Molecular Simulation, Volume 43, Issue 13-16 (2017)

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Molecular Simulation, Volume 43, Issue 13-16 (2017)

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Proceedings of the 4th International Conference on Molecular Simulation

Editorial

Editorial
4th International Conference on Molecular Simulation 2016
Huai Sun
Pages: 969-970
Published online: 09 Aug 2017
Citationfor4th International Conference on Molecular Simulation 2016 | Full Text | PDF (557.2 KB)
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Articles

Article
Combined use of periodic reaction field and coarse-grained molecular dynamics simulations. I. phospholipid monolayer systems
Kazuaki Z. Takahashi
Pages: 971-976
Published online: 09 Mar 2017
AbstractforCombined use of periodic reaction field and coarse-grained molecular dynamics simulations. I. phospholipid monolayer systems | Full Text | References | PDF (760.6 KB)
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Article
Free-energy landscapes of the coupled conformational transition and inclusion processes of altro-cyclodextrins
Tanfeng Zhao, Xueguang Shao & Wensheng Cai
Pages: 977-984
Published online: 09 Mar 2017
AbstractforFree-energy landscapes of the coupled conformational transition and inclusion processes of altro-cyclodextrins | Full Text | References | PDF (3.5 MB) | Supplemental
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Article
Removal of arsenic ions using hexagonal boron nitride and graphene nanosheets: a molecular dynamics study
R. Srivastava, A. Kommu, N. Sinha & J. K. Singh
Pages: 985-996
Published online: 30 May 2017
AbstractforRemoval of arsenic ions using hexagonal boron nitride and graphene nanosheets: a molecular dynamics study | Full Text | References | PDF (2 MB)
  • 536 Views
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Article
A theoretical study on the optical absorption of green fluorescent protein chromophore in solutions
Ken Kajita, Hiroshi Nakano & Hirofumi Sato
Pages: 997-1003
Published online: 12 Jun 2017
AbstractforA theoretical study on the optical absorption of green fluorescent protein chromophore in solutions | Full Text | References | PDF (929.4 KB)
  • 141 Views
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Article
Molecular insight into the micro-behaviors of CH4 and CO2 in montmorillonite slit-nanopores
Haoyang Sun, Hui Zhao, Na Qi, Xiaoqing Qi, Kai Zhang & Ying Li
Pages: 1004-1011
Published online: 06 Jun 2017
AbstractforMolecular insight into the micro-behaviors of CH4 and CO2 in montmorillonite slit-nanopores | Full Text | References | PDF (2.2 MB)
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Article
A theoretical study of isocyanic acid with hydrogen radical (HNCO + OH) catalysed by Aux (x = 0, 1, 3) cluster: dynamic characterisation
Hongxia Liu, Zizhong Liu & Yanhong Zhang
Pages: 1012-1018
Published online: 18 Jun 2017
AbstractforA theoretical study of isocyanic acid with hydrogen radical (HNCO + OH) catalysed by Aux (x = 0, 1, 3) cluster: dynamic characterisation | Full Text | References | PDF (2.8 MB)
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Article
Some insights into the self-assembly patterns of two diamine derivatives as low molecular mass organogelators from molecular dynamics
Bing Zhang, Kaixuan Zhou, Shufan Mo, Lilin Zhu, Zhoucheng Su, Jianxi Yao & Songyuan Dai
Pages: 1019-1025
Published online: 27 Jul 2017
AbstractforSome insights into the self-assembly patterns of two diamine derivatives as low molecular mass organogelators from molecular dynamics | Full Text | References | PDF (3.4 MB)
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Article
Predicting the activity of hydroxamic acid analogues
Qingzhu Jia, Ying Liu, Fangyou Yan, Qiang Wang & Peisheng Ma
Pages: 1026-1033
Published online: 17 Jul 2017
AbstractforPredicting the activity of hydroxamic acid analogues | Full Text | References | PDF (1.7 MB) | Supplemental
  • 73 Views
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Article
