Browsing by Subject "Monolayers"
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Item Open Access Anisotropic electronic, mechanical, and optical properties of monolayer WTe2(American Institute of Physics Inc., 2016) Torun, E.; Sahin, H.; Cahangirov, S.; Rubio, A.; Peeters, F. M.Using first-principles calculations, we investigate the electronic, mechanical, and optical properties of monolayer WTe2. Atomic structure and ground state properties of monolayer WTe2 (Td phase) are anisotropic which are in contrast to similar monolayer crystals of transition metal dichalcogenides, such as MoS2, WS2, MoSe2, WSe2, and MoTe2, which crystallize in the H-phase. We find that the Poisson ratio and the in-plane stiffness is direction dependent due to the symmetry breaking induced by the dimerization of the W atoms along one of the lattice directions of the compound. Since the semimetallic behavior of the Td phase originates from this W-W interaction (along the a crystallographic direction), tensile strain along the dimer direction leads to a semimetal to semiconductor transition after 1% strain. By solving the Bethe-Salpeter equation on top of single shot G0W0 calculations, we predict that the absorption spectrum of Td-WTe2 monolayer is strongly direction dependent and tunable by tensile strain.Item Open Access Attributed relational graphs for cell nucleus segmentation in fluorescence microscopy images(IEEE, 2013) Arslan, S.; Ersahin, T.; Cetin-Atalay, R.; Gunduz-Demir, C.More rapid and accurate high-throughput screening in molecular cellular biology research has become possible with the development of automated microscopy imaging, for which cell nucleus segmentation commonly constitutes the core step. Although several promising methods exist for segmenting the nuclei of monolayer isolated and less-confluent cells, it still remains an open problem to segment the nuclei of more-confluent cells, which tend to grow in overlayers. To address this problem, we propose a new model-based nucleus segmentation algorithm. This algorithm models how a human locates a nucleus by identifying the nucleus boundaries and piecing them together. In this algorithm, we define four types of primitives to represent nucleus boundaries at different orientations and construct an attributed relational graph on the primitives to represent their spatial relations. Then, we reduce the nucleus identification problem to finding predefined structural patterns in the constructed graph and also use the primitives in region growing to delineate the nucleus borders. Working with fluorescence microscopy images, our experiments demonstrate that the proposed algorithm identifies nuclei better than previous nucleus segmentation algorithms. © 2012 IEEE.Item Open Access Characterization and stability of Janus TiXY (X/Y = S, Se, and Te) monolayers(American Chemical Society, 2019) Moğulkoç, A.; Moğulkoç, Y.; Jahangirov, Seymur; Durgun, EnginThe realization of Janus MoSSe monolayers has brought two-dimensional (2D), ternary transition metal dichalcogenides (TMDs) into focus. The addition of a third element can lead to superior properties, hence extensive analyses on the characterization of these sophisticated systems are required to reveal their full potential. In this study, we examine the structural, mechanical, electronic, thermal, and optical properties of TiXY (X/Y = S, Se, and Te) monolayers by using first-principles techniques. In addition to the common 1T form, the 2H phase is considered, and the stability of both phases is revealed by phonon spectrum analysis and molecular dynamics simulations. Following the investigation of the mechanical response, electronic structures are examined together with partial density of states analysis. While monolayers of 1T-TiXY are found to be semimetals, monolayers of 2H-TiXY are semiconductors with indirect band gap. The optical spectrum is obtained by calculating the frequency-dependent imaginary dielectric function and is correlated with the electronic structure. The variation of heat capacity with temperature is investigated, and low-/high-temperature response is shown. Finally, possible structural distortions/transformations are also taken into account, and charge density wave transition in 1T-TiSeS due to Peierls instability is demonstrated. Our results not only reveal the stable Janus monolayers of 2H- and 1T-TiXY but also point out these systems as promising candidates for nanoscale applications.Item Open Access Effective mass of electron in monolayer graphene: Electron-phonon interaction(AIP Publishing LLC, 2013-01-25) Tiras, E.; Ardali, S.; Tiras, T.; Arslan, E.; Cakmakyapan, S.; Kazar, O.; Hassan, J.; Janzén, E.; Özbay, EkmelShubnikov-de Haas (SdH) and Hall effect measurements performed in a temperature range between 1.8 and 275 K, at an electric field up to 35 kV m -1 and magnetic fields up to 11 T, have been used to investigate the electronic transport properties of monolayer graphene on SiC substrate. The number of layers was determined by the use of the Raman spectroscopy. The carrier density and in-plane effective mass of electrons have been