Photonics / Fotonik

Permanent URI for this collectionhttps://hdl.handle.net/11147/2590

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Citation - WoS: 2
Citation - Scopus: 3
1-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, Serdar
Impurities 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.
Citation - WoS: 37
Citation - Scopus: 36
2d Vibrational Properties of Epitaxial Silicene on Ag(111)
(IOP Publishing Ltd., 2017-03) Solonenko, Dmytro; Gordan, Ovidiu D.; Le Lay, Guy; Şahin, Hasan; Cahangirov, Seymur; Zahn, Dietrich R. T.; Vogt, Patrick
The two-dimensional silicon allotrope, silicene, could spur the development of new and original concepts in Si-based nanotechnology. Up to now silicene can only be epitaxially synthesized on a supporting substrate such as Ag(111). Even though the structural and electronic properties of these epitaxial silicene layers have been intensively studied, very little is known about its vibrational characteristics. Here, we present a detailed study of epitaxial silicene on Ag(111) using in situ Raman spectroscopy, which is one of the most extensively employed experimental techniques to characterize 2D materials, such as graphene, transition metal dichalcogenides, and black phosphorous. The vibrational fingerprint of epitaxial silicene, in contrast to all previous interpretations, is characterized by three distinct phonon modes with A and E symmetries. Both, energies and symmetries of theses modes are confirmed by ab initio theory calculations. The temperature dependent spectral evolution of these modes demonstrates unique thermal properties of epitaxial silicene and a significant electron-phonon coupling. These results unambiguously support the purely two-dimensional character of epitaxial silicene up to about 300°C, whereupon a 2D-to-3D phase transition takes place. The detailed fingerprint of epitaxial silicene will allow us to identify it in different environments or to study its modifications.
Citation - WoS: 16
Citation - Scopus: 17
Ab Initio and Semiempirical Modeling of Excitons and Trions in Monolayer Tis3
(American Physical Society, 2018-08) Torun, Engin; Şahin, Hasan; Chaves, A.; Wirtz, Ludger; Peeters, François M.
We explore the electronic and the optical properties of monolayer TiS3, which shows in-plane anisotropy and is composed of a chain-like structure along one of the lattice directions. Together with its robust direct band gap, which changes very slightly with stacking order and with the thickness of the sample, the anisotropic physical properties of TiS3 make the material very attractive for various device applications. In this study, we present a detailed investigation on the effect of the crystal anisotropy on the excitons and the trions of the TiS3 monolayer. We use many-body perturbation theory to calculate the absorption spectrum of anisotropic TiS3 monolayer by solving the Bethe-Salpeter equation. In parallel, we implement and use a Wannier-Mott model for the excitons that takes into account the anisotropic effective masses and Coulomb screening, which are obtained from ab initio calculations. This model is then extended for the investigation of trion states of monolayer TiS3. Our calculations indicate that the absorption spectrum of monolayer TiS3 drastically depends on the polarization of the incoming light, which excites different excitons with distinct binding energies. In addition, the binding energies of positively and the negatively charged trions are observed to be distinct and they exhibit an anisotropic probability density distribution.
Citation - WoS: 1
Citation - Scopus: 1
Adsorption and Diffusion Characteristics of Lithium on Hydrogenated ?- and Ss-Silicene
(Beilstein-Institut Zur Forderung der Chemischen Wissenschaften, 2017-08) İyikanat, Fadıl; Kandemir, Ali; Bacaksız, Cihan; Şahin, Hasan
Using first-principles density functional theory calculations, we investigate adsorption properties and the diffusion mechanism of a Li atom on hydrogenated single-layer α- and β-silicene on a Ag(111) surface. It is found that a Li atom binds strongly on the surfaces of both α- and β-silicene, and it forms an ionic bond through the transfer of charge from the adsorbed atom to the surface. The binding energies of a Li atom on these surfaces are very similar. However, the diffusion barrier of a Li atom on H-α-Si is much higher than that on H-β-Si. The energy surface calculations show that a Li atom does not prefer to bind in the vicinity of the hydrogenated upper-Si atoms. Strong interaction between Li atoms and hydrogenated silicene phases and low diffusion barriers show that α- and β-silicene are promising platforms for Li-storage applications.
Citation - Scopus: 3
Advances 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 Hakan
Recently, 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.
