Physics / Fizik
Permanent URI for this collectionhttps://hdl.handle.net/11147/6
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Article Citation - WoS: 11Citation - Scopus: 13Proteolysis of Micellar Β-Casein by Trypsin: Secondary Structure Characterization and Kinetic Modeling at Different Enzyme Concentrations(MDPI, 2023) Vorob’ev, Mikhail M.; Açıkgöz, Burçin Dersu; Güler, Günnur; Golovanov, Andrey V.; Sinitsyna, Olga V.Tryptic proteolysis of protein micelles was studied using β-casein (β-CN) as an example. Hydrolysis of specific peptide bonds in β-CN leads to the degradation and rearrangement of the original micelles and the formation of new nanoparticles from their fragments. Samples of these nanoparticles dried on a mica surface were characterized by atomic force microscopy (AFM) when the proteolytic reaction had been stopped by tryptic inhibitor or by heating. The changes in the content of β-sheets, α-helices, and hydrolysis products during proteolysis were estimated by using Fourier-transform infrared (FTIR) spectroscopy. In the current study, a simple kinetic model with three successive stages is proposed to predict the rearrangement of nanoparticles and the formation of proteolysis products, as well as changes in the secondary structure during proteolysis at various enzyme concentrations. The model determines for which steps the rate constants are proportional to the enzyme concentration, and in which intermediate nano-components the protein secondary structure is retained and in which it is reduced. The model predictions were in agreement with the FTIR results for tryptic hydrolysis of β-CN at different concentrations of the enzyme.Article Citation - WoS: 11Citation - Scopus: 10Intercalation Leads To Inverse Layer Dependence of Friction on Chemically Doped Mos2(IOP Publishing, 2023) Açıkgöz, Oğulcan; Guerrero, Enrique; Yanılmaz, Alper; Dağdeviren, Ömür E.; Çelebi, Cem; Strubbe, David A.; Baykara, Mehmet Z.We present results of atomic-force-microscopy-based friction measurements on Re-doped molybdenum disulfide (MoS2). In stark contrast to the widespread observation of decreasing friction with increasing number of layers on two-dimensional (2D) materials, friction on Re-doped MoS2 exhibits an anomalous, i.e. inverse, dependence on the number of layers. Raman spectroscopy measurements combined with ab initio calculations reveal signatures of Re intercalation. Calculations suggest an increase in out-of-plane stiffness that inversely correlates with the number of layers as the physical mechanism behind this remarkable observation, revealing a distinctive regime of puckering for 2D materials.Article Citation - WoS: 5Citation - Scopus: 4Electromagnetically Induced Transparency and Absorption Cross-Over With a Four-Level Rydberg System(IOP Publishing, 2022) Oyun, Yağız; Çakır, Özgür; Sevinçli, SevilayElectromagnetically induced transparency (EIT) and absorption (EIA) are quantum coherence phenomena which result from the interference of excitation pathways. Combining these with Rydberg atoms have opened up many possibilities for various applications. We introduce a theoretical model to study Rydberg-EIT and Rydberg-EIA effects in cold Cs and Rb atomic ensembles in a four-level ladder type scheme taking into account van der Waals type interactions between the atoms. The proposed many-body method for analysis of such systems involves a self-consistent mean field approach and it produces results which display a very good agreement with recent experiments. Our calculations also successfully demonstrate experimentally observed EIT-EIA cross-over in the Rb case. Being able to simulate the interaction effects in such systems has significant importance, especially for controlling the optical response of these.Article Citation - WoS: 14Citation - Scopus: 17Enhancement of Thermoelectric Efficiency of T-Hfse2 Via Nanostructuring(American Physical Society, 2021) Ünsal, Elif; Senger, Ramazan Tuğrul; Sevinçli, HaldunIn this work, ab initio calculations based on density functional theory and the Landauer formalism are carried out to investigate ballistic thermoelectric properties of T-HfSe2 nanoribbons (NRs). The zigzag-edged NRs are metallic, and they are not included in this study. The armchair NRs possess two types of edge symmetries depending on the number of atoms present in a row; odd-numbered NRs have mirror symmetry, whereas the even-numbered NRs