbH, 2025-04-07) Samiei, Sadaf; Lin, Jidong; Soheyli, Ehsan; Nabiyouni, Gholamreza; Chen, DaqinEncapsulation of perovskite nanocrystals (PeNCs) within metal oxide glasses and fabrication of PeNCs@glass composites has emerged as a transformative approach to enhance the stability and functionality of these promising luminescent materials. This review comprehensively examines the current state of research on encapsulation techniques, highlighting their effectiveness in preserving the structural integrity, and optical properties of PeNCs. The advantages and mechanisms by which metal oxide glasses mitigate the degradation of PeNCs are discussed and the tunable properties of metal oxide glass structures for optimizing the photoluminescence and quantum efficiency of encapsulated PeNCs are explored. The review further explores the various experimental techniques for characterizing composites made by nanoscale extreme crystalline species within the short-range ordered (amorphous) microstructures. As the ultimate aim of any advanced material for commercialization, diverse optoelectronic devices of these encapsulated systems, emphasize the potential for improved device performance and longevity. Finally, key challenges and future directions in the field are identified, including the need for scalable fabrication methods and the exploration of novel glass compositions to enhance the encapsulation efficacy. This review aims to provide a comprehensive overview of the advancements in the encapsulation of PeNCs with metal oxide glasses, underscoring their significance in developing next-generation optoelectronic devices.Article Citation - WoS: 1Citation - Scopus: 1Quenchable Amorphous Diamond: A Novel High-Pressure Route to Tetrahedral Amorphous Carbon(Wiley-VCH Verlag GmbH, 2025-05-03) Durandurdu, MuratThis study presents a groundbreaking theoretical prediction: the high-pressure transformation of amorphous graphite into a high-fraction sp3-bonded amorphous diamond phase. Employing ab initio molecular dynamics simulations, it is demonstrated that under extreme pressures, amorphous graphite undergoes an irreversible transition to an amorphous diamond phase. Thermodynamic analysis confirms the first-order nature of this sp2-to-sp3 transformation, with the transition predicted to occur at approximate to 33 GPa under experimental conditions. This transformation offers a novel pathway toward the synthesis of amorphous carbon with a high fraction of sp3 bonding, a long-standing challenge in materials science. This work expands understanding of carbon's high-pressure behavior and provides a compelling theoretical foundation for future experimental investigations aimed at synthesizing and characterizing this novel material.Article Discovery of New Candidates Targeting the SH2 Domains of Spleen Tyrosine Kinase (Syk) Through in Silico Studies(Wiley-VCH Verlag GmbH, 2025-06) Sansacar, Merve; Sari, Ceyhun; Yucel, Muhsin Samet; Akcok, Emel Basak Gencer; Akcok, Ismail; Gencer Akçok, Emel BaşakSrc homology 2 (SH2) domains have become an increasingly popular candidate for researchers to search for novel therapeutics to target different diseases. Spleen tyrosine kinase (Syk) is one of the proteins with two SH2 domains that has a role in the pathogenesis of many diseases. Here, we report the discovery of a promising natural product (NP) inhibitor that targets the N-terminal SH2 (N-SH2) and C-terminal SH2 (C-SH2) domains of Syk simultaneously, through structure-based drug discovery approach. Molecular docking studies, followed by molecular dynamics (MD) simulations and molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) calculations, were utilized to reveal the interactions between NPs from "the COlleCtion of Open NatUral producTs (COCONUT)" database and Syk enzyme. Five natural products that have lowest Scoring and Minimization with AutoDock Vina (SMINA) scores against both SH2 domains of Syk were selected for further studies and compound CNP0265345 has the best binding free energies toward both C-SH2 and N-SH2 of Syk enzyme with -44.54 and -55.98 kcal/mol, respectively. Drug-likeness properties, absorption, distribution, metabolism, and excretion (ADME) and carcinogenicity predictions were also studied. In conclusion, our work highlights a novel drug candidate to target the Syk enzyme of SH2 domains using in silico methods.Article Citation - WoS: 5Citation - Scopus: 5Development of Buckwheat Starch-Capric Acid Complex-Based Film: Process Optimization and Film Characterization(Wiley-VCH Verlag GmbH, 2025-02-26) Koca, Esra; Kahraman, Kevser; Oskaybas-Emlek, Betul; Ozbey, Ayse; Aydemir, Levent YurdaerTo overcome the limitations of starch usage alone, the film formation ability of the buckwheat starch-capric acid complex (BS-CA) was optimized, and the films were characterized. Significant models were obtained for tensile strength (TS) and Young's modulus (YM) of BS-CA film (p < 0.0001). The glycerol/starch ratio, temperature, and their interactions were significant in the YM model (R-2 is 0.9851). The BS-CA film had a better water vapor barrier (0.463 +/- 0.02 g mm/m(2) h kPa), with lower water solubility (WS) (34.18 +/- 1.70%) and moisture content (MC) (16.87 +/- 0.09%) than the buckwheat starch (BS) film (p < 0.05). It had lower thickness (0.073 +/- 0.00 mm) and TS (0.624 +/- 0.04 MPa) but higher elasticity (114.60 +/- 3.12%). The non-covalent interactions were determined between BS and CA, since new peaks were not observed in the film's FTIR spectrum. BS-CA film had a typical V-type crystalline structure and had slightly lower decomposition temperatures than the BS film. Contact angle measurements (55.19 degrees +/- 1.7), and images of AFM topography and SEM showed that the BS-CA film surface was hydrophilic; height and average roughness values were 1014 and 276 nm, respectively, which were quite higher than those of BS film. The results reveal that starch modification with fatty acid is a promising way to develop starch-based films to be used in practical applications.