obtained from the periods and temperature dependencies of the amplitude of the SdH oscillations, respectively. The effective mass is in good agreement with the current results in the literature. The two-dimensional (2D) electron energy relaxations in monolayer graphene were also investigated experimentally. The electron temperature (Te) of hot electrons was obtained from the lattice temperature (TL) and the applied electric field dependencies of the amplitude of SdH oscillations. The experimental results for the electron temperature dependence of power loss indicate that the energy relaxation of electrons is due to acoustic phonon emission via mixed unscreened piezoelectric interaction and deformation-potential scattering.Item Open Access Enhanced interactions of amino acids and nucleic acid bases with bare black phosphorene monolayer mediated by coadsorbed species(American Chemical Society, 2019) Kadıoğlu, Y.; Görkan, T.; Üzengi-Aktürk, O.; Aktürk, E.; Çıracı, SalimIn this paper, we characterize amino acids and nucleic acid bases (nucleobases), such as glutamine, histidine, tyrosine, adenine, guanine, cytosine, and thymine, and examine their interaction with bare, as well as with gold cluster and Ti adatom covered, black phosphorene (α-P) monolayers using density functional theory. The binding of these amino acids and nucleobases to the bare α-P monolayer is realized generally through weak van der Waals interaction and comprises only a small amount of charge exchange. Accordingly, the electronic energy structures of adsorbates and underlying substrate are not affected significantly. However, the electronic structure of bare α-P is significantly affected upon adsorption of a gold cluster and a single Ti adatom; depending on the size of the adsorbate and the symmetry of their coverage, the energy band gap can be tuned and permanent magnetic moments can be attained. Additionally, the adsorption of amino acids or nucleobases to these adsorbates on an α-P monolayer results in enhanced binding and hence makes their sustainable fixation on α-P monolayer possible. In particular, a semiconducting Au decorated α-P monolayer undergoes a metal–insulator transition upon the adsorption of tyrosine. This and similar effects favor the α-P monolayer in biosensor applications. In contrast to the situation with adsorbates, the binding of amino acid is not enhanced when it adsorb to patterned vacancy or divacancy sites of the α-P monolayer. Our study shows that the absorbance of the bare α-P monolayer can be enhanced by coating with amino acid and nucleobases. The absorbance spectrum can be further modified by the adsorption of these molecules to gold atoms on the α-P monolayer.Item Open Access Finite temperature studies of Te adsorption on Si(0 0 1)(Elsevier, 2002) Sen, P.; Çıracı, Salim; Batra, I. P.; Grein, C. H.; Sivananthan, S.We perform first principles density functional calculations to investigate the adsorption of Te on the Si(0 0 1) surface from low coverage up to a monolayer coverage. At low coverage, a Te atom is adsorbed on top of the Si surface dimer bond. At higher coverages, Te atoms adsorption causes the Si-Si dimer bond to break, lifting the (2 × 1) reconstruction. We find no evidence of the Te-Te dimer bond formation as a possible source of the (2 × 1) reconstruction at a monolayer coverage. Finite temperature ab initio molecular dynamics calculations show that Te covered Si(0 0 1) surfaces do not have any definitive reconstruction. Vibrations of the bridged Te atoms in the strongly anharmonic potentials prevent the reconstruction structure from attaining any permanent, two-dimensional periodic geometry. This explains why experiments attempting to find a definite model for the reconstruction reached conflicting conclusions. © 2002 Elsevier Science B.V. All rights reserved.Item Open Access Functional carbon and silicon monolayers in biphenylene network(American Chemical Society, 2022-06-28) Gorkan, T.; Çallıoǧlu, Şafak; Demirci, S.; Aktürk, E.; Ciraci, S.We investigated the effects of vacancy, void, substitutional impurity, isolated adsorption of selected adatoms, and their patterned coverage on the physical and chemical properties of metallic carbon and silicon monolayers in a biphenylene network. These monolayers can acquire diverse electronic and magnetic properties to become more functional depending on the repeating symmetry, size of the point defects, and on the type of adsorbed adatoms. While a carbon monovacancy attains a local magnetic moment, its void can display closed edge states with interesting physical effects. Adsorbed light-transition or rare-earth metal atoms attribute magnetism to these monolayers. The opening of a gap in the metallic density of states, which depends on the pattern and density of adsorbed hydrogen, oxygen, and carbon adatoms, can be used as the band gap engineering of these two-dimensional materials. The energy barriers against the passage of oxygen atoms through the centers of hexagon and octagon rings are investigated, and the coating of the active surfaces with carbon monolayers is exploited as a means of