Browsing by Author "Ozdogan, Cem"

Now showing 1 - 12 of 12

Citation - WoS: 23
Citation - Scopus: 24
An investigation of hydrogen bonded neutral B4Hn (n=1-11) and anionic B4H11(-1) clusters: Density functional study
(Elsevier Science Bv, 2007) Boyukata, Mustafa; Özdoğan, Cem; Ozdogan, Cem; Guvenc, Ziya B.; 120207; Ortak Dersler Bölümü
In this study, detailed analysis of the structural stability of hydrogen bonded four-atom boron clusters within the framework of density functional theory (DFT) is presented. Effects of the number of hydrogen atoms on the structural stability of 134, binding energy of the clusters, and also on the boron-hydrogen binding energy are investigated. Attention is also paid to the determination of energetically the most stable geometries of B4Hn (n = 1-11) boron hydrides, and to their isomers. The lower-lying electronic states of the B4Hn structures are investigated. In addition natural electron configurations of the most stable clusters and charge transfer between the atoms in the cluster are also analyzed. Furthermore, the stability of anionic form of B4H11(-1) cluster is examined. (c) 2006 Elsevier B.V. All rights reserved.
Citation - WoS: 17
Citation - Scopus: 18
Boron doped graphene nanostructures
(Wiley-v C H verlag Gmbh, 2008) Quandt, Alexander; Özdoğan, Cem; Ozdogan, Cem; Kunstmann, Jens; Fehske, Holger; Ortak Dersler Bölümü
We 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
Citation - WoS: 30
Density 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 Bölümü
Boron 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.
Citation - WoS: 4
Citation - Scopus: 5
Feynman, biominerals and graphene - basic aspects of nanoscience
(Elsevier, 2010) Quandt, Alexander; Özdoğan, Cem; Ozdogan, Cem; Ortak Dersler Bölümü
This article is about writing small. Inspired by R.P. Feynman's legendary talk There's plenty of room at the bottom, we recapitulate his famous Gedanken experiment of condensing a lot of useful information on the head of a pin [see Feymnan R, J. MEMS 1 (1992) 60]. These considerations will familiarize LIS with the length scales for a future downsizing of technological components, and they allow for some speculations about ultimate physical or chemical limits of the corresponding nanodevices. Furthermore we will analyze the nano-technological capabilities of Mother Nature in the case of magnetotactic bacteria, and briefly sketch the cornerstones of the rapidly growing field of biomineralization, which might open up a new science of complex functional nanomaterials in the near future. Finally we describe a general scheme to shrink integrated microelectronic circuits towards the very size limits of nanotechnology. (C) 2009 Elsevier B.V. All rights reserved.
Citation - WoS: 22
Citation - Scopus: 21
Functionalizing graphene by embedded boron clusters
(Iop Publishing Ltd, 2008) Quandt, Alexander; Özdoğan, Cem; Ozdogan, Cem; Kunstmann, Jens; Fehske, Holger; 40569; Ortak Dersler Bölümü
We present a model system that might serve as a blueprint for the controlled layout of graphene based nanodevices. The systems consists of chains of B-7 clusters implanted in a graphene matrix, where the boron clusters are not directly connected. We show that the graphene matrix easily accepts these alternating B-7-C-6 chains and that the implanted boron components may dramatically modify the electronic properties of graphene based nanomaterials. This suggests a functionalization of graphene nanomaterials, where the semiconducting properties might be supplemented by parts of the graphene matrix itself, but the basic wiring will be provided by alternating chains of implanted boron clusters that connect these areas.
