Özdoğan, Cem
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Doç. Dr.
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Ortak Dersler Bölümü
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Scholarly Output
24
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42
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596
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0
24 results
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Now showing 1 - 10 of 24
Article Citation - WoS: 8Citation - Scopus: 8Localization of metallicity and magnetic properties of graphene and of graphene nanoribbons doped with boron clusters(Taylor & Francis Ltd, 2014) Ozdogan, Cem; Özdoğan, Cem; Kunstmann, Jens; Quandt, Alexander; 40569; Ortak Dersler BölümüAs a possible way of modifying the intrinsic properties of graphene, we study the doping of graphene by embedded boron clusters with density functional theory. Cluster doping is technologically relevant as the cluster implantation technique can be readily applied to graphene. We find that B-7 clusters embedded into graphene and graphene nanoribbons are structurally stable and locally metallize the system. This is done both by the reduction of the Fermi energy and by the introduction of boron states near the Fermi level. A linear chain of boron clusters forms a metallic "wire" inside the graphene matrix. In a zigzag edge graphene nanoribbon, the cluster-related states tend to hybridize with the edge and bulk states. The magnetism in boron-doped graphene systems is generally very weak. The presence of boron clusters weakens the edge magnetism in zigzag edge graphene nanoribbon, rather than making the system appropriate for spintronics. Thus, the doping of graphene with the cluster implantation technique might be a viable technique to locally metallize graphene without destroying its attractive bulk properties.Article Structural stability and energetics of single-walled carbon nanotubes under uniaxial strain(2003) Özdoğan, Cem; Özdoğan, Cem; 40569; Ortak Dersler BölümüA (10x10) single-walled carbon nanotube consisting of 400 atoms with 20 layers is simulated under tensile loading using our developed O(N) parallel tight-binding molecular-dynamics algorithms. It is observed that the simulated carbon nanotube is able to carry the strain up to 122% of the relaxed tube length in elongation and up to 93% for compression. Young's modulus, tensile strength, and the Poisson ratio are calculated and the values found are 0.311 TPa, 4.92 GPa, and 0.287, respectively. The stress-strain curve is obtained. The elastic limit is observed at a strain rate of 0.09 while the breaking point is at 0.23. The frequency of vibration for the pristine (10x10) carbon nanotube in the radial direction is 4.71x10(3) GHz and it is sensitive to the strain rate.Article Citation - WoS: 0Citation - Scopus: 0Synthesis, molecular structure and DFT study of 2-(N-Benzoylbenzamido)pyridine-3-yl benzoate(Springer/plenum Publishers, 2011) Yuksektepe, Cigdem; Özdoğan, Cem; Kazak, Canan; Ozdogan, Cem; Guvenc, Ziya B.; Buyukgungor, Orhan; Arslan, Figen; Odabasoglu, Mustafa; 42359; 22620; 4292; 49272; 13249; Ortak Dersler BölümüThe biologically important 2-amino-3-hydroxypyridine reacts with benzoyl chloride to give 2-(N-benzoylbenzamido)pyridine-3-yl benzoate. This synthesized compound has been studied by elemental analysis, X-ray crystallography and also theoretically by density functional theory (DFT) framework with B3LYP/6-311++G(d, p) level of theory. The molecules of this compound crystallize in the orthorhombic space group of P2(1)2(1)2(1) and the crystal packing involves both hydrogen-bonding and C-Ha <-pi interaction. The vibrational normal modes of the molecular structure are investigated by ab initio method for both infrared intensities (IR) and for Raman activities. Furthermore, the corresponding assignments are discussed. Hydrogen and carbon atoms of the benzene rings are found to be highly active. Also, experimentally obtained IR spectrum is presented and compared with the available theoretical data. Experimentally and theoretically obtained IR spectrum are in good agreement.Conference Object Citation - WoS: 5Citation - Scopus: 12Parallel wavelet-based clustering algorithm on GPUs using CUDA(Elsevier Science Bv, 2011) Yildirim, Ahmet Artu; Özdoğan, Cem; Ozdogan, Cem; Ortak Dersler BölümüThere has been a substantial interest in scientific and engineering computing community to speed up the CPU-intensive tasks on graphical processing units (GPUs) with the development of many-core GPUs as having very large memory bandwidth and computational power. Cluster analysis is a widely used technique for grouping a set of objects into classes of "similar" objects and commonly used in many fields such as data mining, bioinformatics and pattern recognition. WaveCluster defines the notion of cluster as a dense region consisting of connected components in the transformed feature space. In this study, we present the implementation of WaveCluster algorithm as a novel clustering approach based on wavelet transform to GPU level parallelization and investigate the parallel performance for very large spatial datasets. The CUDA implementations of two main sub-algorithms of WaveCluster approach; namely extraction of low-frequency component from the signal using wavelet transform and connected component labeling are presented. Then, the corresponding performance evaluations are reported for each sub-algorithm. Divide and conquer approach is followed on the implementation of wavelet transform and multi-pass sliding window approach on the implementation of connected component labeling. The maximum achieved speedup is found in kernel as 107x in the computation of extraction of the low-frequency component and 6x in the computation of connected component labeling with respect to the sequential algorithms running on the CPU. (C) 2010 Published by Elsevier Ltd. Selection and/or peer-review under responsibility of the Guest Editor.Article Citation - WoS: 3Citation - Scopus: 3Parallelization of a molecular dynamics simulation of an ion-surface collision(World Scientific Publ Co Pte Ltd, 2005) Atis, M; Özdoğan, Cem; Özdogan, C; Güvenç, ZB; 40569; Ortak Dersler BölümüParallel molecular dynamics simulation study of the ion-surface collision system is reported. A sequential molecular dynamics simulation program is converted into a parallel code utilizing the concept of parallel virtual