Mitsubishi Chemical Corporation

1998.4 - 2000.3

Japan Society for the Promotion of Science   Research fellow (DC1)

1995.4 - 1998.3

THE SOCIETY OF POLYMER SCIENCE, JAPAN

JAPAN SOCIETY FOR MOLECULAR SCIENCE

溶液化学研究会

NMR and molecular simulation studies on the structure elucidation of the amphotericin B ion channel using 13C and 19F labelling Invited Reviewed

Yuichi Umegawa, Hiroshi Tsuchikawa, Wataru Shinoda, Michio Murata

Organic & Biomolecular Chemistry   2025

Fully atomistic molecular dynamics modeling of photoswitchable azo-PC lipid bilayers: structure, mechanical properties, and drug permeation Reviewed

Kevin A. Alberto, M. N. Hasna Begam, Hejian Xiong, Wataru Shinoda, Paul A. Slesinger, Zhenpeng Qin, Steven O. Nielsen

Nanoscale   2025

Linear ether-based highly concentrated electrolytes for Li–sulfur batteries Reviewed

Toru Ishikawa, Shohei Haga, Keisuke Shigenobu, Taku Sudoh, Seiji Tsuzuki, Wataru Shinoda, Kaoru Dokko, Masayoshi Watanabe, Kazuhide Ueno

Faraday Discussions   253   385 - 406   2024.10

Evolving better solvate electrolytes for lithium secondary batteries Reviewed International coauthorship International journal

Frederik Philippi, Maleen Middendorf, Keisuke Shigenobu, Yuna Matsuyama, Oriele Palumbo, David Pugh, Taku Sudoh, Kaoru Dokko, Masayoshi Watanabe, Monika Schönhoff, Wataru Shinoda, Kazuhide Ueno

Chemical Science   15 ( 19 )   7342 - 7358   2024.4

Discrimination of extracellular miRNA sources for the identification of tumor-related functions based on nanowire thermofluidics Reviewed

Kunanon Chattrairat, Akira Yokoi, Min Zhang, Mikiko Iida, Kosuke Yoshida, Masami Kitagawa, Ayuka Niwa, Masatoshi Maeki, Takeshi Hasegawa, Takeshi Yokoyama, Yoshikazu Tanaka, Yusuke Miyazaki, Wataru Shinoda, Manabu Tokeshi, Kazuki Nagashima, Takeshi Yanagida, Hiroaki Kajiyama, Yoshinobu Baba, Takao Yasui

Device   12   100363 - 100363   2024.4

Light-controllable cell-membrane disturbance for intracellular delivery. Reviewed International journal

Wenting Huo, Koji Miki, Huiying Mu, Takashi Osawa, Harumi Yamaguma, Yuuya Kasahara, Satoshi Obika, Yoshimasa Kawaguchi, Hisaaki Hirose, Shiroh Futaki, Yusuke Miyazaki, Wataru Shinoda, Shuji Akai, Kouichi Ohe

Journal of Materials Chemistry. B   12 ( 17 )   4138 - 4147   2024.3

Protein-lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin. Reviewed International journal

Yuichi Umegawa, Sho Kato, Sangjae Seo, Wataru Shinoda, Satoshi Kawatake, Shigeru Matsuoka, Michio Murata

Biophysical chemistry   308   107204 - 107204   2024.2

pSPICA Force Field Extended for Proteins and Peptides Reviewed

Yusuke Miyazaki, Wataru Shinoda

Journal of Chemical Information and Modeling   64 ( 2 )   532 - 542   2024.1

Understanding the effects of ethanol on the liposome bilayer structure using microfluidic-based time-resolved small-angle X-ray scattering and molecular dynamics simulations Reviewed International journal

Masatoshi Maeki, Niko Kimura, Yuto Okada, Kazuki Shimizu, Kana Shibata, Yusuke Miyazaki, Akihiko Ishida, Kento Yonezawa, Nobutaka Shimizu, Wataru Shinoda, Manabu Tokeshi

Nanoscale Advances   6 ( 8 )   2166 - 2176   2024

Molecular Level Origin of Ion Dynamics in Highly Concentrated Electrolytes Invited Reviewed

Keisuke Shigenobu, Seiji Tsuzuki, Frederik Philippi, Taku Sudoh, Yosuke Ugata, Kaoru Dokko, Masayoshi Watanabe, Kazuhide Ueno, Wataru Shinoda

The Journal of Physical Chemistry B   127 ( 48 )   10422 - 10433   2023.12

Improved Protein Model in SPICA Force Field Reviewed

Teppei Yamada, Yusuke Miyazaki, Shogo Harada, Ashutosh Kumar, Stefano Vanni, Wataru Shinoda

Journal of Chemical Theory and Computation   19 ( 23 )   8967 - 8977   2023.11

Pragmatic Coarse-Graining of Proteins: Models and Applications Reviewed

Luís Borges-Araújo, Ilias Patmanidis, Akhil P. Singh, Lucianna H. S. Santos, Adam K. Sieradzan, Stefano Vanni, Cezary Czaplewski, Sergio Pantano, Wataru Shinoda, Luca Monticelli, Adam Liwo, Siewert J. Marrink, Paulo C. T. Souza

Journal of Chemical Theory and Computation   19 ( 20 )   7112 - 7135   2023.10

HER-2-targeted Boron Neutron Capture Therapy with Carborane-integrated Immunoliposomes Prepared via an Exchanging Reaction. Reviewed International journal

Riku Kawasaki, Ayano Oshige, Keita Yamana, Hidetoshi Hirano, Kotaro Nishimura, Yamato Miura, Ryuji Yorioka, Yu Sanada, Kaori Bando, Anri Tabata, Kazuma Yasuhara, Yusuke Miyazaki, Wataru Shinoda, Tomoki Nishimura, Hideki Azuma, Takushi Takata, Yoshinori Sakurai, Hiroki Tanaka, Minoru Suzuki, Takeshi Nagasaki, Atsushi Ikeda

Chemistry (Weinheim an der Bergstrasse, Germany)   29 ( 72 )   e202302486   2023.10

Elucidation of Ion Channel Structure and Mechanism of Action of Amphotericin B, an Antifungal Agent Invited Reviewed

Yuichi UMEGAWA, Wataru SHINODA, Michio MURATA

KAGAKU TO SEIBUTSU   61 ( 9 )   419 - 431   2023.9

Complex Energy Landscapes of Self-Assembled Vesicles Reviewed

Jiabin Luan, Danni Wang, Shaohua Zhang, Yusuke Miyazaki, Wataru Shinoda, Daniela A. Wilson

Journal of the American Chemical Society   145 ( 28 )   15496 - 15506   2023.7

Molecular Dynamics Simulations of High-Concentration Li[TFSA] Sulfone Solution: Effect of Easy Conformation Change of Sulfolane on Fast Diffusion of Li Ion Invited Reviewed

Seiji Tsuzuki, Shuhei Ikeda, Wataru Shinoda, Keisuke Shigenobu, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe

JOURNAL OF PHYSICAL CHEMISTRY B   127 ( 28 )   6333 - 6341   2023.7

Lithium-Ion Dynamics in Sulfolane-Based Highly Concentrated Electrolytes Invited Reviewed

Shuhei Ikeda, Seiji Tsuzuki, Taku Sudoh, Keisuke Shigenobu, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe, Wataru Shinoda

JOURNAL OF PHYSICAL CHEMISTRY C   127 ( 28 )   13837 - 13845   2023.7

Li-Ion Transport and Solution Structure in Sulfolane-Based Localized High-Concentration Electrolytes Invited Reviewed

Taku Sudoh, Shuhei Ikeda, Keisuke Shigenobu, Seiji Tsuzuki, Kaoru Dokko, Masayoshi Watanabe, Wataru Shinoda, Kazuhide Ueno

JOURNAL OF PHYSICAL CHEMISTRY C   127 ( 25 )   12295 - 12303   2023.6

Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy Reviewed

Hiromi Takahashi, Takao Yasui, Masaki Hirano, Keiko Shinjo, Yusuke Miyazaki, Wataru Shinoda, Takeshi Hasegawa, Atsushi Natsume, Yotaro Kitano, Mikiko Ida, Min Zhang, Taisuke Shimada, Piyawan Paisrisarn, Zetao Zhu, Fumiharu Ohka, Kosuke Aoki, Sakon Rahong, Kazuki Nagashima, Takeshi Yanagida, Yoshinobu Baba

Biosensors and Bioelectronics   234   115318 - 115318   2023.4

Fluorescence Turn‐on of Tetraphenylethylene Derivative by Transfer from Cyclodextrin to Liposomes, HeLa Cells, and E. coli Reviewed

Kosuke Masuda, Riku Omokawa, Riku Kawasaki, Yuta Mise, Yousuke Ooyama, Shogo Harada, Wataru Shinoda, Atsushi Ikeda

Chemistry – A European Journal   29 ( 10 )   e202203071   2023.2

Self-Assembly of Glycerol-Amphiphilic Janus Dendrimers Amplifies and Indicates Principles for the Selection of Stereochemistry by Biological Membranes Reviewed

Dapeng Zhang, Qi Xiao, Mehrnoush Rahimzadeh, Matthew Liu, Cesar Rodriguez-Emmenegger, Yusuke Miyazaki, Wataru Shinoda, Virgil Percec

Journal of the American Chemical Society   145 ( 7 )   4311 - 4323   2023.2

Liquid Structures and Ion Dynamics of Ionic Liquids viewed from Intermolecular Interactions Invited Reviewed