Biogas upgrading using single-walled carbon nanotubes by molecular simulation
Tingting Yang, Linghong Lu, Shanshan Wang, Wei Cao & Xiaohua Lu
Pages: 1034-1044
Published online: 21 Jun 2017
AbstractforBiogas upgrading using single-walled carbon nanotubes by molecular simulation | Full Text | References | PDF (2.1 MB)
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Article
A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM σπ molecular dynamics simulations
Chao Zhang, Dong-Xia Zhao, Qian Wang, Ling Yu, Guo-Hui Li & Zhong-Zhi Yang
Pages: 1045-1055
Published online: 12 Jul 2017
AbstractforA salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM σπ molecular dynamics simulations | Full Text | References | PDF (1.6 MB) | Supplemental
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Article
Role of chemical short-range order in atomic dynamics decoupling
C. H. Li, Y. W. Luan, X. J. Han & J. G. Li
Pages: 1056-1060
Published online: 22 Jun 2017
AbstractforRole of chemical short-range order in atomic dynamics decoupling | Full Text | References | PDF (981.6 KB) | Supplemental
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Article
Evolution of bubbles in decomposition and replacement process of methane hydrate
Yinan Liu, Li Zhao, Shuai Deng & Dongsheng Bai
Pages: 1061-1073
Published online: 03 Aug 2017
AbstractforEvolution of bubbles in decomposition and replacement process of methane hydrate | Full Text | References | PDF (6.1 MB) | Supplemental
  • 650 Views
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Article
Investigation of molecular dissolution mechanism of ketoprofen binary and ternary solid dispersions by molecular dynamics simulations
Weijie Chen & Defang Ouyang
Pages: 1074-1080
Published online: 30 May 2017
AbstractforInvestigation of molecular dissolution mechanism of ketoprofen binary and ternary solid dispersions by molecular dynamics simulations | Full Text | References | PDF (1.9 MB)
  • 308 Views
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Article
Investigation of model scale effects on coal pyrolysis using ReaxFF MD simulation
Mo Zheng, Xiaoxia Li, Fengguang Nie & Li Guo
Pages: 1081-1088
Published online: 26 Jul 2017
AbstractforInvestigation of model scale effects on coal pyrolysis using ReaxFF MD simulation | Full Text | References | PDF (4.1 MB) | Supplemental
  • 532 Views
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Article
Comparison of computational model and X-ray crystal structure of human serotonin transporter: potential application for the pharmacology of human monoamine transporters
Fengyuan Yang, Tingting Fu, Xiaoyu Zhang, Jie Hu, Weiwei Xue, Guoxun Zheng, Bo Li, Yinghong Li, Xiaojun Yao & Feng Zhu
Pages: 1089-1098
Published online: 16 May 2017
AbstractforComparison of computational model and X-ray crystal structure of human serotonin transporter: potential application for the pharmacology of human monoamine transporters | Full Text | References | PDF (5.5 MB)
  • 447 Views
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Article
Study on properties of liquid ammonia via molecular dynamics simulation based on ABEEMσπ polarisable force field
Lan-Lan He, Shi-Yuan Zhang, Ting-Ting Sun, Chong-Li Zhao, Chao Zhang, Zhong-Zhi Yang & Dong-Xia Zhao
Pages: 1099-1106
Published online: 30 May 2017
AbstractforStudy on properties of liquid ammonia via molecular dynamics simulation based on ABEEMσπ polarisable force field | Full Text | References | PDF (1.5 MB) | Supplemental
  • 299 Views
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Article
Study of the molecular array behaviours and interfacial activities of green surfactant alkyl polyglycoside and the mixed systems with other surfactants on oil–water interface
Hui Zhao, Yanyun Bai, Haoyang Sun & Ying Li
Pages: 1107-1115
Published online: 13 Jun 2017
AbstractforStudy of the molecular array behaviours and interfacial activities of green surfactant alkyl polyglycoside and the mixed systems with other surfactants on oil–water interface | Full Text | References | PDF (1.6 MB) | Supplemental
  • 516 Views
