PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - Scopus: 7High-Pressure Structural Studies and Pressure-Induced Sensitisation of 3,4,5-Trinitro(Royal Society of Chemistry, 2023) Atceken, N.; Hemingway, J.; Bull, C.L.; Liu, X.; Michalchuk, A.A.L.; Konar, S.; Morrison, C.A.Herein we report the first high-pressure study of the energetic material 3,4,5-trinitro-1H-pyrazole (3,4,5-TNP) using neutron powder diffraction and single-crystal X-ray diffraction. A new high-pressure phase, termed Form II, was first identified through a substantial change in the neutron powder diffraction patterns recorded over the range 4.6-5.3 GPa, and was characterised further by compression of a single crystal to 5.3 GPa in a diamond-anvil cell using X-ray diffraction. 3,4,5-TNP was found to be sensitive to initiation under pressure, as demonstrated by its unexpected and violent decomposition at elevated pressures in successive powder diffraction experiments. Initiation coincided with the sluggish phase transition from Form I to Form II. Using a vibrational up-pumping model, its increased sensitivity under pressure can be explained by pressure-induced mode hardening. These findings have potential implications for the safe handling of 3,4,5-TNP, on the basis that shock- or pressure-loading may lead to significantly increased sensitivity to initiation. © 2023 The Royal Society of Chemistry.Article Citation - WoS: 8Citation - Scopus: 9Development of Plant-Based Biopolymer Coatings for 3d Cell Culture: Boron-Silica Quince Seed Mucilage Nanocomposites(Royal Society of Chemistry, 2023) Yılmaz, Hilal Deniz; Cengiz, Uğur; Derkuş, Burak; Arslan, Yavuz EmreSpheroid formation with spontaneous aggregation has captured interest in most cell culture studies due to its easy set-up and more reliable results. However, the economic and technical costs of the advanced systems and commercial ultra-low adhesive platforms have pushed researchers into pursuing alternatives. Nowadays, polymeric coatings, including poly-hydroxyethyl methacrylate and agar/agarose, are the commonly used polymers for non-adhesive plate fabrication, yet the costs and working solvent or heat-dependent preparation procedures maintain the need for the development of novel biomaterials. Here, we propose a greener and more economical approach for producing non-adherent surfaces and spheroid formation. For this, a plant waste-based biopolymer from quince fruit (Cydonia oblonga Miller, from Rosaceae family) seeds and boron-silica precursors were introduced. The unique water-holding capacity of quince seed mucilage (Q) was enriched with silanol and borate groups to form bioactive and hydrophilic nanocomposite overlays for spheroid studies. Moreover, 3D gel plates from the nanocomposite material were fabricated and tested in vitro as a proof-of-concept. The surface properties of coatings and the biochemical and mechanical properties of the nanocomposite materials were evaluated in-depth with techniques, and extra hydrophilic coatings were obtained. Three different cell lines were cultured on these nanocomposite surfaces, and spheroid formation with increased cellular viability was recorded on day 3 with a >200 & mu;m spheroid size. Overall, Q-based nanocomposites are believed to be a fantastic alternative for non-adherent surface fabrication due to their low-cost, easy operation, and intrinsic hydration layer forming capacity with biocompatible nature in vitro.Review Citation - WoS: 14Citation - Scopus: 14Recent Advances in Lab-On Systems for Breast Cancer Metastasis Research(Royal Society of Chemistry, 2023) Fıratlıgil Yıldırır, Burcu; Yalçın Özuysal, Özden; NonappaBreast cancer is the leading cause of cancer-related deaths in women. Multiple molecular subtypes, heterogeneity, and their ability to metastasize from the primary site to distant organs make breast cancer challenging to diagnose, treat, and obtain the desired therapeutic outcome. As the clinical importance of metastasis is dramatically increasing, there is a need to develop sustainable in vitro preclinical platforms to investigate complex cellular processes. Traditional in vitro and in vivo models cannot mimic the highly complex and multistep process of metastasis. Rapid progress in micro- and nanofabrication has contributed to soft lithography or three-dimensional printing-based lab-on-a-chip (LOC) systems. LOC platforms, which mimic in vivo conditions, offer a more profound understanding of cellular events and allow novel preclinical models for personalized treatments. Their low cost, scalability, and efficiency have resulted in on-demand design platforms for cell, tissue, and organ-on-a-chip platforms. Such models can overcome the limitations of two- and three-dimensional cell culture models and the ethical challenges involved in animal models. This review provides an overview of breast cancer subtypes, various steps and factors involved in metastases, existing preclinical models, and representative examples of LOC systems used to study and understand breast cancer metastasis and diagnosis and as a platform to evaluate advanced nanomedicine for breast cancer metastasis.Article Citation - WoS: 9Citation - Scopus: 9Fabrication