Photonics / Fotonik
Permanent URI for this collectionhttps://hdl.handle.net/11147/2590
Browse
90 results
Search Results
Article Citation - WoS: 1Citation - Scopus: 1Calcium Indicators With Fluorescence Lifetime-Based Signal Readout: a Structure-Function Study(MDPI, 2024) Simonyan, Tatiana R.; Varfolomeeva, Larisa A.; Mamontova, Anastasia V.; Kotlobay, Alexey A.; Gorokhovatsky, Andrey Y.; Bogdanov, Alexey M.; Boyko, Konstantin M.The calcium cation is a crucial signaling molecule involved in numerous cellular pathways. Beyond its role as a messenger or modulator in intracellular cascades, calcium's function in excitable cells, including nerve impulse transmission, is remarkable. The central role of calcium in nervous activity has driven the rapid development of fluorescent techniques for monitoring this cation in living cells. Specifically, genetically encoded calcium indicators (GECIs) are the most in-demand molecular tools in their class. In this work, we address two issues of calcium imaging by designing indicators based on the successful GCaMP6 backbone and the fluorescent protein BrUSLEE. The first indicator variant (GCaMP6s-BrUS), with a reduced, calcium-insensitive fluorescence lifetime, has potential in monitoring calcium dynamics with a high temporal resolution in combination with advanced microscopy techniques, such as light beads microscopy, where the fluorescence lifetime limits acquisition speed. Conversely, the second variant (GCaMP6s-BrUS-145), with a flexible, calcium-sensitive fluorescence lifetime, is relevant for static measurements, particularly for determining absolute calcium concentration values using fluorescence lifetime imaging microscopy (FLIM). To identify the structural determinants of calcium sensitivity in these indicator variants, we determine their spatial structures. A comparative structural analysis allowed the optimization of the GCaMP6s-BrUS construct, resulting in an indicator variant combining calcium-sensitive behavior in the time domain and enhanced molecular brightness. Our data may serve as a starting point for further engineering efforts towards improved GECI variants with fine-tuned fluorescence lifetimes.Article Citation - WoS: 4Citation - Scopus: 4A Polymeric Copper Complex Based on a Pyrazole Derivative: Synthesis, Spectroscopic, X-Ray, and Biological Activity Studies(John Wiley and Sons Inc., 2024) Amin,M.A.; Diker,H.; Şahin,O.; Varlıklı, Canan; Soliman,A.A.A novel 1D coordination polymeric copper complex based on 4-(4′-nitrophenylhydrazono)-5-trifluoromethyl-2,4-dihydropyrazol-3-one was prepared and characterized spectroscopically and thermally and via X-ray crystallographic investigation. The prepared copper-based structure was proved to have a 1D coordination polymer. X-ray studies showed that the polymeric copper complex was of octahedral geometry, the ligand acted as a bidentate ligand, and the nitro group attached to the ligand acted as a bridging group. The cytotoxic activities of the copper polymer were evaluated including against MCF-7 cells (breast cancer cell line), HepG-2 cells (hepatocellular carcinoma), and HCT-116 cells (colon cancer cell line). The morphological alterations of the complex treated cells were investigated using an inverted microscope. The cell cycle and apoptosis were evaluated and reported. The copper polymer exhibited the best antitumor activity against HepG-2 cells (35.22 ± 4.80 μM) while also causing a decline in the G2/M phase and a remarkable enhancement in the early apoptosis. © 2024 John Wiley & Sons, Ltd.Article Citation - WoS: 3Citation - Scopus: 4A Facile Method for Boosting the Graphitic Carbon Nitride's Photocatalytic Activity Based on 0d/2d S-Scheme Heterojunction Nanocomposite Architecture(Elsevier, 2024) Kahraman, Zeynep; Kartal, Uğur; Gent, Aziz; Alp, EmreGraphitic carbon nitride (g-C 3 N 4 ) has received significant interest as a metal -free photocatalyst. The S -scheme photocatalytic system has great potential to improve the charge separation in semiconductor photocatalysts. In this study, we have fabricated non-toxic and low-cost photocatalytic nanocomposites of 0D/2D S -scheme heterojunction composed of iron oxide and graphitic carbon nitride by a facile method. The developed facile method provides a sustainable way with a high atom economy to further enhance the photocatalytic performance of exfoliated g-C 3 N 4 . The 0D -iron oxide/2D-C 3 N 4 exhibited nearly 10 times better than bulk g-C 3 N 4 and almost 60 % better than exfoliated g-C 3 N 4 under simulated solar light irradiation. The experimental results demonstrated that the effective charge -carrier mechanism led to an improved generation of reactive oxygen species (ROSs), resulting in an impressive photocatalytic performance. A serial photocatalytic test was also conducted to understand photocatalytic reaction mechanisms with various scavengers.Article Citation - Scopus: 