Browsing by Author "Guvenc, Ziya B."

Now showing 1 - 15 of 15

Citation - WoS: 45
Citation - Scopus: 47
Density Functional Study of Albn Clusters for N=1-14
(Elsevier Science Sa, 2011) Boyukata, Mustafa; Guvenc, Ziya B.; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
Density functional theory (DFT) B3LYP at 6-311++G(d,p) level is employed to optimize the structures of AlBn (n = 1-14) microclusters. Analysis of the energetic and structural stability of these clusters and their various isomers are presented. Total and binding energies of the clusters have been calculated. Their harmonic frequencies, point symmetries, and the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) energy gaps have been determined. Results are evaluated by comparing to the previous similar works. (C) 2011 Elsevier B.V. All rights reserved.
Citation - WoS: 30
Density Functional Study of Physical and Chemical Properties of Nano Size Boron Clusters: Bn (n=13-20)
(Chinese Physical Soc, 2009) Ozdogan, Cem; Guvenc, Ziya B.; Atis, Murat; 28225; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi; 09. Rektörlük; 09.01. 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: 13
Dft Study of Al Doped Cage B12hn Clusters
(Pergamon-elsevier Science Ltd, 2011) Boyukata, Mustafa; Guvenc, Ziya B.; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
Density Functional Theory (DFT) with B3LYP/6-311++g** level has been performed to investigate the electronic structures of cage B12Hn for up to n <= 12 and AlB12Hn for up to n <= 13. Moreover, the computations has been extended to the charged clusters of [B12H12](q), [AlB12H12](q) and [AlB12H13](q) where (q = +/- 1 and +/- 2). Their energetics are calculated and structural analysis have been carried out. Cage form of the B-12 remains stable against to hydrogen adsorptions. Copyright (C) 2011, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.
Citation - WoS: 2
Citation - Scopus: 3
Dynamical Analysis of Sputtering at Threshold Energy Range: Modelling of Ar+ni(100) Collision System
(Iop Publishing Ltd, 2008) Hundur, Yakup; Guvenc, Ziya B.; Hippler, Rainer; 29853; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
The sputtering process of Ar+Ni(100) collision systems is investigated by means of constant energy molecular dynamics simulations. The Ni(100) slab is mimicked by an embedded-atom potential, and the interaction between the projectile and the surface is modelled by using the reparametrized ZBL potential. Ni atom emission from the lattice is analysed over the range of 20-50 eV collision energy. Sputtering yield, angular and energy distributions of the scattered Ar and of the sputtered Ni atoms are calculated, and compared to the available theoretical and experimental data.
Citation - WoS: 2
Citation - Scopus: 4
Estimation of Cross Sections for Molecule-Cluster Interactions by Using Artificial Neural Networks
(Springer, 2006) Boyukata, Mustafa; Kocyigit, Yucel; Guvenc, Ziya B.; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
The cross sections Of D-2 (v,j) + Ni-n (T), n = 19 and 20, collision systems have been estimated by using Artificial Neural Networks (ANNs). For training, previously determined cross section values via molecular dynamics simulation have been used. The performance of the ANNs for predicting any quantities in molecule-cluster interaction has been investigated. Effects of the temperature of the clusters and the rovibrational states of the molecule are analyzed. The results are in good agreement with previous studies.
Citation - WoS: 11
Citation - Scopus: 10
H(D) → D(H)+cu Collision System: Molecular Dynamics Study of Surface Temperature Effects
(Amer inst Physics, 2011) Vurdu, Can D.; Guvenc, Ziya B.; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
All the channels of the reaction dynamics of gas-phase H (or D) atoms with D (or H) atoms adsorbed onto a Cu(111) surface have been studied by quasiclassical constant energy molecular dynamics simulations. The surface is flexible and is prepared at different temperature values, such as 30 K, 94 K, and 160 K. The adsorbates were distributed randomly on the surface to create 0.18 ML, 0.28 ML, and 0.50 ML of coverages. The multi-layer slab is mimicked by a many-body embedded-atom potential energy function. The slab atoms can move according to the exerted external forces. Treating the slab atoms non-rigid has an important effect on the dynamics of the projectile atom and adsorbates. Significant energy transfer from the projectile atom to the surface lattice atoms takes place especially during the first impact that modifies significantly the details of the dynamics of the collisions. Effects of the different temperatures of the slab are investigated in this study. Interaction between the surface atoms and the adsorbates is modeled by a modified London-Eyring-Polanyi-Sato (LEPS) function. The LEPS parameters are determined by using the total energy values which were calculated by a density functional theory and a generalized gradient approximation for an exchange-correlation energy for many different orientations, and locations of one-and two-hydrogen atoms on the Cu(111) surface. The rms value of the fitting procedure is about 0.16 eV. Many different channels of the processes on the surface have been examined, such as inelastic reflection of the incident hydrogen, subsurface penetration of the incident projectile and adsorbates, sticking of the incident atom on the surface. In addition, hot-atom and Eley-Rideal direct processes are investigated. The hot-atom process is found to be more significant than the Eley-Rideal process. Furthermore, the rate of subsurface penetration is larger than the sticking rate on the surface. In addition, these results are compared and analyzed as a function of the surface temperatures. (c) 2011 American Institute of Physics. [doi:10.1063/1.3583811]
Citation - WoS: 2
Hybrid Single Walled Carbon Nanotube Fets for High Fidelity Dna Detection
(Springer-verlag Berlin, 2010) Wang, Xu; Ozkan, Mihri; Budak, Gurer; Guvenc, Ziya B.; Ozkan, Cengiz S.; 06.01. Bilgisayar Mühendisliği; 06.07. Malzeme Bilimi ve Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
A novel application for detecting specific biomolecules using SWNT-ssDNA nanohybrid is described. SWNT-ssDNA hybrid is formed by conjugating amino-ended single strand of DNA (ssDNA) with carboxylic group modified SWNTs through a straightforward EDC coupling reaction. ssDNA functionalized SWNT hybrids could be used as high fidelity sensors for biomolecules. The sensing capability is demonstrated by the change in the electronic properties of SWNT. Employing DNA functionalized SWNT FETs could lead to dramatically increased sensitivity in biochemical sensing and medical diagnostics applications.