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Article
Plastic deformation behaviours of CuZr amorphous/crystalline nanolaminate: a molecular dynamics study
Y. W. Luan, C. H. Li, X. J. Han & J. G. Li
Pages: 1116-1124
Published online: 09 Jun 2017
AbstractforPlastic deformation behaviours of CuZr amorphous/crystalline nanolaminate: a molecular dynamics study | Full Text | References | PDF (3.7 MB)
  • 315 Views
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Article
Monte Carlo simulations of vapour–liquid phase equilibrium and microstructure for the system containing azeotropes
Hong Li, Ji Zhang, Dongyang Li, Xingang Li & Xin Gao
Pages: 1125-1133
Published online: 12 Jun 2017
AbstractforMonte Carlo simulations of vapour–liquid phase equilibrium and microstructure for the system containing azeotropes | Full Text | References | PDF (995.5 KB)
  • 195 Views
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Article
Ab initio molecular metadynamics simulation for S-nitrosylation by nitric oxide: S-nitroxide as the key intermediate
Chao Zhou, Juan Liang, Shangli Cheng, Ting Shi, K. N. Houk, Dong-Qing Wei & Yi-Lei Zhao
Pages: 1134-1141
Published online: 19 May 2017
AbstractforAb initio molecular metadynamics simulation for S-nitrosylation by nitric oxide: S-nitroxide as the key intermediate | Full Text | References | PDF (1.4 MB)
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Article
Biomethane storage in activated carbons: a grand canonical Monte Carlo simulation study
Shanshan Wang, Linghong Lu, Di Wu & Xiaohua Lu
Pages: 1142-1152
Published online: 27 Jul 2017
AbstractforBiomethane storage in activated carbons: a grand canonical Monte Carlo simulation study | Full Text | References | PDF (3.1 MB)
  • 185 Views
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Article
Self-assembly of surfactant aqueous solution confined in a Janus amphiphilic nanotube
Yusei Kobayashi & Noriyoshi Arai
Pages: 1153-1159
Published online: 26 May 2017
AbstractforSelf-assembly of surfactant aqueous solution confined in a Janus amphiphilic nanotube | Full Text | References | PDF (1.6 MB)
  • 145 Views
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Article
Self-aggregation of trehalose in the mixed solvents of 1,3-dimethylimidazolium ionic liquid and water
Zigui Kan, Dong Zheng & Jing Ma
Pages: 1160-1171
Published online: 31 May 2017
AbstractforSelf-aggregation of trehalose in the mixed solvents of 1,3-dimethylimidazolium ionic liquid and water | Full Text | References | PDF (5.7 MB) | Supplemental
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Article
Interaction between lattice dislocations and low-angle grain boundaries in Ni via molecular dynamics simulations
Yun Gao & Zhaohui Jin
Pages: 1172-1178
Published online: 26 Jul 2017
AbstractforInteraction between lattice dislocations and low-angle grain boundaries in Ni via molecular dynamics simulations | Full Text | References | PDF (3.3 MB)
  • 430 Views
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Article
Two sterols, two bilayers: insights on membrane structure from molecular dynamics
Viviana Monje-Galvan & Jeffery B. Klauda
Pages: 1179-1188
Published online: 19 Jul 2017
AbstractforTwo sterols, two bilayers: insights on membrane structure from molecular dynamics | Full Text | References | PDF (1.5 MB) | Supplemental
  • 214 Views
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Article
Carbon nanotube prevents the secondary structure formation of amyloid-β trimers: an all-atom molecular dynamics study
Menghua Song, Yanyan Zhu, Guanghong Wei & Huiyu Li
Pages: 1189-1195
Published online: 23 May 2017
AbstractforCarbon nanotube prevents the secondary structure formation of amyloid-β trimers: an all-atom molecular dynamics study | Full Text | References | PDF (2.7 MB) | Supplemental
  • 141 Views
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Article
Critical test of bead–spring model to resolve the scaling laws of polymer melts: a molecular dynamics study
Kazuaki Z. Takahashi, Nobuyoshi Yamato, Kenji Yasuoka & Yuichi Masubuchi
