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: 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: 19Citation - Scopus: 19Biofilm Formation by Staphylococcus Epidermidis on Nitrogen Ion Implanted Cocrmo Alloy Material(John Wiley and Sons Inc., 2007) Öztürk, Orhan; Sudağıdan, Mert; Türkan, UğurStaphylococcus epidermidis is the primary cause of medical device-related infections due to its adhesion and biofilm forming abilities on biomaterial surfaces. For this reason development of new materials and surfaces to prevent bacterial adhesion is inevitable. In this study, the adhesion of biofilm forming S. epidermidis strain YT-169a on nitrogen (N) ion implanted as well as on as-polished CoCrMo alloy materials were investigated. A medical grade CoCrMo alloy was ion implanted with 60 keV N ions to a high dose of 1.9 × 10 18 ions/cm2 at substrate temperatures of 200 and 400°C. The near-surface implanted layer crystal structures, implanted layer thicknesses, and roughnesses were characterized by XRD, SEM and AFM. The number of adherent bacteria on the surfaces of N implanted specimens was found to be 191 × 106 CFU/cm2 for the 200°C and 70 × 106 CFU/cm2 for the 400°C specimens compared to the as-polished specimen (3 × 106 CFU/cm2). The adhesion test results showed that S. epidermidis strain YT-169a adhere much more efficiently to the N implanted surfaces than to the as-polished CoCrMo alloy surface. This was attributed mainly to the rougher surfaces associated with the N implanted specimens in comparison with the relatively smooth surface of the as-polished specimen.Article Citation - WoS: 12Probing Nanoscale Domains of J-Aggregates Deposited on a Mica Surface(American Chemical Society, 2004) Demir, Mustafa Muammer; Özçelik, Serdar; Birkan, BurakJ-aggregates of 1,1′,3,3′-tetraethyl-5,5′,6,6′- tetrachlorobenzimidazolocarbocyanine (TTBC) were deposited on a mica surface and probed by atomic force microscopy operated at tapping mode in air. Optical spectra showed that J-aggregates were formed in aqueous solutions. Atomic force microscopy images revealed that J-aggregates deposited on mica surfaces mainly present single domains with a mean height of 2.00 ± 0.25 nm and an average diameter of 100 ± 20 nm. Quantitative analysis of the morphology of images indicated that the single domain of J-aggregates exhibits very uniform height and diameter distributions with polydispersity indices of 1.02 and 1.04, respectively. Based on the results, we propose a two-dimensional nanostructure in which TTBC J-aggregates could be arranged in a monolayer.