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: 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: 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.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: 18Citation - Scopus: 46Phosphor-Based White Led by Various Glassy Particles:control Over Luminous Efficiency(The Optical Society, 2019) Yüce, Hürriyet; Güner, Tuğrul; Balcı, Sinan; Demir, Mustafa MuammerGenerating white light through a mainstream remote phosphor design suffers from phosphor conversion efficiency loss due to a backscattering of light. Such a loss also reduces luminous efficiency of the resulting white light. To overcome this issue, various glassy scatterers with different morphologies such as glass bubbles, glass beads, and nanosized silica particles were employed as scatterers, together with a fixed amount of yellow phosphor (YAG:Ce3+) and a poly(dimethylsiloxane) (PDMS) matrix. In addition, the simulation of the system validates the rigorous multiple scattering of the incoming light most probably due to refractive index mismatch between the glass bubbles and surrounding PDMS matrix along with the internal reflections. (C) 2019 Optical Society of America