Pages: 1196-1201
Published online: 12 Jun 2017
AbstractforCritical test of bead–spring model to resolve the scaling laws of polymer melts: a molecular dynamics study | Full Text | References | PDF (1.2 MB)
  • 197 Views
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Article
Wetting control through topography and surface hydrophilic/hydrophobic property changes by coarse grained simulation
Zhongyang Dai, Linghong Lu, Yunhao Sun, Ziqian Tang & Xiaohua Lu
Pages: 1202-1208
Published online: 21 Jun 2017
AbstractforWetting control through topography and surface hydrophilic/hydrophobic property changes by coarse grained simulation | Full Text | References | PDF (1.4 MB)
  • 404 Views
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Article
A QM/MM study on the correlation between the polarisations of and electrons in a hydrated benzene
Daiki Suzuoka, Hideaki Takahashi & Akihiro Morita
Pages: 1209-1217
Published online: 18 Jul 2017
AbstractforA QM/MM study on the correlation between the polarisations of and electrons in a hydrated benzene | Full Text | References | PDF (1.2 MB)
  • 65 Views
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Article
Liquid-crystal ordering mediated by self-assembly of surfactant solution confined in nanodroplet: a dissipative particle dynamics study
Takuya Inokuchi & Noriyoshi Arai
Pages: 1218-1226
Published online: 03 Aug 2017
AbstractforLiquid-crystal ordering mediated by self-assembly of surfactant solution confined in nanodroplet: a dissipative particle dynamics study | Full Text | References | PDF (1.7 MB)
  • 209 Views
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Article
Molecular dynamics simulation of the nanofibrils formed by amyloid-based peptide amphiphiles
Rongliang Wu, Jun Liu, Xinlong Qiu & Manli Deng
Pages: 1227-1239
Published online: 01 Jun 2017
AbstractforMolecular dynamics simulation of the nanofibrils formed by amyloid-based peptide amphiphiles | Full Text | References | PDF (3.5 MB)
  • 153 Views
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Article
Theoretical guidance and experimental confirmation on catalytic tendency of M-CeO2 (M = Zr, Mn, Ru or Cu) for NH3-SCR of NO
Phornphimon Maitarad, Jin Han, Supawadee Namuangruk, Liyi Shi, Chirawat Chitpakdee, Jittima Meeprasert, Anchalee Junkaew, Nawee Kungwan & Dengsong Zhang
Pages: 1240-1246
Published online: 15 Jun 2017
AbstractforTheoretical guidance and experimental confirmation on catalytic tendency of M-CeO2 (M = Zr, Mn, Ru or Cu) for NH3-SCR of NO | Full Text | References | PDF (2.1 MB) | Supplemental
  • 597 Views
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Article
Structural ordering of lipid bilayers induced by surfactant molecules with small hydrophilic head group
Yoshimichi Andoh, Siti Nor Syafawani Mohamed, Sakiho Kitou & Susumu Okazaki
Pages: 1247-1255
Published online: 24 May 2017
AbstractforStructural ordering of lipid bilayers induced by surfactant molecules with small hydrophilic head group | Full Text | References | PDF (1.4 MB) | Supplemental
  • 114 Views
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Article
The switch of the binding behaviours between Xe and π system induced by the change of oxidation state of Cu ion
Junjian Miao & Yi Gao
Pages: 1256-1259
Published online: 15 Jun 2017
AbstractforThe switch of the binding behaviours between Xe and π system induced by the change of oxidation state of Cu ion | Full Text | References | PDF (564.5 KB) | Supplemental
  • 54 Views
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Article
Classical cumulant dynamics for statistical chemical physics
Yasuteru Shigeta, Ryuhei Harada, Ryuma Sato, Hirotaka Kitoh-Nishioka, Thi Kieu My Bui, Akimasa Sato, Takaki Tokiwa, Akane Kyan, Yuki Ishii, Masato Kimatsuka, Sotaro Yamasaki, Megumi Kayanuma & Mitsuo Shoji
Pages: 1260-1268
Published online: 26 May 2017
AbstractforClassical cumulant dynamics for statistical chemical physics | Full Text | References | PDF (1.3 MB)
  • 105 Views
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Article