1A Perspective on the State-Of Functionalized 2d Materials(American Institute of Physics, 2023) Duran, Tuna; Yayak, Yankı Öncü; Aydın, Hasan; Peeters, François M.; Yağmurcukardeş, MehmetTwo-dimensional (2D) ultra-thin materials are more crucial than their bulk counterparts for the covalent functionalization of their surface owing to atomic thinness, large surface-to-volume ratio, and high reactivity of surface atoms having unoccupied orbitals. Since the surface of a 2D material is composed of atoms having unoccupied orbitals, covalent functionalization enables one to improve or precisely modify the properties of the ultra-thin materials. Chemical functionalization of 2D materials not only modifies their intrinsic properties but also makes them adapted for nanotechnology applications. Such engineered materials have been used in many different applications with their improved properties. In the present Perspective, we begin with a brief history of functionalization followed by the introduction of functionalized 2D materials. Our Perspective is composed of the following sections: the applications areas of 2D graphene and graphene oxide crystals, transition metal dichalcogenides, and in-plane anisotropic black phosphorus, all of which have been widely used in different nanotechnology applications. Finally, our Perspectives on the future directions of applications of functionalized 2D materials are given. The present Perspective sheds light on the current progress in nanotechnological applications of engineered 2D materials through surface functionalization. © 2023 Author(s).Article Citation - WoS: 9Citation - Scopus: 11Electrospun Polyacrylonitrile (pan)/Polypyrrole (ppy) Nanofiber-Coated Quartz Crystal Microbalance for Sensing Volatile Organic Compounds(Springer, 2023) Yağmurcukardeş, Nesli; İnce Yardımcı, Atike; Yağmurcukardeş, Mehmet; Çapan, İnci; Erdoğan, Matem; Çapan, Rifat; Açıkbaş, YaserIn this study, electrospun polyacrylonitrile (PAN)/polypyrrole (PPy) nanofibers (NFs) coated quartz crystal microbalance (QCM) were investigated for their sensing characteristics against six different volatile organic compounds (VOCs): chloroform, dichloromethane, carbon tetrachloride, benzene, toluene and xylene. SEM, TEM, FT-IR and TGA analysis were carried out for the characterization of PAN/PPy nanofibers and characterization results of PAN/PPy NFs showed that these nanofibers were morphologically well-arranged and straightforward with a cylindrical shape with the average fiber diameter of 253.17 +/- 27 nm. Among all the gas measurement tests, dichloromethane displayed the highest response values for PAN/PPy coated QCM sensors. When the reproducibility of kinetic studies for PAN/PPy NFs coated QCM sensors were examined, the most repetitive results were obtained by this QCM sensor during dichloromethane investigation and the diffusion coefficients of VOCs for the first and second regions increased with the order of xylene < toluene < benzene < carbontetrachloride < chloroform < dichloromethane. The sensitivities of the PAN/PPy nanofibers-coated QCM sensor against organic vapors are determined between 4.71 and 6.17 (Hz ppm(-1)) x 10(-4). As a result, PAN/PPy nanofibers exhibited high sensitivity and selectivity for VOCs sensor applications, especially for dichloromethane.Article Citation - WoS: 1Citation - Scopus: 1Experimental and Theoretical Investigation of Synthesis and Properties of Dodecanethiol-Functionalized Mos<sub>2</Sub>(Royal Soc Chemistry, 2023) Duran, Tuna A.; Şahin, Hasan; Sabani, Denis; Milosevic, Milorad V.; Sahin, HasanHerein, we investigate the DDT (1-dodecanethiol) functionalization of exfoliated MoS2 by using experimental and theoretical tools. For the functionalization of MoS2, DDT treatment was incorporated into the conventional NMP (N-methyl pyrrolidone) exfoliation procedure. Afterward, it has been demonstrated that the functionalization process is successful through optical, morphological and theoretical analysis. The D, G and 2LA peaks seen in the Raman spectrum of exfoliated NMP-MoS2 particles, indicate the formation of graphitic species on MoS2 sheets. In addition, as the DDT ratio increases, the vacant sites on MoS2 sheets diminish. Moreover, at an optimized ratio of DDT-NMP, the maximum number of graphitic quantum dots (GQDs) is observed on MoS2 nanosheets. Specifically, the STEM and AFM data confirm that GQDs reside on the MoS2 nano-sheets and also that the particle size of the DDT-MoS2 is mostly fixed, while the NMP-MoS2 show many smaller and distributed sizes. The comparison of PL intensities of the NMP-MoS2 and DDT-MoS2 samples states a 10-fold increment is visible, and a 60-fold increment in NIR region photoluminescent properties. Moreover, our results lay out understanding and perceptions on the surface and edge chemistry of exfoliated MoS2 and open up more opportunities for MoS2 and GQD particles with