Scopus İndeksli Yayınlar Koleksiyonu / Scopus Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7148
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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: 3Citation - Scopus: 3Manipulating the Frequency Response of Small High-Frequency Atomic Force Microscope Cantilevers(IOP Publishing, 2020) Brar, Harpreet Singh; Balantekin, MüjdatWe study small (less than 10 mu m-long) high-frequency (greater than 1 MHz) cantilevers specially designed for visualization of biomolecular processes in high-speed atomic force microscopes. The frequency responses of the first three flexural eigenmodes are investigated for the modified geometries. It is found that the Q-factors can be significantly altered in the desired way by reengineering the cantilever geometry without affecting its main operational parameters, such as the spring constant and the resonance frequency of the first flexural eigenmode in an air environment. In addition, higher-order flexural resonances can be moved away from the fundamental resonance with these geometrical modifications. The Q-factors in liquid, on the other hand, do not show a significant difference due to high viscous damping of the medium. Regular cantilevers modified by a focused ion beam are used to demonstrate the validity of the finite element simulation model.Article Citation - WoS: 5Citation - Scopus: 5Determination of Electrostatic Potential Distribution by Atomic Force Microscopy (afm) on Model Silica and Alumina Surfaces in Aqueous Electrolyte Solutions(Elsevier Ltd., 2014) Yelken Özek, Gülnihal; Polat, MehmetAFM was employed as a physicochemical probe to determine the electrostatic potential distribution quantitatively on selected ideal oxide surfaces (quartz 0 0 0 1 and sapphire 0 0 0 1) in aqueous media. The force of interaction between a silicon nitride tip and the oxide surface was measured at a given point under well-defined solution conditions. Relevant theories were used to isolate the electrostatic component from the total force of interaction which was then employed to estimate the surface potential at that point. Repeating the procedure on selected locations generated a potential map of the surface. Comparison of these potentials with those obtained from independent electrokinetic measurements confirmed the validity of the approach. © 2014 Elsevier B.V. All rights reserved.Article Citation - WoS: 12Citation - Scopus: 16Humidity Adsorption Kinetics of a Trypsin Gel Film(Elsevier Ltd., 2012) Okur, Salih; Ceylan, Çağatay; Çulcular, EvrenThis study focuses on the humidity adsorption kinetics of an isopropanol-induced and pH-triggered bovine pancreatic trypsin gel (BPTG). The BPTG was adsorbed on a gold coated Quartz Crystal Microbalance (QCM) substrate with a thickness of 376nm. The morphology of the film was characterized using Atomic Force Microscopy (AFM). QCM was used to investigate the humidity sensing properties of the BPTG film. The response of the humidity sensor was explained using the Langmuir model. The average values of adsorption and desorption rates between 11% RH (relative humidity) and 97% RH were calculated as 2482.5M -1s -1 and 0.02s -1, respectively. The equilibrium constant and average Gibbs Free Energy of humidity adsorption and desorption cycles were obtained as 133,000 and -11.8kJ/mol, respectively. © 2011 Elsevier Inc..Article Citation - WoS: 82Citation - Scopus: 92Metal Ion Release From Nitrogen Ion Implanted Cocrmo Orthopedic Implant Material(Elsevier Ltd., 2006) Öztürk, Orhan; Türkan, Uğur; Eroğlu, Ahmet EminCoCrMo alloys are used as orthopedic implant materials because of their excellent mechanical and corrosion properties. However, when placed in vivo, these alloys release Co, Cr, Mo ions to host tissues, which may give rise to significant health concerns over time. Nitrogen ion implantation can be used to form protective layers on the surface of CoCrMo orthopedic alloys by modifying the near surface layers of these materials. In this study, medical grade CoCrMo alloy (IS0 5832-12) was ion implanted with 60 keV nitrogen ions to a high dose of 1.9 × 10 18 ions/cm 2 at substrate temperatures of 100, 200 and 400 °C. The N implanted layer microstructures, implanted layer phases, and thicknesses were studied by a combination of Bragg-Brentano (θ/2θ) and grazing incidence (Seeman-Bohlin) X-ray diffraction (XRD and GIXRD) and cross-sectional scanning electron microscopy (SEM). Atomic force microscopy (AFM) was used for roughness analysis of N implanted as well as as-polished surfaces. Static immersion tests were performed to investigate metal ion release into simulated body fluid (SBF) by electrothermal atomic absorption spectrometry (ETAAS) and inductively coupled plasma optical emission spectrometry (ICP-OES). XRD and SEM analyses indicated that the N implanted layers were ∼ 150-450 nm thick and composed of the (Co,Cr,Mo) 2+xN nitride phase and a high N concentration Co-based FCC phase, γ N depending on the substrate temperature. ETAAS analysis results showed that in vitro exposure of the N implanted surfaces resulted in higher levels of cobalt ion release into the simulated body fluid compared to the untreated, polished alloy. The higher Co release from the N implanted specimens is attributed to the nature of the implanted layer phases as well as to the rougher surfaces associated with the N implanted specimens compared to the relatively smooth surface of the untreated material. SEM analysis of N implanted and untreated specimens after immersion tests clearly indicated calcium phosphate formation on the as-polished CoCrMo alloy, indicating a degree of bioactivity of the untreated metal surface which is absent in the N implanted specimens.Article Citation - WoS: 2Dimensions of Polystyrene Particles Deposited on Mica From Dilute Cyclohexane Solution at Different Temperatures(American Chemical Society, 2002) Demir, Mustafa Muammer; Erman, BurakUsing atomic force microscopy, the height, diameter, and volume of polystyrene particles deposited on mica from dilute cyclohexane solution at different temperatures are determined. Dimensions exhibit a strong temperature dependence. The heights of the deposited particles are only a few atomic diameters, the major dimension being parallel to the mica surface. The number of single polystyrene molecules in a deposited particle cannot be determined directly by atomic force microscopy. However, the maximum number of molecules that may be present in a particle may be estimated. Below 35 °C, the particles possibly consist of single collapsed molecules. This number increases with temperature and becomes as large as about 30 molecules per particle at 80 °C. The volume occupied by a single chain in solvent is calculated as a function of temperature and compared with observed volumes of dry particles on mica. A linear relationship is observed between single chain volumes in solvent and corresponding particle volumes on mica. On the average, the volume of a single chain in solution is 10 times the volume of a dry particle at the corresponding temperature. Fluctuations of chain volumes that are dominant in solution are also present in the volumes of particles deposited and dried on mica.