Seiji Tsuzuki, Wataru Shinoda

CHEMICAL RECORD   23 ( 8 )   e202200272   2023.2

Liquid Structures and Ion Dynamics of Ionic Liquids viewed from Intermolecular Interactions Invited Reviewed

Seiji Tsuzuki, Wataru Shinoda

THE CHEMICAL RECORD Chem.Rec.2023   e202200272   2023.1

Fluorescence Turn-on of Tetraphenylethylene Derivative by Transfer from Cyclodextrin to Liposomes, HeLa cells, and E. coli Reviewed

Kosuke Masuda, Riku Omokawa, Riku Kawasaki, Yuta Mise, Yousuke Ooyama, Shogo Harada, Wataru Shinoda, Atsushi Ikeda

Chemistry - A European Journal   2022.11

SPICA Force Field for Proteins and Peptides Reviewed

Shuhei Kawamoto, Huihui Liu, Yusuke Miyazaki, Sangjae Seo, Mayank Dixit, Russell DeVane, Christopher MacDermaid, Giacomo Fiorin, Michael L. Klein, Wataru Shinoda

Journal of Chemical Theory and Computation   18 ( 5 )   3204 - 3217   2022.5

Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study. Reviewed International journal

Yusuke Miyazaki, Wataru Shinoda

Biochimica et biophysica acta. Biomembranes   1864 ( 9 )   183955 - 183955   2022.5

Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study Reviewed

Hari O. S. Yadav, An-Tsung Kuo, Shingo Urata, Kosuke Funahashi, Yutaka Imamura, Wataru Shinoda

Physical Chemistry Chemical Physics   24   14805 - 14815   2022.5

Effects of Li ion-solvent interaction on ionic transport and electrochemical properties in highly concentrated cyclic carbonate electrolytes Reviewed

Keisuke Shigenobu, Taku Sudoh, Mayu Tabuchi, Seiji Tsuzuki, Wataru Shinoda, Kaoru Dokko, Masayoshi Watanabe, Kazuhide Ueno

Journal of Non-Crystalline Solids: X   11-12   100071   2021.11

Domain Formation in Charged Polymer Vesicles Reviewed International coauthorship

Kaushik Chakraborty, Prabir Khatua, Wataru Shinoda, Sharon M. Loverde

Macromolecules   54 ( 20 )   9258 - 9267   2021.10

Hemimicelle formation of semi-fluorocarbon chains at air–water interface: coarse-grained molecular dynamics study with an extension of the SPICA force field Reviewed

Hari O. S. Yadav, Shogo Harada, An-Tsung Kuo, Shingo Urata, Wataru Shinoda

Molecular Physics   119 ( 19-20 )   e1910355   2021.10

All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution Reviewed

Kazushi Fujimoto, Youhei Yamaguchi, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, Susumu Okazaki

The Journal of Chemical Physics   155 ( 14 )   145101   2021.10

Analyzing the Role of Surfactants in the Colloidal Stability of Nanoparticles in Oil through Coarse-Grained Molecular Dynamics Simulations Reviewed

Mark Z. Griffiths, Wataru Shinoda

The Journal of Physical Chemistry B   125 ( 23 )   6315 - 6321   2021.6

Chain-End Modification: A Starting Point for Controlling Polymer Crystal Nucleation Reviewed

Kyle Wm. Hall, Simona Percec, Wataru Shinoda, Michael L. Klein

Macromolecules   54 ( 4 )   1599 - 1610   2021.2

Thermodynamic aspect of sulfur, polysulfide anion and lithium polysulfide: plausible reaction path during discharge of lithium–sulfur battery Reviewed

Seiji Tsuzuki, Tomoaki Kaneko, Keitaro Sodeyama, Yasuhiro Umebayashi, Wataru Shinoda, Shiro Seki, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe

Physical Chemistry Chemical Physics   23 ( 11 )   6832 - 6840   2021

GLASS MICROFLUIDIC PLATFORM FOR NANOWIRE-ASSISTED URINARY CELL-FREE DNA ISOLATION

Hiromi Takahashi, Takao Yasui, Keiko Shinjo, Yusuke Miyazaki, Wataru Shinoda, Takeshi Hasegawa, Yotaro Kitano, Yoshinobu Baba

MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences   1401 - 1402   2021

Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement Reviewed

Tetsuro Nagai, Shuhei Tsurumaki, Ryo Urano, Kazushi Fujimoto, Wataru Shinoda, Susumu Okazaki

Journal of Chemical Theory and Computation   16 ( 12 )   7239 - 7254   2020.12

Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure Reviewed

Valeria Zoni, Wataru Shinoda, Stefano Vanni

Proceedings of the National Academy of Sciences   118 ( 10 )   e2017205118   2020.10

Conformation and Orientation of Branched Acyl Chains Responsible for the Physical Stability of Diphytanoylphosphatidylcholine Reviewed International journal

Hiroshi Tsuchikawa, Takuya Ono, Masaki Yamagami, Yuichi Umegawa, Wataru Shinoda, Michio Murata

Biochemistry   59 ( 40 )   3929 - 3938   2020.10

Effect of the Packing Density on the Surface Hydrophobicity of ω-Functionalized (−CF3, −CH3, −OCH3, and −OH) Self-Assembled Monolayers: A Molecular Dynamics Study Reviewed

Hari O. S. Yadav, An-Tsung Kuo, Shingo Urata, Wataru Shinoda

The Journal of Physical Chemistry C   124 ( 26 )   14237 - 14244   2020.7

Pivotal Role of Interdigitation in Interleaflet Interactions: Implications from Molecular Dynamics Simulations Reviewed International journal

Sangjae Seo, Michio Murata, Wataru Shinoda

The Journal of Physical Chemistry Letters   11 ( 13 )   5171 - 5176   2020.7

Effects of Anion on Liquid Structures of Ionic Liquids at Graphene Electrode Interface Analyzed by Molecular Dynamics Simulations Reviewed

Seiji Tsuzuki, Takenobu Nakamura, Tetsuya Morishita, Wataru Shinoda, Shiro Seki, Yasuhiro Umebayashi, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe

Batteries & Supercaps   3 ( 7 )   658 - 667   2020.7

Exact long-range Coulombic energy calculation for net charged systems neutralized by uniformly distributed background charge using fast multipole method and its application to efficient free energy calculation Reviewed

Ryo Urano, Wataru Shinoda, Noriyuki Yoshii, Susumu Okazaki

The Journal of Chemical Physics   152 ( 24 )   244115   2020.6

Property Decoupling across the Embryonic Nucleus–Melt Interface during Polymer Crystal Nucleation Reviewed

Kyle Wm. Hall, Simona Percec, Wataru Shinoda, Michael L. Klein

The Journal of Physical Chemistry B   124 ( 23 )   4793 - 4804   2020.6

Monodisperse Polymer Melts Crystallize via Structurally Polydisperse Nanoscale Clusters: Insights from Polyethylene Reviewed

Kyle Wm. Hall, Timothy W. Sirk, Simona Percec, Michael L. Klein, Wataru Shinoda

Polymers   12 ( 2 )   447   2020.2

pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model Reviewed

Yusuke Miyazaki, Susumu Okazaki, Wataru Shinoda

Journal of Chemical Theory and Computation   16 ( 1 )   782 - 793   2020.1

Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation Reviewed

Kazushi Fujimoto, Motohiro Fukai, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, Susumu Okazaki

Pure and Applied Chemistry   92 ( 10 )   1584 - 1594   2020

Molecular simulation of the shape deformation of a polymersome Reviewed

Kaushik Chakraborty, Wataru Shinoda, Sharon M. Loverde

Soft Matter   16 ( 13 )   3234 - 3244   2020

The Amphotericin B–Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly Reviewed

Tomoya Yamamoto, Yuichi Umegawa, Hiroshi Tsuchikawa, Shinya Hanashima, Nobuaki Matsumori, Kosuke Funahashi, Sangjae Seo, Wataru Shinoda, Michio Murata

Biochemistry   58 ( 51 )   5188 - 5196   2019.12

Heteroaryldihydropyrimidines Alter Capsid Assembly By Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein Reviewed

Huihui Liu, Susumu Okazaki, Wataru Shinoda

Journal of Chemical Information and Modeling   59 ( 12 )   5104 - 5110   2019.12

Effects of Packing Density and Chain Length on the Surface Hydrophobicity of Thin Films Composed of Perfluoroalkyl Acrylate Chains: A Molecular Dynamics Study Reviewed

Hari O. S. Yadav, An-Tsung Kuo, Shingo Urata, Wataru Shinoda

Langmuir   35 ( 44 )   14316 - 14323   2019.11

Development of dissociative force field for all-atomistic molecular dynamics calculation of fracture of polymers Reviewed

Kazushi Fujimoto, Rajdeep Singh Payal, Tomonori Hattori, Wataru Shinoda, Masayuki Nakagaki, Sigeyoshi Sakaki, Susumu Okazaki

Journal of Computational Chemistry   40   2571-2576   2019.11

Divining the shape of nascent polymer crystal nuclei Reviewed

Kyle Wm. Hall, Timothy W. Sirk, Simona Percec, Michael L. Klein, Wataru Shinoda

The Journal of Chemical Physics   151 ( 14 )   144901   2019.10

Large-scale molecular dynamics simulation of perfluorosulfonic acid membranes: Remapping coarse-grained to all-atomistic simulations Reviewed

An-Tsung Kuo, Yusuke Miyazaki, Changwoon Jang, Tatsuya Miyajima, Shingo Urata, Steven O. Nielsen, Susumu Okazaki, Wataru Shinoda

