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: 6Tuning the Structural, Electronic and Dynamical Properties of Janus M4x3y3 (m = Pd, Ni and Co; X,y = S, Se and Te) Monolayers: a Dft Study(Royal Society of Chemistry, 2021) Eren, İsmail; Akgenç, BernaBased on density functional theory, the structural, electronic and vibrational properties of two-dimensional transition metal chalcogenides M2X3 and their Janus type M4X3Y3, where M = Pd, Co and Ni and X = Se, S and Te, are investigated. Motivated by the successful synthesis of a 2D Pd2Se3 monolayer and the proof of the dynamical stability of Ni2Se3 and Co2Se3 monolayers, in terms of the phonon band dispersions, we have systemically studied the fundamental physical properties of Janus transition metal chalcogenides, such as their structural, phonon and thermodynamic stability and their electronic and mechanical properties. Our results show that Janus structures of M4X3Y3 are energetically favorable and dynamically stable. The ab initio molecular dynamic simulations (AIMD) results clearly prove that they kept their thermal stability at room temperature. We have demonstrated their structural, electronic and vibrational properties and Raman spectra. The electronic band dispersions show that monolayer Co2Se3 shows half-metal properties with a moderate band gap (1.01 eV), Pd2Se3 has a 1.42 eV direct band gap, while Ni2Se3 has a 1.38 eV indirect band gap. Pd4Se3S3, Pd4Se3Te3 and Pd4S3Te3 are indirect band gap semiconductors with band gaps of 1.22 eV, 1.05 eV and 0.61 eV, respectively. Ni4Se3S3, Ni4Se3Te3 and Ni4S3Te3 are indirect band gap semiconductors with band gaps of 1.61 eV, 0.77 eV and 0.49 eV, respectively. While pristine Co2Se3 is shown to have half-metallicity (HM), the HM behaviour of the Janus Co4Se3Te3 and Co4S3Te3 monolayers disappear and Co4Se3S3 remains a HM with a moderate band gap of 0.85 eV. In addition, the Raman spectra of these Janus materials are shown to exhibit totally distinctive features as compared to those of the pristine materials. This work reveals the important material properties of Janus type M4X3Y3 monolayers, where M = Pd, Co and Ni and X = Se, S and Te, which could have wide applications in new functional devices.Article Citation - WoS: 24Citation - Scopus: 24Defect Tolerant and Dimension Dependent Ferromagnetism in Mnse2(Royal Society of Chemistry, 2019) Eren, İsmail; İyikanat, Fadıl; Şahin, HasanBy performing density functional theory-based calculations, we investigate the structural, vibrational, electronic and magnetic properties of 2D monolayers, nanoribbons and quantum dots of MnSe2. Vibrational spectrum analysis reveals the dynamical stability of not only ferromagnetic but also antiferromagnetic phases of single layer MnSe2 crystal structures. Electronically, calculations show that 1T-MnSe2 is a ferromagnetic structure displaying metallic behavior. It is also found that the structure preserves its dynamical stability and metallic behavior even under the presence of high density Se vacancies. Moreover, it was predicted that, differing from the 2D MnSe2, metal-metal interaction driven reconstructions result in ferromagnetic-to-antiferromagnetic crossover in the ground state of nanoribbons and quantum dots. With its robust ferromagnetic metallic character in the 2D ultra-thin limit and dimension-dependent magnetic properties, MnSe2 is an important candidate for spintronic device applications.Article Citation - WoS: 22Citation - Scopus: 22Characterization of Cd133(+)/Cd44(+) Human Prostate Cancer Stem Cells With Atr-Ftir Spectroscopy(Royal Society of Chemistry, 2019) Güler, Günnur; Güven, Ümmü; Öktem, GülperiCurrent cancer treatments destroy the tumor mass but cannot prevent the recurrence of cancer. The heterogeneous structure of the tumor mass includes cancer stem cells that are responsible for tumor relapse, treatment resistance, invasion and metastasis. The biology of these cells is still not fully understood; therefore, effective treatments cannot be developed sufficiently. Herein, attenuated total reflection- Fourier transform infrared (ATR-FTIR) spectroscopy, combined with unsupervised multivariate analysis, was