Citation - WoS: 17
Citation - Scopus: 22
Aluminum and Lithium Sulfur Batteries: a Review of Recent Progress and Future Directions
(IOP Publishing, 2021) Akgenç, Berna; Sarıkurt, Sevil; Yağmurcukardeş, Mehmet; Ersan, Fatih
Advanced materials with various micro-/nanostructures have attracted plenty of attention for decades in energy storage devices such as rechargeable batteries (ion- or sulfur based batteries) and supercapacitors. To improve the electrochemical performance of batteries, it is uttermost important to develop advanced electrode materials. Moreover, the cathode material is also important that it restricts the efficiency and practical application of aluminum-ion batteries. Among the potential cathode materials, sulfur has become an important candidate material for aluminum-ion batteries cause of its considerable specific capacity. Two-dimensional materials are currently potential candidates as electrodes from lab-scale experiments to possible pragmatic theoretical studies. In this review, the fundamental principles, historical progress, latest developments, and major problems in Li-S and Al-S batteries are reviewed. Finally, future directions in terms of the experimental and theoretical applications have prospected.
Citation - WoS: 13
Citation - Scopus: 13
Analysis 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, Serkan
The 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.
Citation - WoS: 64
Citation - Scopus: 67
Angle Resolved Vibrational Properties of Anisotropic Transition Metal Trichalcogenide Nanosheets
(Royal Society of Chemistry, 2017-03) Kong, Wilson; Bacaksız, Cihan; Chen, Bin; Wu, Kedi; Blei, Mark; Fan, Xi; Shen, Yuxia; Şahin, Hasan; Wright, David; Narang, Deepa S.; Tongay, Sefaattin
Layered transition metal trichalcogenides (TMTCs) are a new class of anisotropic two-dimensional materials that exhibit quasi-1D behavior. This property stems from their unique highly anisotropic crystal structure where vastly different material properties can be attained from different crystal directions. Here, we employ density functional theory predictions, atomic force microscopy, and angle-resolved Raman spectroscopy to investigate their fundamental vibrational properties which differ significantly from other 2D systems and to establish a method in identifying anisotropy direction of different types of TMTCs. We find that the intensity of certain Raman peaks of TiS3, ZrS3, and HfS3 have strong polarization dependence in such a way that intensity is at its maximum when the polarization direction is parallel to the anisotropic b-axis. This allows us to readily identify the Raman peaks that are representative of the vibrations along the b-axis direction. Interestingly, similar angle resolved studies on the novel TiNbS3 TMTC alloy reveal that determination of anisotropy/crystalline direction is rather difficult possibly due to loss of anisotropy by randomization distribution of quasi-1D MX6 chains by the presence of defects which are commonly found in 2D alloys and also due to the complex Raman tensor of TMTC alloys. Overall, the experimental and theoretical results establish non-destructive methods used to identify the direction of anisotropy in TMTCs and reveal their vibrational characteristics which are necessary to gain insight into potential applications that utilize direction dependent thermal response, optical polarization, and linear dichroism.
Citation - WoS: 34
Citation - Scopus: 34
Anisotropic and Outstanding Mechanical, Thermal Conduction, Optical, and Piezoelectric Responses in a Novel Semiconducting Bcn Monolayer Confirmed by First-Principles and Machine Learning
(Elsevier, 2022-11) Mortazavi, Bohayra; Fazel Shojaei; Yağmurcukardeş, Mehmet; Alexander Shapeev; Xiaoying Zhuang
Graphene-like nanomembranes made of the neighboring elements of boron, carbon and nitrogen elements, are well-known of showing outstanding physical properties. Herein, with the aid of density functional theory (DFT) calculations, various atomic configurations of the graphene-like BCN nanosheets are investigated. DFT results reveal that depending on the atomic arrangement, the BCN monolayers may display semimetallic Dirac cone or semiconducting electronic nature. BCN nanosheets are also found to exhibit high piezoelectricity and carrier mobilities with considerable in-plane anisotropy, depending on the atomic arrangement. For the predicted most stable BCN monolayer, thermal and mechanical properties are explored using machine learning interatomic potentials. The room temperature tensile strength and lattice thermal conductivity of the most stable BCN monolayer are estimated to be orientation-dependent and remarkably high, over 78 GPa and 290 W/m.K, respectively. In addition, the thermal expansion coefficient of the monolayer BCN at room temperature is estimated to be −3.2 × 10−6 K−1, which is close to that of the graphene. The piezoelectric response of the herein proposed BCN lattice is also predicted to be close to that of the h-BN monolayer. Presented results highlight outstanding physics of the BCN nanosheets.
