Molecular Simulation, Volume 41, Issue 10-12 (2015)

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Molecular Simulation, Volume 41, Issue 10-12 (2015)

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Proceedings of the 3rd International Conference on Molecular Simulation

Editorial

Editorial
Editorial: ICMS2013
Yuko Okamoto
Page: 779
Published online: 15 Jun 2015
CitationforEditorial: ICMS2013 | Full Text | PDF (124.7 KB)
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Proceedings of the 3rd International Conference on Molecular Simulation

Article
Learning chemistry with multiple first-principles simulations
Giovanni La Penna, Christelle Hureau & Peter Faller
Pages: 780-787
Published online: 07 Jul 2014
AbstractforLearning chemistry with multiple first-principles simulations | Full Text | References | PDF (166.6 KB)
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Article
Structure, dynamics and hydrogen bonding of acetonitrile in nanoscale silica pores
Ward H. Thompson
Pages: 788-794
Published online: 07 Jul 2014
AbstractforStructure, dynamics and hydrogen bonding of acetonitrile in nanoscale silica pores | Full Text | References | PDF (564.9 KB)
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Article
A determination of liquid–vapour interfacial properties for methanol using a linear-combination-based isotropic periodic sum
Kazuaki Z. Takahashi & Kenji Yasuoka
Pages: 795-800
Published online: 03 Jul 2014
AbstractforA determination of liquid–vapour interfacial properties for methanol using a linear-combination-based isotropic periodic sum | Full Text | References | PDF (359.5 KB)
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Article
An efficiently extendable and fine-grain parallelised molecular dynamics simulation program: Mid
Takahiro Koishi & Hironori Takeichi
Pages: 801-807
Published online: 03 Jul 2014
AbstractforAn efficiently extendable and fine-grain parallelised molecular dynamics simulation program: Mid | Full Text | References | PDF (275.4 KB)
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Article
Analytical expressions on harmonic oscillators for variational path integrals
Yuki Kamibayashi & Shinichi Miura
Pages: 808-812
Published online: 05 Aug 2014
AbstractforAnalytical expressions on harmonic oscillators for variational path integrals | Full Text | References | PDF (204.3 KB)
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Article
Vibrational spectra of deuterated methane and water molecules in structure I clathrate hydrate from ab initio MD simulation
Masaki Hiratsuka, Ryo Ohmura, Amadeu K. Sum & Kenji Yasuoka
Pages: 813-817
Published online: 08 Jul 2014
AbstractforVibrational spectra of deuterated methane and water molecules in structure I clathrate hydrate from ab initio MD simulation | Full Text | References | PDF (230.6 KB)
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Article
Density of states estimation for soft core system
Hisashi Shimizu
Pages: 818-821
Published online: 08 Jul 2014
AbstractforDensity of states estimation for soft core system | Full Text | References | PDF (242.1 KB)
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Article
The observation of the longitudinal wave velocity in a model supercooled liquid
T. Muranaka, J. Matsui & Y. Hiwatari
Pages: 822-826
Published online: 28 Jul 2014
AbstractforThe observation of the longitudinal wave velocity in a model supercooled liquid | Full Text | References | PDF (254.8 KB)
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Article
Quasi-boundary based on exchange symmetry theory for multilevel simulations
Motoyuki Shiga & Marco Masia
Pages: 827-831
Published online: 01 Aug 2014
AbstractforQuasi-boundary based on exchange symmetry theory for multilevel simulations | Full Text | References | PDF (236.5 KB)
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Article
Quantum simulation for muoniated and deuterated methyl radicals in implicit water solvent: combined ab initio path integral molecular dynamics and the polarizable continuum model simulation study
Kenta Yamada, Yukio Kawashima & Masanori Tachikawa
Pages: 832-839
Published online: 14 Aug 2014
AbstractforQuantum simulation for muoniated and deuterated methyl radicals in implicit water solvent: combined ab initio path integral molecular dynamics and the polarizable continuum model simulation study | Full Text | References | PDF (406.5 KB)
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Article