Polymer   181   121766 - 121766   2019.10

tSPICA: Temperature- and Pressure-Dependent Coarse-Grained Force Field for Organic Molecules Reviewed

Mark Z. Griffiths, Wataru Shinoda

Journal of Chemical Information and Modeling   59 ( 9 )   3829 - 3838   2019.9

Average Conformation of Branched Chain Lipid PGP-Me That Accounts for the Thermal Stability and High-Salinity Resistance of Archaeal Membranes Reviewed

Masaki Yamagami, Hiroshi Tsuchikawa, Jin Cui, Yuichi Umegawa, Yusuke Miyazaki, Sangjae Seo, Wataru Shinoda, Michio Murata

Biochemistry   58 ( 37 )   3869 - 3879   2019.9

All-atom molecular dynamics study of impact fracture of glassy polymers. I: Molecular mechanism of brittleness of PMMA and ductility of PC Reviewed

Kazushi Fujimoto, Zhiye Tang, Wataru Shinoda, Susumu Okazaki

Polymer   178   121570 - 121570   2019.9

Hydrogen Permeation in Hydrated Perfluorosulfonic Acid Polymer Membranes: Effect of Polymer Crystallinity and Equivalent Weight Reviewed

Kotono Takeuchi, An-Tsung Kuo, Takeshi Hirai, Tatsuya Miyajima, Shingo Urata, Shinji Terazono, Susumu Okazaki, Wataru Shinoda

The Journal of Physical Chemistry C   123 ( 33 )   20628 - 20638   2019.8

Molecular Behavior of Linear Alkylbenzene Sulfonate in Hydrated Crystal, Tilted Gel, and Liquid Crystal Phases Studied by Molecular Dynamics Simulation Reviewed

Kosuke Takeda, Yoshimichi Andoh, Wataru Shinoda, Susumu Okazaki

Langmuir   35 ( 33 )   10877 - 10884   2019.8

Structure of Hydrated Crystal (Lc), Tilted Gel (Lβ′), and Liquid Crystal (Lα) Phases of Linear Alkylbenzene Sulfonate (LAS) Studied by X-ray Diffraction and Molecular Dynamics Simulation Reviewed

Kosuke Takeda, Yoshimichi Andoh, Wataru Shinoda, Susumu Okazaki

Langmuir   35 ( 27 )   9011 - 9019   2019.7

Free energy analysis of membrane pore formation process in the presence of multiple melittin peptides Reviewed

Y. Miyazaki, S. Okazaki, W. Shinoda

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES   1861 ( 7 )   1409-1419 - 1419   2019.7

Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup Reviewed

Shinya Hanashima, Kazuhiro Murakami, Michihiro Yura, Yo Yano, Yuichi Umegawa, Hiroshi Tsuchikawa, Nobuaki Matsumori, Sangjae Seo, Wataru Shinoda, Michio Murata

Biophysical Journal   117 ( 2 )   307 - 318   2019.7

A coarse-grain model for entangled polyethylene melts and polyethylene crystallization Reviewed

Kyle Wm. Hall, Timothy W. Sirk, Michael L. Klein, Wataru Shinoda

The Journal of Chemical Physics   150 ( 24 )   244901 - 244901   2019.6

Molecular mechanism of material deformation and failure in butadiene rubber: Insight from all-atom molecular dynamics simulation using a bond breaking potential model Reviewed

Rajdeep Singh Payal, Kazushi Fujimoto, Changwoon Jang, Wataru Shinoda, Yuki Takei, Hiroshi Shima, Katsuhiko Tsunoda, Susumu Okazaki

Polymer   170   113 - 119   2019.4

SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol Reviewed

Sangjae Seo, Wataru Shinoda

Journal of Chemical Theory and Computation   151 ( 10 )   762 - 774   2019.1

Direct Evidence for Li Ion Hopping Conduction in Highly Concentrated Sulfolane-Based Liquid Electrolytes Reviewed

Kaoru Dokko, Daiki Watanabe, Yosuke Ugata, Morgan L. Thomas, Seiji Tsuzuki, Wataru Shinoda, Kei Hashimoto, Kazuhide Ueno, Yasuhiro Umebayashi, Masayoshi Watanabe

The Journal of Physical Chemistry B   122 ( 47 )   10736 - 10745   2018.11

Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids Reviewed

Wataru Shinoda, Yuta Hatanaka, Masashi Hirakawa, Susumu Okazaki, Seiji Tsuzuki, Kazuhide Ueno, Masayoshi Watanabe

The Journal of Chemical Physics   148 ( 19 )   193809 - 193809   2018.5

Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals Reviewed

Soumya Lipsa Rath, Huihui Liu, Susumu Okazaki, Wataru Shinoda

Journal of Chemical Information and Modeling   58 ( 2 )   328 - 337   2018.2

Polymer Electrolytes Containing Solvate Ionic Liquids: A New Approach to Achieve High Ionic Conductivity, Thermal Stability, and a Wide Potential Window Reviewed

Yuzo Kitazawa, Kaori Iwata, Ryosuke Kido, Satoru Imaizumi, Seiji Tsuzuki, Wataru Shinoda, Kazuhide Ueno, Toshihiko Mandai, Hisashi Kokubo, Kaoru Dokko, Masayoshi Watanabe

Chemistry of Materials   30 ( 1 )   252 - 261   2018.1

Exploring the effect of pendent side chain length on the structural and mechanical properties of hydrated perfluorosulfonic acid polymer membranes by molecular dynamics simulation Reviewed

Kuo, A.-T., Takeuchi, K., Tanaka, A., Urata, S., Okazaki, S., Shinoda, W.

Polymer   146   53 - 62   2018

Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction Reviewed

Morishita, T., Nakamura, T., Shinoda, W., Ito, A.M.

Chemical Physics Letters   706   633 - 640   2018

Molecular Dynamics Study on the Mechanical Deformation of Hydrated Perfluorosulfonic Acid Polymer Membranes Reviewed

An-Tsung Kuo, Atsushi Tanaka, Jun Irisawa, Wataru Shinoda, Susumu Okazaki

JOURNAL OF PHYSICAL CHEMISTRY C   121 ( 39 )   21374 - 21382   2017.10

Transferable coarse-grained model for perfluorosulfonic acid polymer membranes Reviewed

An-Tsung Kuo, Susumu Okazaki, Wataru Shinoda

JOURNAL OF CHEMICAL PHYSICS   147 ( 9 )   2017.9

Janus dendrimersomes coassembled from fluorinated, hydrogenated, and hybrid Janus dendrimers as models for cell fusion and fission Reviewed

Qi Xiao, Samuel E. Sherman, Samantha E. Wilner, Xuhao Zhou, Cody Dazen, Tobias Baumgart, Ellen H. Reed, Daniel A. Hammer, Wataru Shinoda, Michael L. Klein, Virgil Percec

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA   114 ( 34 )   E7045 - E7053   2017.8

Effect of the cation on the stability of cation-glyme complexes and their interactions with the [TFSA](-) anion Reviewed

Seiji Tsuzuki, Toshihiko Mandai, Soma Suzuki, Wataru Shinoda, Takenobu Nakamura, Tetsuya Morishita, Kazuhide Ueno, Shiro Seki, Yasuhiro Umebayashi, Kaoru Dokko, Masayoshi Watanabe

PHYSICAL CHEMISTRY CHEMICAL PHYSICS   19 ( 28 )   18262 - 18272   2017.7

Molecular Dynamics Study of the Morphology of Hydrated Perfluorosulfonic Acid Polymer Membranes Reviewed

An-Tsung Kuo, Wataru Shinoda, Susumu Okazaki

JOURNAL OF PHYSICAL CHEMISTRY C   120 ( 45 )   25832 - 25842   2016.11

Permeability across lipid membranes Invited Reviewed

Wataru Shinoda

BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES   1858 ( 10 )   2254 - 2265   2016.10

Coarse-grained molecular dynamics study of membrane fusion: Curvature effects on free energy barriers along the stalk mechanism Reviewed

Shuhei Kawamoto, Michael L. Klein, Wataru Shinoda

JOURNAL OF CHEMICAL PHYSICS   143 ( 24 )   2015.12

Molecular dynamics simulations of cholesterol-rich membranes using a coarse-grained force field for cyclic alkanes Reviewed

Christopher M. MacDermaid, Hemant K. Kashyap, Russell H. DeVane, Wataru Shinoda, Jeffery B. Klauda, Michael L. Klein, Giacomo Fiorin

JOURNAL OF CHEMICAL PHYSICS   143 ( 24 )   2015.12

Precise calculation of the local pressure tensor in Cartesian and spherical coordinates in LAMMPS Reviewed

Takenobu Nakamura, Shuhei Kawamoto, Wataru Shinoda

COMPUTER PHYSICS COMMUNICATIONS   190   120 - 128   2015.5

Structures of [Li(glyme)](+) complexes and their interactions with anions in equimolar mixtures of glymes and Li[TFSA]: analysis by molecular dynamics simulations Reviewed

Seiji Tsuzuki, Wataru Shinoda, Masaru Matsugami, Yasuhiro Umebayashi, Kazuhide Ueno, Toshihiko Mandai, Shiro Seki, Kaoru Dokko, Masayoshi Watanabe

PHYSICAL CHEMISTRY CHEMICAL PHYSICS   17 ( 1 )   126 - 129   2015

[70]Fullerenes Assist the Formation of Phospholipid Bice Iles at Low Lipid Concentrations Reviewed