have glide reflection symmetry. The armchair-edged NRs are dynamically stable and show semiconducting properties with varying band gap values in the infrared and visible regions. Detailed transport analyses show that the n-type Seebeck coefficient and the power factor differ because of the structural symmetry, whereas the p-type thermoelectric coefficients are not significantly influenced. It is shown that the phonon thermal conductance is reduced to a third of its two-dimensional value via nanostructuring. The p-type Seebeck coefficient and the power factor for T-phase HfSe(2 )are enhanced in NRs. We report that the p-type ZT value of HfSe2 NRs at 300 and 800 K are enhanced by factors of 4 and 3, respectively.Article Citation - WoS: 12Citation - Scopus: 14Laser Assisted Synthesis of Anisotropic Metal Nanocrystals and Strong Light-Matter Coupling in Decahedral Bimetallic Nanocrystals(Royal Society of Chemistry, 2021) Mert Balcı, Fadime; Sarısözen, Sema; Polat, Nahit; Güvenç, Çetin Meriç; Karadeniz, Uğur; Tertemiz, Necip Ayhan; Balcı, SinanThe advances in colloid chemistry and nanofabrication allowed us to synthesize noble monometallic and bimetallic nanocrystals with tunable optical properties in the visible and near infrared region of the electromagnetic spectrum. In the strong coupling regime, surface plasmon polaritons (SPPs) of metal nanoparticles interact with excitons of quantum dots or organic dyes and plasmon-exciton hybrid states called plexcitons are formed. Until now, various shaped metal nanoparticles such as nanorods, core-shell nanoparticles, hollow nanoparticles, nanoprisms, nanodisks, nanorings, and nanobipyramids have been synthesized to generate plasmon-exciton mixed states. However, in order to boost plasmon-exciton interaction at nanoscale dimensions and expand the application of plexcitonic nanocrystals in a variety of fields such as solar cells, light emitting diodes, and nanolasers, new plexcitonic nanocrystals with outstanding optical and chemical properties remain a key goal and challenge. Here we report laser-assisted synthesis of decahedral shaped noble metal nanocrystals, tuning optical properties of the decahedral shaped nanocrystals by galvanic replacement reactions, colloidal synthesis of bimetallic decahedral shaped plexcitonic nanocrystals, and strong plasmon-plasmon interaction in bimetallic decahedral shaped noble metal nanocrystals near a metal film. We photochemically synthesize decahedral Ag nanoparticles from spherical silver nanoparticles by using a 488 nm laser. The laser assisted synthesis of silver nanoparticles yields decahedral (bicolored) and prism (monocolored) shaped silver nanocrystals. The decahedral shaped nanoparticles were selectively separated from prism shaped nanoparticles by centrifugation. The optical properties of decahedral nanocrystals were tuned by the galvanic replacement reaction between gold ions and silver atoms. Excitons of J-aggregate dyes and SPPs of decahedral bimetallic nanoparticles strongly couple and hence decahedral shaped plexcitonic nanoparticles are prepared. In addition, localized SPPs of decahedral shaped bimetallic nanocrystals interact strongly with the propagating SPPs of a flat silver film and hence new hybrid plasmonic modes (plasmonic nanocavities) are generated. The experimental results are further fully corroborated by theoretical calculations including decahedral shaped plexcitonic nanoparticles and decahedral nanoparticles coupled to flat metal films.Article Fine-Tuned Spin-3/2 and the Hierarchy Problem(Hindawi Publishing Corporation, 2020) Sargın, OzanIn the past, Kundu et al. and Chakraborty et al. used extra scalar fields to cancel the quadratic divergences in the Higgs mass squared and they determined the mass of the required scalar field. In this work, a spin-3/2 particle has been used in the same manner to nullify the power-law divergences, and it is determined that the mass of the spin-3/2 particle resides in the ball park of the GUT scale.Article Citation - WoS: 3Citation - Scopus: 3Atomic Collapse in Disordered Graphene Quantum Dots(American Physical Society, 2020) Polat, Mustafa; Güçlü, Alev DevrimIn this paper, we numerically study a Coulomb impurity problem for interacting Dirac fermions restricted in disordered graphene quantum dots. In the presence of randomly distributed lattice defects and spatial potential fluctuations, the response of