Abdullah Kepceoglu

All Publications

• Rapid and efficient ambient temperature X-ray crystal structure determination at Turkish Light Source SCIENTIFIC REPORTS Gul, M., Ayan, E., Destan, E., Johnson, J., Shafiei, A., Kepceoglu, A., Yilmaz, M., Ertem, F., Yapici, I., Tosun, B., Baldir, N., Tokay, N., Nergiz, Z., Karakadioglu, G., Paydos, S., Kulakman, C., Ferah, C., Guven, O., Atalay, N., Akcan, E., Cetinok, H., Arslan, N., Sabanoglu, K., Asci, B., Tavli, S., Gumusboga, H., Altuntas, S., Otsuka, M., Fujita, M., Tekin, S., Ciftci, H., Durdagi, S., Karaca, E., Turkoz, B., Kabasakal, B., Kati, A., DeMirci, H. 2023; 13 (1): 8123

  Abstract

  High-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 min with resolution extending to 2.39 Å and 100% completeness. Combined with our previous cryogenic structure (PDB ID: 7Y6A), the ambient temperature structure provides invaluable information about the structural dynamics of the lysozyme. Turkish DeLight provides robust and rapid ambient temperature biomacromolecular structure determination with limited radiation damage.

  View details for DOI 10.1038/s41598-023-33989-0

  View details for Web of Science ID 001001529400055

  View details for PubMedID 37208392

  View details for PubMedCentralID PMC10198979

• Comparative Study of High-Resolution LysB29(Nε-myristoyl) des(B30) Insulin Structures Display Novel Dynamic Causal Interrelations in Monomeric-Dimeric Motions CRYSTALS Ayan, E., Destan, E., Kepceoglu, A., Ciftci, H., Kati, A., DeMirci, H. 2023; 13 (4)

  View details for DOI 10.3390/cryst13040648

  View details for Web of Science ID 000979164900001

• Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish Light Source "Turkish DeLight" TURKISH JOURNAL OF BIOLOGY Atalay, N., Akcan, E., Gul, M., Ayan, E., Destan, E., Ertem, F., Tokay, N., Cakilkaya, B., Nergiz, Z., Karakadioglu, G., Kepceoglu, A., Yapici, I., Tosun, B., Baldir, N., Yildirim, G., Johnson, J., Guven, O., Shafiei, A., Arslan, N., Yilmaz, M., Kulakman, C., Paydos, S., Cinal, Z., Sabanoglu, K., Pazarceviren, A., Yilmaz, A., Canbay, B., Asci, B., Kartal, E., Tavli, S., Caliseki, M., Goc, G., Mermer, A., Yesilay, G., Altuntas, S., Tateishi, H., Otsuka, M., Fujita, M., Tekin, S., Ciftci, H., Durdagi, S., Doganay, G., Karaca, E., Turkoz, B., Kabasakal, B., Kati, A., Demirci, H. 2023; 47 (1): 1-+

  Abstract

  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 cryocrystallography 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, İstanbul, 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 for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis.

  View details for DOI 10.55730/1300-0152.2637

  View details for Web of Science ID 000938252000002

  View details for PubMedID 37529114

  View details for PubMedCentralID PMC10387866

• Experimental and theoretical study of the characteristics of LSPR peaks for metal NPs produced by controlling Ar ambient gas pressure to enhance the efficiency of solar cells CANADIAN JOURNAL OF PHYSICS Gezgin, S., Kepceoglu, A., Kilic, H. 2021; 99 (10): 907-912

  View details for DOI 10.1139/cjp-2020-0626

  View details for Web of Science ID 000704761000009

• Rhenium/rhenium oxide nanoparticles production using femtosecond pulsed laser ablation in liquid. Turkish journal of chemistry Kepceoğlu, A., Gündoğdu, Y., Sarilmaz, A., Ersöz, M., Özel, F., Kiliç, H. Ş. 2021; 45 (2): 485-492

  Abstract

  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.

