PublicationsPapers

2024

7.	"Discrimination of extracellular miRNA sources for the identification of tumor-related functions based on nanowire thermofluidics", K. Chattrairat, A. Yokoi, M. Zhang, M. Iida, K. Yoshida, M. Kitagawa, A. Niwa, M, Maeki, T. Hasegawa, T. Yokoyama, Y. Tanaka, Y. Miyazaki, W. Shinoda, M. Tokeshi, K. Nagashima, T. Yanagida, H. Kajiyama, Y. Baba, and T. Yasui Device, 2 100363 (2024).
6.	"Evolving Better Solvate Electrolytes for Lithium Secondary Batteries", F. Philippi, M. Middendorf, K. Shigenobu, Y. Matsuyama, O. Palumbo, D. Pugh, T. Sudoh, K. Dokko, M. Watanabe, M. Schonhoff, W. Shinoda, and K. Ueno, Chem. Sci., 15 7342-7358 (2024).
5.	"Linear ether-based highly concentrated electrolytes for Li-sulfur batteries", Toru Ishikawa , Shohei Haga , Keisuke Shigenobu , Taku Sudoh , Seiji Tsuzuki , Wataru Shinoda , Kaoru Dokko , Masayoshi Watanabe and Kazuhide Ueno* Faraday Discuss. in press (2024). DOI:10.1039/D4FD00024B
4.	"Light-controllable cell-membrane disturbance for intracellular delivery", 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, and Kouichi Ohe* J. Mater. Chem. B 12 4138-4147 (2024).
3.	"Understanding the effects of ethanol on structural changes in liposomes using microfluidic-based time-resolved small-angle X-ray scattering and MD simulations", Masatoshi Maeki, Niko Kimura, Yuto Okada, Kazuki Shimizu, Kana Shibata, Yusuke Miyazaki, Akihiko Ishida, Kento Yonezawa, Nobutaka Shimizu, Wataru Shinoda, Manabu Tokeshi Nanoscale Adv. 6 2166-2176 (2024).
2.	"Protein–lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin", Yuichi Umegawa, Sho Kato, Sangjae Seo, Wataru Shinoda, Satoshi Kawatake, Shigeru Matsuoka, Michio Murata, Biophys. Chem. 308, 107204 (2024).
1.	"pSPICA Force Field Extended for Proteins and Peptides", Yusuke Miyazaki and Wataru Shinoda J. Chem. Inf. Model. 64, 532-542 (2024).

2023

12.	"Molecular Level Origin of Ion Dynamics in Highly Concentrated Electrolytes", Keisuke Shigenobu, Seiji Tsuzuki, Frederik Philippi, Taku Sudoh, Yosuke Ugata, Kaoru Dokko, Masayoshi Watanabe, Kazuhide Ueno, Wataru Shinoda J. Phys. Chem. B 127, 10422-10433 (2023).
11.	"Improved Protein Model in SPICA Force Field", Teppei Yamada, Yusuke Miyazaki, Shogo Harada, Ashutosh Kumar, Stefano Vanni, and Wataru Shinoda J. Chem. Theory Comput. 19, 8967-8977 (2023).
10.	"HER-2-targeted Boron Neutron Capture Therapy with Carborane-integrated Immunoliposomes Prepared via an Exchanging Reaction", 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 Chem. Eur. J. 29 e202302486 (2023).
9.	"Pragmatic Coarse-Graining of Proteins: Models and Applications", Luis Borges-Araujo, 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, and Paulo C. T. Souza J. Chem. Theory Comput. 19, 7112-7135 (2023).
8.	"Complex Energy Landscapes of Self-Assembled Vesicles", Jiabin Luan, Danni Wang, Shaohua Zhang, Yusuke Miyazaki, Wataru Shinoda, and Daniela Wilson, J. Am. Chem. Soc. 145, 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", Seiji Tsuzuki, Shuhei Ikeda, Wataru Shinoda, Keisuke Shigenobu, Kazuhide Ueno, Kaoru Dokko, and Masayoshi Watanabe, J. Phys. Chem. B 127, 6333-6341(2023).
6.	"Lithium-Ion Dynamics in Sulfolane-based Highly Concentrated Electrolyte", Shuhei Ikeda, Seiji Tsuzuki, Taku Sudoh, Keisuke Shigenobu, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe, and Wataru Shinoda J. Phys. Chem. C 127, 13837-13845(2023).
5.	"Li-Ion Transport and Solution Structure in Sulfolane-Based Localized High-Concentration Electrolytes", Taku Sudoh, Shuhei Ikeda, Keisuke Shigenobu, Seiji Tsuzuki, Kaoru Dokko, Masayoshi Watanabe, Wataru Shinoda, and Kazuhide Ueno J. Phys. Chem. C, 127, 12295-12303 (2023).
4.	"Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy", 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 Biosens. Bioelectron. 234, 115318 (2023).
3.	"Liquid Structures and Ion Dynamics of Ionic Liquids viewed from Intermolecular Interactions", Seiji Tsuzuki and Wataru Shinoda, Chem. Rec. 23, e202200272 (2023).
2.	"Self-Assembly of Glycerol-Amphiphilic Janus Dendrimers Amplifies and Indicates Principles for the Selection of Stereochemistry by Biological Membranes", Dapeng Zhang, Qi Xiao, Mehrnoush Rahimzadeh, Matthew Liu, Cesar Rodriguez-Emmenegger, Yusuke Miyazaki, Wataru Shinoda, and Virgil Percec J. Am. Chem. Soc 145, 4311-4323 (2023).
1.	"Fluorescence Turn-on of Tetraphenylethylene Derivative by Transfer from Cyclodextrin to Liposomes, Hela cells, and E. Coli", Kosuke Masuda, Riku Omokawa, Riku Kawasaki, Yuta Mise, Yousuke Ooyama, Shogo Harada, Wataru Shinoda, and Atsushi Ikeda, Chem. Eur. J. 29, e2022203071 (2023).

