Abdullah Kepceoglu | Stanford University (original) (raw)

Papers by Abdullah Kepceoglu

Lasers in Medical Science, 2015

Journal of Adhesion Science and Technology, 2014

bioRxiv (Cold Spring Harbor Laboratory), Nov 20, 2022

In this study, a quartz crystal microbalance (QCM) sensor surface was coated with biotin and/or s... more In this study, a quartz crystal microbalance (QCM) sensor surface was coated with biotin and/or streptavidin using the electrospinning method. The coated surfaces were analyzed using the Raman spectroscopy method. QCM measurements were carried out using the OpenQCM platform. The results indicate that the electrospinning method can be used to coat QCM surfaces with biotin and/or streptavidin and that the coated surfaces exhibit distinct morphological and spectroscopic properties. The QCM measurements showed that the coated surfaces are highly sensitive to changes in mass, indicating their potential for use in biosensing applications. Overall, this study provides new insights into the use of QCM sensors coated with biotin and/or streptavidin for biological sensing and detection applications.

Selçuk-Teknik Dergisi, Dec 6, 2017

Selçuk-Teknik Dergisi, Feb 23, 2018

Turkish Journal of Chemistry, Apr 28, 2021

In this study, rhenium/rhenium oxide nanoparticles (Re / ReO3 NPs) have been produced for the fir... more In this study, rhenium/rhenium oxide nanoparticles (Re / ReO3 NPs) have been produced for the first time in ultrapure water by using Femtosecond Pulsed Laser Ablation in Liquid (fsPLAL) method. X-Ray Diffraction (XRD) measurements and results obtained for NPs show the existence of well-crystallized peaks and preferred phases. Re NPs have hexagonal structure while ReO3 NPs have the perovskite-like cubic crystal structures. The Re / ReO3 ratio is also determined to be 53 / 47 with ~ 20 nm crystallite size, while pure ReO3 crystallite sizes were measured to be ~ 25 nm. The TEM results have shown that the produced particles have a spherical shape, and particle sizes changes between ~ 20 nm and ~ 60 nm. The crystallite size is similar due to XRD results. Obtained nanoparticles exhibit promising applications for photonic devices with broad bandgap values which have measured to be 4.71 eV for Re / ReO3 NPs mixture and 4.36 eV for pure ReO3 NPs.

Canadian Journal of Physics, Oct 1, 2021

In this study, silver (Ag) nanoparticle thin films were deposited on microscope slide glass and S... more In this study, silver (Ag) nanoparticle thin films were deposited on microscope slide glass and Si wafer substrates using the pulsed-laser deposition (PLD) technique in Ar ambient gas pressures of 1 × 10−3 and 7.5 × 10−1 mbar. AFM analysis has shown that the number of Ag nanoparticles reaching the substrate decreased with increasing Ar gas pressure. As a result of Ar ambient gas being allowed into the vacuum chamber, it was observed that the size and height of Ag nanoparticles decreased and the interparticle distances decreased. According to the absorption spectra taken by a UV–vis spectrometer, the wavelength where the localised surface plasmon resonance (LSPR) peak appeared was shifted towards the longer wavelength region in the solar spectrum as Ar background gas pressure was decreased. This experiment shows that LSPR wavelength can be tuned by adjusting the size of metal nanoparticles, which can be controlled by changing Ar gas pressure. The obtained extinction cross section spectra for Ag nanoparticle thin film was theoretically analysed and determined by using the metal nanoparticle–boundary element method (MNPBEM) toolbox simulation program. In this study, experimental spectrum and simulation data for metal nanoparticles were acquired, compared, and determined to be in agreement.

Journal of Adhesion Science and Technology, May 9, 2018

Abstract The bonding of resin cement to ceramic materials plays an important role in dentistry. T... more Abstract The bonding of resin cement to ceramic materials plays an important role in dentistry. The purpose of this study is to evaluate the effects of various surface treatments on the shear bond strength (SBS) of zirconia ceramic and metal alloy. A total of 60 specimens were prepared from Y-TZP ceramic and metal alloy. The specimens were divided into three subgroups (n = 10) that received different surface treatments for each material. An Er:YAG laser (ER), a femtosecond laser (FS), and air-borne particle abrasion (A) were employed as surface treatments. One specimen from each group was analyzed using a scanning electron microscope (SEM) at 500 x magnification after surface treatments. The self-adhesive resin cement was then bonded to the treated surfaces using a Teflon mold. The specimens were thermocycled for 5,000 cycles at 5–55 °C, and then the SBS test was performed. Kruskal–Wallis and Mann–Whitney U tests were used to determine the differences between the groups (p = 0.05), and failure modes were evaluated for each specimen. Statistical analyses revealed significant differences between the surface treatment methods. The mean SBS values of the air-borne particle-abraded groups were higher than those of the other groups. The femtosecond-irradiated groups of each material showed significantly higher SBS values than the Er:YAG-irradiated groups (p < 0.05). Within the limitations of this study, air-borne particle abrasion and the femtosecond laser were more effective than Er:YAG laser treatment.

Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi, Aug 1, 2014

ABSTRACTHigh-resolution biomacromolecular structure determination is essential to better understa... more ABSTRACTHigh-resolution biomacromolecular structure determination is essential to better understand protein function and dynamics. Serial crystallography is an emerging structural biology technique which has fundamental limitations due to either sample volume requirements or immediate access to the competitive X-ray beamtime. Obtaining a high volume of well-diffracting, sufficient-size crystals while mitigating radiation damage remains a critical bottleneck of serial crystallography. As an alternative, we introduce the plate-reader module adapted for using a 72-well Terasaki plate for biomacromolecule structure determination at a convenience of a home X-ray source. We also present the first ambient temperature lysozyme structure determined at the Turkish Light Source (Turkish DeLight). The complete dataset was collected in 18.5 mins with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature struct...

Renewable energy sources will play an important role in the energy supply in a near future. Solar... more Renewable energy sources will play an important role in the energy supply in a near future. Solar energy is the primary energy source among renewable energy sources. The solar energy systems are became the most compelling topic, understanding the parameters of the Photovoltaic (PV) panels using the experimental data plays an important role in the design and evaluation of the PV panels and its efficiencies. Obtaining the performance characteristics of the photovoltaic panels in different operating conditions and parametric studies, have attract attention in the last decade. In this study, we determined the unknown parameters of photovoltaic panels using the single diode Rs model via applying two different methods, by using catalog information of the commercial solar panel obtained from manufacturers. Thus, these were compared with the experimental data by plotting I-V and P-V characteristics in MATLAB at the different solar radiation conditions. Eventually, temperature dependent I-V ...

Nanomaterials, 2020

In this study, the thin films were produced by using pulsed laser deposition (PLD) technique from... more In this study, the thin films were produced by using pulsed laser deposition (PLD) technique from gold (Au) nanoparticles deposited on two kinds of substrates under different argon (Ar) gas pressure. Microscope glass slides and silicon (100) wafers were used as amorphous and crystal substrates. The films were deposited under 2 × 10−3 mbar, 1 × 10−2 mbar, 2 × 10−2 mbar argon (Ar) ambient gas pressure. Effect of the background gas pressure on the plasma plume of the ablated Au nanoparticles was investigated in details. Morphology of Au nanoparticle thin films was investigated by means of atomic force microscopy (AFM) technique. Absorption spectra of Au nanoparticles were examined by using UV-Vis spectrometry. Extinction spectra of Au nanoparticles were calculated by using metallic nano particles boundary element method (MNPBEM) simulation programme. Both experimental spectra and simulation data for Au nanoparticles were obtained and compared in this work. It was concluded that they ar...

X-ray crystallography is a robust and powerful structural biology technique that provides high-re... more X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g. proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryo-crystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, Istanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample fo...

The treatment of insulin-dependent diabetes mellitus is characterized by artificial supplementati... more The treatment of insulin-dependent diabetes mellitus is characterized by artificial supplementation of pancreatic β-cell ability to regulate sugar levels in the blood. Even though various insulin analogs are crucial for reasonable glycemic control, understanding the dynamic mechanism of the insulin analogs may help to improve the best-protracted insulin analog to assist people with Type 1 Diabetes (T1D) to live comfortably while maintaining tight glycemic control. Here we present the high-resolution crystal structure of NN304, known as insulin detemir, to 1.7 A resolution at cryogenic temperature. We computationally further investigated our crystal structure's monomeric-dimeric conformation and dynamic profile by comparing it with a previously available detemir structure (PDB ID: 1XDA). Our structure (PDB ID: 8HGZ) obtained at elevated pH provides a distinct alternative dimeric conformation compared to the previous structure, suggesting it might induce an intermediate state in t...

The driven force of this work is to found a statistical approach for the identification of the di... more The driven force of this work is to found a statistical approach for the identification of the different chemicals by using Femtosecond Laser Mass Spectrometry (FLMS) method. A major problem in the field of the mass spectrometry is the identification or the discrimination of similar chemicals with the same molecular weight or even chemical isomers. Mass spectrometry systems are using a variety of ionisation techniques and their modification. It is really hard to distinguish the differences of the investigated sample when using most of the current ionising techniques. In this thesis, the multiphoton ionisation/dissociation method is used to create ions. The varying dissociation channels opened gave very useful information about the structure of the investigated chemical. In this study, it is shown that isomers can be distinguished by using multivariate statistical analysis on the mass spectral data obtained by FLMS method. In addition, after constructing a mass spectral database which consists of mass spectra of the isomers which are recorded under different experimental conditions (laser wavelength, laser pulse power and sample pressure), distinguishing in real-time the unknown isomers by comparing obtained mass spectral information with the database has been performed As a result, supporting the philosophy of this work, it is revealed the fact that the FLMS method is suitable for mass spectral identification applications (cancer diagnostic research, material analysis, chemical detection etc.) and keen alternative to the other mass spectrometry methods use different ionisations techniques.