machine (PVM). An effective and favorable algorithm is developed. Our parallelization of the algorithm shows that it is more efficient because of the optimal pair listing, linear scaling, and constant behavior of the internode communications. The code is tested in a distributed memory system consisting of a cluster of eight PCs that run under Linux (Debian 2.4.20 kernel). Our results on the collision system are discussed based on the speed up, efficiency and the system size. Furthermore, the code is used for a full simulation of the Ar-Ni(100) collision system and calculated physical quantities are presented.Article Citation - WoS: 52Citation - Scopus: 59Structure and energetic of Bn (n 2–12) clusters: electronic structure calculations(Wiley, 2007) Atis, Murat; Özdoğan, Cem; Oezdogan, Cem; Guevenc, Ziya B.; Ortak Dersler BölümüThe electronic and geometric structures, total and binding energies, first and second energy differences, harmonic frequencies, point symmetries, and highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gaps of small and neutral B-n (n = 2-12) clusters have been investigated using density functional theory (DFT), B3LYP with 6-311 + + G(d,p) basis set. Linear, planar, convex, quasi-planar, three-dimensional (3D) cage, and open-cage structures have been found. None of the lowest energy structures and their isomers has an inner atom; i.e., all the atoms are positioned at the surface. Within this size range, the planar and quasi-planar (convex) structures have the lowest energies. The first and the second energy differences are used to obtain the most stable sizes. A simple growth path is also discussed with the studied sizes and isomers. The results have been compared with previously available theoretical and experimental works. (C) 2006 Wiley Periodicals, Inc.Article Citation - WoS: 10Citation - Scopus: 1(Formula Presented) Algorithms In Tight-Binding Molecular-Dynamics Simulations of the Electronic Structure of Carbon Nanotubes(American Physical Soc, 2003) Dereli, G; Özdoğan, Cem; Ozdogan, C; 40569; Ortak Dersler BölümüThe O(N) and parallelization techniques have been successfully applied in tight-binding molecular-dynamics simulations of single-walled carbon nanotubes (SWNT's) of various chiralities. The accuracy of the O(N) description is found to be enhanced by the use of basis functions of neighboring atoms (buffer). The importance of buffer size in evaluating the simulation time, total energy, and force values together with electronic temperature has been shown. Finally, through the local density of state results, the metallic and semiconducting behavior of (10x10) armchair and (17x0) zigzag SWNT's, respectively, has been demonstrated.Article Citation - WoS: 203Citation - Scopus: 212Stability of edge states and edge magnetism in graphene nanoribbons(Amer Physical Soc, 2011) Kunstmann, Jens; Özdoğan, Cem; Ozdogan, Cem; Quandt, Alexander; Fehske, Holger; Ortak Dersler BölümüWe critically discuss the stability of edge states and edge magnetism in zigzag edge graphene nanoribbons (ZGNRs). We point out that magnetic edge states might not exist in real systems and show that there are at least three very natural mechanisms-edge reconstruction, edge passivation, and edge closure-which dramatically reduce the effect of edge states in ZGNRs or even totally eliminate them. Even if systems with magnetic edge states could be made, the intrinsic magnetism would not be stable at room temperature. Charge doping and the presence of edge defects further destabilize the intrinsic magnetism of such systems.Article Citation - WoS: 30Density functional study of physical and chemical properties of nano size Boron Clusters: B-n (n=13-20)(Chinese Physical Soc, 2009) Atis, Murat; Özdoğan, Cem; Ozdogan, Cem; Guvenc, Ziya B.; 28225; Ortak Dersler BölümüBoron is an element that has ability to build strong and highly directional bonds with boron itself. As a result, boron atoms form diverse structural motifs, ultimately can yield distinct nano structures, such as planar, quasi-planar, convex, cage, open-cage, tubular, spherical., ring, dome-like, shell, capsule, and so on, i.e., it can take almost any shape. Therefore, a deep understanding of the physical and chemical properties becomes important in boron cluster chemistry. Electronic and geometric structures, total and binding energies, harmonic frequencies, point symmetries, charge distributions, dipole moments, chemical bondings and the highest occupied molecular orbital-lowest unoccupied molecular orbital energy gaps of neutral B-n (n=13-20) clusters have been investigated by, density functional theory (DFT), B3LYP with 6-311++G(d,p) basis set. Furthermore, the first and the second energy differences are used to obtain the most stable sizes. We have observed that almost all physical properties are size dependent, and double-ring tubular form of B-20 has the highest binding energy per atom. The icosahedral structure with an inside atom is found as impossible as a stable structure for the size thirteen. This structure transforms to an open-cage form. The structural transition from two-dimensional to three-dimensional is found at the size of 20 and consistent with the literature. The calculated charges by the Mulliken analysis show that there is a symmetry pattern with respect to the x-z and y-z planes for the charge distributions. The unusual planar stability of the boron clusters may be explained by the delocalized pi and sigma bonding characteristic together with the existence of the multicentered bonding. The results have been compared to available studies in the literature.Article Citation - WoS: 17Citation - Scopus: 18Boron doped graphene nanostructures(Wiley-v C H verlag Gmbh, 2008) Quandt, Alexander; Özdoğan, Cem; Ozdogan, Cem; Kunstmann, Jens; Fehske, Holger; Ortak Dersler BölümüWe present results from an ab initio study of metallized semiconducting graphene nanostructures. Our model system consists of an alternating chain of quasi-planar B-7 clusters embedded into a semiconducting arm-chair nanoribbon. We observe the appearance of overlapping bands around the Fermi-level, with crystal momenta pointing into the direction of these boron chains. This observation could be a vantage point for the development of graphene nanodevices and integrated nanocircuits, based on existing technologies. (C) 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim
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