Wataru Shinoda

Scopus Author ID Researcher Name Resolver ID ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 42

Top Topics

Hepatitis B Virus

Top Venues

Journal of chemical information and modeling

Journal of chemical theory and computation

The journal of physical chemistry. B

This page only lists publications with an associated author ORCID identifier.

Publications

Wenting Huo, Koji Miki, Huiying Mu, Takashi Osawa, Harumi Yamaguma, Yusuke Tamenori, Satoshi Obika, Yoshimasa Kawaguchi, Hisaaki Hirose, Shiroh Futaki, Yusuke Miyazaki, Wataru Shinoda, Shuji Akai, Kouichi Ohe
Light-controllable cell-membrane disturbance for intracellular delivery. Journal of materials chemistry. B (2024)
Masatoshi Maeki, Niko Kimura, Yuto Okada, Kazuki Shimizu, Kana Shibata, Yusuke Miyazaki, Akihiko Ishida, Kento Yonezawa, Nobutaka Shimizu, Wataru Shinoda, Manabu Tokeshi
Understanding the effects of ethanol on the liposome bilayer structure using microfluidic-based time-resolved small-angle X-ray scattering and molecular dynamics simulations. Nanoscale advances 6 (8) (2024)
Toru Ishikawa, Shohei Haga, Keisuke Shigenobu, Taku Sudoh, Seiji Tsuzuki, Wataru Shinoda, Kaoru Dokko, Masayoshi Watanabe, Kazuhide Ueno
Linear ether-based highly concentrated electrolytes for Li-sulfur batteries. Faraday discussions (2024)
Frederik Philippi, Maleen Middendorf, Keisuke Shigenobu, Yuna Matsuyama, Oriele Palumbo, David Pugh, Taku Sudoh, Kaoru Dokko, Masayoshi Watanabe, Monika Schönhoff, Wataru Shinoda, Kazuhide Ueno
Evolving better solvate electrolytes for lithium secondary batteries. Chemical science 15 (19) (2024)
Frederik Philippi, Maleen Middendorf, Keisuke Shigenobu, Yuna Matsuyama, Oriele Palumbo, David Pugh, Taku Sudoh, Kaoru Dokko, Masayoshi Watanabe, Monika Schönhoff, Wataru Shinoda, Kazuhide Ueno
Evolving better solvate electrolytes for lithium secondary batteries. Chemical science 15 (19) (2024)
Masatoshi Maeki, Niko Kimura, Yuto Okada, Kazuki Shimizu, Kana Shibata, Yusuke Miyazaki, Akihiko Ishida, Kento Yonezawa, Nobutaka Shimizu, Wataru Shinoda, Manabu Tokeshi
Understanding the effects of ethanol on the liposome bilayer structure using microfluidic-based time-resolved small-angle X-ray scattering and molecular dynamics simulations. Nanoscale advances 6 (8) (2024)
Wenting Huo, Koji Miki, Huiying Mu, Takashi Osawa, Harumi Yamaguma, Yusuke Tamenori, Satoshi Obika, Yoshimasa Kawaguchi, Hisaaki Hirose, Shiroh Futaki, Yusuke Miyazaki, Wataru Shinoda, Shuji Akai, Kouichi Ohe
Light-controllable cell-membrane disturbance for intracellular delivery. Journal of materials chemistry. B 12 (17) (2024)
Yusuke Miyazaki, Wataru Shinoda
pSPICA Force Field Extended for Proteins and Peptides. Journal of chemical information and modeling 64 (2) (2023)
Jiabin Luan, Danni Wang, Shaohua Zhang, Yusuke Miyazaki, Wataru Shinoda, Daniela A Wilson
Complex Energy Landscapes of Self-Assembled Vesicles. Journal of the American Chemical Society (2023)
Seiji Tsuzuki, Shuhei Ikeda, Wataru Shinoda, Keisuke Shigenobu, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe
Molecular Dynamics Simulations of High-Concentration Li[TFSA] Sulfone Solution: Effect of Easy Conformation Change of Sulfolane on Fast Diffusion of Li Ion. The journal of physical chemistry. B (2023)
Keisuke Shigenobu, Seiji Tsuzuki, Frederik Philippi, Taku Sudoh, Yosuke Ugata, Kaoru Dokko, Masayoshi Watanabe, Kazuhide Ueno, Wataru Shinoda
Molecular Level Origin of Ion Dynamics in Highly Concentrated Electrolytes. The journal of physical chemistry. B (2023)
