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: 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: 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: 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.Conference Object Citation - WoS: 6Citation - Scopus: 6Fabrication of Array of Mesas on Superconducting Bi2sr 2cacu2o8+? Single Crystals(National Institute of Optoelectronics, 2005) Kurter, Cihan; Özyüzer, LütfiThe superconducting properties of multi-layered high temperature superconductors (HTS) result mainly from the CuO2 planes, while the other structural components behave simply as charge reservoirs. Using these perfect-layered structures of HTS, arrays of mesas have been fabricated on the surfaces of Bi2Sr2CaCu2O8+δ (Bi2212) single crystals using hotolithography and argon ion beam etching techniques. These arrays have current-voltage (I-V) characteristics that consist of some branches corresponding to different intrinsic Josephson junctions in the mesas, The surface topography and heights of the mesas were examined with atomic force microscopy. Due to the small mesa area, conventional wire bonding techniques are not applicable. A novel method, point contact tunneling apparatus with a sharp Au tip, was used to obtain the I-V characteristics of the fabricated intrinsic Josephson junctions, below the critical temperature of Bi2212. Since the ultimate goal was to obtain an ordered group of mesas with small lateral dimensions, to eliminate heating effects during I-V measurements, we showed that submicron-sized mesas could be characterized by the new technique.