and Development of a Microfluidic Paper-Based Immunosorbent Assay Platform (μpisa) for Colorimetric Detection of Hepatitis C(Royal Society of Chemistry, 2023) Özefe, Fatih; Arslan Yıldız, AhuPaper-based microfluidics is an emerging analysis tool used in various applications, especially in point-of-care (PoC) diagnostic applications, due to its advantages over other types of microfluidic devices in terms of simplicity in both production and operation, cost-effectiveness, rapid response time, low sample consumption, biocompatibility, and ease of disposal. Recently, various techniques have been developed and utilized for the fabrication of paper-based microfluidics, such as photolithography, micro-embossing, wax and PDMS printing, etc. In this study, we offer a fabrication methodology for a microfluidic paper-based immunosorbent assay (μPISA) platform and the detection of Hepatitis C Virus (HCV) was carried out to validate this platform. A laser ablation technique was utilized to form hydrophobic barriers easily and rapidly, which was the major advantage of the developed fabrication methodology. The characterization of the μPISA platform was performed in terms of micro-channel properties using bright-field (BF) microscopy, and surface properties using scanning electron microscopy (SEM). At the same time, sample volume and liquid handling capacity were analyzed quantitatively. Ablation speed (S) and laser power (P) were optimized, and it was shown that one combination (10P60S) provided minimal deviation in micro-channel dimensions and prevented deterioration of hydrophobic barriers. Also, the minimum hydrophobic barrier width, which prevents cross-barrier bleeding, was determined to be 255.92 ± 10.01 μm. Furthermore, colorimetric HCV NS3 detection was implemented to optimize and validate the μPISA platform. Here, HCV NS3 in both PBS and human blood plasma was successfully detected by the naked eye at concentrations as low as 1 ng mL−1 and 10 ng mL−1, respectively. Moreover, the limit of detection (LoD) values for HCV NS3 were acquired as 0.796 ng mL−1 in PBS and 2.203 ng mL−1 in human blood plasma with a turnaround time of 90 min. In comparison with conventional ELISA, highly sensitive and rapid HCV NS3 detection was accomplished colorimetrically on the developed μPISA platform.Article Citation - WoS: 2Citation - Scopus: 2Size Driven Barrier To Chirality Reversal in Electric Control of Magnetic Vortices in Ferromagnetic Nanodiscs(Royal Society of Chemistry, 2022) Aldulaimi, W. A. S.; Okatan, Mahmut Barış; Şendur, Kürşat; Onbaşlı, Mehmet Cengiz; Mısırlıoğlu, İbrahim BurçNew high density storage media and spintronic devices come about with a progressing demand for the miniaturization of ferromagnetic structures. Vortex ordering of magnetic dipoles in such structures has been repeatedly observed as a stable state, offering the possibility of chirality in these states as a means to store information at high density. Electric pulses and magnetoelectric coupling are attractive options to control the chirality of such states in a deterministic manner. Here, we demonstrate the chirality reversal of vortex states in ferromagnetic nanodiscs via pulsed electric fields using a micromagnetic approach and focus on the analysis of the energetics of the reversal process. A strong thickness dependence of the chirality reversal in the nanodiscs is found that emanates from the anisotropy of the demagnetizing fields. Our results indicate that chiral switching of the magnetic moments in thin discs can give rise to a transient vortex-antivortex lattice not observed in thicker discs. This difference in the chirality reversal mechanism emanates from profoundly different energy barriers to overcome in thin and thicker discs. We also report the polarity-chirality correlation of a vortex that appears to depend on the aspect ratio of the nanodiscs.Article Citation - WoS: 2Citation - Scopus: 2High-Throughput Analysis of Tetragonal Transition Metal Xenes(Royal Society of Chemistry, 2022) Šabani, Denis; Milošević, Milorad V.; Yorulmaz, Uğur; Yağmurcukardeş, Mehmet; Sevik, CemWe report a high-throughput first-principles characterization of the structural, mechanical, electronic, and vibrational properties of tetragonal single-layer transition metal Xenes (t-TMXs). Our calculations revealed 22 dynamically, mechanically and chemically stable structures among the 96 possible free-standing layers present in the t-TMX family. As a fingerprint for their structural identification, we identified four characteristic Raman active phonon modes, namely three in-plane and one out-of-plane optical branches, with various intensities and frequencies depending on the material in question. Spin-polarized electronic calculations demonstrated that anti-ferromagnetic (AFM) metals, ferromagnetic (FM) metals, AFM semiconductors, and non-magnetic semiconductor materials exist within this family, evidencing the potential of t-TMXs for further use in multifunctional heterostructures.Article Citation - WoS: 17Citation - Scopus: 18Development of a Hydrocolloid Bio-Ink for 3d Bioprinting(Royal Society of Chemistry, 2022) Yıldırım, Özüm; Arslan Yıldız, AhuA new generation