applied to prostate cancer stem cells (CSCs), non-stem cancer cells (non-CSCs) and normal prostate epithelial cells to elucidate the molecular mechanisms and features of CSCs, which are crucial to improving the target specific therapies. This work revealed the spectral differences in the cellular mechanisms and biochemical structures among three different cell types. Particularly, prostate CSCs exhibit differences in the lipid composition and dynamics when compared to other cell types. CSCs also harbor pronounced differences in their major cellular macromolecules, including differences in the protein amount and content (mainly a-helices), the abundance of nucleic acids (DNA/RNA), altered nucleic acid conformation and carbohydrate composition. Interestingly, macromolecules containing the CvO groups and negatively charged molecules having the COO-groups are abundant in prostate CSCs in comparison to prostate non-CSCs and normal prostate cells. Overall, this study demonstrates the potential use of ATR-FTIR spectroscopy as a powerful tool to obtain new insights into the understanding of the CSC features, which may provide new strategies for cancer treatment by selectively targeting the CSCs.Article Citation - WoS: 28Citation - Scopus: 30P3HT-graphene bilayer electrode for Schottky junction photodetectors(IOP Publishing Ltd., 2018) Aydın, Hasan; Kalkan, Sırrı Batuhan; Varlıklı, Canan; Çelebi, CemWe have investigated the effect of a poly (3-hexylthiophene-2.5-diyl)(P3HT)-graphene bilayer electrode on the photoresponsivity characteristics of Si-based Schottky photodetectors. P3HT, which is known to be an electron donor and absorb light in the visible spectrum, was placed on CVD grown graphene by dip-coating method. The results of the UV-vis and Raman spectroscopy measurements have been evaluated to confirm the optical and electronic modification of graphene by the P3HT thin film. Current-voltage measurements of graphene/Si and P3HT-graphene/Si revealed rectification behavior confirming a Schottky junction formation at the graphene/Si interface. Time-resolved photocurrent spectroscopy measurements showed the devices had excellent durability and a fast response speed. We found that the maximum spectral photoresponsivity of the P3HT-graphene/Si photodetector increased more than three orders of magnitude compared to that of the bare graphene/Si photodetector. The observed increment in the photoresponsivity of the P3HT-graphene/Si samples was attributed to the charge transfer doping from P3HT to graphene within the spectral range between near-ultraviolet and near-infrared. Furthermore, the P3HT-graphene electrode was found to improve the specific detectivity and noise equivalent power of graphene/Si photodetectors. The obtained results showed that the P3HT-graphene bilayer electrodes significantly improved the photoresponsivity characteristics of our samples and thus can be used as a functional component in Si-based optoelectronic device applications.Article Citation - WoS: 18Citation - Scopus: 19Oxyhydroxide of Metallic Nanowires in a Molecular H2o and H2o2 Environment and Their Effects on Mechanical Properties(Royal Society of Chemistry, 2018) Aral, Gürcan; İslam, Md Mahbubul; Wang, Yun-Jiang; Ogata, Shigenobu; van Duin, Adri C. T.To avoid unexpected environmental mechanical failure, there is a strong need to fully understand the details of the oxidation process and intrinsic mechanical properties of reactive metallic iron (Fe) nanowires (NWs) under various aqueous reactive environmental conditions. Herein, we employed ReaxFF reactive molecular dynamics (MD) simulations to elucidate the oxidation of Fe NWs exposed to molecular water (H2O) and hydrogen peroxide (H2O2) environment, and the influence of the oxide shell layer on the tensile mechanical deformation properties of Fe NWs. Our structural analysis shows that oxidation of Fe NWs occurs with the formation of different iron oxide and hydroxide phases in the aqueous molecular H2O and H2O2 oxidizing environments. We observe that the resulting microstructure due to pre-oxide shell layer formation reduces the mechanical stress via increasing the initial defect