protection against oxidation. We showed that the repulsive forces exerting even at distant separations between two parallel, hydrogenated carbon monolayers in a biphenylene network can lead to the superlow friction features in their sliding motion. All these results obtained from the calculations using the density functional theory herald critical applications.Item Open Access Hybridization of fano and vibrational resonances in surface-enhanced infrared absorption spectroscopy of streptavidin monolayers on metamaterial substrates(2014) Alici, K. B.We present spectral hybridization of organic and inorganic resonant materials and related bio-sensing mechanism. We utilized a bound protein (streptavidin) and a Fano-resonant metasurface to illustrate the concept. The technique allows us to investigate the vibrational modes of the streptavidin and how they couple to the underlying metasurface. This optical, label-free, nonperturbative technique is supported by a coupled mode-theory analysis that provides information on the structure and orientation of bound proteins. We can also simultaneously monitor the binding of analytes to the surface through monitoring the shift of the metasurface resonance. All of this data opens up interesting opportunities for applications in biosensing, molecular electronics and proteomics. © 2014 IEEE.Item Open Access Hydrogenated carbon monolayer in biphenylene network offers a potential paradigm for nanoelectronic devices(American Chemical Society, 2022-09-15) Demirci, S.; Gorkan, T.; Çallıoǧlu, Şafak; Özçelik, V. O.; Barth, J.; Aktürk, E.; Çıracı, SalimA metallic carbon monolayer in the biphenylene network (specified as C ohs) becomes an insulator upon hydrogenation (specified as CH ohs). Patterned dehydrogenation of this CH ohs can offer a variety of intriguing functionalities. Composite structures constituted by alternating stripes of C and CH ohs with different repeat periodicity and chirality display topological properties and can form heterostructures with a tunable band-lineup or Schottky barrier height. Alternating arrangements of these stripes of finite size enable one to also construct double barrier resonant tunneling structures and 2D, lateral nanocapacitors with high gravimetric capacitance for an efficient energy storage device. By controlled removal of H atom from a specific site or dehydrogenation of an extended zone, one can achieve antidoping or construct 0D quantum structures like antidots, antirings/loops, and supercrystals, the energy level spacing of which can be controlled with their geometry and size for optoelectronic applications. Conversely, all these device functions can be acquired also by controlled hydrogenation of a bare C ohs monolayer. Since all these processes are applied to a monolayer, the commensurability of electronically different materials is assured. These features pertain not only to CH ohs but also to fully hydrogenated Si ohs.Item Open Access Infrared absorption spectroscopy of monolayers with thin film interference coatings(Optical Society of America, 2017) Ayas, Sencer; Bakan, Gökhan; Ozgur, E.; Celebi, Kemal; Dana, AykutluWe report high performance Infrared spectroscopy platforms based on interference coatings on metal using CaF2 dielectric films and Ge2Sb2Te5 (GST) phase-change films. IR vibrational bands of proteins and organic monolayers are also detected.Item Open Access Mechanical and electrical monitoring in the dynamics of twisted phosphorene nanoflakes on 2D monolayers(American Chemical Society, 2019) Görkan, T.; Kadıoğlu, Y.; Üzengi-Aktürk, O.; Gökoğlu, G.; Aktürk, E.; Çıracı, SalimWe investigated the rotational and translational dynamics of hydrogen-passivated, black phosphorene and blue phosphorene nanoflakes of diverse size and geometry anchored to graphene, black phosphorene, blue phosphorene, and MoS2 monolayer substrates. The optimized attractive interaction energy between each nanoflake and monolayer substrates are harmonic for small angular displacements, leading to libration frequencies. We showed that the relevant dynamical parameters and resulting libration frequencies, which vary with the size/geometry of nanoflakes, as well as with the type of substrate, can be monitored by charging, external electric field, pressure, and also by a molecule anchored to the flake. The optimized energy profiles and energy barriers thereof have been calculated in translational and in large angle rotational dynamics. Owing to the weak interaction between the flakes and monolayers the energy barriers are particularly small for incommensurate systems and can renders nearly frictionless rotation and translation, which is crucial for nanoscale mechanics. Even if small for particular combined nanoflake + monolayer heterostructures, the energy band gaps exhibit variations with angular and linear displacements of nanoflakes. However, these band gaps undergo considerable reduction under pressure. With tunable dynamics, electronic structure, and low friction coefficients, individual or periodically repeating nanoflakes on a monolayer substrate constitute critical composite structures offering