broader applications.Article Citation - WoS: 9Citation - Scopus: 9Non-Hermitian Hamiltonians for Linear and Nonlinear Optical Response: a Model for Plexcitons(AIP Publishing LLC, 2023) Finkelstein-Shapiro, Daniel; Mante, Pierre-Adrien; Balcı, Sinan; Zigmantas, Donatas; Pullerits, TonuIn polaritons, the properties of matter are modified by mixing the molecular transitions with light modes inside a cavity. Resultant hybrid light-matter states exhibit energy level shifts, are delocalized over many molecular units, and have a different excited-state potential energy landscape, which leads to modified exciton dynamics. Previously, non-Hermitian Hamiltonians have been derived to describe the excited states of molecules coupled to surface plasmons (i.e., plexcitons), and these operators have been successfully used in the description of linear and third order optical response. In this article, we rigorously derive non-Hermitian Hamiltonians in the response function formalism of nonlinear spectroscopy by means of Feshbach operators and apply them to explore spectroscopic signatures of plexcitons. In particular, we analyze the optical response below and above the exceptional point that arises for matching transition energies for plasmon and molecular components and study their decomposition using double-sided Feynman diagrams. We find a clear distinction between interference and Rabi splitting in linear spectroscopy and a qualitative change in the symmetry of the line shape of the nonlinear signal when crossing the exceptional point. This change corresponds to one in the symmetry of the eigenvalues of the Hamiltonian. Our work presents an approach for simulating the optical response of sublevels within an electronic system and opens new applications of nonlinear spectroscopy to examine the different regimes of the spectrum of non-Hermitian Hamiltonians.Article Citation - WoS: 49Citation - Scopus: 54Highly Porous Poly(o-Phenylenediamine) Loaded Magnetic Carboxymethyl Cellulose Hybrid Beads for Removal of Two Model Textile Dyes(Springer, 2022) Arıca, Tuğçe Aybüke; Balcı, Fadime Mert; Balcı, Sinan; Arıca, Mehmet YakupEnsuring the removal of complex dyes from wastewater is a topic of great interest as it is vital for the environment. The present study reports a facile preparation method for poly(o-phenylenediamine) [p(o-PDA)] micro-particles loaded to magnetic carboxymethyl cellulose (CMC) hydrogel beads as adsorbents. The prepared products were characterized by FTIR, TGA, VSM, SEM, BET, and zeta sizer. The Fe3O4@p(o-PDA)@CMC beads were used for the removal of Reactive Blue 4 (RB-4) and Congo Red (CR) textile dyes from an aqueous medium. Different factors, such as adsorbent dose, initial pH, ionic strength, contact time, temperatures, and initial RB-4 and CR concentrations were examined. The maximum adsorption capacities of the RB-4 dye and CR at optimum pH 5 reached 398.7 and 524.6 mg/g in 120 min, respectively. The adsorption of RB-4 and CR on the hybrid magnetic beads can be due to the electrostatic, hydrogen bonding, and π-π interactions. Moreover, the magnetic hybrid beads showed easy regeneration ability and good reusability. The adsorbent can be a very good candidate for the efficient removal of micro-pollutant from wastewater.Article Citation - WoS: 3Citation - Scopus: 3Stable Single Layer Structures of Aluminum Oxide: Vibrational and Electronic Characterization of Magnetic Phases(Elsevier, 2022) Özyurt, A. Kutay; Molavali, Deniz; Şahin, HasanThe structural, magnetic, vibrational and electronic properties of single layer aluminum oxide (AlO2) are investigated by performing state-of-the-art first-principles calculations. Total energy optimization and phonon calculations reveal that aluminum oxide forms a distorted octahedral structure (1T′-AlO2) in its single layer limit. It is also shown that surfaces of 1T′-AlO2 display magnetic behavior originating from the O atoms. While the ferromagnetic (FM) state is the most favorable magnetic order for 1T′-AlO2, transformation to a dynamically stable antiferromagnetic (AFM) state upon a slight distortion in the crystal structure is also possible. It is also shown that Raman activities (350–400 cm−1) obtained from the vibrational spectrum can be utilized to distinguish the possible magnetic phases of the crystal structure. Electronically, both FM and the AFM phases are semiconductors with an indirect band gap and they can form a type-III vdW heterojunction with graphene-like ultra-thin materials. Moreover, it is predicted that presence of oxygen defects that inevitably occur during synthesis and production do not alter the magnetic state, even at high vacancy density. Apparently, ultra-thin 1T′-AlO2 with its stable crystal structure, semiconducting nature and robust magnetic state is a quite promising material for nanoscale device applications.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.