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.Book Part Citation - Scopus: 3Advances and Future Perspective of Graphene Field Effect Transistors (gfets) for Medical Diagnostics and Point-Of Tools(World Scientific Publishing, 2022) İnanç, Dilce; Mutlu, Mustafa Umut; Karabacak, Soner; Yıldız, Ümit HakanRecently, major focus has been centered to enhance the capability of graphenebased devices and to facilitate utilization of graphene for biological applications by lowering its toxicity. In this chapter, from synthesis to applications, many of the conspicuous characteristics of graphene have been elaborately reviewed. We primarily focused on graphene-based field effect transistor (FET) for medical diagnostics and point-of-care applications. The device configurations and their application potential as well as sensing capability of various graphene FETs (GFETs) have been discussed. Here, we have also presented several aspects and advantages of GFETs in medical applications while discussing their pros and cons in commercialization. We address the advances and challenges for GFET-based sensing platforms for the medical applications and elaborate the combination strategy of GFETs with the existing commercial systems. © 2023 by World Scientific Publishing Co. Pte. 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: 5Citation - Scopus: 4Polarity Induced Vapochromism and Vapoluminescence of Polythiophene Derivatives for Volatile Organic Compounds Classification(Elsevier, 2023) Karabacak, Soner; Qun, David Lee Chao; Ammanath, Gopal; Yeasmin, Sanjida; Yağmurcukardeş, Mehmet; Palaniappan, Alagappan; Liedberg, Bo; Yıldız, Ümit HakanPolarity induced vapochromic and vapoluminescent properties of cationic poly-3-alkoxythiophene derivatives (PT) casted on polyvinylidene fluoride (PVDF) membranes are reported. PT with six different pendant groups are designed to differentially interact with volatile organic compounds (VOC) of varying polarities, thereby enabling their classification. PT exhibit a rapid vapochromic response with a concurrent modulation of vapoluminescence due to the non-covalent cation-? interactions between the pendant groups and the PT backbone. Adsorption of VOC on pendant groups alters the conformation of PT backbone, thus resulting in an increase in intensity and blue shifting of fluorescence emission within the visible spectrum. The vapoluminescent responses are found to be more sensitive with a limit of detection (LOD) of ?7 ppm and a wider dynamic range as compared to the vapochromic responses with a LOD of ?60 ppm for the detection of a model VOC: chloroform. Notably, all the PT illustrate an instantaneous recovery of colour and luminescence upon desorption of VOC. PT interaction with VOC of varying polarities was ascertained using density functional theory (DFT) and principal component analysis (PCA) methodologies. In summary, the polarity induced vapochromic and vapoluminescent properties of PT could yield a selective and sensitive vapochromic and fluorometric dual-mode VOC detection platform. © 2023Article Citation - WoS: 5Citation - Scopus: 5Thickness-Dependent Piezoelecticity of Black Arsenic From Few-Layer To Monolayer(Elsevier, 2023) Akgenç Hanedar, Berna; Ersan, Fatih; Altalhi, Tariq; Yağmurcukardeş, Mehmet; Yakobson, BorisUltra-thin forms of black phosphorus (b-P) have been widely investigated due to its unique properties arising from the in-plane anisotropy in its crystal structure. Recently, two-dimensional (2D) forms of black arsenic (b-As) have also been added to the 2D family. In this study, the thickness-dependent structural, electronic, and piezoelectric properties of layered b-As are investigated by means of ab-initio calculations. The structural optimizations confirm the van der Waals type layered structure for both these structures. In addition, increasing the thickness is shown to result in the decreasing of the band gap arising from the confinement of electrons in the layers. In contrast to the case of b-P, it is revealed that a transition from indirect-to-direct band gap behavior can be found in b-As which can be important for optically identifying the single-layer structure. Moreover, the piezoelectric properties are investigated as a function of the number of layers. It is shown that while a single-layer of b-As does not exhibit piezoelectric features, even in the case of bilayer structures the piezoelectricity is created. Our results revealed the strong in-plane anisotropy in piezoelectric coefficients for the three-layer and thicker structures. We have shown that the out-of-plane piezoelectric properties can be achieved by non-centrosymmetric features in the out-of-plane direction in thicker structures of b-As.Article Citation - WoS: 1Citation - Scopus: 1A Multi-Layered Graphene Based Gas Sensor Platform for Discrimination of Volatile Organic Compounds Via Differential Intercalation(Royal Society of Chemistry, 2023) Özkendir İnanç, Dilce; Ng, Zhi Kai; Başkurt, Mehmet; Keleş, Berfin; Vardar, Gökay; Şahin, Hasan; Tsang, Siu Hon; Palaniappan, Alagappan; Yıldız, Ümit Hakan; Teo, EhtSelective and sensitive detection of volatile organic compounds (VOCs) is of critical importance for environmental monitoring, disease diagnosis and industrial applications. Among VOCs, assay development for primary alcohols has captured significant research attention since their toxicity causes adverse effects on gastrointestinal and central nerve systems, resulting in irreversible blindness, and coma, and can be even fatal at high exposure levels. However, selective detection of primary alcohols is extremely challenging owing to the similarity in their molecular structure and characteristic groups. Herein, we have attempted to investigate the differential methanol (MeOH)-ethanol (EtOH) discriminative properties of single-layer, bi-layer, and multi-layer graphene morphologies. Chemiresistors fabricated using the three morphologies of graphene illustrate discriminative MeOH-EtOH responses, which is attributed to the phenomenon of differential intercalation of MeOH within layered graphene morphologies as compared to that of EtOH. This hypothesis is verified by density functional theory calculations, which revealed that the adsorption of EtOH molecules on the graphene surface is more energetically favorable as compared to that of MeOH molecules, thereby inhibiting their intercalation within the layered graphene morphologies. It is further evaluated that the degree of MeOH intercalation increases with increasing layers of graphene for obtaining differential MeOH-EtOH responses. Experimental results suggest possibilities to develop selective and sensitive MeOH assays fabricated using various graphene morphologies in a combinatorial sensor array format.Article Citation - WoS: 6Citation - Scopus: 6Ion and Molecule Sieving Through Highly Stable Graphene-Based Laminar Membranes(Amer Chemical Soc, 2023) Yuan, Gang; Jiang, Yu; Wang, Xiao; Ma, Jiaojiao; Ma, Hao; Wang, Xiang; Hu, ShengBiological ion channels use both their sizes and residual groups to reject large ions and molecules and allow highly selective permeation of small species with similar sizes. To realize these properties in artificial membranes, the main challenge is the precise control of both the channel size and the interior at the nanoscale. Here we report the permeation of ions and molecules through interlayer channels in graphene-based laminar membranes. The amino groups decorated on channel walls are found to form hydrogen bond networks with intercalated water molecules, thus providing a highly stable laminate structure and a controlled channel size. Solutes with hydration diameters of >10 angstrom are precisely sieved out. Small species permeate through with selectivities of up to a few thousand, governed by their distinct electrical interactions with channels depending on the atomistic distance from the charged species to the channel walls. Our work offers important insights into manipulating channel structures for enhanced separation performance at the nanoscale.