Scopus İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12416/8651
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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: 3Citation - Scopus: 2Molecular Dynamics of Thermal Vibration Effects: Ar + Ni(100) Collision System(Elsevier Science Bv, 2010) Hundur, Yakup; Guvenc, Ziya B.; Hippler, RainerIn 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.