Atsushi Ikeda, Kazuya Kiguchi, Tomohiro Hida, Kazuma Yasuhara, Kazuyuki Nobusawa, Motofusa Akiyama, Wataru Shinoda

LANGMUIR   30 ( 41 )   12315 - 12320   2014.10

Thermodynamic Stability of [60]Fullerene and gamma-Cyclodextrin Complex in Aqueous Solution: Free Energy Simulation Reviewed

Shunsuke Mieda, Atsushi Ikeda, Yasushi Shigeri, Wataru Shinoda

JOURNAL OF PHYSICAL CHEMISTRY C   118 ( 23 )   12555 - 12561   2014.6

Effective interaction between small unilamellar vesicles as probed by coarse-grained molecular dynamics simulations Reviewed

Wataru Shinoda, Michael L. Klein

PURE AND APPLIED CHEMISTRY   86 ( 2 )   215 - 222   2014.2

Free energy analysis along the stalk mechanism of membrane fusion Reviewed

Shuhei Kawamoto, Wataru Shinoda

SOFT MATTER   10 ( 17 )   3048 - 3054   2014

Effect of different substituents on the water-solubility and stability properties of 1:2 [60]fullerene derivative·gamma-cyclodextrin complexes Reviewed

Atsushi Ikeda, Akiko Hirata, Michiko Ishikawa, Jun-Ichi Kikuchi, Shunsuke Mieda, Wataru Shinoda

Organic and Biomolecular Chemistry   11 ( 45 )   7843 - 7851   2013.12

Interactions in ion pairs of protic ionic liquids: Comparison with aprotic ionic liquids Reviewed

Seiji Tsuzuki, Wataru Shinoda, Md. Shah Miran, Hiroshi Kinoshita, Tomohiro Yasuda, Masayoshi Watanabe

Journal of Chemical Physics   139 ( 17 )   2013.11

Intermolecular interactions in Li+-glyme and Li +-glyme-TFSA- complexes: Relationship with physicochemical properties of [Li(glyme)][TFSA] ionic liquids Reviewed

Seiji Tsuzuki, Wataru Shinoda, Shiro Seki, Yasuhiro Umebayashi, Kazuki Yoshida, Kaoru Dokko, Masayoshi Watanabe

ChemPhysChem   14 ( 9 )   1993 - 2001   2013.6

Regioselective recognition of a [60]fullerene-bisadduct by cyclodextrin Reviewed

Atsushi Ikeda, Michiko Ishikawa, Ryota Aono, Jun-Ichi Kikuchi, Motofusa Akiyama, Wataru Shinoda

Journal of Organic Chemistry   78 ( 6 )   2534 - 2541   2013.3

Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory Reviewed

Takenobu Nakamura, Wataru Shinoda

JOURNAL OF CHEMICAL PHYSICS   138 ( 12 )   124903   2013.3

Computer Simulation of Self-Assembling Macromolecules Reviewed

Giacomo Fiorin, Michael L. Klein, Russell DeVane, Wataru Shinoda

HIERARCHICAL MACROMOLECULAR STRUCTURES: 60 YEARS AFTER THE STAUDINGER NOBEL PRIZE II   262   93 - 107   2013

Probing the structure of PEGylated-lipid assemblies by coarse-grained molecular dynamics Reviewed

Wataru Shinoda, Dennis E. Discher, Michael L. Klein, Sharon M. Loverde

SOFT MATTER   9 ( 48 )   11549 - 11556   2013

A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation Reviewed

Shuhei Kawamoto, Takenobu Nakamura, Steven O. Nielsen, Wataru Shinoda

Journal of Chemical Physics   139 ( 3 )   2013

Effect of Carboxylation on Carbon Nanotube Aqueous Dispersibility: A Predictive Coarse-Grained Molecular Dynamics Approach Reviewed

Chi-cheng Chiu, Russell H. DeVane, Michael L. Klein, Wataru Shinoda, Preston B. Moore, Steven O. Nielsen

JOURNAL OF PHYSICAL CHEMISTRY C   116 ( 43 )   23102 - 23106   2012.11

Molecular Dynamics Study of Catanionic Bilayers Composed of Ion Pair Amphiphile with Double-Tailed Cationic Surfactant Reviewed

An-Tsung Kuo, Chien-Hsiang Chang, Wataru Shinoda

LANGMUIR   28 ( 21 )   8156 - 8164   2012.5

Computer simulation studies of self-assembling macromolecules Reviewed

Wataru Shinoda, Russell DeVane, Michael L. Klein

CURRENT OPINION IN STRUCTURAL BIOLOGY   22 ( 2 )   175 - 186   2012.4

Premicelles and monomer exchange in aqueous surfactant solutions above and below the critical micelle concentration Reviewed

David N. LeBard, Benjamin G. Levine, Russell DeVane, Wataru Shinoda, Michael L. Klein

CHEMICAL PHYSICS LETTERS   522   38 - 42   2012.1

Effects of spherical fullerene nanoparticles on a dipalmitoyl phosphatidylcholine lipid monolayer: a coarse grain molecular dynamics approach Reviewed

Chi-cheng Chiu, Wataru Shinoda, Russell H. DeVane, Steven O. Nielsen

SOFT MATTER   8 ( 37 )   9610 - 9616   2012

Free energy of cell-penetrating peptide through lipid bilayer membrane: coarse-grained model simulation Reviewed

S. Kawamoto, M. Takasu, T. Miyakawa, T. Oda, H. Saito, S. Futaki, H. Nagao, W. Shinoda

Progress in Theoretical Chemistry and Physics   26   503 - 511   2012

Micellization Studied by GPU-Accelerated Coarse-Grained Molecular Dynamics Reviewed

Benjamin G. Levine, David N. LeBard, Russell DeVane, Wataru Shinoda, Axel Kohlmeyer, Michael L. Klein

JOURNAL OF CHEMICAL THEORY AND COMPUTATION   7 ( 12 )   4135 - 4145   2011.12

Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers: A Molecular Dynamics Study Reviewed

Hiroaki Saito, Wataru Shinoda

JOURNAL OF PHYSICAL CHEMISTRY B   115 ( 51 )   15241 - 15250   2011.12

Novel numerical method for calculating the pressure tensor in spherical coordinates for molecular systems Reviewed

Takenobu Nakamura, Wataru Shinoda, Tamio Ikeshoji

JOURNAL OF CHEMICAL PHYSICS   135 ( 9 )   2011.9

Molecular Simulation of Lipid Membranes and Liposomes : A Coarse-Grained Molecular Modeling Approach

SHINODA Wataru

MEMBRANE   36 ( 1 )   31 - 37   2011.1

Coarse-grained force field for ionic surfactants Reviewed

Wataru Shinoda, Russell DeVane, Michael L. Klein

SOFT MATTER   7 ( 13 )   6178 - 6186   2011

Molecular dynamics study of nanoparticles and non-ionic surfactant at an oil-water interface Reviewed

R. J. K. Udayana Ranatunga, Chuong T. Nguyen, Blake A. Wilson, Wataru Shinoda, Steven O. Nielsen

SOFT MATTER   7 ( 15 )   6942 - 6952   2011

Free energy analysis of vesicle-to-bicelle transformation Reviewed

Wataru Shinoda, Takenobu Nakamura, Steven O. Nielsen

SOFT MATTER   7 ( 19 )   9012 - 9020   2011

Paper supplement: Study on the pan carbon-fiber-innovation for modeling a successful R&D management - An excited-oscillation management model Reviewed

Nakamura O, Ohana T, Tazawa M, Yokota S, Shinoda W, Nakamura O, Itoh J

Synthesiology   4 ( 2 )   111 - 114   2011

Nanoscale carbon particles and the stability of lipid bilayers Reviewed

Arben Jusufi, Russell H. DeVane, Wataru Shinoda, Michael L. Klein

SOFT MATTER   7 ( 3 )   1139 - 1146   2011

Effects of conformational flexibility of alkyl chains of cations on diffusion of ions in ionic liquids Reviewed

Seiji Tsuzuki, Hajime Matsumoto, Wataru Shinoda, Masuhiro Mikami

PHYSICAL CHEMISTRY CHEMICAL PHYSICS   13 ( 13 )   5987 - 5993   2011

Molecular Dynamics Simulations of Nanoparticles and Surfactants at Oil/Water Interfaces A Qualitative Overview Reviewed

R. J. K. Udayana Ranatunga, Chuong T. Nguyen, Chi-cheng Chiu, Wataru Shinoda, Steven O. Nielsen

AMPHIPHILES: MOLECULAR ASSEMBLY AND APPLICATIONS   1070   295 - +   2011

Paper supplement: Study on the pan carbon-fiber-innovation for modeling a successful R&D management - An excited-oscillation management model

Osamu Nakamura, Tsuguyori Ohana, Masato Tazawa, Shinji Yokota, Wataru Shinoda, Osamu Nakamura, Junji Itoh

Synthesiology   4 ( 2 )   111 - 114   2011

Parametrization and Application of a Coarse Grained Force Field for Benzene/Fullerene Interactions with Lipids Reviewed

Russell DeVane, Arben Jusufi, Wataru Shinoda, Chi-cheng Chiu, Steven O. Nielsen, Preston B. Moore, Michael L. Klein

JOURNAL OF PHYSICAL CHEMISTRY B   114 ( 49 )   16364 - 16372   2010.12

Molecular Dynamics Study of Isoprenoid-Chained Lipids: Salient Features of Isoprenoid Chains As Compared with Ordinary Alkyl Chains Reviewed