Velocity auto-correlation function of ions and water molecules in different concentrations, anions and ion clusters
Katsufumi Tomobe, Eiji Yamamoto, Dusan Kojic, Masato Yasui & Kenji Yasuoka
Pages: 840-844
Published online: 16 Sep 2014
AbstractforVelocity auto-correlation function of ions and water molecules in different concentrations, anions and ion clusters | Full Text | References | PDF (357.4 KB)
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Article
Molecular dynamics simulation of self-assembled nanocubes in methanol
Takako Mashiko, Kenta Yamada, Shuichi Hiraoka, Umpei Nagashima & Masanori Tachikawa
Pages: 845-849
Published online: 12 Aug 2014
AbstractforMolecular dynamics simulation of self-assembled nanocubes in methanol | Full Text | References | PDF (2.1 MB)
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Article
Free energy surface for rotamers of cis-enol malonaldehyde in aqueous solution studied by molecular dynamics calculations
Hidekazu Kojima, Atsushi Yamada & Susumu Okazaki
Pages: 850-856
Published online: 16 Sep 2014
AbstractforFree energy surface for rotamers of cis-enol malonaldehyde in aqueous solution studied by molecular dynamics calculations | Full Text | References | PDF (290.5 KB)
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Article
Influencing the direct formation of ‘Janus’ particles in molecular dynamics simulations
Jan-Hubert Wittmann & Reinhard Strey
Pages: 857-860
Published online: 01 Oct 2014
AbstractforInfluencing the direct formation of ‘Janus’ particles in molecular dynamics simulations | Full Text | References | PDF (284.2 KB)
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Article
The isotope effects on a hydrogen transfer using path integral instanton method
Tsutomu Kawatsu & Shinichi Miura
Pages: 861-867
Published online: 16 Sep 2014
AbstractforThe isotope effects on a hydrogen transfer using path integral instanton method | Full Text | References | PDF (352.7 KB)
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Article
Structure, dynamics and thermodynamic stability of high-pressure ices and clathrate hydrates
Takuma Yagasaki, Kazuhiro Himoto, Tatsuya Nakamura, Masakazu Matsumoto & Hideki Tanaka
Pages: 868-873
Published online: 17 Sep 2014
AbstractforStructure, dynamics and thermodynamic stability of high-pressure ices and clathrate hydrates | Full Text | References | PDF (540.5 KB)
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Article
GPU-accelerated replica exchange molecular simulation on solid–liquid phase transition study of Lennard-Jones fluids
Kentaro Nomura, Minoru Oikawa, Atsushi Kawai, Tetsu Narumi & Kenji Yasuoka
Pages: 874-880
Published online: 17 Sep 2014
AbstractforGPU-accelerated replica exchange molecular simulation on solid–liquid phase transition study of Lennard-Jones fluids | Full Text | References | PDF (347.8 KB)
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Article
A molecular level study of selective cation capture by a host–guest mechanism for 25,26,27,28-tetramethoxycalix[4]arene in MClO4 solution (M = Na, K)
Kentaro Kido, Kento Kasahara, Hirofumi Sato & Shigeyoshi Sakaki
Pages: 881-891
Published online: 07 Jul 2014
AbstractforA molecular level study of selective cation capture by a host–guest mechanism for 25,26,27,28-tetramethoxycalix[4]arene in MClO4 solution (M = Na, K) | Full Text | References | PDF (2 MB)
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Article
First-principles study of surface states in topological insulators Bi2Te3 and Bi2Se3: film thickness dependence
Takehiro Kato, Hiroki Kotaka & Fumiyuki Ishii
Pages: 892-895
Published online: 09 Oct 2014
AbstractforFirst-principles study of surface states in topological insulators Bi2Te3 and Bi2Se3: film thickness dependence | Full Text | References | PDF (448.1 KB)
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Article
Nanoscale droplet vaporisation by molecular dynamics
Donguk Suh & Kenji Yasuoka
Pages: 896-904
Published online: 20 Oct 2014
AbstractforNanoscale droplet vaporisation by molecular dynamics | Full Text | References | PDF (885.5 KB)
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Article
Molecular dynamics simulation of the melting processes of core–shell and pure nanoparticles
Yuki Tamura & Noriyoshi Arai
Pages: 905-912
Published online: 31 Oct 2014
AbstractforMolecular dynamics simulation of the melting processes of core–shell and pure nanoparticles | Full Text | References | PDF (825.1 KB)
  • 411 Views