the design of novel detectors, nanomechanical, electromechanical, and electronic devices.Item Open Access Mo2C as a high capacity anode material: a first-principles study(Royal Society of Chemistry, 2016) Çakir, D.; Sevik, C.; Gülseren, O.; Peeters, F. M.The adsorption and diffusion of Li, Na, K and Ca atoms on a Mo2C monolayer are systematically investigated by using first principles methods. We found that the considered metal atoms are strongly bound to the Mo2C monolayer. However, the adsorption energies of these alkali and earth alkali elements decrease as the coverage increases due to the enhanced repulsion between the metal ions. We predict a significant charge transfer from the ad-atoms to the Mo2C monolayer, which indicates clearly the cationic state of the metal atoms. The metallic character of both pristine and doped Mo2C ensures a good electronic conduction that is essential for an optimal anode material. Low migration energy barriers are predicted as small as 43 meV for Li, 19 meV for Na and 15 meV for K, which result in the very fast diffusion of these atoms on Mo2C. For Mo2C, we found a storage capacity larger than 400 mA h g-1 by the inclusion of multilayer adsorption. Mo2C expands slightly upon deposition of Li and Na even at high concentrations, which ensures the good cyclic stability of the atomic layer. The calculated average voltage of 0.68 V for Li and 0.30 V for Na ions makes Mo2C attractive for low charging voltage applications.Item Open Access Model study of a surfactant on the GaAs(100) surface(Elsevier, 2002-11-01) Consorte, C. D.; Fong, C. Y.; Watson, M. D.; Yang, L. H.; Çıracı, SalimBased on the facts that: (a) the transverse acoustic vibrational branch frequency is softened at the Brillouin zone boundaries of crystalline GaAs; (b) at the surface, the Ga-As bond is stronger than Ga-Te bond; and (c) the requirement that the final bond orientation of the Te surfactant should be rotated by 90degrees with respect to its initial orientation, we carried out a model study of an exchange process in epitaxial growth of GaAs (100). Even with very restrictive conditions imposed on the atomic movements, this study explains why Te is an effective surfactant for this type of growth. (C) 2002 Elsevier Science B.V. All rights reserved.Item Open Access Peculiar piezoelectric properties of soft two-dimensional materials(American Chemical Society, 2016-06) Sevik, C.; Çakır, D.; Gülseren, O.; Peeters, F. M.Group II-VI semiconductor honeycomb monolayers have a noncentrosymmetric crystal structure and therefore are expected to be important for nano piezoelectric device applications. This motivated us to perform first-principles calculations based on density functional theory to unveil the piezoelectric properties (i.e., piezoelectric stress (e11) and piezoelectric strain (d11) coefficients) of these monolayer materials with chemical formula MX (where M = Be, Mg, Ca, Sr, Ba, Zr, Cd and X = S, Se, Te). We found that these two-dimensional materials have peculiar piezoelectric properties with d11 coefficients 1 order of magnitude larger than those of commercially utilized bulk materials. A clear trend in their piezoelectric properties emerges, which originates mainly from their mechanical properties. We establish a simple correlation between the piezoelectric strain coefficients and the physical properties, as the natural elemental polarizabilities, the Bader charges, and lattice constants of the individual M/X atoms and MX monolayers.Item Open Access The response of mechanical and electronic properties of graphane to the elastic strain(AIP Publishing LLC, 2010) Topsakal, M.; Cahangirov, S.; Çıracı, SalimBased on first-principles calculations, we resent a method to reveal the elastic properties of recently synthesized monolayer hydrocarbon, graphane. The in-plane stiffness and Poisson’s ratio values are found to be smaller than those of graphene, and its yielding strain decreases in the presence of various vacancy defects and also at high ambient temperature. We also found that the band gap can be strongly modified by applied strain in the elastic range.Item Open Access Structural and electronic properties of MoS2, WS2, and WS2/MoS2 heterostructures encapsulated with hexagonal boron nitride monolayers(American Institute of Physics Inc., 2017) Yelgel, C.; Yelgel, Ö. C.; Gülseren, O.In this study, we investigate the structural and electronic properties of MoS2, WS2, and WS2/MoS2 structures encapsulated within hexagonal boron nitride (h-BN) monolayers with first-principles calculations based on density functional theory by using the recently developed non-local van der Waals density functional (rvv10). We find that the heterostructures are thermodynamically stable with the interlayer distance ranging from 3.425 Å to 3.625 Å implying van der Waals type interaction between the layers. Except for the WS2/h-BN heterostructure which exhibits direct band gap character with the value of 1.920 eV at the K point, all proposed heterostructures show indirect band gap behavior from the valence band maximum at the Γ point to the conduction band minimum at