Wataru Shinoda, Masakatsu Hato

Self-Organized Surfactant Structures   175 - 194   2010.11

Self-assembled Structure of Amphiphiles by Coarse-grained Molecular Model

SHINODA Wataru

Seibutsu Butsuri   50 ( 5 )   232 - 235   2010.9

Interactions of Perfluoroalkyltrifluoroborate Anions with Li Ion and Imidazolium Cation: Effects of Perfluoroalkyl Chain on Motion of Ions in Ionic Liquids Reviewed

Seiji Tsuzuki, Tatsuya Umecky, Hajime Matsumoto, Wataru Shinoda, Masuhiro Mikami

JOURNAL OF PHYSICAL CHEMISTRY B   114 ( 35 )   11390 - 11396   2010.9

Coarse-Grained Potential Models for Phenyl-Based Molecules: I. Parametrization Using Experimental Data Reviewed

Russell DeVane, Michael L. Klein, Chi-cheng Chiu, Steven O. Nielsen, Wataru Shinoda, Preston B. Moore

JOURNAL OF PHYSICAL CHEMISTRY B   114 ( 19 )   6386 - 6393   2010.5

Coarse-Grained Potential Models for Phenyl-Based Molecules: II. Application to Fullerenes Reviewed

Chi-cheng Chiu, Russell DeVane, Michael L. Klein, Wataru Shinoda, Preston B. Moore, Steven O. Nielsen

JOURNAL OF PHYSICAL CHEMISTRY B   114 ( 19 )   6394 - 6400   2010.5

Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field Reviewed

Wataru Shinoda, Russell DeVane, Michael L. Klein

JOURNAL OF PHYSICAL CHEMISTRY B   114 ( 20 )   6836 - 6849   2010.5

A mean field approach for computing solid-liquid surface tension for nanoscale interfaces Reviewed

Chi-cheng Chiu, R. J. K. Udayana Ranatunga, David Torres Flores, D. Vladimir Perez, Preston B. Moore, Wataru Shinoda, Steven O. Nielsen

JOURNAL OF CHEMICAL PHYSICS   132 ( 5 )   2010.2

Paramaterization of a coarse-grained model for linear alkylbenzene sulfonate surfactants and molecular dynamics studies of their self-assembly in aqueous solution Reviewed

Xibing He, Wataru Shinoda, Russell DeVane, Kelly L. Anderson, Michael L. Klein

CHEMICAL PHYSICS LETTERS   487 ( 1-3 )   71 - 76   2010.2

The shear hysteresis in lamellar structure of surfactant-water binary system Reviewed

Takenobu Nakamura, Wataru Shinoda, Masuhiro Mikami

CHEMICAL PHYSICS   367 ( 1 )   20 - 26   2010.1

Exploring the utility of coarse-grained water models for computational studies of interfacial systems Reviewed

Xibing He, Wataru Shinoda, Russell DeVane, Michael L. Klein

MOLECULAR PHYSICS   108 ( 15 )   2007 - 2020   2010

Size-dependent hydrophobic to hydrophilic transition for nanoparticles: A molecular dynamics study Reviewed

Chi-cheng Chiu, Preston B. Moore, Wataru Shinoda, Steven O. Nielsen

JOURNAL OF CHEMICAL PHYSICS   131 ( 24 )   2009.12

Molecular Dynamics Simulations of Ionic Liquids: Cation and Anion Dependence of Self-Diffusion Coefficients of Ions Reviewed

Seiji Tsuzuki, Wataru Shinoda, Hiroaki Saito, Masuhiro Mikami, Hiroyuki Tokuda, Masayoshi Watanabe

JOURNAL OF PHYSICAL CHEMISTRY B   113 ( 31 )   10641 - 10649   2009.8

Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids Reviewed

Russell DeVane, Wataru Shinoda, Preston B. Moore, Michael L. Klein

JOURNAL OF CHEMICAL THEORY AND COMPUTATION   5 ( 8 )   2115 - 2124   2009.8

Models for Phosphatidylglycerol Lipids Put to a Structural Test Reviewed

Jerome Henin, Wataru Shinoda, Michael L. Klein

JOURNAL OF PHYSICAL CHEMISTRY B   113 ( 19 )   6958 - 6963   2009.5

Area per Ligand as a Function of Nanoparticle Radius: A Theoretical and Computer Simulation Approach Reviewed

Robert J. B. Kalescky, Wataru Shinoda, Preston B. Moore, Steven O. Nielsen

LANGMUIR   25 ( 3 )   1352 - 1359   2009.2

Fluorination effects on structure and dynamics of phospholipid bilayer: A molecular dynamics study Reviewed

Hiroaki Saito, Wataru Shinoda, Masuhiro Mikami

CHEMICAL PHYSICS LETTERS   468 ( 4-6 )   260 - 263   2009.1

Calculating the surface tension between a flat solid and a liquid: a theoretical and computer simulation study of three topologically different methods Reviewed

Uriel Octavio Moreles Vazquez, Wataru Shinoda, Preston B. Moore, Chi-cheng Chiu, Steven O. Nielsen

JOURNAL OF MATHEMATICAL CHEMISTRY   45 ( 1 )   161 - 174   2009.1

Computational Exploration of Novel Silicon Nanostructures Reviewed

Kengo Nishio, Taisuke Ozaki, Tetsuya Morishita, Wataru Shinoda, Masuhiro Mikami

ULIS 2009: 10TH INTERNATIONAL CONFERENCE ON ULTIMATE INTEGRATION OF SILICON   61 - +   2009

Study on the PAN carbon-fiber-innovation for modeling a successful R&D management Reviewed

Osamu Nakamura, Tsuguyori Ohana, Masato Tazawa, Shinji Yokota, Wataru Shinoda, Junji Itoh

Synthesiology   2 ( 2 )   154 - 164   2009

Enhanced hydrophobicity of fluorinated lipid bilayer: A molecular dynamics study Reviewed

Hiroaki Saito, Wataru Shinoda, Masuhiro Mikami

JOURNAL OF PHYSICAL CHEMISTRY B   112 ( 36 )   11305 - 11309   2008.9

Efficient free energy calculation of water across lipid membranes Reviewed

Keiko Shinoda, Wataru Shinoda, Masuhiro Mikami

JOURNAL OF COMPUTATIONAL CHEMISTRY   29 ( 12 )   1912 - 1918   2008.9

Large-scale molecular dynamics simulations of self-assembling systems Reviewed

Michael L. Klein, Wataru Shinoda

SCIENCE   321 ( 5890 )   798 - 800   2008.8

United-atom acyl chains for CHARMM phospholipids Reviewed

Jerome Henin, Wataru Shinoda, Michael L. Klein

JOURNAL OF PHYSICAL CHEMISTRY B   112 ( 23 )   7008 - 7015   2008.6

Free-energy analysis of the molecular binding into lipid membrane with the method of energy representation Reviewed

Nobuyuki Matubayasi, Wataru Shinoda, Masaru Nakahara

JOURNAL OF CHEMICAL PHYSICS   128 ( 19 )   2008.5

Electronic and optical properties of polyicosahedral Si nanostructures: A first-principles study Reviewed

Kengo Nishio, Taisuke Ozaki, Tetsuya Morishita, Wataru Shinoda, Masuhiro Mikami

PHYSICAL REVIEW B   77 ( 7 )   2008.2

Coarse-grained molecular modeling of non-ionic surfactant self-assembly Reviewed

Wataru Shinoda, Russell DeVane, Michael L. Klein

SOFT MATTER   4 ( 12 )   2454 - 2462   2008

Multi-property fitting and parameterization of a coarse grained model for aqueous surfactants Reviewed

W. Shinoda, R. Devane, M. L. Klein

MOLECULAR SIMULATION   33 ( 1-2 )   27 - 36   2007.1

Molecular dynamics simulation of an archaeal lipid bilayer with sodium chloride Reviewed

Keiko Shinoda, Wataru Shinoda, Masuhiro Mikami

PHYSICAL CHEMISTRY CHEMICAL PHYSICS   9 ( 5 )   643 - 650   2007

Molecular dynamics study of bipolar tetraether lipid membranes Reviewed

W Shinoda, K Shinoda, T Baba, M Mikami

BIOPHYSICAL JOURNAL   89 ( 5 )   3195 - 3202   2005.11

Calculation of heat capacities of light and heavy water by path-integral molecular dynamics Reviewed

Motoyuki Shiga, Wataru Shinoda

Journal of Chemical Physics   123 ( 13 )   134502   2005.10

Quantum simulation of the heat capacity of water Reviewed

Wataru Shinoda, Motoyuki Shiga

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics   71 ( 4 )   2005.4

Spatial confinement effect on the atomic structure of solid argon Reviewed

K Nishio, W Shinoda, T Morishita, M Mikami

JOURNAL OF CHEMICAL PHYSICS   122 ( 12 )   2005.3

Can such long time steps really be used in dissipative particle dynamics simulations? Reviewed

B Hafskjold, CC Liew, W Shinoda

MOLECULAR SIMULATION   30 ( 13-15 )   879 - 885   2004.11

Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers Reviewed

K Shinoda, W Shinoda, T Baba, M Mikami

JOURNAL OF CHEMICAL PHYSICS   121 ( 19 )   9648 - 9654   2004.11

Stress-assisted grain boundary sliding and migration at finite temperature: A molecular dynamics study Reviewed

M Shiga, W Shinoda

PHYSICAL REVIEW B   70 ( 5 )   054102   2004.8

Molecular dynamics study on the effects of chain branching on the physical properties of lipid bilayers: 2. Permeability Reviewed

W Shinoda, M Mikami, T Baba, M Hato

JOURNAL OF PHYSICAL CHEMISTRY B   108 ( 26 )   9346 - 9356   2004.7

Two-dimensional self-assembled structures of adenine molecules: modeling and simulation Reviewed

K Shinoda, W Shinoda, CC Liew, S Tsuzuki, Y Morikawa, M Mikami

SURFACE SCIENCE   556 ( 2-3 )   109 - 120   2004.5

Dynamics of a highly branched lipid bilayer: a molecular dynamics study Reviewed

W Shinoda, M Mikami, T Baba, M Hato

CHEMICAL PHYSICS LETTERS   390 ( 1-3 )   35 - 40   2004.5

Rapid estimation of elastic constants by molecular dynamics simulation under constant stress Reviewed

W Shinoda, M Shiga, M Mikami

PHYSICAL REVIEW B   69 ( 13 )   134103   2004.4

Molecular dynamics study of the lipid bilayers: Effects of the chain branching on the structure and dynamics Reviewed

W Shinoda, M Mikami, T Baba, M Hato

SLOW DYNAMICS IN COMPLEX SYSTEMS   708   352 - 353   2004

1P108 MD Simulation of Halorhodopsin in Lipid bilayer

Hayashi M., Miyagawa Y., Shinoda W., Sakurai M.