Lasers in Medical Science, 2015

Journal of Adhesion Science and Technology, 2014

bioRxiv (Cold Spring Harbor Laboratory), Nov 20, 2022

Selçuk-Teknik Dergisi, Dec 6, 2017

Selçuk-Teknik Dergisi, Feb 23, 2018

Turkish Journal of Chemistry, Apr 28, 2021

Canadian Journal of Physics, Oct 1, 2021

Journal of Adhesion Science and Technology, May 9, 2018

Afyon Kocatepe Üniversitesi Fen Ve Mühendislik Bilimleri Dergisi, Aug 1, 2014

Nanomaterials, 2020

AIP Conference Proceedings, 2017

Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel... more Succinonitrile (i.e. butanedinitrile) is a colorless nitrile compound that can be used in the gel polymer batteries as a solid-state solvent electrolytes and has a plastic crystal structure. Prior to the molecular structure calculation of the succinonitrile molecule, the conformer analysis were calculated by using semi empirical method PM3 core type Hamiltonian and eight different conformer structures were determined. Molecular structure with energy related properties of these conformers having the lowest energy was calculated by using DFT (B3LYP) methods with 6-311++G(d,p) basis set. Possible radicals, can be formed experimentally, were modeled in this study. EPR parameters of these model radicals were calculated and then compared with that obtained experimentally.

T.C. ULUDAĞ ÜNİVERSİTESİ FEN BİLİMLERİ ENSTİTÜSÜ, 2012

Bu çalışmada amaç, EEG/fMRI’de kullanılan fantom üzerine yerleştirilmiş iki farklı tip Ag/AgCl el... more Bu çalışmada amaç, EEG/fMRI’de kullanılan fantom üzerine yerleştirilmiş iki farklı tip Ag/AgCl elektrotların (ilki 1,5mm-sıkıştırılabilir güvenlik soketi ve 150cm uzun ömürlü kablolu B10-S-150 Ag/AgCl sintere edilmiş halka elektrot ve ikincisi, 100cm light-duty leadwire ve 1,5mm-touchproof güvenlik soketi ve sensöre yakın noktada 5 kOhm değerinde direnç bulunan B12-LS-100 Ag/AgCl sintere edilmiş FE-elektrot) ısınma etkilerinin incelenmesidir. Bu amaç doğrultusunda önce FDTD programı (XFDTD, REMCOM Co., State College, PA) ile phantomda soğrulan güç hesaplanmıştır. Daha sonra 3T Siemens Trio (Erlangen, Germany) MRI cihazında EPI (ep2d_seg/ ep_seg_fid) sekansında 60 dakika taranmış ve elde edilen görüntülerden fantomdaki sıcaklık değişimi hesaplanmıştır. İstatistiksel olarak bu sonuçlar karşılaştırılmış ve sonucunda Ag/AgCl sintere edilmiş pin elektrotun (B12-LS-100) EEG/fMRI’de kullanılmasının daha iyi olduğu ve daha az ısınmaya yol açacağı belirlenmiştir.

The aim of this study is investigate the heating effects on the two different types of Ag/AgCl electrodes (the first B10-S-150 Ag/AgCl sintered ring electrode with 1,5mm-touchproof safety socket and 150cm heavy-duty lead wire and the second, B12-LS-100 Ag/AgCl sintered FE-electrode with 100cm light-duty lead wire and 1,5mm-touchproof safety socket with 5 k resistor near sensor) mounted on the surface of the phantom, used in EEG/fMRI. For this purpose, firstly RF deposited power has been simulated using FDTD method (XFDTD, REMCOM Co., State College, PA). Then, phantom scanned in 3T Siemens Trio (Erlangen, Germany) MRI scanner with EPI (ep2d_seg/ ep_seg_fid) sequence for 60 minute and temperature change has been calculated using obtained images. These results are compared statistically and it is obtained that Ag/AgCl Pin electrode (B12-LS-100) is better to be use in EEG/fMRI for reducing temperature increase.

T.C. SELÇUK UNIVERSITY THE GRADUATE SCHOOL OF NATURAL SCIENCES, 2020

The driven force of this work is to found a statistical approach for the identification of the di... more The driven force of this work is to found a statistical approach for the identification of the different
chemicals by using Femtosecond Laser Mass Spectrometry (FLMS) method. A major problem in the field
of the mass spectrometry is the identification or the discrimination of similar chemicals with the same
molecular weight or even chemical isomers.
Mass spectrometry systems are using a variety of ionisation techniques and their modification. It
is really hard to distinguish the differences of the investigated sample when using most of the current
ionising techniques. In this thesis, the multiphoton ionisation/dissociation method is used to create ions.
The varying dissociation channels opened gave very useful information about the structure of the
investigated chemical.
In this study, it is shown that isomers can be distinguished by using multivariate statistical analysis
on the mass spectral data obtained by FLMS method. In addition, after constructing a mass spectral database
which consists of mass spectra of the isomers which are recorded under different experimental conditions
(laser wavelength, laser pulse power and sample pressure), distinguishing in real-time the unknown isomers
by comparing obtained mass spectral information with the database has been performed
As a result, supporting the philosophy of this work, it is revealed the fact that the FLMS method is
suitable for mass spectral identification applications (cancer diagnostic research, material analysis,
chemical detection etc.) and keen alternative to the other mass spectrometry methods use different
ionisations techniques.