  View details for DOI 10.3906/kim-2008-59

  View details for PubMedID 34104059

  View details for PubMedCentralID PMC8164208

• Effect of Ar Gas Pressure on LSPR Property of Au Nanoparticles: Comparison of Experimental and Theoretical Studies. Nanomaterials (Basel, Switzerland) Gezgin, S. Y., Kepceoğlu, A., Gündoğdu, Y., Zongo, S., Zawadzka, A., Kiliç, H. Ş., Sahraoui, B. 2020; 10 (6)

  Abstract

  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 are also in good agreement with literature data. The measurements and the simulation results showed that localized surface plasmon resonance (LSPR) peaks for Au nanoparticles were located in the near infrared region (NIR) because of the larger size of the disk-like shape of Au nanoparticles, and the near-field coupling between Au nanoparticles. It was demonstrated that as the ambient gas (Ar) pressure was increased, the size and the density of Au nanoparticles on the substrate were decreased and the LSPR peak shifts toward the short wavelength region in the spectrum. This shift has been explained by the changes in the morphology of produced thin films.

  View details for DOI 10.3390/nano10061071

  View details for PubMedID 32486386

  View details for PubMedCentralID PMC7352769

• Real-Time Distinguishing of the Xylene Isomers Using Photoionization and Dissociation Mass Spectra Obtained by Femtosecond Laser Mass Spectrometry (FLMS) ANALYTICAL LETTERS Kepceoglu, A., Gundogdu, Y., Ledinghama, K., kilic, H. 2020; 53 (2): 290-307

  View details for DOI 10.1080/00032719.2019.1647227

  View details for Web of Science ID 000478218000001

• Nonlinear Optical Properties of Zinc Oxide Thin Films Produced by Pulsed Laser Deposition Kepceoglu, A., Gezgin, S., Gundogdu, Y., Kucukcelebi, H., Kilic, H. S. ELSEVIER. 2019: 1819-1825

  View details for Web of Science ID 000495858400005

• Molecular Structure and TD-DFT Study of the Xylene Isomers GAZI UNIVERSITY JOURNAL OF SCIENCE Kepceoglu, A., Gundogdu, Y., Dereli, O., Kilic, H. 2019; 32 (1): 300-308

  View details for Web of Science ID 000460061400022

• Investigation of Conversion Efficiency of n-ZnO/p-Si Heterojunction Device Produced by Pulsed Laser Deposition (PLD) Gezgin, S., Kepceoglu, A., Toprak, A., Kilic, H. ELSEVIER. 2019: 1996-2002

  View details for Web of Science ID 000495858400027

• Femtosecond Laser Ablation Synthesis of Nanoparticles and Nano-Hybrides in Ethanol Medium Gundogdu, Y., Kepceoglu, A., Gezgin, S., Kucukcelebi, H., Kilic, H. ELSEVIER. 2019: 1803-1810

  View details for Web of Science ID 000495858400003

• An Experimental and Theoretical Comparison of Plasmonic Properties of Metallic Nano-Particles Have Different Morphological Properties Gezgin, S., Kepceoglu, A., Kucukcelebi, H., Kilic, H. ELSEVIER. 2019: 1896-1902

  View details for Web of Science ID 000495858400015

• Analysis of the xylenol isomers by femtosecond laser time of flight mass spectrometry Kepceoglu, A., Koklu, N., Gundogdu, Y., Dereli, O., Kilic, H. S. CANADIAN SCIENCE PUBLISHING. 2018: 711-715

  View details for DOI 10.1139/cjp-2017-0762

  View details for Web of Science ID 000437293500010

• Effect of different surface treatments on the shear bond strength of resin cement to zirconia ceramic and metal alloy JOURNAL OF ADHESION SCIENCE AND TECHNOLOGY Yucel, M., Kilic, I., Okutan, Y., Tobi, E., Kilic, H., Kepceoglu, A., Donmez, M. 2018; 32 (20): 2232-2243