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) Ozdogan, Cem; Guvenc, Ziya B.; Boyukata, Mustafa; 120207; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi; 09. Rektörlük; 09.01. 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: 11
Citation - Scopus: 10
Md Study of Energetics, Melting and Isomerization of Aluminum Microclusters
(Springer, 2006) Boyukata, Mustafa; Guvenc, Ziya B.; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
Voter and Chen version of an Embedded Atom Model has been applied to study the locally stable structures, energies, melting, isomerization and growth patterns of small aluminum clusters, Al(n), in the size range of n = 2 - 13. Using molecular dynamics and thermal quenching simulations, the global minima and the other locally stable structures have been distinguished from those stationary structures that correspond to saddle points of the potential energy surface. A large number (10000) of independent initial configurations generated at high temperatures has been used to obtain the stable isomers, and the probabilities of sampling different basins of attractions, for each size of the clusters. Their energy spectra have been determined and melting, and isomerization dynamics are investigated.
Citation - WoS: 3
Citation - Scopus: 2
Molecular Dynamics of Thermal Vibration Effects: Ar + Ni(100) Collision System
(Elsevier Science Bv, 2010) Hundur, Yakup; Guvenc, Ziya B.; Hippler, Rainer; 29853; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
In this work constant energy molecular dynamics simulations are achieved for investigating sputtering process of Ar + Ni(1 0 0) collision system. The Ni crystal is imitated by an embedded-atom potential, whereas the interaction between the projectile and the surface is modeled by re-parameterized ZBL potential. Seven hundred eighty-four Ar atoms carrying 20-50 eV are sent towards a Ni(1 0 0) surface at normal incidence. Each projectile meets with different initial coordinates (phase) of the nickel atoms because of thermal vibrations in the slab. Effects of the different initial phases of the surface are compared with the available theoretical and experimental data. (C) 2009 Elsevier B.V. All rights reserved.
Citation - WoS: 7
Citation - Scopus: 7
Retracted: a Simple Analytical Eam Model for Some Bcc Metals (Retracted Article. See Vol. 16, Pg. 4547, 2011)
(Elsevier, 2010) Dursun, Ibrahim H.; Guvenc, Ziya B.; Kasap, E.; 47800; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
An analytical embedded atom method which can treat bcc transition metal iron has been developed. In this model, a new potential was presented and a modified term has been introduced to fit the negative Cauchy pressure P-C = (C-12 - C-44)/2 for Fe element. The new model was applied to calculate thermodynamic properties of binary alloys of the bcc transition metals: Fe, V and Cr. The calculated dilute-solution enthalpies and formation enthalpies of random alloys are in good agreement with the results of first principles calculations and that of the thermodynamic calculations. (C) 2009 Elsevier B.V. All rights reserved.
A Simple Analytical Eam Model for Some Bcc Metals (Retraction of Vol 15, Pg 1259, 2010)
(Elsevier Science Bv, 2011) Dursun, Ibrahim H.; Guvenc, Ziya B.; Kasap, E.; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
Citation - WoS: 1
Citation - Scopus: 1
Structures and Energetics of Cu21-Cu71 Clusters: a Molecular Dynamics Study
(Gazi Univ, 2009) Güvenç, Ziya Burhanettin; Cetin, Saime Sebnem; Ozcelik, Suleyman; Guvenc, Ziya B.; Bilgisayar Mühendisliği; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi
Using Molecular Dynamics and thermal quenching simulations the stable geometrical structures and energies of Cun (n=21-71) clusters are identified. The interaction between the cluster atoms is modeled by an EmbeddedAtom Potential Surface, Voter and Chen's version. The stable geometrical structures and energies are obtained from 500 phase space coordinates generated along high-energy trajectories. The internal energy (about T=2500 K) is above the melting temperature of the Cun clusters. The thermal quenching technique is employed to remove slowly the internal kinetic energy of the clusters. Because of this slow minimization process the locally stable isomers are separated from those meta-stable ones.
Citation - Scopus: 1
Surface Modification by 1 Kev Ion Impact: Molecular Dynamics Study of an Ar⁺-ni(100) Collision System
(Iop Publishing Ltd, 2008) Atis, Murat; Guvenc, Ziya B.; Ozdogan, Cem; 28225; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi; 09. Rektörlük; 09.01. 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.
Synthesis, Molecular Structure and Dft Study of 2-(n Benzoate
(Springer/plenum Publishers, 2011) Kazak, Canan; Ozdogan, Cem; Guvenc, Ziya B.; Buyukgungor, Orhan; Arslan, Figen; Odabasoglu, Mustafa; Yuksektepe, Cigdem; 42359; 22620; 4292; 49272; 13249; 06.01. Bilgisayar Mühendisliği; 06. Mühendislik Fakültesi; 01. Çankaya Üniversitesi; 09. Rektörlük; 09.01. 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.