sites in the vicinity of the oxide region to facilitate the onset of plastic deformation during tensile loading. Specifically, the oxide layer of Fe NWs formed in the H2O2 environment has a relatively significant effect on the deterioration of the mechanical properties of Fe NWs. The weakening of the yield stress and Young modulus of H2O2 oxidized Fe NWs indicates the important role of local oxide microstructures on mechanical deformation properties of individual Fe NWs. Notably, deformation twinning is found as the primary mechanical plastic deformation mechanism of all Fe NWs, but it is initially observed at low strain and stress level for the oxidized Fe NWs.Article Citation - WoS: 7Citation - Scopus: 8Hydrogenation-driven phase transition in single-layer TiSe2(IOP Publishing Ltd., 2017) İyikanat, Fadıl; Kandemir, Ali; Özaydın, H. Duygu; Senger, Ramazan Tuğrul; Şahin, HasanFirst-principles calculations based on density-functional theory are used to investigate the effects of hydrogenation on the structural, vibrational, thermal and electronic properties of the charge density wave (CDW) phase of single-layer TiSe2. It is found that hydrogenation of single-layer TiSe2 is possible through adsorption of a H atom on each Se site. Our total energy and phonon calculations reveal that a structural phase transition occurs from the CDW phase to the T d phase upon full hydrogenation. Fully hydrogenated TiSe2 presents a direct gap semiconducting behavior with a band gap of 119 meV. Full hydrogenation also leads to a significant decrease in the heat capacity of single-layer TiSe2.Article Citation - WoS: 7Citation - Scopus: 7Stable Ultra-Thin Cdte Crystal: a Robust Direct Gap Semiconductor(IOP Publishing Ltd., 2017) İyikanat, Fadıl; Akbalı, Barış; Kang, J.; Senger, Ramazan Tuğrul; Selamet, Yusuf; Şahin, HasanEmploying density functional theory based calculations, we investigate structural, vibrational and strain-dependent electronic properties of an ultra-thin CdTe crystal structure that can be derived from its bulk counterpart. It is found that this ultra-thin crystal has an 8-atom primitive unit cell with considerable surface reconstructions. Dynamic stability of the structure is predicted based on its calculated vibrational spectrum. Electronic band structure calculations reveal that both electrons and holes in single layer CdTe possess anisotropic in-plane masses and mobilities. Moreover, we show that the ultra-thin CdTe has some interesting electromechanical features, such as strain-dependent anisotropic variation of the band gap value, and its rapid increase under perpendicular compression. The direct band gap semiconducting nature of the ultra-thin CdTe crystal remains unchanged under all types of applied strain. With a robust and moderate direct band gap, single-layer CdTe is a promising material for nanoscale strain dependent device applications.Article Citation - WoS: 6Citation - Scopus: 6Few-Layer Mos2 as Nitrogen Protective Barrier(IOP Publishing Ltd., 2017) Akbalı, Barış; Yanılmaz, Alper; Tomak, Aysel; Tongay, Sefaattin; Çelebi, Cem; Şahin, HasanWe report experimental and theoretical investigations of the observed barrier behavior of few-layer MoS2 against nitrogenation. Owing to its low-strength shearing, low friction coefficient, and high lubricity, MoS2 exhibits the demeanor of a natural N-resistant coating material. Raman spectroscopy is done to determine the coating capability of MoS2 on graphene. Surface morphology of our MoS2/graphene heterostructure is characterized by using optical microscopy, scanning electron microscopy, and atomic force microscopy. In addition, density functional theory-based calculations are performed to understand the energy barrier performance of MoS2 against nitrogenation. The penetration of nitrogen atoms through a defect-free MoS2 layer is prevented by a very high vertical diffusion barrier, indicating that MoS2 can serve as a protective layer for the nitrogenation of graphene. Our experimental and theoretical results show that MoS2 material can be used both as an efficient nanocoating material and as a nanoscale mask for selective nitrogenation of graphene layer.