  View details for DOI 10.1080/01694243.2018.1470363

  View details for Web of Science ID 000445077400004

• Molecular Structure and the EPR Calculation of the Gas Phase Succinonitrile Molecule Kepceoglu, A., Kilic, H. S., Dereli, O., Akkus, B., Oktem, Y., Dogan, G. S., Guzelcimen, F. AMER INST PHYSICS. 2017

  View details for DOI 10.1063/1.4976356

  View details for Web of Science ID 000435205100012

• Production and Characterization of Titanium (Ti), Platinum (Pt) and Tantalum (Ta) Thin Films for Native DNA Biosensors Genc, E., Kepceoglu, A., Gezgin, S., Kars, M., Kilic, H., Akkus, B., Oktem, Y., Dogan, G. S., Guzelcimen, F. AMER INST PHYSICS. 2017

  View details for DOI 10.1063/1.4976460

  View details for Web of Science ID 000435205100116

• An Experimental Investigation of Localised Surface Plasmon Resonance (LSPR) for Cu Nanoparticles Depending as a Function of Laser Pulse Number in Pulsed Laser Deposition Gezgini, S., Kepceoglu, A., Kilic, H., Akkus, B., Oktem, Y., Dogan, G. S., Guzelcimen, F. AMER INST PHYSICS. 2017

  View details for DOI 10.1063/1.4976368

  View details for Web of Science ID 000435205100024

• An Investigation of Localised Surface Plasmon Resonance (LSPR) of Ag Nanoparticles Produced by Pulsed Laser Deposition (PLD) Technique Gezgin, S., Kepceoglu, A., Kilic, H., Akkus, B., Oktem, Y., Dogan, G. S., Guzelcimen, F. AMER INST PHYSICS. 2017

  View details for DOI 10.1063/1.4976367

  View details for Web of Science ID 000435205100023

• Identification of the Isomers Using Principal Component Analysis (PCA) Method Kepceoglu, A., Gundogdu, Y., Ledingham, K., Kilic, H., Akkus, B., Oktem, Y., Yalcin, L. S., Mutlu, R. B., Dogan, G. S. AMER INST PHYSICS. 2016

  View details for DOI 10.1063/1.4944149

  View details for Web of Science ID 000375923300030

• Plasmonic Tuning of Gold Doped Thin Films for Layers of Photovoltaic Devices Gezgin, S., Kilic, H., Kepceoglu, A., Bayir, S., Nalbantoglu, I., Toprak, A., Akkus, B., Oktem, Y., Yalcin, L. S., Mutlu, R. B., Dogan, G. S. AMER INST PHYSICS. 2016

  View details for DOI 10.1063/1.4944228

  View details for Web of Science ID 000375923300109

• Effect of femtosecond laser beam angle on bond strength of zirconia-resin cement. Lasers in medical science Akpinar, Y. Z., Kepceoglu, A., Yavuz, T., Aslan, M. A., Demirtag, Z., Kılıc, H. S., Usumez, A. 2015; 30 (8): 2123-8

  Abstract

  Yttrium-stabilized tetragonal zirconia polycrystalline (Y-TZP) ceramic is widely used as an all-ceramic core material because of its enhanced mechanical and aesthetic properties. The bond strength of Y-TZP restorations affects long-term success; hence, surface treatment is required on ceramic boundaries. This study evaluated the effect of different laser beam angles on Y-TZP-resin cement shear bond strength (SBS). Forty plates of Y-TZP ceramics were randomly assigned to four groups (n = 10). A femtosecond amplifier laser pulse was applied on Y-TZP surface with different incidence angles (90°, 75°, 60°, 45°). The resin cement was adhered onto the zirconia surfaces. The SBS of each sample was measured using universal testing machine at crosshead speed of 1 mm/min. The SBS was analyzed through one-way analysis of variance (ANOVA)/Tukey tests. The results showed that the degree of laser beam angle affects the SBS of resin cement to Y-TZP. The laser beam was applied to a surface with a 45° angle which resulted in significantly higher SBS (18.2 ± 1.43 MPa) than other groups (at 90° angulation (10.79 ± 1.8 MPa), at 75° (13.48 ± 1.2 MPa) and at 60° (15.85 ± 0.81 MPa); p < 0.001). This study shows that decreasing of the angle between the ceramic surface and the laser beam increased the SBS between the resin cement and the ceramic material, as well as the orifice.

