Photonics / Fotonik
Permanent URI for this collectionhttps://hdl.handle.net/11147/2590
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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: 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: 16Citation - Scopus: 16Silylethynyl substitution for preventing aggregate formation in perylene diimides(American Chemical Society, 2021) Aksoy, Erkan; Danos, Andrew; Li, Chunyong; Monkman, Andrew P.; Varlıklı, CananEthynylene-bridged perylene diimides (PDIs) with different sized silane groups have been synthesized as a steric blocking group to prevent the formation of non-radiative trap sites, for example, strong H-aggregates and other dimers or excimers. Excited singlet-state exciton dynamics were investigated by time-resolved photoluminescence and ultrafast pump-probe transient absorption spectroscopy. The spectra of the excimer or dimer aggregates formed by the PDIs at high concentrations were also determined. Although the photophysical properties of the bare and shielded PDIs are identical at micromolar concentrations, more shielded PDI2 and PDI3 exhibited resistance to aggregation, retaining higher photoluminescence quantum yield even at 10 mM concentration and in neat films. The PDIs also exhibited high photostability (1 h of continuous excitation), as well as electrochemical stability (multiple cycles with cyclic voltammetry). Prevention of dimer/aggregate formation in this manner will extend the uses of PDIs to a variety of high concentration photonics and optoelectronic applications, such as organic light-emitting diodes, organic photovoltaics, and luminescent solar concentrators.Article Citation - WoS: 21Citation - Scopus: 21Prediction of Monoclinic Single-Layer Janus Ga2tex (x = S and Se): Strong In-Plane Anisotropy(American Physical Society, 2021) Yağmurcukardeş, Mehmet; Moğulkoç, Yeşim; Akgenç, Berna; Moğulkoç Aybey; Peeters, François M.By using density functional theory (DFT) based first-principles calculations, electronic, vibrational, piezo-electric, and optical properties of monoclinic Janus single-layer Ga2TeX (X = S or Se) are investigated. The dynamical, mechanical, and thermal stability of the proposed Janus single layers are verified by means of phonon bands, stiffness tensor, and quantum molecular dynamics simulations. The calculated vibrational spectrum reveals the either pure or coupled optical phonon branches arising from Ga-Te and Ga-X atoms. In addition to the in-plane anisotropy, single-layer Janus Ga2TeX exhibits additional out-of-plane asymmetry, which leads to important consequences for its electronic and optical properties. Electronic band dispersions indicate the direct band-gap semiconducting nature of the constructed Janus structures with energy band gaps falling into visible spectrum. Moreover, while orientation-dependent linear-elastic properties of Janus single layers indicate their strong anisotropy, the calculated in-plane stiffness values reveal the ultrasoft nature of the structures. In addition, predicted piezoelectric coefficients show that while there is a strong in-plane anisotropy between piezoelectric constants along armchair (AC) and zigzag (ZZ) directions, there exists a tiny polarization along the out-of-plane direction as a result of the formation of Janus structure. The optical response to electromagnetic radiation has been also analyzed through density functional theory by considering the independent-particle approximation. Finally, the optical spectra of Janus Ga2TeX structures is investigated and it showed a shift from the ultraviolet region to the visible region. The fact that the spectrum is between these regions will allow it to be used in solar energy and many nanoelectronics applications. The predicted monoclinic single-layer Janus Ga2TeX are relevant for promising applications in optoelectronics, optical dichroism, and anisotropic nanoelasticity.Article Citation - WoS: 2Citation - Scopus: 2Ultra-Thin Structures of Manganese Fluorides: Conversion From Manganese Dichalcogenides by Fluorination(Royal Society of Chemistry, 2021) Başkurt, Mehmet; Nair, Rahul R.; Peeters, François