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: 11Citation - Scopus: 13Effect of Cnt Incorporation on Pan/Ppy Nanofibers Synthesized by Electrospinning Method(TÜBİTAK, 2020) İnce Yardımcı, Atike; Tanoğlu, Metin; Yılmaz, Selahattin; Selamet, YusufIn this study, carbon nanotubes (CNTs) added polyacrylonitrile/polypyrrole (PAN/PPy) electrospun nanofibers were produced. Average diameters of the nanofibers were measured as 268 and 153 nm for 10 and 25 wt% of PPy contents, respectively. A relatively higher strain to failure values (23.3%) were observed for the low PPy content. When as-grown CNTs (1 and 4 wt%) were added into the PAN/PPy blends, disordered nanofibers were observed to form within the microstructure. To improve the interfacial properties of CNTs/PAN/PPy composites, CNTs were functionalized with H2SO4/HNO3/HCl solution. The functionalized CNTs were well dispersed within the nanofibers and aligned along the direction of nanofibers. Therefore, beads formation on nanofibers decreased. The impedance of the nanofibers was found to decrease with the PPy content and CNT addition. These nanofibers had a great potential to be used as an electrochemical actuator or a tissue engineering scaffold.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: 16Citation - Scopus: 16Temperature and Gate Dependence of Carrier Diffusion in Single Crystal Methylammonium Lead Iodide Perovskite Microstructures(American Chemical Society, 2020) McClintock, Luke; Xiao, Rui; Hou, Yasen; Gibson, Clinton; Travaglini, Henry Clark; Abramovitch, David; Tan, Liang Z.; Senger, Ramazan Tuğrul; Fu, Yongping; Jin, SongWe investigate temperature-dependent photogenerated carrier diffusion in single-crystal methylammonium lead iodide microstuctures via scanning photocurrent microscopy, Carrier diffusion lengths increased abruptly across the tetragonal to orthorhombic phase transition and reached 200 +/- 50 mu m at 80 K. In combination with the microsecond carrier lifetime measured by a transient photocurrent method, an enormous carrier mobility value of 3 x 10(4) cm(2)/V s was extracted at 80 K. The observed highly nonlocal photocurrent and the rapid increase of the carrier diffusion length at low temperatures can be understood by the formation and efficient transport of free excitons in the orthorhombic phase as a result of reduced optical phonon scattering due to the dipolar nature of the excitons. Carrier diffusion lengths were tuned by a factor of 8 by gate voltage and increased with increasing majority carrier (electron) concentration, consistent with the exciton model.Article Citation - WoS: 12Citation - Scopus: 15Magnetic Mechanism for the Biological Functioning of Hemoglobin(Nature Publishing Group, 2020) Mayda, Selma; Kandemir, Zafer; Bulut, Nejat; Maekawa, SadamichiThe role of magnetism in the biological functioning of hemoglobin has been debated since its discovery by Pauling and Coryell in 1936. The hemoglobin molecule contains four heme groups each having a porphyrin layer with a Fe ion at the center. Here, we present combined density-functional theory and quantum Monte Carlo calculations for an effective model of Fe in a heme cluster. In comparison with these calculations, we analyze the experimental data on human adult hemoglobin (HbA) from the magnetic susceptibility, Mossbauer and magnetic circular dichroism (MCD) measurements. In both the deoxygenated (deoxy) and the oxygenated (oxy) cases, we show that local magnetic moments develop in the porphyrin layer with antiferromagnetic coupling to the Fe moment. Our calculations reproduce the magnetic susceptibility measurements on deoxy and oxy-HbA. For deoxy-HbA, we show that the anomalous MCD signal in the UV region is an experimental evidence for the presence of antiferromagnetic Fe-porphyrin correlations. The functional properties of hemoglobin such as the binding of O-2, the Bohr effect and the cooperativity are explained based on the magnetic correlations. This analysis suggests that magnetism could be involved in the functioning of hemoglobin.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: 150Citation - Scopus: 7Correlation of Tunneling Spectra in Bi2sr2cacu2o8+? With the Resonance Spin Excitation(American Physical Society, 2001) Zasadzinski, John F.; Özyüzer, Lütfi; Miyakawa, Nobuaki; Gray, Kenneth E.; Hinks, David G.; Kendziora, Christopher A.New break-junction tunneling data are reported in Bi2Sr2CaCu2O8+δ over a wide range of hole concentration from underdoped (Tc=74k) to optimal doped (Tc=95k) to overdoped (Tc=48k). The conductances exhibit sharp dips at a voltage, Ω/e, measured with respect to the superconducting gap. Clear trends are found such that the dip strength is maximum at optimal doping and that Ω scales as 4.9kTc over the entire doping range. These features link the dip to the resonance spin excitation and suggest quasiparticle interactions with this mode are important for superconductivity.