WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12416/8653
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Article Citation - WoS: 1Citation - Scopus: 1Determination of Chemisorption Probabilities of Hydrogen Molecules on a Nickel Surface by Artificial Neural Network(Croatian Chemical Soc, 2008) Güvenç, Ziya Burhanettin; Boeyuekata, Mustafa; Kocyigit, Yuecel; Guevenc, Ziya B.; Böyükata, Mustafa; Bilgisayar MühendisliğiDissociative chemisorption probabilities for H-2(v, j) + Ni(100) collision systems have been estimated by using Artificial Neural Network (ANN). For training, previously determined probability values via molecular dynamics simulations have been used. Performance of the ANN, for predicting any quantities in the molecule-surface interaction, has been investigated. Effects of the surface sites and the rovibrational states of the molecule on the process are analyzed. The results are in good agreement with the related previous studies.Article Citation - WoS: 1Citation - Scopus: 1Structures 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 MühendisliğiUsing 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.Article Citation - WoS: 13Citation - Scopus: 15O(N) Parallel Tight Binding Molecular Dynamics Simulation of Carbon Nanotubes(Elsevier, 2002) Özdogan, C; Dereli, G; Çagin, TWe report an O(N) parallel tight binding molecular dynamics simulation study of (10 x 10) structured carbon nanotubes (CNT) at 300 K. We converted a sequential O(N-3) TBMD simulation program into an O(N) parallel code, utilizing the concept of parallel virtual machines (PVM). The code is tested in a distributed memory system consisting of a cluster with 8 PC's that run under Linux (Slackware 2.2.13 kernel). Our results on the speed up, efficiency and system size are given. (C) 2002 Elsevier Science B.V. All rights reserved.Article Citation - WoS: 4Citation - Scopus: 4The Molecular Dynamics Study of Atomic Structure Behavior of Ll-37 Peptide as the Antimicrobial Agent, Derived From the Human Cathelicidin, Inside a Nano Domain Filled by the Aqueous Environment(Elsevier, 2022) Liu, Xinglong; Othman, Ahmad Razi; Abu-Hamdeh, Nidal H.; Abusorrah, Abdullah M.; Karimipour, Arash; Li, Zhixiong; Baleanu, Dumitru; H. Abu-Hamdeh, Nidal; Razi Othman, AhmadThe LL-37 peptide is an antimicrobial agent derived from human cathelicidin. In addition to their antimicrobial properties, these peptides can activate the immune system through various mechanisms and contribute to autoimmune diseases. In the current study, we describe the atomic behavior of this protein in an aqueous environment inside of metallic nanochannel (Fe nanochannel). For this purpose, Molecular Dynamics (MD) approach was implemented in equilibrium conditions. A Large Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used in this computational study. Computationally, the various atoms interaction described by Universal Force Field (UFF), TIP4P, and Embedded Atom Model (EAM). Furthermore, physical factors like potential energy, temperature, Radial Distribution Function (RDF), density/velocity/temperature profiles, and protein volume were calculated for atomic behavior description of the LL-37 protein-water system. MD outputs indicated the atomic stability of protein structure in an aqueous environment inside metallic nanochannels. Numerically, the LL-37 protein volume changes from 3906.81 angstrom(3) to 3900.11 angstrom(3) value after t= 10 ns. Also, the maximum density and velocity/temperature profiles reach 0.0225 atoms/angstrom(3) and 0.0124 angstrom/fs/435.22 K (respectively), values detected in the initial/final and middle bins MD box. (C) 2021 Elsevier B.V. All rights reserved.Article Citation - WoS: 4Citation - Scopus: 4Phase Changes in Icosahedral 54-, 55-, 56-Atom Platinum Clusters(World Scientific Publ Co Pte Ltd, 2004) Güvenç, ZB; Kökten, H; Sebetci, AUsing the Voter and Chen version of an embedded-atom model, derived by fitting simultaneously to experimental data both the diatomic molecule and bulk platinum, we have studied the melting behavior of free, icosahedral, 54-, 55- and 56-atom platinum clusters in the molecular dynamics simulation technique. We present an atom-resolved analysis method that includes physical quantities such as the root-mean-square bond-length fluctuation and coordination number for individual atoms as functions of temperature. The effect of a central atom in the icosahedral structure to the melting process is discussed. The results show that the global minimum structures of the 54-, 55- and 56-atom Pt clusters do not melt at a specific temperature, rather, melting processes take place over a finite temperature range. The heat capacity peaks are not delta-functions, but instead remain finite. An ensemble of clusters in the melting region is a mixture of solid-like and liquid-like clusters.Conference Object Citation - WoS: 3Citation - Scopus: 5Reactivity of the Nin(T) (N=54,55,56) Clusters