2022

2021

9.	"Effects of Li ion-solvent interaction on ionic transport and electrochemical properties in highly concentrated cyclic carbonate electrolytes", Keisuke Shigenobu, Taku Sudoh, Mayu Tabuchi, Seiji Tsuzuki, Wataru Shinoda, Kaoru Dokko, Masayoshi Watanabe, and Kazuhide Ueno, J. Non-Cryst. Solids: X, 11-12 100071 (2021).
8.	"Domain Formation in Charged Polymer Vesicles", Kaushik Chakraborty, Prabir Khatua, Wataru Shinoda, and Sharon M Loverde, Macromolecules, 54 9258–9267 (2021).
7.	"All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution", Kazushi Fujimoto, Youhei Yamaguchi, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, and Susumu Okazaki, J. Chem. Phys. 155 145101 (2021).
6.	"Properties and Dynamics by Computer Simulation", Seiji Tsuzuki, and Wataru Shinoda, in "Next Generation Batteries: Realization of High Energy Density Rechargeable Batteries" K. Kanamura ed. Springer Nature Singapore, 2021; pp. 301-310.
5.	"Analyzing the Role of Surfactants in the Colloidal Stability of Nanoparticles in Oil through Coarse-Grained Molecular Dynamics Simulations", Mark Griffiths and Wataru Shinoda, J. Phys. Chem. B 125 6315-6321 (2021).
4.	"Hemimicelle Formation of Semi-fluorocarbon Chains at Air–Water Interface: Coarse-Grained Molecular Dynamics Study with an Extension of the SPICA Force Field", Hari O. S. Yadav, Shogo Harada, An-Tsung Kuo, Shingo Urata, and Wataru Shinoda, Mol. Phys. e1910355 (2021).
3.	"Thermodynamic aspect of sulfur, polysulfide anion and lithium polysulfide: Plausible reaction path during discharge of lithium-sulfur battery", Seiji Tsuzuki, Tomoaki Kaneko, Keitaro Sodeyama, Yasuhiro Umebayashi, Wataru Shinoda, Shiro Seki, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe, Phys. Chem. Chem. Phys. 23 6832-6840 (2021).
2.	"Seipin Accumulates and Traps Diacylglycerols and Triglycerides in Its Ring-Like Structure", Valeria Zoni, Rasha Khaddaj, Ivan Lukmantara, Wataru Shinoda, Hongyuan Yang, Roger Schneiter, and Stefano Vanni, Proc. Natl. Acad. Sci. USA, 118 e2017205118 (2021).
1.	"Chain-End Modification: A Starting Point for Controlling Polymer Crystal Nucleation", Kyle Wm. Hall, Simona Percec, Wataru Shinoda, and Michael L. Klein, Macromolecules, 54 1599-1610 (2021).