Citation - WoS: 31
Citation - Scopus: 30
Ionization energies, Coulomb explosion, fragmentation, geometric, and electronic structures of multicharged boron clusters B-n (n=2-13)
(Amer Physical Soc, 2011) Akman, Nurten; Özdoğan, Cem; Tas, Murat; Ozdogan, Cem; Boustani, Ihsan; 27617; Ortak Dersler Bölümü
Based on the ab initio quantum chemical methods, we have determined fragmentation channels, ionization energies, and the Coulomb explosion of multicharged boron clusters B-n (n = 2-13), where n is the cluster size. The electron-deficient boron clusters sustain more stability and hardly fragment when they are negatively charged. Stability of boron clusters decreases with increasing ionization. Only by the first ionization the odd-size clusters are more stable than the even-size clusters. Further ionizations cause the repulsive Coulomb force between the constituent atoms to get stronger, and lead first to metastable states, then to the Coulomb explosion of clusters. None of the cationic boron clusters studied remain stable after six times ionization. The critical charge for metastability is estimated as Q(m) <= n/2 for even-size clusters, and Q(m) <= 1/2 (n - 1) for odd-size clusters. In addition, the critical charge for the Coulomb explosion is found to be Q(c) = n/2 + 1 for even-size clusters, and Q(c) = 1/2(n + 1) for odd-size clusters. Relative stability of clusters with respect to their nearest neighbors is determined from the analysis of their second energy difference data. Several dissociation channels of B-n(+) and B-13(Q) isomers with the lowest fragmentation energies are presented. All of the vibrational frequencies are found positive indicating that no transition state is possible for the clusters studied. Reliability of our data is verified with a good agreement with experimental results.
Citation - WoS: 8
Citation - Scopus: 8
Localization 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 Bölümü
As 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.
Citation - WoS: 6
Citation - Scopus: 15
Parallel WaveCluster: A linear scaling parallel clustering algorithm implementation with application to very large datasets
(Academic Press inc Elsevier Science, 2011) Yildirim, Ahmet Artu; Özdoğan, Cem; Ozdogan, Cem; Ortak Dersler Bölümü
A linear scaling parallel clustering algorithm implementation and its application to very large datasets for cluster analysis is reported. WaveCluster is a novel clustering approach based on wavelet transforms. Despite this approach has an ability to detect clusters of arbitrary shapes in an efficient way, it requires considerable amount of time to collect results for large sizes of multi-dimensional datasets. We propose the parallel implementation of the WaveCluster algorithm based on the message passing model for a distributed-memory multiprocessor system. In the proposed method, communication among processors and memory requirements are kept at minimum to achieve high efficiency. We have conducted the experiments on a dense dataset and a sparse dataset to measure the algorithm behavior appropriately. Our results obtained from performed experiments demonstrate that developed parallel WaveCluster algorithm exposes high speedup and scales linearly with the increasing number of processors. (C) 2011 Elsevier Inc. All rights reserved.
Citation - WoS: 5
Citation - Scopus: 12
Parallel wavelet-based clustering algorithm on GPUs using CUDA
(Elsevier Science Bv, 2011) Yildirim, Ahmet Artu; Özdoğan, Cem; Ozdogan, Cem; Ortak Dersler Bölümü
There 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.
Citation - WoS: 203
Citation - Scopus: 212
Stability 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 Bölümü
We 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.
Citation - WoS: 0
Citation - Scopus: 1
Surface modification by 1 keV ion impact: molecular dynamics study of an Ar+-Ni(100) collision system
(Iop Publishing Ltd, 2008) Ozdogan, Cem; Özdoğan, Cem; Atis, Murat; Guvenc, Ziya B.; 28225; Ortak Dersler Bölümü
An Ar+-Ni(1 0 0) collision system at 1 keV impact energy was investigated by using realistic isoenergetic molecular dynamics (MD) simulations. The sputtering process upon Ar+ ion impact and damage to the Ni(1 0 0) surface are examined in detail. Studying of high bombarding energy regions leads to the necessity of larger and thick enough slabs, otherwise incoming ions can easily pass through the slab; as a result, investigated physical properties may not be revealed. In addition the simulation time should be long enough to observe and to calculate a reliable macroscopic property such as sputtering yield that is addressed in this study. In order to preserve the total energy in the simulation at this collision energy a small time-step (0.1 fs) is used. We have made use of our developed linear scaling parallel MD program to overcome these demands. The Ni(1 0 0) slab is formed by 63700 atoms (122 angstrom x 122 angstrom x 44 angstrom) and the total observation time for each collision event is about 2.25 ps. Several properties such as penetration depths, angular and energy distributions of the reflected Ar and sputtered Ni atoms as well as dissociation time, embedded, scattering, sputtering patterns and geometries of the sputtered clusters are also reported, and the calculated sputtering yield is found to be in good agreement with the available experimental results.
Citation - WoS: 0
Citation - Scopus: 0
Synthesis, 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 Bölümü
The 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.