Citation - WoS: 6
Citation - Scopus: 6
Anisotropic Etching of Cvd Grown Graphene for Ammonia Sensing
(Institute of Electrical and Electronics Engineers Inc., 2022-03) Yağmurcukardeş, Nesli; Bayram, Abdullah; Aydın, Hasan; Yağmurcukardeş, Mehmet; Açıkbaş, Yaser; Peeters, François M.; Çelebi, Cem
Bare chemical vapor deposition (CVD) grown graphene (GRP) was anisotropically etched with various etching parameters. The morphological and structural characterizations were carried out by optical microscopy and the vibrational properties substrates were obtained by Raman spectroscopy. The ammonia adsorption and desorption behavior of graphene-based sensors were recorded via quartz crystal microbalance (QCM) measurements at room temperature. The etched samples for ambient NH3 exhibited nearly 35% improvement and showed high resistance to humidity molecules when compared to bare graphene. Besides exhibiting promising sensitivity to NH3 molecules, the etched graphene-based sensors were less affected by humidity. The experimental results were collaborated by Density Functional Theory (DFT) calculations and it was shown that while water molecules fragmented into H and O, NH3 interacts weakly with EGPR2 sample which reveals the enhanced sensing ability of EGPR2. Apparently, it would be more suitable to use EGRP2 in sensing applications due to its sensitivity to NH3 molecules, its stability, and its resistance to H2O molecules in humid ambient.
Anisotropic Tunability of Vibrational Modes in Black Phosphorus Under Uniaxial Compressive/Tensile Strain
(Wiley, 2023) Li, Hao; Kutlu, Tayfun; Carrascoso, Felix; Şahin, Hasan; Munuera, Carmen; Castellanos Gomez, Andres
Strain engineering is a powerful strategy for tuning the optical, electrical, vibrational properties of 2D nanomaterials. In this work, a four-point bending apparatus is constructed to apply both compressive and tensile strain on 2D anisotropic black phosphorus flake. Further polarized Raman spectroscopy is used to study the vibrational modes of black phosphorus flakes under uniaxial strain applied along various crystalline orientations. Here, a strong anisotropic blue/redshift of A1g, B2g, and A2g modes is found under compressive/tensile strain, respectively. Interestingly, mode A1g exhibits the maximum/minimum shift while mode B2g and mode A2g present the minimum/maximum shift when the strain is applied along armchair/zigzag direction. Density functional theory calculations are carried out to investigate the anisotropic strain response mechanism, finding that the strain-induced regulation of the PP bond angle, bond length, and especially interlayer interaction has a giant influence on the Raman shift. A four-point bending apparatus is constructed to study the effect of uniaxial strain on the vibrational property of anisotropic black phosphorus. Particularly, strong anisotropy on the Raman blueshift/redshift rate upon compressive/tensile strain can be observed, which results from the strain-induced regulation of the bond angle, bond length, and interlayer interactions according to density functional theory calculation analysis.image
Citation - WoS: 2
Citation - Scopus: 2
Atomic-scale understanding of dichlorobenzene-assisted poly 3-hexylthiophene-2,5-diyl nanowire formation mechanism
(Elsevier Ltd., 2017-04) Yağmurcukardeş, Mehmet; Kıymaz, D.; Zafer, C.; Senger, Ramazan Tuğrul; Şahin, Hasan
Low-dimensional Poly 3-hexylthiophene-2,5-diyl (P3HT) structures that serve efficient exciton dissociation in organic solar cells, play a major role in increasing the charge collection, and hence, the efficiency of organic devices. In this study, we theoretically and experimentally investigate the Dichlorobenzene (DCB)-assisted formation of P3HT nanowires. Our experiments show that the solution of DCB molecules drive randomly oriented P3HT polymers to form well-stacked nanowires by stabilizing tail-tail and π−π interactions. Here the question is how DCB molecules migrate into the P3HT layers while forming the nanowire structure. Our density functional theory-based calculations reveal that the vertical migration of the DCB molecules between P3HT layers is forbidden due to a high energy barrier that stems from strong alkyl chain-DCB interaction. In contrast to vertical diffusion, lateral diffusion of DCB molecules in between P3HT layers is much more likely. Our results show that migration of a DCB molecule occurs through the alkyl groups with a low energy barrier. Therefore, laterally diffused DCB molecules assist nucleation of top-to-top stacking of P3HT polymers and formation of well-ordered nanowires.