  View details for DOI 10.1007/s10103-015-1762-1

  View details for PubMedID 25958172

• Effect of different surface shapes formed by femtosecond laser on zirconia-resin cement shear bond strength JOURNAL OF ADHESION SCIENCE AND TECHNOLOGY Akpinar, Y., Yavuz, T., Aslan, M., Kepceoglu, A., Kilic, H. 2015; 29 (3): 149-157

  View details for DOI 10.1080/01694243.2014.977697

  View details for Web of Science ID 000345442600001

• Optical and structural characterization of thin films containing metallophthalocyanine chlorides DYES AND PIGMENTS Zawadzka, A., Karakas, A., Plociennik, P., Szatkowski, J., Lukasiak, Z., Kapceoglu, A., Ceylan, Y., Sahraoui, B. 2015; 112: 116-126

  View details for DOI 10.1016/j.dyepig.2014.06.029

  View details for Web of Science ID 000343687300017

• Femtosecond laser induced photodynamic therapy on 5-ALA treated SKMEL-30 cells: an efficient theranostic strategy to combat melanoma. Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie Kars, M. D., Kara, R., Gündoğdu, Y., Kepceoğlu, A., Kılıç, H. Ş. 2014; 68 (5): 657-62

  Abstract

  Photodynamic therapy (PDT) is a type of photo-chemotherapy that is based on the application of photosensitizer and irradiation of the region by laser sources. Photosensitizer and light interaction will develop reactive oxygen radicals ((1)O2) in the cells and elimination of cells by apoptosis or necrosis.Metastatic skin cancer cells SKMEL-30 were treated by 5-ALA in dark and then they were irradiated by 90-femtosecond (fs) laser with different pulse powers for different durations. The effects of 5-ALA mediated photodynamic therapy on the cells were determined by XTT proliferation kit and by flow cytometry measurements of Annexin V, 7-AAD and mitochondrial membrane potential alterations. Fluorescent accumulation of protoporphyrin IX was investigated by fluorometry and confocal laser microscope.The viability tests for SKMEL-30 cells treated with different 5-ALA doses and femtosecond laser power and durations demonstrated that 635 nm, 45 mW pulse energy at 90 fs laser pulse applications for 60 sec to 1mM 5-ALA exposed cells decreased the cell proliferation by 30%. Flow cytometric measurements exhibit that PDT caused 63% of mitochondria membrane potential alteration, 30% of cell death in the population by apoptosis and 39% of cells by necrosis. There was 1mM 5-ALA exposure that also exhibited about 32% accumulation of fluorescence in the cells.The pretreatment of the cells with the precursor 5-ALA lets the imaging due to increased protoporphyrin IX fluorescence. This treatment method may be proposed as an effective theranostic strategy for melanoma because of its rapid and effective anticancer consequences.

  View details for DOI 10.1016/j.biopha.2014.04.001

  View details for PubMedID 24835696

• Ag/AgCl electrodes in the EEG/fMRI method in 3T MRI scanner EUROPEAN PHYSICAL JOURNAL-APPLIED PHYSICS Akay, C., Kepceoglu, A. 2013; 64 (1)

  View details for DOI 10.1051/epjap/2013130173

  View details for Web of Science ID 000325535600007