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, Jozef Adam Liwo, Siewert-Jan Marrink, Paulo Cesar Telles de Souza
Pragmatic Coarse-Graining of Proteins: Models and Applications. Journal of chemical theory and computation (2023)
Teppei Yamada, Yusuke Miyazaki, Shogo Harada, Ashutosh Kumar, Stefano Vanni, Wataru Shinoda
Improved Protein Model in SPICA Force Field. Journal of chemical theory and computation (2023)
Yusuke Miyazaki, Wataru Shinoda
pSPICA Force Field Extended for Proteins and Peptides. Journal of chemical information and modeling (2023)
Yusuke Miyazaki, Wataru Shinoda
pSPICA Force Field Extended for Proteins and Peptides. Journal of chemical information and modeling 64 (2) (2023)
Yusuke Miyazaki, Wataru Shinoda
pSPICA Force Field Extended for Proteins and Peptides. Journal of chemical information and modeling 64 (2) (2023)
Dapeng Zhang, Qi Xiao, Mehrnoush Rahimzadeh, Matthew Liu, Cesar Rodriguez-Emmenegger, Yusuke Miyazaki, Wataru Shinoda, Virgil Percec
Self-Assembly of Glycerol-Amphiphilic Janus Dendrimers Amplifies and Indicates Principles for the Selection of Stereochemistry by Biological Membranes. Journal of the American Chemical Society (2023)
Yuichi Umegawa, Tomoya Yamamoto, Mayank Dixit, Kosuke Funahashi, Sangjae Seo, Yasuo Nakagawa, Taiga Suzuki, Shigeru Matsuoka, Hiroshi Tsuchikawa, Shinya Hanashima, Tohru Oishi, Nobuaki Matsumori, Wataru Shinoda, Michio Murata
Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study. Science advances 8 (24) (2022)
Shuhei Kawamoto, Huihui Liu, Yusuke Miyazaki, Sangjae Seo, Mayank Dixit, Russell DeVane, Christopher MacDermaid, Giacomo Fiorin, Michael L Klein, Wataru Shinoda
SPICA Force Field for Proteins and Peptides. Journal of chemical theory and computation 18 (5) (2022)
Hari O S Yadav, An-Tsung Kuo, Shingo Urata, Kosuke Funahashi, Yutaka Imamura, Wataru Shinoda
Adsorption characteristics of peptides on ω-functionalized self-assembled monolayers: a molecular dynamics study. Physical chemistry chemical physics : PCCP 24 (24) (2022)
Valeria Zoni, Rasha Khaddaj, Ivan Lukmantara, Wataru Shinoda, Hongyuan Yang, Roger Schneiter, Stefano Vanni
Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure. Proceedings of the National Academy of Sciences of the United States of America 118 (10) (2021)
Mark Z Griffiths, Wataru Shinoda
Analyzing the Role of Surfactants in the Colloidal Stability of Nanoparticles in Oil through Coarse-Grained Molecular Dynamics Simulations. The journal of physical chemistry. B 125 (23) (2021)
Kazushi Fujimoto, Youhei Yamaguchi, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, Susumu Okazaki
All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution. The Journal of chemical physics 155 (14) (2021)
Kaushik Chakraborty, Wataru Shinoda, Sharon M Loverde
Molecular simulation of the shape deformation of a polymersome. Soft matter 16 (13) (2020)
Hiroshi Tsuchikawa, Takuya Ono, Masaki Yamagami, Yuichi Umegawa, Wataru Shinoda, Michio Murata
Conformation and Orientation of Branched Acyl Chains Responsible for the Physical Stability of Diphytanoylphosphatidylcholine. Biochemistry 59 (40) (2020)
Kyle Wm Hall, Simona Percec, Wataru Shinoda, Michael L Klein
Property Decoupling across the Embryonic Nucleus-Melt Interface during Polymer Crystal Nucleation. The journal of physical chemistry. B 124 (23) (2020)
Tetsuro Nagai, Shuhei Tsurumaki, Ryo Urano, Kazushi Fujimoto, Wataru Shinoda, Susumu Okazaki
Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement. Journal of chemical theory and computation 16 (12) (2020)
Sangjae Seo, Michio Murata, Wataru Shinoda
Pivotal Role of Interdigitation in Interleaflet Interactions: Implications from Molecular Dynamics Simulations. The journal of physical chemistry letters 11 (13) (2020)
Kyle Wm Hall, Timothy W Sirk, Simona Percec, Michael L Klein, Wataru Shinoda
Monodisperse Polymer Melts Crystallize via Structurally Polydisperse Nanoscale Clusters: Insights from Polyethylene. Polymers 12 (2) (2020)
Yusuke Miyazaki, Susumu Okazaki, Wataru Shinoda
pSPICA: A Coarse-Grained Force Field for Lipid Membranes Based on a Polar Water Model. Journal of chemical theory and computation 16 (1) (2019)
Huihui Liu, Susumu Okazaki, Wataru Shinoda
Heteroaryldihydropyrimidines Alter Capsid Assembly By Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein. Journal of chemical information and modeling 59 (12) (2019)
Mark Z Griffiths, Wataru Shinoda
tSPICA: Temperature- and Pressure-Dependent Coarse-Grained Force Field for Organic Molecules. Journal of chemical information and modeling 59 (9) (2019)
Hari O S Yadav, An-Tsung Kuo, Shingo Urata, Wataru Shinoda
Effects of Packing Density and Chain Length on the Surface Hydrophobicity of Thin Films Composed of Perfluoroalkyl Acrylate Chains: A Molecular Dynamics Study. Langmuir : the ACS journal of surfaces and colloids 35 (44) (2019)
Kosuke Takeda, Yoshimichi Andoh, Wataru Shinoda, Susumu Okazaki
Molecular Behavior of Linear Alkylbenzene Sulfonate in Hydrated Crystal, Tilted Gel, and Liquid Crystal Phases Studied by Molecular Dynamics Simulation. Langmuir : the ACS journal of surfaces and colloids 35 (33) (2019)
Tomoya Yamamoto, Yuichi Umegawa, Hiroshi Tsuchikawa, Shinya Hanashima, Nobuaki Matsumori, Kosuke Funahashi, Sangjae Seo, Wataru Shinoda, Michio Murata
The Amphotericin B-Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly. Biochemistry 58 (51) (2019)
Kosuke Takeda, Yoshimichi Andoh, Wataru Shinoda, Susumu Okazaki
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. Langmuir : the ACS journal of surfaces and colloids 35 (27) (2019)
Kyle Wm Hall, Timothy W Sirk, Simona Percec, Michael L Klein, Wataru Shinoda
Divining the shape of nascent polymer crystal nuclei. The Journal of chemical physics 151 (14) (2019)
Masaki Yamagami, Hiroshi Tsuchikawa, Jin Cui, Yuichi Umegawa, Yusuke Miyazaki, Sangjae Seo, Wataru Shinoda, Michio Murata
Average Conformation of Branched Chain Lipid PGP-Me That Accounts for the Thermal Stability and High-Salinity Resistance of Archaeal Membranes. Biochemistry 58 (37) (2019)
Kaoru Dokko, Daiki Watanabe, Yosuke Ugata, Morgan L Thomas, Seiji Tsuzuki, Wataru Shinoda, Kei Hashimoto, Kazuhide Ueno, Yasuhiro Umebayashi, Masayoshi Watanabe
Direct Evidence for Li Ion Hopping Conduction in Highly Concentrated Sulfolane-Based Liquid Electrolytes. The journal of physical chemistry. B 122 (47) (2018)
Wataru Shinoda, Yuta Hatanaka, Masashi Hirakawa, Susumu Okazaki, Seiji Tsuzuki, Kazuhide Ueno, Masayoshi Watanabe
Molecular dynamics study of thermodynamic stability and dynamics of [Li(glyme)]+ complex in lithium-glyme solvate ionic liquids. The Journal of chemical physics 148 (19) (2018)
Sangjae Seo, Wataru Shinoda
SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol. Journal of chemical theory and computation 15 (1) (2018)
Soumya Lipsa Rath, Huihui Liu, Susumu Okazaki, Wataru Shinoda
Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals. Journal of chemical information and modeling 58 (2) (2018)