Citation - WoS: 66
Citation - Scopus: 66
Bilayers of Janus Wsse: Monitoring the Stacking Type: Via the Vibrational Spectrum
(Royal Society of Chemistry, 2018) Kandemir, Ali; Şahin, Hasan
Motivated by the recent successful synthesis of Janus type single layers of transition metal dichalcogenides, we investigate the stability, vibrational and electronic properties of the Janus single layer structure of WSSe and its bilayers by means of density functional theory. The structural and vibrational analysis show that the Janus single layer of WSSe forms a dynamically stable structure in the 2H phase. Owing to its non-centrosymmetric structure, the Janus WSSe single layer has two in-plane (E) and two out-of-plane (A) Raman active phonon modes. The eigen-frequencies of the prominent Raman active modes are calculated to be 277 (A) and 322 (E) cm-1. Similar to single layer WS2 and WSe2, Janus WSSe is a direct band gap semiconductor that has two electronically different faces. In addition, the possible bilayer stacking orders of the Janus WSSe single layers are investigated. It is found that there are 3 stacking types of bilayer Janus WSSe and each stacking type has distinctive Raman characteristics in its vibrational spectrum. Our results show that thanks to the vibrational characteristics, which stem from the distinctive interlayer interactions at different sides, the stability and stacking types of the bilayer of WSSe Janus structure can be monitored.
Citation - WoS: 26
Citation - Scopus: 28
Biocomposite Scaffolds for 3d Cell Culture: Propolis Enriched Polyvinyl Alcohol Nanofibers Favoring Cell Adhesion
(John Wiley and Sons Inc., 2021-05) Bilginer, Rumeysa; Özkendir İnanç, Dilce; Yıldız, Ümit Hakan; Arslan Yıldız, Ahu
The objective of this work is generation of propolis/polyvinyl alcohol (PVA) scaffold by electrospinning for 3D cell culture. Here, PVA used as co-spinning agent since propolis alone cannot be easily processed by electrospinning methodology. Propolis takes charge in maximizing biological aspect of scaffold to facilitate cell attachment and proliferation. Morphological analysis showed size of the electrospun nanofibers varied between 172-523 nm and 345-687 nm in diameter, for non-crosslinked and crosslinked scaffolds, respectively. Incorporation of propolis resulted in desired surface properties of hybrid matrix, where hybrid scaffolds highly favored protein adsorption. To examine cell compatibility, NIH-3T3 and HeLa cells were seeded on propolis/PVA hybrid scaffold. Results confirmed that integration of propolis supported cell adhesion and cell proliferation. Also, results indicated electrospun propolis/PVA hybrid scaffold provide suitable microenvironment for cell culturing. Therefore, developed hybrid scaffold could be considered as potential candidate for 3D cell culture and tissue engineering.
Bir Ameliyat Robotunun Denetimi için Basitleştirilmiş Dinamik Modeli
(Otomatik Kontrol Türk Milli Komitesi, 2018-09) Ayit, Orhan; Yaşır, Abdullah; Vardarlı, Eren; Kiper, Gökhan; Dede, Mehmet İsmet Can
Bu çalışmanın temel konusu minimal invaziv tipi bir ameliyat olan endoskopik hipofiz tümörü ameliyatında kullanılan endoskopun hareket denetimi için geliştirilen robotik sistemdir. Geliştirilen sistemin bu bildiride ele alınan kısmı, ameliyat sırasında sadece ameliyat bölgesi içinde endoskopu cerrahın anlık isteklerine göre yönlendiren, aktif robot yapısıdır. Söz konusu robot uzak hareket merkezli, 3 serbestlik dereceli, paralel kinematik mimariye sahiptir. Bu çalışmada robotun denetimi için uygun görülen hesaplanmış tork yöntemi için gerekli robotun dinamik analizi sunulmaktadır. Denetim algoritmasının yüksek frekansta çalışabilmesi için dinamik denklemlerde yapılan basitleştirmeler ve bunun sonucunda elde edilen hesaplama zamanı sunulmaktadır.
Citation - WoS: 22
Citation - Scopus: 22
Bodipy-Vinyl Dibromides as Triplet Sensitisers for Photodynamic Therapy and Triplet-Triplet Annihilation Upconversion
(Royal Society of Chemistry, 2021) Dartar, Suay; Üçüncü, Muhammed; Karakuş, Erman; Hou, Yuqi; Zhao, Jianzhang; Emrullahoğlu, Mustafa
We devised a new generation of halogen-based triplet sensitisers comprising geminal dibromides at the vinyl backbone of a BODIPY fluorophore. Incorporating geminal dibromides into the pi-conjugation of BODIPY enhanced intersystem crossing due to the heavy atom effect, which in turn improved the extent of excited triplet states.