Seibutsu Butsuri   44   S56   2004

Molecular dynamics study on the effect of chain branching on the physical properties of lipid bilayers: Structural stability Reviewed

W Shinoda, M Mikami, T Baba, M Hato

JOURNAL OF PHYSICAL CHEMISTRY B   107 ( 50 )   14030 - 14035   2003.12

A comparison of straight- and branch-chained lipid bilayers for static and dynamic properties: A molecular dynamics study Reviewed

W Shinoda, M Mikami, T Baba, M Hato

NANOTECH 2003, VOL 3   3   512 - 515   2003

1G0930 A comparison of straight- and branch-chained lipid bilayers for the static and dynamic properties a molecular dynamics study.

Shinoda W., Mikami M., Baba T., Hato M.

Seibutsu Butsuri   42 ( 2 )   S35   2002

Self-guided molecular dynamics in the isothermal-isobaric ensemble Reviewed

W Shinoda, M Mikami

CHEMICAL PHYSICS LETTERS   335 ( 3-4 )   265 - 272   2001.2

Molecular dynamics study of the dipalmitoyl phosphatidylcholine bilayer in the liquid crystal phase: An effect of the potential force fields on the membrane structure. Reviewed

W Shinoda, S Okazaki

JOURNAL OF MOLECULAR LIQUIDS   90 ( 1-3 )   95 - 103   2001.2

Molecular dynamics study on mechanism of selective permeation of water through aquaporin-1

Shinoda W, Tateno M, Ohfuku Y, Mikami M

Seibutsu Butsuri   41   S178   2001

Molecular dynamics study of structure and dynamics of lipid bilayer in the liquid crystal phase Reviewed

W Shinoda, S Okazaki

ELECTROCHEMISTRY   68 ( 2 )   129 - 133   2000.2

Parallel molecular dynamics simulation: implementation of PVM for a lipid membrane Reviewed

ZW Fang, ADJ Haymet, W Shinoda, S Okazaki

COMPUTER PHYSICS COMMUNICATIONS   116 ( 2-3 )   295 - 310   1999.2

Molecular dynamics study on electrostatic properties of a lipid bilayer: Polarization, electrostatic potential, and the effects on structure and dynamics of water near the interface Reviewed

W Shinoda, M Shimizu, S Okazaki

JOURNAL OF PHYSICAL CHEMISTRY B   102 ( 34 )   6647 - 6654   1998.8

A Voronoi analysis of lipid area fluctuation in a bilayer Reviewed

W Shinoda, S Okazaki

JOURNAL OF CHEMICAL PHYSICS   109 ( 4 )   1517 - 1521   1998.7

Molecular dynamics study of a lipid bilayer: Convergence, structure, and long-time dynamics Reviewed

W Shinoda, N Namiki, S Okazaki

JOURNAL OF CHEMICAL PHYSICS   106 ( 13 )   5731 - 5743   1997.4

MOLECULAR-DYNAMICS SIMULATION OF THE DIPALMITOYLPHOSPHATIDYLCHOLINE (DPPC) LIPID BILAYER IN THE FLUID-PHASE USING THE NOSE-PARRINELLO-RAHMAN NPT ENSEMBLE Reviewed

W SHINODA, T FUKADA, S OKAZAKI, OKADA, I

CHEMICAL PHYSICS LETTERS   232 ( 3 )   308 - 312   1995.1

pgRNAを内包したB型肝炎ウイルスの全原子分子動力学シミュレーション

山口陽平, 今井甫, 藤本和士, 浦野諒, 篠田渉, 尾曲克己, 田中靖人, 石川哲也, 中川敦史, 岡崎進

分子シミュレーション討論会講演要旨集   31st   2017

分子動力学法による界面活性剤水和結晶の融解挙動に関する研究

武田康助, 武田康助, 田渕友季子, 安藤嘉倫, 篠田渉, 岡崎進, 岡崎進

分子シミュレーション討論会講演要旨集   31st   2017

分子動力学法を用いた生体膜の水透過における自由エネルギーの解析

山崎隼也, 伊藤太一, 安藤嘉倫, 篠田渉, 岡崎進

分子シミュレーション討論会講演要旨集   29th   2015

全原子分子動力学計算によるポリオウイルスカプシドの溶液内安定性についての研究

安藤嘉倫, 吉井範行, 山田篤志, 藤本和士, 小嶋秀和, 水谷圭佑, 中川敦史, 野本明男, 篠田渉, 岡崎進

日本膜学会年会講演要旨集   37th   2015

分子動力学法を用いた生体膜の水透過における自由エネルギーの解析

山崎隼也, 伊藤太一, 安藤嘉倫, 篠田渉, 岡崎進

分子科学討論会講演プログラム&要旨(Web)   9th   2015

脂質膜間距離による膜の物性変化

井上未知子, 安藤嘉倫, 篠田渉, 岡崎進, 岡崎進

分子シミュレーション討論会講演要旨集   29th   2015

Lipid bilayer energetics, deformations, and interaction with carbon nanoparticles studied by molecular dynamics simulations

Steven O. Nielsen, Wataru Shinoda

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   247   2014.3

スフィンゴ脂質膜の構造とダイナミクス-コレステロール含有による変化-

永山日菜, 安藤嘉倫, 篠田渉, 岡崎進

分子シミュレーション討論会講演要旨集   28th   2014

スフィンゴミエリン/コレステロール/DOPC3成分膜のLo,Ld相の分子動力学計算

柴山総一郎, 篠田渉, 安藤嘉倫, 岡崎進

分子シミュレーション討論会講演要旨集   28th   2014

Coarse-grained molecular dynamics of PEGylated assemblies

Sharon M. Loverde, Wataru Shinoda, Dennis E. Discher, Michael L. Klein

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   245   2013.4

26pBJ-8 Analysis of physical properties of liposome aiming at bridging the molecular theory to continuous elastic theory II

Nakamura Takenobu, Shinoda Wataru

Meeting abstracts of the Physical Society of Japan   67 ( 1 )   416 - 416   2012.3

22pJF-2 The evaluation of material properties of liposome From Molecular description to continuous description

Nakamura Takenobu, Shinoda Wataru

Meeting abstracts of the Physical Society of Japan   66 ( 2 )   319 - 319   2011.8

24aPS-18 The choice of contours to calculate the local pressure for the spherical coordinate

Nakamura Takenobu, Shinoda Wataru

Meeting abstracts of the Physical Society of Japan   66 ( 2 )   342 - 342   2011.8

21pJF-11 Novel numerical method to calculate the local pressure tensor in the spherical coordinates for Molecular systems

Nakamura Takenobu, Shinoda Wataru

Meeting abstracts of the Physical Society of Japan   66 ( 2 )   309 - 309   2011.8

23aGN-11 The O(N) first-principles calculations on a large system of gramicidin-A II

Arita M., Miyazaki T., Todorovic M., Shinoda W., Bowler D. R.

Meeting abstracts of the Physical Society of Japan   66 ( 2 )   325 - 325   2011.8

28aGV-12 The implementation of the calculation method of pressure profile for the spherically symmetric systems and material property of liposome

Nakamura Takenobu, Shinoda Wataru

Meeting abstracts of the Physical Society of Japan   66 ( 1 )   417 - 417   2011.3

28aGV-3 The O(N) first-principles calculations on a large system of gramicidin-A

Arita M., Miyazaki T., Todorovic M., Shinoda W., Bowler D. R.