With D2(V,j) Molecule: Molecular Dynamics Simulations(Elsevier Science Bv, 2004) Özçelik, S; Güvenç, ZB; Durmus, P; Jellinek, JThe reactive channel of the D(2) (v, j) + Ni(n) (T) (n = 54, 55, 56) collision system is studied via quasiclassical molecular dynamics simulations. The cluster is described using an embedded-atom potential, and the interaction between the molecule and the cluster is modeled by a LEPS (London-Eyring-Polanyi-Sato) potential energy function. Dissociative chemisorption probabilities are computed as functions of the impact parameter and the collision energy, and are used to evaluate the reaction cross-sections. Effects of the initial rovibrational states of the molecule and the temperatures of the clusters on the reactive channel are analyzed. Reaction rate constants are also computed and compared with those measured experimentally. (C) 2004 Elsevier B.V. All rights reserved.Article Citation - WoS: 7Citation - Scopus: 7Structure and Dynamical Properties of Aun, N=12-14 Clusters: Molecular Dynamics Simulation(World Scientific Publ Co Pte Ltd, 2005) Yildirim, EK; Atis, M; Güvenç, ZBUsing molecular dynamics and thermal quenching methods on the basis of Voter-Chen version of the embedded-atom method, we have studied the melting behavior of Au-N (N = 12, 13, 14) clusters. This behavior is described in terms of overall and atom resolved root-mean-square bond-length fluctuations, specific-heat, short- and long-time average coordination numbers of each atom and short-time average temperatures of the clusters. The isomer sampling probabilities are obtained from the thermal quenching of the molten clusters, and their energy-spectrum widths are investigated. Phase change of a cluster takes place with the collective and simultaneous motion of all the atoms.Article Citation - WoS: 7Citation - Scopus: 8Molecule-Surface Interaction: Dissociative Chemisorption of a D2 (V=0, J=0) Molecule on Rigid Low Index Ni Surfaces(Elsevier Science Bv, 2004) Böyükata, M; Güvenç, ZBD(2) + Ni-surface collision system has been studied by a quasiclassical molecular dynamic simulation method. Dissociative adsorption of a D(2) molecule on rigid Ni(1 0 0), Ni(1 1 0) and Ni(1 1 1) surfaces are investigated. Interactions between the molecule and Ni surfaces were described by a LEPS potential. The contour plots of the LEPS function is presented as functions of the distances between the center of mass of the D(2) and surface, and between the two deuterium atoms (D-D) for topologically different sites of the surfaces. Dissociative chemisorption probabilities of the D(2) (nu = 0, j = 0) molecule on various sites of the surfaces are presented for different translation energies between 0.001 and 1.0 eV. The probabilities obtained at each collision site have unique behavior. At low collision energies indirect processes enhance the reactivity. The results are compared with the available studies. The physical mechanisms underlying the results are discussed. (C) 2004 Elsevier B.V. All rights reserved.Article Citation - WoS: 6Citation - Scopus: 7Bombardment of Ni(100) Surface With Low-Energy Argons: Molecular Dynamics Simulations(Elsevier Science Sa, 2005) Güvenç, ZB; Hippler, R; Jackson, BResults of molecular dynamics simulations of the sputtering of Ni(100) by Ar atoms are reported. The solid is described by an embedded atom potential, and the interaction between the projectile and the metal atoms is modelled by a Morse-like function. Processes leading to Ni atom emissions from the lattice are analysed over the energy range of 70-80 eV In this energy range cluster (larger than three atoms) emission is not observed. The maximum penetration depth of Ar, the kinetic energy and angular distributions of the reflected Ar, and the sputtered Ni atoms are evaluated as functions of the impact energy and sputtering time. The computed sputtering yield is compared with the available theoretical and experimental data. (C) 2004 Elsevier B.V. All rights reserved.Conference Object Citation - WoS: 14Citation - Scopus: 13Structures and Energetics of Pd21-Pd55 Clusters(Elsevier Science Bv, 2003) Karabacak, M; Özçelik, S; Güvenç, ZBUsing molecular dynamics and thermal quenching simulations the stable geometrical structures and energies of Pd-n (n = 21-55) clusters are identified. The interaction between the cluster atoms is modeled by an embedded-atom (EA) potential energy surface, Voter and Chen's version. The stable geometrical structures and their minimum energies are obtained from 500 phase space coordinates generated along high-energy trajectories. The internal energies (about T = 2500 K) are above the melting temperature of the Pd-n 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. Stability of the clusters is examined by the first and the second energy differences. The average bond lengths are obtained and analyzed as a function of the size of the clusters. (C) 2003 Elsevier Science B.V. All rights reserved.