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: 4Lipid Bilayer on Wrinkled-Interfaced Graphene Field Effect Transistor(Elsevier Ltd., 2021) Özkendir İnanç, Dilce; Çelebi, Cem; Yıldız, Ümit HakanThis study describes lipid bilayer-based sensor interface on SiO2 encapsulated graphene field effect transistors (GFET). The SiO2 layer was utilized as a lipid compatible surface that drives bilayer formation. The two types of surface morphologies i) wrinkled morphology by thermal evaporation (TE) and ii) flat morphology by pulsed electron deposition (PED) were obtained. The sensing performance of wrinkled and flat interfaced-GFETs were investigated, pH sensitivity of wrinkled interfaced-GFETs were found to be ten fold larger than the flat ones. The enhanced sensitivity is attributed to thinning of the oxide layer by formation of wrinkles thereby facilitating electrostatic gating on graphene. We foresee that described wrinkled SiO2 interfaced-GFET holds promise as a cell membrane mimicking sensing platform for novel bioelectronic applications. © 2020Article 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: 2Citation - Scopus: 2Morphology of Sodium Salt of Calf Thymus Dna on Mica, Alumina, and Silica Surfaces: Effect of Solvent and Drying Method(Taylor and Francis Ltd., 2017) Yetgin, Senem; Balköse, DevrimInvestigation of morphology of deoxyribonucleotide triphosphate (DNA) dried on different surfaces by atomic force microscopy (AFM) is important in DNA research that is focused on subjects of condensation for gene therapy, sizing, DNA mapping, and cancer examination. The solvent, the surface type, and the method of drying effect the morphology of DNA on solid surfaces. Ethanol and water were used as solvents, flat mica, silica, and alumina surfaces were used as the substrates in the present study. Different methods such as ambient air-drying, N2-forced flow regime drying, and freeze-drying have been applied to droplets of DNA solutions in water or ethanol on the substrates. Forced flow drying regime causes nonlinear DNA attachment on the surface and self-assembly. DNA vertical distance on mica surface was found to be 6 and 1.4 nm for DNA dried in ambient air from ethanol and water solutions, respectively. It was 1.6 nm for N2 flow drying of aqueous DNA solution on mica surface. It was 4.6, 4.6, and 1.99 nm for ambient, N2 flow, and freeze-dried aqueous DNA on alumina surfaces, respectively. Aqueous solution of DNA dried under N2 flow on silica surface had 0.8 nm vertical distance. The smallest standard deviation of 0.05 nm was observed for DNA dried under N2 flow on alumina surface.Article Citation - WoS: 4Citation - Scopus: 4Formation and Characterisation of Nanoporous Tio2 Layers on Microroughened Titanium Surfaces by Electrochemical Anodisation(Institution of Engineering and Technology, 2014) Dikici, Tuncay; Güzelaydın, Abdurrahman Halis; Toparlı, MustafaNanoporous titanium dioxide (TiO2) layers were successfully formed by an electrochemical anodisation method on microroughened titanium (Ti) surfaces in fluoride containing aqueous electrolyte. Microroughened Ti surfaces were produced by sandblasting with Al2O3 particles of 50 μm in diameter and acid-etching in a blend of HCl/H2SO4 solution. The surface morphology, topography and chemical composition of the specimens were analysed by scanning electron microscopy, atomic force microscopy and X-ray photoelectron spectroscopy. The surface roughness and the wettability of treated Ti surfaces were measured using profilometry and a contact angle measurement system, respectively. With anodising of sandblasted-/acid etched surfaces, micrometre- and nanometre-scale textures on titanium specimens were created. Results showed that these developed nanoporous-microroughened surfaces exhibited lower contact angle values than the other treated Ti surfaces. The sandblasted/acid-etched/anodised Ti specimen had a surface morphology with distinctively formed hills and valleys and higher surface roughness than the other anodised specimens. This study indicated that nanoporous TiO2 structures fabricated on microroughened Ti can be an effective way to modify the titanium surfaces for the future development of implant applications.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: 3Citation - Scopus: 3High-Speed Tapping-Mode Atomic Force Microscopy Using a Q-Controlled Regular Cantilever Acting as the Actuator: Proof-Of Experiments(American Institute of Physics, 2014) Balantekin, Müjdat; Satır, Sarp; Torello, David; Değertekin, F. L.We present the proof-of-principle experiments of a high-speed actuationmethod to be used in tapping-mode atomic force microscopes (AFM). In this method, we do not employ a piezotube actuator to move the tip or the sample as in conventional AFM systems, but, we utilize a Q-controlled eigenmode of a cantilever to perform the fast actuation. We show that the actuation speed can be increased even with a regular cantilever.Article Citation - WoS: 3Citation - Scopus: 4Electrical Characterizations of Schottky Diodes on Ito Modified by Aromatic Sams(Polish Academy of Sciences, 2013) Havare, A. Kemal; Okur, Salih; Yağmurcukardeş, Nesli; Can, M.; Aydın, H.; Şeker, M.; Demiç, ŞerafettinIn order to understand the electronic properties of the organic Schottky diode, ITO/TPD/Al and ITO/SAM/ TPD/Al organic Schottky devices were fabricated to obtain currentffvoltage characteristics. From the slopes and y-axis intercepts of the plots, the values of the ideality factor, barrier heights of the ITO/SAM/TPD/Al diode were determined as 2.03 and 0.56 eV, respectively. The surface characterizations of modified and unmodified ITO were performed via atomic force microscopy.Conference Object Citation - Scopus: 3Characterization of Polysulfone Based Hemodialysis Membranes by Afm(Elsevier Ltd., 2012) Uz, Metin; Yaşar Mahlıçlı, Filiz; Polat, Mehmet; Alsoy Altınkaya, SacideMost of the hemodialysis membrane materials are hydrophobic in nature and allow protein adsorption on the surface easily due to hydrophobic interaction between membrane surface and protein molecules when in contact with blood. Adsorbed proteins can affect platelet and leukocyte adhesion, and modulate the response of plasmatic reactions followed by the activation of different defense systems in blood (Sun et al. 2003).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..