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.Conference Object Citation - WoS: 12Citation - Scopus: 11Md Study of Energetics, Melting and Isomerization of Aluminum Microclusters(Springer, 2006) Boyukata, Mustafa; Guvenc, Ziya B.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.Conference Object Citation - WoS: 2Citation - Scopus: 4Estimation of Cross Sections for Molecule-Cluster Interactions by Using Artificial Neural Networks(Springer, 2006) Boyukata, Mustafa; Kocyigit, Yucel; Guvenc, Ziya B.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.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.Article Citation - WoS: 58Citation - Scopus: 66Molecular Dynamics Simulation of Sintering and Surface Premelting of Silver Nanoparticles(Japan inst Metals & Materials, 2013) Ozdogan, C.; Hu, A.; Yavuz, M.; Zhou, Y.; Atis, M.; Alarifi, H. A.Sintering of Ag nanoparticles (NPs) is increasingly being used as a driving mechanism for joining in the microelectronics industry. We therefore performed molecular dynamics simulations based on the embedded atom method (EAM) to study pressureless sintering kinetics of two Ag NPs in the size range of (4 to 20 nm), and sintering of three and four Ag NPs of 4 nm diameter. We found that the sintering process passed through three main stages. The first was the neck formation followed by a rapid increase of the neck radius at 50K for 20 nm particles and at 10 K for smaller NPs. The second was characterized by a gradual linear increase of the neck radius to particle radius ratio as the temperature of the sintered structure was increased to the surface premelting point. Different than previous sintering studies, a twin boundary was formed during the second stage that relaxed the sintered structure and decreased the average potential energy (PE). The third stage of sintering was a rapid shrinkage during surface premelting of the sintered structure. Based on pore geometry, densification occurred during the first stage for three 4 nm particles and during the second stage for four 4 nm particles. Sintering rates obtained by our simulation were higher than those obtained by theoretical models generally used for predicting sintering rates of microparticles.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.
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