the K point with values varying from 0.907 eV to 1.710 eV. More importantly, it is found that h-BN is an excellent candidate for the protection of intrinsic properties of MoS2, WS2, and WS2/MoS2 structures.Item Open Access TiO2 assisted sensitivity enhancement in photosensitive nanocrystal skins(IEEE, 2014-10) Yeltik, Aydan; Akhavan, Shahab; Demir, Hilmi VolkanSolution-processable semiconductor nanocrystals (NCs) have been widely used to create novel devices for the photovoltaic, light-emission, light-detection and biosensing applications. They are good candidates especially to develope more efficient and novel optoelectronic devices owing to the high absorption cross-section, spectral tunability, deposition easiness and low cost properties. In recent years, NC integrated photodetectors have been developed to be used in large-area light-sensing applications [1]. These NC-based photodetectors have the ability to convert an optical signal to an electrical signal using the NCs as the optical absorbers. These low-cost devices were initially operated on the basis of charge collection, where an electric field imposed on the detector dissociates the photogenerated excitons into electrons and holes, in which an electric current is produced [2]. On the other hand, as an alternative device structure, we have recently developed the light-sensitive nanocrystal skin (LS-NS) [3]. These LS-NS platforms, which were fabricated over areas up to 48 cm2, are operated on the basis of photogenerated potential buildup, as opposed to conventional charge collection. In operation, close interaction of the monolayer NCs of the LS-NS with the top interfacing contact, while the bottom one is isolated using a high dielectric spacing layer, results in highly sensitive photosensing in the absence of external bias application. Furthermore, NC monolayer of the LS-NS makes the device semi-transparent with sufficient absorption, while reducing the noise generation and dark current. In our other recent work, we also reported that, by using a thick photoactive NC layer, a much lower photovoltage buildup was observed in the LS-NSs and it was attributed to the self-absorption effect [4]. In addition, we demonstrated the sensitivity increase in the LS-NSs via the absorption enhancement of NC film with the integration of plasmonic nanoparticles [5]. However, the localized plasmonic resonance band strongly limits the observed enhancement factor and the resultant operating wavelength range. Furthermore, in the absence of an external bias in the LS-NSs, each exciton tends to remain in the NC layer, where it was created, and recombine with the photogenerated holes that accumulate at the top interfacing contact, which causes also lower voltage buildup in the device. To overcome all these problems, in this study, we propose a thin TiO2 layer as the electron-accepting material and demonstrate the first account of electron transfer in NC-based light-sensitive skins, which leads to significant broadband sensitivity enhancement in the active device architecture. Here, we prove that favorable conduction band offset aids in transferring photogenerated electrons from a monolayer of NCs to an electron-accepting layer, which is ultimately useful for photosensing platforms and the next generation of light-sensing NC devices. © 2014 IEEE.Item Open Access Ultrasensitive label-free microcavity biosensors with high selectivity(IEEE, 2011) Özgür, Erol; Bayındır, Mehmet; Aktaş, OzanHigh quality factor whispering gallery mode microresonators have been recently shown to exhibit detection sensitivity of single molecule; however, the selectivity of these sensors among different types of analytes remains as an important issue, obscuring the broad applicability of optical microcavities. We demonstrate a surface modification strategy for fabrication of high selectivity and sensitivity microcavity biosensors in this study. © 2011 IEEE.Item Open Access Variable energy x-ray photoemission studies of alkylsilane based monolayers on gold(American Chemical Society, 2003) Owens, T. M.; Süzer, S.; Banaszak Holl, M. M.Gaseous n-hexylsilane (C6H13SiH3), n-octylsilane (C8H17SiH3), and n-octadecylsilane (C18H37SiH3) have been vapor deposited in ultrahigh vacuum (UHV) on freshly evaporated gold surfaces to form monolayers. Surface sensitive X-ray photoemission studies utilizing synchrotron radiation in the 160-360 eV range have been used to characterize these systems. Analyses of the C 1s, Si 2p, and Au 4f and valence band regions permit a structural assessment of the monolayer. The full width at half-maximum of the Si 2p and C 1s core levels, 0.4 and 1.2 or 1.1 eV, respectively, suggest the monolayers are chemically homogeneous. The intensity variation of the Au 4f and Si 2p core levels at different photon energies indicate the surface coverage of the monolayer is ∼96% and the chain orientation is upright on the surface, not parallel to the surface. The valence band of the alkylsilane monolayers exhibit features at ∼-13.2, -14.6, -16.3, -17.6, and -18.9 eV that agree well with those observed for alkyl chains of the same length.