Quantum chemical molecular dynamics simulation of carbon nanotube–graphene fusion
Hu-Jun Qian, Gyula Eres & Stephan Irle
Pages: 1269-1276
Published online: 01 Jun 2017
AbstractforQuantum chemical molecular dynamics simulation of carbon nanotube–graphene fusion | Full Text | References | PDF (3.2 MB)
  • 163 Views
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Article
Prediction of chemical biodegradability using computational methods
Zhixiong Zhan, Linlang Li, Sheng Tian, Xuechu Zhen & Youyong Li
Pages: 1277-1290
Published online: 12 Jun 2017
AbstractforPrediction of chemical biodegradability using computational methods | Full Text | References | PDF (6.2 MB) | Supplemental
  • 415 Views
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Article
On computational efficiency of the hybrid Monte Carlo method applied to the multicanonical ensemble
Tsugumichi Tagawa, Toshihiro Kaneko & Shinichi Miura
Pages: 1291-1294
Published online: 28 Jun 2017
AbstractforOn computational efficiency of the hybrid Monte Carlo method applied to the multicanonical ensemble | Full Text | References | PDF (614.4 KB)
  • 92 Views
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Article
Surface structure of ionic liquids under an external electric field
Rui Shi & Yanting Wang
Pages: 1295-1299
Published online: 12 Jun 2017
AbstractforSurface structure of ionic liquids under an external electric field | Full Text | References | PDF (992.9 KB)
  • 356 Views
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Article
pH-mediated gating and formate transport mechanism in the Escherichia coli formate channel
Siladitya Padhi, Lekkala Karthik Reddy & U. Deva Priyakumar
Pages: 1300-1306
Published online: 18 Jul 2017
AbstractforpH-mediated gating and formate transport mechanism in the Escherichia coli formate channel | Full Text | References | PDF (2.4 MB)
  • 111 Views
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Article
Finite element analysis of the Poisson–Boltzmann equation coupled with chemical equilibriums: redistribution and transport of protons in nanophase separated polymeric acid–base proton exchange membranes
Xuejiao Li, Liuming Yan & Baohua Yue
Pages: 1307-1314
Published online: 16 Jun 2017
AbstractforFinite element analysis of the Poisson–Boltzmann equation coupled with chemical equilibriums: redistribution and transport of protons in nanophase separated polymeric acid–base proton exchange membranes | Full Text | References | PDF (1.4 MB) | Supplemental
  • 140 Views
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Article
How one-dimensional diffusion of transcription factors are affected by obstacles: coarse-grained molecular dynamics study
Mami Saito, Tsuyoshi Terakawa & Shoji Takada
Pages: 1315-1321
Published online: 12 Jun 2017
AbstractforHow one-dimensional diffusion of transcription factors are affected by obstacles: coarse-grained molecular dynamics study | Full Text | References | PDF (1.4 MB)
  • 153 Views
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Article
Solvent-responsiveness of PS–PEO binary mixed polymer brushes: a coarse-grained molecular dynamics study
Li Wang, Tianping Zhong, Xuebo Quan & Jian Zhou
Pages: 1322-1330
Published online: 16 Jul 2017
AbstractforSolvent-responsiveness of PS–PEO binary mixed polymer brushes: a coarse-grained molecular dynamics study | Full Text | References | PDF (3 MB)
  • 337 Views
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Article
Molecular dynamics study of the aggregation rate for zwitterionic dodecyldimethylamine oxide and cationic dodecyltrimethylammonium chloride micelles
Kazushi Fujimoto, Yousuke Kubo, Shinji Kawada, Noriyuki Yoshii & Susumu Okazaki
Pages: 1331-1337
Published online: 25 Jun 2017
AbstractforMolecular dynamics study of the aggregation rate for zwitterionic dodecyldimethylamine oxide and cationic dodecyltrimethylammonium chloride micelles | Full Text | References | PDF (1.5 MB)
  • 147 Views
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Article