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Article
Molecular simulation study of structure and dynamical properties of nitrate anion in sodium chloride aqueous solution
Shigeki Matsunaga
Pages: 913-917
Published online: 06 Nov 2014
AbstractforMolecular simulation study of structure and dynamical properties of nitrate anion in sodium chloride aqueous solution | Full Text | References | PDF (676.1 KB)
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Article
Analysis of crystal growth of methane hydrate using molecular dynamics simulation
Daisuke Yuhara, Masaki Hiratsuka, Daisuke Takaiwa & Kenji Yasuoka
Pages: 918-922
Published online: 02 Dec 2014
AbstractforAnalysis of crystal growth of methane hydrate using molecular dynamics simulation | Full Text | References | PDF (732.1 KB)
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Article
First-principles study of Rashba effect in the (LaAlO3)2/(SrTiO3)2
Miho Nishida, Fumiyuki Ishii, Hiroki Kotaka & Mineo Saito
Pages: 923-926
Published online: 13 Dec 2014
AbstractforFirst-principles study of Rashba effect in the (LaAlO3)2/(SrTiO3)2 | Full Text | References | PDF (351.7 KB)
  • 164 Views
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Article
Application of isotropic periodic sum method for 4-pentyl-4′-cyanobiphenyl liquid crystal
Takuma Nozawa, Kazuaki Z. Takahashi, Shun Kameoka, Tetsu Narumi & Kenji Yasuoka
Pages: 927-935
Published online: 22 Jan 2015
AbstractforApplication of isotropic periodic sum method for 4-pentyl-4′-cyanobiphenyl liquid crystal | Full Text | References | PDF (1.7 MB)
  • 142 Views
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Article
A hybrid-type approach with MD and DFT calculations for evaluation of redox potential of molecules
Masashi Iwayama, Isman Kurniawan, Kazutomo Kawaguchi, Hiroaki Saito & Hidemi Nagao
Pages: 936-941
Published online: 05 Mar 2015
AbstractforA hybrid-type approach with MD and DFT calculations for evaluation of redox potential of molecules | Full Text | References | PDF (159.5 KB)
  • 236 Views
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Article
Tribology of polymer brush: microscale modelling and simulation
Mitsuho Ide & Mitsuhiro Matsumoto
Pages: 942-947
Published online: 01 Aug 2014
AbstractforTribology of polymer brush: microscale modelling and simulation | Full Text | References | PDF (686 KB)
  • 211 Views
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Article
Molecular dynamics simulations of palmitoyloleoylphosphatidylglycerol bilayers
Hojin Kang & Jeffery B. Klauda
Pages: 948-954
Published online: 07 Jul 2014
AbstractforMolecular dynamics simulations of palmitoyloleoylphosphatidylglycerol bilayers | Full Text | References | PDF (426.4 KB)
  • 283 Views
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Article
Molecular dynamics study of changes in physico-chemical properties of DMPC lipid bilayers by addition of nonionic surfactant C12E10
Yoshimichi Andoh, Shun Muraoka & Susumu Okazaki
Pages: 955-960
Published online: 07 Jul 2014
AbstractforMolecular dynamics study of changes in physico-chemical properties of DMPC lipid bilayers by addition of nonionic surfactant C12E10 | Full Text | References | PDF (374.6 KB)
  • 87 Views
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Article
Spontaneous self-assembly of diblock copolymers in nanoconfined geometries by dissipative particle dynamics
Koji Takahashi & Takahiro Koishi
Pages: 961-967
Published online: 07 Jul 2014
AbstractforSpontaneous self-assembly of diblock copolymers in nanoconfined geometries by dissipative particle dynamics | Full Text | References | PDF (340.9 KB)
  • 137 Views
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Article
Simulation studies of microstructure of colloids in sedimentation
Adnan Hamid, John Jairo Molina & Ryoichi Yamamoto
Pages: 968-973
Published online: 08 Jul 2014
AbstractforSimulation studies of microstructure of colloids in sedimentation | Full Text | References | PDF (508.9 KB)
  • 144 Views
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Article
Diffusion mechanism of CO2 in a crystalline polymer membrane studied using model gases
Shunsuke Asahi & Yoshinori Tamai
Pages: 974-979
Published online: 08 Jul 2014
AbstractforDiffusion mechanism of CO2 in a crystalline polymer membrane studied using model gases | Full Text | References | PDF (229.6 KB)
  • 170 Views
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Article
Diffusion of cations in salt solutions between ice walls