Citation - WoS: 5
Citation - Scopus: 6
Boosting Up Printability of Biomacromolecule Based Bio-Ink by Modulation of Hydrogen Bonding Pairs
(Elsevier Ltd., 2020) Köksal, Büşra; Önbaş, Rabia; Başkurt, Mehmet; Şahin, Hasan; Arslan Yıldız, Ahu; Yıldız, Ümit Hakan
This study describes low dose UV curable and bioprintable new bioink made of hydrogen bond donor-acceptor adaptor molecule 2-isocyanatoethyl methacrylate (NCO)modified gelatin (NCO-Gel). Our theoretical calculations demonstrate that insertion of 2-isocyanatoethyl methacrylate doubles the interaction energy (500 meV) between gelatin chains providing significant contribution in interchain condensation and self-organization as compared to methacrylic anhydride modified gelatin (GelMA). The NCO-Gel exhibits peak around 1720 cm?1 referring to bidentate hydrogen bonding between H-NCO and its counterpart O[dbnd]CN[sbnd]H. These strong interchain interactions drive chains to be packed and thereby facilitating UV crosslinking. The NCO-Gel is exhibiting a rapid, 10 s gelation process by the exposure of laser (3 W, 365 nm). The dynamic light scattering characterization also reveals that NCO-Gel has faster sol to gel transition as compared to GelMA depending on the UV curing time. The NCO-Gel was found to be more firm and mechanically strong that provides advantages in molding as well as bioprinting processes. Bioprinted NCO-Gel has shown sharp borders and stable 3D geometry as compared to GelMA ink under 10 s UV curing time. The cell viability tests confirm that NCO-Gel facilitates cell proliferation and supports cell viability. We foresee that NCO-Gel bioink formulation provides a promising opportunity when low dose UV curing and rapid printing are required. © 2020 Elsevier Ltd
Citation - WoS: 5
Citation - Scopus: 5
Breaking the Boundaries of the Goldschmidt Tolerance Factor With Ethylammonium Lead Iodide Perovskite Nanocrystals
(American Chemical Society, 2024) Güvenç, Çetin Meriç; Toso, Stefano; Ivanov, Yurii P.; Saleh, Gabriele; Balcı, Sinan; Divitini, Giorgio; Manna, Liberato
We report the synthesis of ethylammonium lead iodide (EAPbI3) colloidal nanocrystals as another member of the lead halide perovskites family. The insertion of an unusually large A-cation (274 pm in diameter) in the perovskite structure, hitherto considered unlikely due to the unfavorable Goldschmidt tolerance factor, results in a significantly larger lattice parameter compared to the Cs-, methylammonium- and formamidinium-based lead halide perovskite homologues. As a consequence, EAPbI3 nanocrystals are highly unstable, evolving to a nonperovskite delta-EAPbI3 polymorph within 1 day. Also, EAPbI3 nanocrystals are very sensitive to electron irradiation and quickly degrade to PbI2 upon exposure to the electron beam, following a mechanism similar to that of other hybrid lead iodide perovskites (although degradation can be reduced by partially replacing the EA+ ions with Cs+ ions). Interestingly, in some cases during this degradation the formation of an epitaxial interface between (EA x Cs1-x )PbI3 and PbI2 is observed. The photoluminescence emission of the EAPbI3 perovskite nanocrystals, albeit being characterized by a low quantum yield (similar to 1%), can be tuned in the 664-690 nm range by regulating their size during the synthesis. The emission efficiency can be improved upon partial alloying at the A site with Cs+ or formamidinium cations. Furthermore, the morphology of the EAPbI3 nanocrystals can be chosen to be either nanocube or nanoplatelet, depending on the synthesis conditions.
A Brief History of Silicene
(Springer Verlag, 2017-11) Cahangirov, Seymur; Şahin, Hasan; Le Lay, Guy; Rubio, Angel
Research on silicene shows a fast and steady growth that has increased our tool-box of novel 2D materials with exceptional potential applications in materials science. Especially after the experimental synthesis of silicene on substrates in 2012 it has attracted substantial interest from both theoretical and experimental communities. Every day, new people from various disciplines join this rapidly growing field. The aim of this book is to serve as a fast entry to the field to these newcomers and as a long-living reference to the growing community. To achieve this goal, the book is designed to emphasize the most crucial developments from both theoretical and experimental point of view since the starting of the silicene field back in 1994 with the first theoretical paper proposing the structure of silicene. We provide the general concepts and ideas such that the book is accessible to everybody from graduate students to senior researchers and we refer the reader interested in the detail to the relevant literature. We now start with a brief history of silicene where we highlight, in the chronological order, the important works that shaped our understanding of silicene.
Citation - WoS: 1
Citation - Scopus: 1
Calcium 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.

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