Meeting abstracts of the Physical Society of Japan   66 ( 1 )   416 - 416   2011.3

Advantages of using implicit solid models in the study of nano-scaled interfaces

Udayana Ranatunga, Chi-Cheng Chiu, Preston B. Moore, Wataru Shinoda, Steven Nielsen

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   241   2011.3

Simulating nanoparticles and surfactant in the vicinity of oil/water interfaces

Udayana Ranatunga, Chuong T. Nguyen, Blake A. Wilson, Wataru Shinoda, Steven O. Nielsen

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   241   2011.3

Influence of solvation and interparticle interactions on the aggregation behavior of nanoparticles in membranes

Udayana Ranatunga, Arben Jusufi, Russell H. DeVane, Wataru Shinoda, Michael L. Klein, Steven O. Nielsen

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   241   2011.3

Aggregation behavior of nanoparticles constrained at oil/water interfaces

Udayana Ranatunga, Wataru Shinoda, Steven Nielsen

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   241   2011.3

Development of a Coarse-Grained Model for the Surfactant Family of Linear Alkylbenzene Sulfonates

Xibing He, Wataru Shinoda, Russell Devane, Olgun Guvench, Kelly L. Anderson, Alexander D. MacKerell, Michael L. Klein

BIOPHYSICAL JOURNAL   100 ( 3 )   147 - 147   2011.2

Graphical processing unit acceleration of coarse grained molecular dynamics and data analysis

David N. LeBard, Benjamin G. Levine, Russell DeVane, Wataru Shinoda, John E. Stone, Axel Kohlmeyer, Klein L. Michael

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   240   2010.8

Coarse grained molecular dynamics of biological and soft matter systems

Russell H. DeVane, Wataru Shinoda, Michael L. Klein

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   240   2010.8

Effect of spherical fullerenes on pulmonary lipid monolayers: Molecular dynamics simulations

Steven O. Nielsen, Chi-cheng Chiu, Preston B. Moore, Russell DeVane, Michael L. Klein, Wataru Shinoda

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   240   2010.8

20pEC-4 Molecular Dynamics of Vesicles : Coarse-grained molecular modeling on the basis of all-atomic simulation

Shinoda Wataru

Meeting abstracts of the Physical Society of Japan   65 ( 1 )   368 - 368   2010.3

20aEF-11 Elastic moduli of vesicles from particle simulations (II)

Nakamura Takenobu, Shinoda Wataru, Mikami Masuhiro

Meeting abstracts of the Physical Society of Japan   65 ( 1 )   366 - 366   2010.3

Mean field approach for computing solid-liquid surface tension for nanoscale interfaces

Steven O. Nielsen, Chi-cheng Chiu, Udayana Ranatunga, Preston B. Moore, Wataru Shinoda

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   239   2010.3

COLL 458-Area per ligand as a function of nanoparticle radius: A theoretical and computer simulation approach

Robert J. B. Kalescky, Wataru Shinoda, Preston Moore, Steven O. Nielsen

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   238   2009.8

合成脂質膜の分子シミュレーション - フッ素化脂質 Invited

齋藤大明, 篠田渉

分子シミュレーション研究会会誌 アンサンブル   11 ( 4 )   22 - 25   2009.4

COMP 2-Coarse grain models for molecular dynamics simulation

Russell DeVane, Wataru Shinoda, Michael L. Klein

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   236   2008.8

PHYS 116-Calculation of the surface tension between water and a flat solid

Uriel Vazquez, Chi-cheng Chiu, Wataru Shinoda, D. Vladimir Perez, Preston B. Moore, Steven O. Nielsen

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   236   2008.8

COLL 43-Nanoparticle localization energy at the oil/water interface: Effect of the deformable organic ligand coating

Udayana Ranathunga Jayasekara, Robert J. B. Kalescky, Chi-cheng Chiu, Wataru Shinoda, Preston B. Moore, Steven O. Nielsen

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   236   2008.8

PHYS 324-Measurement of the contact angle of a water droplet on a flat surface

Uriel Vazquez, Chi-cheng Chiu, Wataru Shinoda, D. Vladimir Perez, Preston B. Moore, Steven O. Nielsen

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   236   2008.8

COLL 378-Correlating surfactant hydrophilic-lipophilic balance and nanoparticle radii via coarse-grained molecular dynamics simulations

Robert J. B. Kaleseky, Wataru Shinoda, Preston B. Moore, Steven O. Nielsen

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   235   2008.4

COLL 372-Theory of nanoparticle self-assembly at oil/water interfaces: The role of curvature

Steven O. Nielsen, Preston B. Moore, Wataru Shinoda, Robert J. B. Kalescky, Chi-cheng Chiu

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   235   2008.4

23pTG-4 Electronic band structure of polyicosahedral Si nanowire

Nishio K., Ozaki T., Morishita T., Shinoda W., Mikami M.

Meeting abstracts of the Physical Society of Japan   63 ( 1 )   804 - 804   2008.2

22aRL-1 The shear hysteresis in the lamellar phase by dissipative particle dynamics

Nakamura Takenobu, Shinoda Wataru, Mikami Masuhiro

Meeting abstracts of the Physical Society of Japan   62 ( 2 )   366 - 366   2007.8

COLL 26-Coarse-grained molecular simulation of surfactant self-assembly

Wataru Shinoda, Michael L. Klein

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   234   2007.8

COMP 384-Multiproperty parametrization of a coarse grained model for proteins

Russell DeVane, Wataru Shinoda, Michael L. Klein

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   234   2007.8

COMP 258-Multi-terascale molecular modeling of biological systems

Russell DeVane, Wataru Shinoda, Jerome Henin, Matteo Dal Peraro, Axel Kohlmeyer, Michael L. Klein

ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY   234   2007.8

21aTG-5 Molecular dynamics simulation of polyicosahedral Si nanowire formation

Nishio K., Morishita T., Shinoda W., Mikami M.

Meeting abstracts of the Physical Society of Japan   62 ( 1 )   919 - 919   2007.2

ナノとバイオ領域における膜科学 高度含フッ素リン脂質液晶膜の創製と特性化

馬場照彦, 高井克毅, 高木俊之, 金森敏幸, 篠田渉, 齋藤大明, 三上益弘

膜シンポジウム   ( 18 )   41 - 44   2006.10

Molecular dynamics simulations of self-organized polyicosahedral Si nanowire

Kengo Nishio, Tetsuya Morishita, Wataru Shinoda, Masuhiro Mikami

JOURNAL OF CHEMICAL PHYSICS   125 ( 7 )   074712-1-074712-4   2006.8

28aXJ-5 Molecular dynamics simulation of the icosahedral Si nano cluster formation

Nishio K., Morishita T., Shinoda W., Mikami M.

Meeting abstracts of the Physical Society of Japan   61 ( 1 )   877 - 877   2006.3

28pPSB-39 Calculation of free energy of a water molecule in a lipid bilayer using overlapping method

Shinoda Keiko, Shinoda Wataru, Mikami Masuhiro

Meeting abstracts of the Physical Society of Japan   61 ( 1 )   370 - 370   2006.3

Molecular dynamics simulation of icosahedral Si quantum dot formation from liquid droplets

K Nishio, T Morishita, W Shinoda, M Mikami

PHYSICAL REVIEW B   72 ( 24 )   245321-1-4   2005.12

Intermolecular interaction between the pendant chain of perfluorinated ionomer and methanol

S Urata, J Irisawa, A Takada, S Tsuzuki, W Shinoda, M Mikami

JOURNAL OF FLUORINE CHEMISTRY   126 ( 9-10 )   1312 - 1320   2005.10

Molecular dynamics study of the methanol effect on the membrane morphology of perfluorosulfonic ionomers

S Urata, J Irisawa, A Takada, W Shinoda, S Tsuzuki, M Mikami

JOURNAL OF PHYSICAL CHEMISTRY B   109 ( 36 )   17274 - 17280   2005.9

24aYW-5 Molecular Dynamics study on the freezing phenomena of Ar confined in nanopores

Nishio K., Shinoda W., Morishita T., Mikami M.

Meeting abstracts of the Physical Society of Japan   60 ( 1 )   347 - 347   2005.3

Molecular dynamics simulation of swollen membrane of perfluorinated ionomer

S Urata, J Irisawa, A Takada, W Shinoda, S Tsuzuki, M Mikami

JOURNAL OF PHYSICAL CHEMISTRY B   109 ( 9 )   4269 - 4278   2005.3

15aTA-13 Molecular dynamics simulation of an ether-linked lipid bilayer

Shinoda Keiko, Shinoda Wataru, Mikami Masuhiro

Meeting abstracts of the Physical Society of Japan   59 ( 2 )   311 - 311   2004.8

Intermolecular interaction between the pendant chain of perfluorinated ionomer and water

S Urata, J Irisawa, A Takada, S Tsuzuki, W Shinoda, M Mikami

PHYSICAL CHEMISTRY CHEMICAL PHYSICS   6 ( 13 )   3325 - 3332   2004.7

水の比熱:経路積分分子動力学法による研究

篠田渉, 志賀基之

分子シミュレーション討論会講演要旨集   18th   2004

経路積分分子動力学法による比熱の精密計算

志賀基之, 篠田渉

分子構造総合討論会講演要旨集(CD-ROM)   2004   2004

温度と応力を制御した分子動力学法による粒界すべりの研究

志賀基之, 篠田渉

分子シミュレーション討論会講演要旨集   18th   2004

Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency

W Shinoda, M Mikami

JOURNAL OF COMPUTATIONAL CHEMISTRY   24 ( 8 )   920 - 930   2003.6

分子動力学法による温度とストレスの制御とその応用

志賀基之, 篠田渉, 三上益弘, 蕪木英雄

分子構造総合討論会講演要旨集(CD-ROM)   2003   2003

Development of General Purpose Molecular Dynamics Simulation System TACPACK 2000 III - Systematization technologies -

Minami Kazuyoshi, Morikawa Yoshitada, Ogawa Hiroshi, Tanaka Shingo, Terakura Kiyoyuki, Masuda Hirotoshi, Mitsui Takashi, Sasaki Mikio, Mikami Masuhiro, Shinoda Wataru, Liew Chie Chin, Kawata Masaaki, Ikeshoji Tamio

Symposium on Chemical Information and Computer Sciences   0 ( 0 )   J25 - J25   2001