Theoretical study on the topotactic transformation and memory effect of M (II) M (III)-layered double hydroxides
Qingting Meng & Hong Yan
Pages: 1338-1347
Published online: 22 Aug 2017
AbstractforTheoretical study on the topotactic transformation and memory effect of M (II) M (III)-layered double hydroxides | Full Text | References | PDF (2.4 MB) | Supplemental
  • 381 Views
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Article
A multi-scale computational study on the mechanism of protonation of isobutene and 2-butene over HY zeolite
Kui Ren, Jun Long, Qiang Ren, Yongxiang Li & Zhenyu Dai
Pages: 1348-1355
Published online: 25 Jul 2017
AbstractforA multi-scale computational study on the mechanism of protonation of isobutene and 2-butene over HY zeolite | Full Text | References | PDF (1.4 MB)
  • 171 Views
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Article
Structural dynamics and binding free energy of neral-cyclodextrins inclusion complexes: molecular dynamics simulation
Peerapong Wongpituk, Bodee Nutho, Wanwisa Panman, Nawee Kungwan, Peter Wolschann, Thanyada Rungrotmongkol & Nadtanet Nunthaboot
Pages: 1356-1363
Published online: 26 Jul 2017
AbstractforStructural dynamics and binding free energy of neral-cyclodextrins inclusion complexes: molecular dynamics simulation | Full Text | References | PDF (1.5 MB)
  • 536 Views
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Article
Elevation/depression mechanism of freezing points of liquid confined in slit nanopores
Toshihiro Kaneko
Pages: 1364-1369
Published online: 16 Jul 2017
AbstractforElevation/depression mechanism of freezing points of liquid confined in slit nanopores | Full Text | References | PDF (1.4 MB)
  • 179 Views
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Article
Two major stable structures of amyloid-forming peptides: amorphous aggregates and amyloid fibrils
Naohiro Nishikawa, Yoshitake Sakae, Takuya Gouda, Yuichiro Tsujimura & Yuko Okamoto
Pages: 1370-1376
Published online: 22 Aug 2017
AbstractforTwo major stable structures of amyloid-forming peptides: amorphous aggregates and amyloid fibrils | Full Text | References | PDF (1,019.7 KB)
  • 164 Views
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Article
Effect of water molecules on nanoscale wetting behaviour of molecular ethanol on hydroxylated SiO2 substrate
Xuechuan Nie, Jige Chen, Nan Sheng, Li Zeng, Haijun Yang & Chunlei Wang
Pages: 1377-1384
Published online: 18 Jul 2017
AbstractforEffect of water molecules on nanoscale wetting behaviour of molecular ethanol on hydroxylated SiO2 substrate | Full Text | References | PDF (2 MB) | Supplemental
  • 325 Views
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Article
The mechanism for the complexation and dissociation between siRNA and PMAL: a molecular dynamics simulation study based on a coarse-grained model
Yanfei Lu, Jipeng Li & Diannan Lu
Pages: 1385-1393
Published online: 13 Jul 2017
AbstractforThe mechanism for the complexation and dissociation between siRNA and PMAL: a molecular dynamics simulation study based on a coarse-grained model | Full Text | References | PDF (3.4 MB) | Supplemental
  • 229 Views
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Article
Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF
Chamila C. Dharmawardhana, Krishan Kanhaiya, Tzu-Jen Lin, Amanda Garley, Marc R. Knecht, Jihan Zhou, Jianwei Miao & Hendrik Heinz
Pages: 1394-1405
Published online: 19 Jun 2017
AbstractforReliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF | Full Text | References | PDF (2.8 MB)
  • 716 Views
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Article
Comparative study of 3D-RISM theory and molecular dynamics calculations for the free-energy landscape of a hydrated dipeptide
Hiroshi Iwasaki, Satoshi Yamaguchi & Shinichi Miura
Pages: 1406-1411
Published online: 28 Jun 2017
AbstractforComparative study of 3D-RISM theory and molecular dynamics calculations for the free-energy landscape of a hydrated dipeptide | Full Text | References | PDF (1.2 MB)
  • 171 Views
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