M.; Şahin, HasanIn this study, it is predicted by density functional theory calculations that graphene-like novel ultra-thin phases of manganese fluoride crystals, that have nonlayered structures in their bulk form, can be stabilized by fluorination of manganese dichalcogenide crystals. First, it is shown that substitution of fluorine atoms with chalcogens in the manganese dichalcogenide host lattice is favorable. Among possible crystal formations, three stable ultra-thin structures of manganese fluoride, 1H-MnF2, 1T-MnF2 and MnF3, are found to be stable by total energy optimization calculations. In addition, phonon calculations and Raman activity analysis reveal that predicted novel single-layers are dynamically stable crystal structures displaying distinctive characteristic peaks in their vibrational spectrum enabling experimental determination of the corresponding phases. Differing from 1H-MnF2 antiferromagnetic (AFM) large gap semiconductor, 1T-MnF2 and MnF3 single-layers are semiconductors with ferromagnetic (FM) ground state.Article Citation - WoS: 14Citation - Scopus: 14Analysis of Illumination Dependent Electrical Characteristics of Α- Styryl Substituted Bodipy Dye-Based Hybrid Heterojunction(Springer, 2021) Kaplan, Nazmiye; Taşcı, Enis; Emrullahoğlu, Mustafa; Gökçe, Halil; Tuğluoğlu, Nihat; Eymur, SerkanThe alpha-styryl substituted BODIPY compound (BDP-Sty) was synthesized and characterized. The optimize ground state structure, HOMO and LUMO simulations, MEP surface map, and various molecular descriptors of the isolated BDP-Sty compound were investigated by Density Functional Theory at the B3LYP/6-311G (d,p) level. The reverse and forward bias current-voltage (I-V) characteristics of the Au/BDP-Sty/n-Si/In diode showed Schottky diode-like characteristics. An ideality factor (n) and barrier height (phi(b)) values of prepared diode for dark were found as 2.32 and 0.828, respectively. The series resistance (R-s) values were attained from the dV/dln(I) plot and Cheung's H(I) function and their values found for dark as 4.95 k omega and 4.59 k omega, respectively. The lnI - lnV and ln(I-R) - V-R(1/2) characteristics of the Au/BDP-Sty/n-Si/In diode reveal that the conduction mechanism is ohmic at low voltage and that of trap-filled space charge limited current and space charge limited current at higher voltage. The characteristic photodiode parameters of the prepared diode such as open circuit voltage (V-oc), short circuit current density (J(sc)), and photosensitivity (S) have also been investigated. All these results indicate the applicability for Au/BDP-Sty/n-Si/In diode in the field optoelectronic device applications.Article Citation - WoS: 2Citation - Scopus: 31-Octanol Is a Functional Impurity Modifying Particle Size and Photophysical Properties of Colloidal Zncdsse/Zns Nanocrystals(American Chemical Society, 2021) Sevim Ünlütürk, Seçil; Çağır, Ali; Varlıklı, Canan; Özçelik, SerdarImpurities in trioctylphophine (TOP) strongly affect nanocrystal synthesis. 1-Octanol among other contaminants in TOP is identified for the first time as a functional impurity by H-1 NMR. The deliberate addition of 1-octanol into trioctylphosphine reduced particle size and modified photophysical properties of ZnCdSSe/ZnS colloidal nanocrystals. NMR analysis furthermore revealed that 1-octanol is bonded to the nanocrystal surfaces. The ratio of integrals for the O-CH2 protons of 1-octanol, which is the lowest compared to the other ligands, suggests that 1-octanol plays a critical role to tune the particle size of nanocrystals. The increased amount of 1-octanol added into TOP reduces the particle size from 9.8 to 7.2 nm, causing a progressive blue shift in the UV-vis and PL spectra but leaving the alloy composition unaffected. The rate of nonradiative processes is enhanced with the amount of 1-octanol added into TOP, correlating with higher dislocation density observed in the nanocrystals. As a conclusion, 1-octanol is proposed as a functional impurity that varies particle size and nonradiative photophysical processes in the ZnCdSSe/ZnS colloidal nanocrystals.
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