of bio-inks that are soft, viscous enough, stable in cell culture, and printable at low printing pressures is required in the current state of 3D bioprinting technology. Hydrogels can meet these features and can mimic the microenvironment of soft tissues easily. Hydrocolloids are a group of hydrogels which have a suitable gelling capacity and rheological properties. According to the literature, polysaccharide-based hydrocolloids are used in the food industry, wound healing technologies, and tissue engineering. Quince seed hydrocolloids (QSHs), which consist of mostly glucuronoxylan, can easily be obtained from quince seeds by water extraction. In this study, the use of a QSH as a bio-ink was investigated. The suitability of QSH for the printing process was assessed by rheological, uniformity and pore factor analyses. Appropriate printing parameters were determined and the characterization of the bioprinted QSHs was performed by SEM analysis, water uptake capacity measurement, and protein adsorption assay. The bioprinted QSHs had excellent water uptake capacity and showed suitable protein adsorption behaviour. Analyses of the biocompatibility and cellular viability of bioprinted QSHs were conducted using NIH-3T3 fibroblast cells and the results were found to be high during short and long-term cell culture periods. It was proved that QSH is a highly promising bio-ink for 3D bioprinting and further tissue engineering applications.Article Citation - WoS: 16Citation - Scopus: 15Ultrasound-Assisted Dopamine Polymerization: Rapid and Oxidizing Agent-Free Polydopamine Coatings on Membrane Surfaces(Royal Society of Chemistry, 2021) Cihanoğlu, Aydın; Schiffman, Jessica D.; Alsoy Altınkaya, SacideHerein, we report a controllable pathway to accelerate the polymerization kinetics of dopamine using ultrasound as a trigger. The use of ultrasound was demonstrated to dramatically accelerate the slow liquid phase reaction kinetics and increase the deposition rate of the polydopamine coating on the surface of polymeric membranes.Article Citation - WoS: 6Citation - Scopus: 7Interface-Dependent Phononic and Optical Properties of Geo/Moso Heterostructures(Royal Society of Chemistry, 2022) Yağmurcukardeş, Mehmet; Sözen, Yiğit; Başkurt, Mehmet; Peeters, François M.; Şahin, HasanThe interface-dependent electronic, vibrational, piezoelectric, and optical properties of van der Waals heterobilayers, formed by buckled GeO (b-GeO) and Janus MoSO structures, are investigated by means of first-principles calculations. The electronic band dispersions show that O/Ge and S/O interface formations result in a type-II band alignment with direct and indirect band gaps, respectively. In contrast, O/O and S/Ge interfaces give rise to the formation of a type-I band alignment with an indirect band gap. By considering the Bethe-Salpeter equation (BSE) on top of G0W0 approximation, it is shown that different interfaces can be distinguished from each other by means of the optical absorption spectra as a consequence of the band alignments. Additionally, the low-and high-frequency regimes of the Raman spectra are also different for each interface type. The alignment of the individual dipoles, which is interface-dependent, either weakens or strengthens the net dipole of the heterobilayers and results in tunable piezoelectric coefficients. The results indicate that the possible heterobilayers of b-GeO/MoSO asymmetric structures possess various electronic, optical, and piezoelectric properties arising from the different interface formations and can be distinguished by means of various spectroscopic techniques.Article Citation - WoS: 10Citation - Scopus: 10Vibrational and Optical Identification of Geo2 and Geo Single Layers: a First-Principles Study(Royal Society of Chemistry, 2021) Sözen, Yiğit; Yağmurcukardeş, Mehmet; Şahin, HasanIn the present work, the identification of two hexagonal phases of germanium oxides (namely GeO2 and GeO) through the vibrational and optical properties is reported using density functional theory calculations. While structural optimizations show that single-layer GeO2 and GeO crystallize in 1T and buckled phases, phonon band dispersions reveal the dynamical stability of each structure. First-order off-resonant Raman spectral predictions demonstrate that each free-standing single-layer possesses characteristic peaks that are representative for the identification of the germanium oxide phase. On the other hand, electronic band dispersion analysis shows the insulating and large-gap semiconducting nature of single-layer GeO2 and GeO, respectively. Moreover, optical absorption, reflectance, and transmittance spectra obtained by means of G(0)W(0)-BSE calculations reveal the existence of tightly bound excitons in each phase, displaying strong optical absorption. Furthermore, the excitonic gaps are found to be at deep UV and visible portions of the spectrum, for GeO2 and GeO crystals, with energies of 6.24 and 3.10 eV, respectively. In addition, at the prominent excitonic resonances, single-layers display high reflectivity with a zero transmittance, which is another indication of the strong light-matter interaction inside the crystal medium.