分子動力学シミュレーションによる脂質二重層膜の構造と動力学

篠田 渉, 岡崎 進

電気化学および工業物理化学 : denki kagaku   68 ( 2 )   129 - 133   2000.2

抗菌ペプチドがもつ膜選択性の分子論的研究

川端一正, 宮崎裕介, 山田哲平, 篠田渉

第36回分子シミュレーション討論会  2022.12.6  分子シミュレーション学会

エンベロープ型ウイルス粒子の粗視化シ ミュレーション: B 型肝炎ウイルスのビリ オン構造とエンベロープ膜

浦野諒, 篠田渉

第36回分子シミュレーション討論会  2022.12.6  分子シミュレーション学会

スルホラン系濃厚電解液における Li イオン伝導における溶媒効果

池田周平, 都築誠二, 上野和英, 渡邉正義, 篠田渉

第36回分子シミュレーション討論会  2022.12.5  分子シミュレーション学会

環境依存の構造変化を取り込んだ粗視化タンパク質モデルの開発と脂質膜吸着現象への応用

山田哲平, 篠田渉

第36回分子シミュレーション討論会  2022.12.5  分子シミュレーション学会

分子動力学計算による脂質ナノ粒子を用いた核酸エンドソーム脱出機構の解明

柴田果奈, Akhil Pratap Singh, 宮崎裕介, 篠田渉

第36回分子シミュレーション討論会  2022.12.5  分子シミュレーション学会

高濃度Li塩溶液に用いる溶媒のドナー性と溶液構造・Liイオン輸送の関係

重信 圭佑、 都築 誠二、 篠田 渉、 獨古 薫、 渡邉 正義、 上野 和英

第63回 電池討論会  2022.11.10  （公社）電気化学会 電池技術委員会

鎖状エーテル系電解液の基礎物性とリチウム硫黄電池への適用

石川 遼、 重信 圭佑、 須藤 拓、 都築 誠二、 篠田 渉、 獨古 薫、 渡邉 正義、 上野 和英

第63回 電池討論会  2022.11.8  （公社）電気化学会 電池技術委員会

分極力場を用いたスルホラン系濃厚電解液の輸送物性の解析

都築 誠二、 篠田 渉、 池田 周平、 重信 圭佑、 関 志朗、 上野 和英、 獨古 薫、 渡邉 正義

第63回 電池討論会  2022.11.8  （公社）電気化学会 電池技術委員会

Coarse-grained molecular dynamics of lipid self-assembly. Invited International conference

CECAM workshop: Ions, membrane and channels: Multiscale simulations from quantum to coarse-grain. A symposium in honor of Mike Klein.  2022.10.29  CECAM

補助溶媒希釈スルホラン系濃厚Li塩電解液におけるLiイオン拡散機構の解析

池田周平，都築誠二， 上野和英，渡邉正義， 篠田 渉

第44回溶液化学シンポジウム  2022.10.28  溶液化学研究会

分子動力学計算による抗菌ペプチドの膜選択性解析

川端一正，宮崎裕介，篠田　渉

第44回溶液化学シンポジウム  2022.10.28  溶液化学研究会

脂質ナノ粒子を用いた核酸エンドソーム脱出の分子動力学

柴田果奈，Akhil Pratap Singh，宮崎裕介，篠田 渉

第44回溶液化学シンポジウム  2022.10.27  溶液化学研究会

生体膜・脂質膜の分子シミュレーション Invited

篠田渉

「計算生命科学の基礎９」  2022.11.16  神戸大学大学院システム情報学研究科 計算科学教育研究センター

分子動力学シミュレーションを用いた脂質膜におけるメリチンの抗菌作用の研究

宮崎 裕介，篠田 渉

第60回生物物理学会年会  2022.9.30  一般社団法人日本生物物理学会

エンベロープ型ウイルス粒子の粗視化シミュレーション: B型肝炎ウイルス

浦野 諒，篠田 渉

第60回生物物理学会年会  2022.9.29  一般社団法人日本生物物理学会

分子動力学シミュレーションによるエンドソーム脱出分子機構の解明

柴田果奈, Akhil Pratap Singh, 篠田渉

第60回生物物理学会年会  2022.9.29  一般社団法人日本生物物理学会

環境変化によるタンパク質の構造変化を取り込んだ粗視化タンパク質モデル

山田 哲平，篠田 渉

第60回生物物理学会年会  2022.9.29  一般社団法人日本生物物理学会

抗菌ペプチドによる膜細孔形成の分子シミュレーション研究

川端一正、宮﨑裕介、篠田渉

第60回生物物理学会年会  2022.9.29  一般社団法人日本生物物理学会

分子動力学法を用いた脂質ナノ粒子のエンドソーム脱出機構の解明

柴田 果奈, Pratap Singh Akhil, 宮崎 裕介 , 篠田 渉

第 73 回コロイドおよび界面化学討論会  2022.9.20  公益社団法人 日本化学会 コロイドおよび界面化学部会

環境依存の構造変化を取り入れた粗視化タンパク質モデルの開発

山田 哲平，篠田 渉

第16回分子科学会  2022.9.21  分子科学会

ウイルス粒子の粗視化分子動力学シミュレーション：B型肝炎ウイルス粒子構造

浦野諒，篠田 渉

第16回分子科学会  2022.9.20  分子科学会

粗視化分子力場SPICAのタンパク質系への拡張と応用

宮崎 裕介，篠田 渉

第16回分子科学会  2022.9.19  分子科学会

ドナー性の異なる溶媒を用いた高濃度Li塩溶液における溶液構造とLiイオン輸送の関係性

重信 圭佑、 都築 誠二、 篠田 渉、 獨古 薫、 渡邉 正義、 上野 和英

2022年電気化学秋季大会  2022.9.9  公益社団法人 電気化学会

アンフォテリシンBが脂質膜中で形成するイオンチャネル複合体の構造と活性発現機構

梅川雄一、 山本智也、 Mayank Dixit、 中川泰男、 土川博史、 花島慎弥、 松森信明、 篠田　渉、 村田道雄

第64回天然有機化合物討論会  2022.9.8  第64回天然有機化合物討論会

粗視化分子モデルとその応用

篠田渉

第16回分子シミュレーションスクール  2022.9.6  計算科学研究センター

固体 NMR による脂質二重膜におけるリン脂質不飽和脂肪鎖の配 座・配向解析

安田 貴也 ・ 梅川 雄・ 篠田 渉 ・ 村田 道雄

日本化学会 第102春季年会(2022)  2022.3.26  公益社団法人日本化学会

アンフォテリシン B 会合体と構造化した リン脂質の相互作用の解明

片山 綾人 ・ 梅川 雄・ 篠田 渉 ・ 村田 道雄

日本化学会 第102春季年会(2022)  2022.3.25  公益社団法人日本化学会

2H-13C二重標識体を用いた固体 NMRによる飽 和リン脂質sn-1、sn-2アシル鎖の配座配向解析

○齋藤 宣樹、 梅川 雄、 篠田 渉、 村田 道雄

日本化学会 第102春季年会(2022)  2022.3.23  公益社団法人日本化学会

マルチスケール分子シミュレーションによる電解質系 の物性解析：高分子電解質の物性解析とリチウムイオ ン電池系のイオン伝導機構 Invited

篠田渉

第410回電池技術委員会  2022.2.4  公益社団法人 電気化学会 　電池技術委員会

生体膜・脂質膜の分子シミュレーション Invited

篠田渉

高分子計算機科学研究会  2022.1.13  公益社団法人 高分子学会

生体高分子自己集合系の分子シミュレーション Invited

篠田渉

スーパーコンピュータワークショップ2021 「 生体分子の構造・機能・デザインの計算科学」  2022.1.12  自然科学研究機構　岡崎共通研究施設　計算科学研究センター

MDシミュレーションによるスルホラン系Li塩高濃度電解液中のLiイオン拡散機構の調査

池田周平、都築誠二、上野和英、渡邉正義、篠田渉

溶液化学研究会若手の会 第1回冬季発表会  2021.12  溶液化学研究会若手の会

粗視化力場 pSPICA による抗菌ペプチドの細菌膜選択性の解明

川端一正、宮﨑裕介、篠田渉

溶液化学研究会若手の会 第1回冬季発表会  2021.12  溶液化学研究会若手の会

全原子分子動力学計算による PMMA の溶剤破壊の分子論

下岡稔，篠田渉，三宅大輝，原光生，河原聡平，眞弓皓一，藤本和士

溶液化学研究会若手の会 第1回冬季発表会  2021.12  溶液化学研究会若手の会

分子動力学法を用いたエタノール混合によるベシクル構造転移機構の解明

柴田果奈，真栄城正寿，渡慶次学，篠田渉

溶液化学研究会若手の会 第1回冬季発表会  2021.12  溶液化学研究会若手の会

Coarse-Grained Molecular Dynamics of Biomolecular Self-Assembly: Membranes, Vesicles, Lipid Nanoparticles, Virus Capsids Invited International conference

Wataru Shinoda

Pacifichem2021  2021.12.21  The Chemical Society of Japan

生体分子集合系の粗視化分子シミュレーション Invited

篠田渉

第16回理研「バイオものづくり」シンポジウム  2021.12.9  国立研究開発法人理化学研究所

分子動力学法を用いたスルホラン系 Li 塩濃厚電解液 における Li イオンダイナミクスの解析

池田周平、都築誠二、上野和英、渡邉正義、篠田渉

第35回分子シミュレーション討論会  2021.11  分子シミュレーション学会