the critical coupling constant for atomic collapse is mainly investigated by local density of states calculations within the extended mean-field Hubbard model. We find that both types of disorder cause an amplification of the critical threshold. As a result, up to a 34% increase in the critical coupling constant is reported. This numerical result may explain why the Coulomb impurities remain subcritical in experiments, even if they are supercritical in theory. Our results also point to the possibility that atomic collapse can be observed in defect-rich samples such as Ar+ ion bombarded, He+ ion irradiated, and hydrogenated graphene.Article Citation - WoS: 1Citation - Scopus: 2Reactive Wetting of Metallic/Ceramic (al/Α-al2 O3 ) Systems: a Parallel Molecular Dynamics Simulation Study(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2020) Aral, GürcanThe reactive wetting process of a flat solid alumina (?-Al2 O3) ceramic surface by metallic aluminum (Al) nanodroplets with different shapes (spherical, cylindrical, and layer) is studied using parallel molecular dynamics (MD) simulations based on a variable charge MD method, with focuses on heat transfer, mass transfer, and the structure of the reactive region at the Al/?-Al2 O3 interface. We find that the diffusion of oxygen (O) atoms from the substrate into the droplet leads to the formation of a continuous layer of reaction product at the interface. The diffusion length of oxygen atoms into the spherical Al droplet is found to be ~7.3 Å, and the number density of O atoms at the ~5 top layers of the substrate decreases substantially. As a result, the structural correlations near the reactive region differ considerably from those in the solid substrate. Heat generated by the exothermic reactions in the reactive region is transferred to both the substrate and the droplet. The heat transfer is found to be sensitive to droplet shape.Article Citation - WoS: 3Citation - Scopus: 3Local Vibrational Modes of Natural Isotopes of Substitutional Oxygen in Cdte(TÜBİTAK - Türkiye Bilimsel ve Teknolojik Araştırma Kurumu, 2020) Tarhan, Enver; Ramdas, Anant K.We investigated the localized vibrational modes (LVM) of natural oxygen containing ${}^{16}O,\;{}^{17}O$ and ${}^{18}O$ isotopes at a substitutional tellurium site in cadmium telluride using infrared absorption spectroscopy at cryogenic temperatures. The main absorption peak observed at 350 cm ?1 was formerly attributed to a fundamental LVM mode (?0) of oxygen at a tellurium site. The relatively weak absorption peaks observed at 331 $cm^{-1}$ and 340 $cm^{-1}$ are assigned as the same $\nu_0$ mode of the ${}^{17}O$ and ${}^{18}O$ isotopes, respectively, based on their relative intensities and spectral positions. The spectral positions were confirmed with theoretical calculations using a linear chain model where the peak position at 350$cm^{-1}$ was taken as the reference for the ${}^{16}O$ isotope. From a least square analysis of the observed peak positions we were able to calculate the force constants from perturbation theory. A Lorentzian line shape analysis of each $\nu_0$ absorption peak, considering the effects of isotopic mass and natural abundance variations of the host Cd atoms, was also carried out to further confirm their assignments. Reasonably good line shape fittings were obtained for $\nu_0$ modes of all isotopes of oxygen.Article Citation - WoS: 10Citation - Scopus: 10The Comparison of Transient Photocurrent Spectroscopy Measurements of Pulsed Electron Deposited Zno Thin Film for Air and Vacuum Ambient Conditions(Elsevier, 2019) Özdoğan, Mehmet; Yiğen, Serap; Çelebi, Cem; Utlu, GökhanPhotoconduction mechanism of ZnO thin films that produced by Pulsed Electron Deposition method is systematically investigated by taking Transient Photocurrent Spectroscopy measurements for different atmospheres including high vacuum and air environments. Response and recovery rates of photocurrent in the air are faster than the rates in high vacuum condition. The results in the presented work clearly indicate that the photoconduction of ZnO thin films with high surface-area-to-volume ratio are surface-related and mostly governed by adsorption/desorption of oxygen and water molecules in the atmosphere. Therefore, the high surface interaction tendency of ZnO surface with the atmosphere inevitably leads to charge transfer from surface to adsorbates and/or vice versa.