Karel Svadlenka

Rinovia Simanjuntak

Shinichi Miura

Veinardi Suendo

Miura Shinichi

三浦 伸一

Kanazawa University Repository for Academic Resources

RECENT DEVELOPMENT IN COMPUTATIONAL SCIENCEVolume 4Selected Papers from the International Symposium on Computational ScienceInternational Symposium on Computational Science Kanazawa University, JapanFebruary 2013Editors  Veinardi Suendo  Karel Svadlenka  Rinovia Simanjuntak  Shinichi Miura  RECENT DEVELOPMENT  IN COMPUTATIONAL SCIENCE  Volume 4  Selected Papers  from International Symposium on Computational Science   International Symposium on Computational Science Kanazawa University, Japan February 2013     Editors  Veinardi Suendo  Karel Svadlenka  Rinovia Simanjuntak  Shinichi Miura International Symposium on Computational Science 2013 18-21 February 2013, Kanazawa University, Japan  ISCS 2013 Organizing Committee l Kanazawa University (Japan)   T. Ito, S. Omata, H. Nagao, T. Oda, M. Saito, K. Svadlenka, S. Miura, H. Iwasaki,   H. Saito, K. Kawaguchi, F. Ishii, Mayu Winnie Rachmawati l Bandung Institute of Technology (Indonesia)   Muhamad A. Martoprawiro, Daryono Hadi Tjahjono, Acep Purqon, Suprijadi l Gadjah Mada University (Indonesia)   Harno Dwi Pranowo  International Advisory Board E. T. Baskoro, M. A. Martoprawiro, S. Miura, H. Nagao, S. Omata, M. Saito, Suprijadi, K. Svadlenka  _____________________________________________________   Volume Editors l Veinardi Suendo Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Indonesia l Karel Svadlenka Institute of Science and Engineering, Kanazawa University, Japan l Rinovia Simanjuntak Faculty of Mathematics and Natural Sciences, Bandung Institute of Technology, Indonesia l Shinichi Miura Institute of Science and Engineering, Kanazawa University, Japan  ISSN 2223-0785  Published by Kanazawa e-Publishing Co., Ltd © Organizing Committee of ISCS 2013 Printed in Japan Typesetting: Camera-ready by author. Printed on acid-free paper.  i CONTENTS  Agra Barecasco, Hanifa Terissa and Christian Fredy Naa    Simple Free-surface Detection in Two and Three-dimensional SPH Solver 1   Ahmad Rio Adriansyah    On the Farthest Subconstituent of the q-Johnson Graph Jq(n, k) 11   Cometta S. Guritno and Shinichi Miura    Structural Fluctuation of a Protonated Water Cluster 17   Ely Aprilia, Acep Purqon and Suprijadi  The Geometrical Effects of Substitutional Impurities on Electric and Magnetic Properties of (10,0) Carbon Nanotube by using Density Functional Theory 23   Hanifa Terissa, Agra Barecasco and Christian Fredy Naa  Three-dimensional Smoothed Particle Hydrodynamics Simulation for Liquid Droplet with Surface Tension 29   Indra Gunawan, Masao Obata, Makoto Nakamura, Muhamad A. Martoprawiro and  Tatsuki Oda    Implementation of Parallel Matrix Diagonalization for Ab-Initio Molecular Dynamics    Program using ScaLAPACK 39   Isman Kurniawan, Hiroaki Saito, Kazutomo Kawaguchi and Hidemi Nagao    Computational Study of Oxidation Potential Fluctuation of Ketone Molecule 45   Marhamni Syaputra and Mineo Saito    First-Principle Density-Functional-Theory Calculation of Water Molecule    on Graphene Defects 53   Masashi Iwayama, Kazutomo Kawaguchi, Hiroaki Saito and Hidemi Nagao    Structure and Hydration Free Energy of Ketone Compound in Neutral and Cationic State    by Molecular Dynamics Simulation 59        ii  Meidy Triana Pakpahan, Hiroaki Saito, Kazutomo Kawaguchi, and Hidemi Nagao    Binding Free Energy of Protein-Ligand by Combining Docking and MD Simulation:    A Comparison of Calculation Methods 71   Micke Rusmerryani, Masako Takasu, Kazutomo Kawaguchi, Hiroaki Saito, and  Hidemi Nagao    Coarse-grained Simulation of Azurin Crystal Complex System:    Protein-protein Interactions 79   Muhamad Koyimatu, Hideto Shimahara, Kazutomo Kawaguchi, Hirosaki Saito,  Kimikazu Sugimori, and Hidemi Nagao    Theoretical Study of a π-stacking Interaction in Carbonic Anhydrase 87   Nurul Ikhsan, Yuusaku Taguchi, Masao Obata, Makoto Nakamura, Suprijadi, and Tatsuki Oda    Magnetic, Structural, and Electronic Properties of Co doped Fe/MgO Interface:    Density Functional Approach 95   Raden Ahnaf Faqih S. and Christian Fredy Naa    Three-dimensional Smoothed Particle Hydrodynamics Simulation for Liquid Metal    Solidification Process 105   Rhudaina Z. Mohammad    Multiphase Mean Curvature Flow: Signed Distance Vector Approach 115   Rizal Dwi Prayogo and Christian Fredy Naa    Three-dimensional Smoothed Particle Hydrodynamics Method for Simulating Free    Surface Flows 125   Robbi Nur Rakhman    Stability Change of Periodic Orbits and the Phase Space Structure of Buckled Beam and    Hénon-Heiles System 135         iii Sasfan Arman Wella, Makoto Nakamura, Masao Obata, Suprijadi, and Tatsuki Oda    Tight-Binding Molecular Dynamics with Fermi Operator Expansion: Application to     Vacancy Defects in Silicon 145   Suprijadi, F. Faizal, C.F. Naa and A. Trisnawan  3D Simulation of Dam-break Effect on a Solid Wall using Smoothed Particle Hydrodynamics 155   Program of “International Symposium on Computational Science 2013” ⅴ List of Participants ⅻ  

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