Yuta Nohara & Yoshimichi Hagiwara
Pages: 980-985
Published online: 08 Jul 2014
AbstractforDiffusion of cations in salt solutions between ice walls | Full Text | References | PDF (499.3 KB)
  • 139 Views
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Article
Molecular dynamics simulation for shape change of water-in-oil droplets
Naohito Urakami, Akio Takaki, Masayuki Imai & Takashi Yamamoto
Pages: 986-992
Published online: 09 Jul 2014
AbstractforMolecular dynamics simulation for shape change of water-in-oil droplets | Full Text | References | PDF (525.4 KB)
  • 380 Views
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Article
Monte Carlo simulations of structure and entanglements in polymer melts
Krzysztof Moorthi, Kazunori Kamio, Javier Ramos & Doros N. Theodorou
Pages: 993-995
Published online: 28 Jul 2014
AbstractforMonte Carlo simulations of structure and entanglements in polymer melts | Full Text | References | PDF (141 KB)
  • 276 Views
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Article
Structural analysis of telechelic polymer solution using dissipative particle dynamics simulations
Noriyoshi Arai
Pages: 996-1001
Published online: 15 Sep 2014
AbstractforStructural analysis of telechelic polymer solution using dissipative particle dynamics simulations | Full Text | References | PDF (522.1 KB)
  • 222 Views
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Article
Multiscale simulation for thermo-hydrodynamic lubrication of a polymeric liquid between parallel plates
Shugo Yasuda & Ryoichi Yamamoto
Pages: 1002-1005
Published online: 22 Sep 2014
AbstractforMultiscale simulation for thermo-hydrodynamic lubrication of a polymeric liquid between parallel plates | Full Text | References | PDF (169.5 KB)
  • 161 Views
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Article
Exposure of thiol groups in the heat-induced denaturation of β-lactoglobulin
Rosanne N.W. Zeiler & Peter G. Bolhuis
Pages: 1006-1014
Published online: 07 Jul 2014
AbstractforExposure of thiol groups in the heat-induced denaturation of β-lactoglobulin | Full Text | References | PDF (1.1 MB)
  • 323 Views
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Article
A 3D-RISM integral equation study of a hydrated dipeptide
Hiroshi Iwasaki, Shinnosuke Gyoubu, Tsutomu Kawatsu & Shinichi Miura
Pages: 1015-1020
Published online: 14 Aug 2014
AbstractforA 3D-RISM integral equation study of a hydrated dipeptide | Full Text | References | PDF (266.5 KB)
  • 79 Views
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Article
Replica-permutation method to enhance sampling efficiency
Satoru G. Itoh & Hisashi Okumura
Pages: 1021-1026
Published online: 04 Jul 2014
AbstractforReplica-permutation method to enhance sampling efficiency | Full Text | References | PDF (320 KB)
  • 78 Views
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Article
Effects of initial settings on computational protein–ligand docking accuracies for several docking programs
Akifumi Oda, Noriyuki Yamaotsu, Shuichi Hirono, Yurie Watanabe, Shuichi Fukuyoshi & Ohgi Takahashi
Pages: 1027-1034
Published online: 27 May 2014
AbstractforEffects of initial settings on computational protein–ligand docking accuracies for several docking programs | Full Text | References | PDF (270.6 KB)
  • 159 Views
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Article
Molecular dynamics simulation study on the high-pressure behaviour of an AK16 peptide
Yoshiharu Mori & Hisashi Okumura
Pages: 1035-1040
Published online: 12 Aug 2014
AbstractforMolecular dynamics simulation study on the high-pressure behaviour of an AK16 peptide | Full Text | References | PDF (333.1 KB)
  • 169 Views
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Article
Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation
Naohiro Nishikawa, Phuong H. Nguyen, Philippe Derreumaux & Yuko Okamoto
Pages: 1041-1044
Published online: 15 Sep 2014
AbstractforReplica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation | Full Text | References | PDF (295.2 KB)
  • 249 Views
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Article
Conformational search simulations of Trp-cage using genetic crossover
Yoshitake Sakae, Tomoyuki Hiroyasu, Mitsunori Miki, Katsuya Ishii & Yuko Okamoto
Pages: 1045-1049
Published online: 19 May 2015
AbstractforConformational search simulations of Trp-cage using genetic crossover | Full Text | References | PDF (265.3 KB)
  • 92 Views
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