2020

11.	"Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement", Tetsuro Nagai, Shuhei Tsurumaki, Ryo Urano, Kazushi Fujimoto, Wataru Shinoda, and Susumu Okazaki, J. Chem. Theory Comput. 16 7239-7254 (2020).
10.	"Conformation and orientation of branched acyl chains responsible for the physical stability of diphytanoylphosphatidylcholine", Hiroshi Tsuchikawa, Takuya Ono, Masaki Yamagami, Yuichi Umegawa, Wataru Shinoda, and Michio Murata Biochemistry, 59 3929-3938 (2020).
9.	"Pivotal Role of Interdigitation in Interleaflet Interactions: Implications from Molecular Dynamics Simulations", Sangjae Seo, Michio Murata, Wataru Shinoda, J. Phys. Chem. Lett., 11 5171-5176 (2020).
8.	"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", Ryo Urano, Wataru Shinoda, Noriyuki Yoshii, Susumu Okazaki, J. Chem. Phys., 152 244115 (2020).
7.	"Effect of Packing Density on the Surface Hydrophobicity of ω-Functionalized (–CF3, –CH3, –OCH3, and –OH) Self-assembled Monolayers: A Molecular Dynamics Study", Hari Yadav, An-Tsung Kuo, Shingo Urata, Wataru Shinoda, J. Phys. Chem. C, 124 14237-14244 (2020).
6.	"Property Decoupling across the Embryonic Nucleus-Melt Interface during Polymer Crystal Nucleation", Kyle Wm Hall, Simona Percec, Wataru Shinoda, Michael L Klein, J. Phys. Chem. B, 124 4793-4804 (2020).
5.	"Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation", Kazushi Fujimoto, Motohiro Fukai, Ryo Urano, Wataru Shinoda, Tetsuya Ishikawa, Katsumi Omagari, Yasuhito Tanaka, Atsushi Nakagawa, Susumu Okazaki, Pure & Appl. Chem. 92 1585-1594 (2020).
4.	"Molecular Simulation of the Shape Deformation of a Polymersome", Kaushik Chakraborty, Wataru Shinoda, Sharon M. Loverde, Soft Matter, 16 3234-3244 (2020).
3.	"Effects of anion on liquid structures of ionic liquids at graphene electrode interface analyzed by molecular dynamics simulations", Seiji Tsuzuki, Takenobu Nakamura, Tetsuya Morishita, Wataru Shinoda, Shiro Seki, Yasuhiro Umebayashi, Kazuhide Ueno, Kaoru Dokko, Masayoshi Watanabe, Batteries & Supercaps, 3 658-667 (2020).
2.	"Monodisperse Polymer Melts Crystallize via Structurally Polydisperse Nanoscale Clusters: Insights from Polyethylene", Kyle Wm Hall, Timothy W Sirk, Simona Percec, Michael L Klein, Wataru Shinoda, Polymers, 12 447 (2020).
1.	"pSPICA: A coarse-grained force field for lipid membranes based on a polar water model", Yusuke Miyazaki, Susumu Okazaki, and Wataru Shinoda, J. Chem. Theory Comput. 16 782-793 (2020).

2019

17.	"Amphotericin B-Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly", Tomoya Yamamoto, Yuichi Umegawa, Hiroshi Tsuchikawa, Shinya Hanashima, Nobuaki Matsumori, Kosuke Funahashi, Sangjae Seo, Wataru Shinoda, Michio Murata, Biochemistry, 58 5188-5196 (2019).
16.	"Heteroaryldihydropyrimidines Alter Capsid Assembly by Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein", Huihui Liu, Susumu Okazaki and Wataru Shinoda, J. Chem. Inf. Model. 59 5104-5110 (2019).
15.	"Large-scale molecular dynamics simulation of perfluorosulfonic acid membranes: Remapping coarse-grained to all-atomistic simulations", An-Tsung Kuo, Yusuke Miyazaki, Changwoon Jang, Tatsuya Miyajima, Shingo Urata, Steven O Nielsen, Susumu Okazaki, Wataru Shinoda, Polymer, 181 121766 (2019).
14.	"Average Conformation of Branched-Chain Lipid PGP-Me that Accounts for the Thermal Stability and High-Salinity Registance of Archaeal Membranes", Masaki Yamagami, Hiroshi Tsuchikawa, Jin Cui, Yuichi Umegawa, Yusuke Miyazaki, Sangjae Seo, Wataru Shinoda, Michio Murata, Biochemistry, 58 3869-3879 (2019).
13.	"Effects of Packing Density and Chain Length on the Surface Hydrophobicity of Thin-Films Composed of Perfluoroalkyl Acrylate Chains: A Molecular Dynamics Study", Hari Yadav, An-Tsung Kuo, Shingo Urata, Wataru Shinoda, Langmuir, 35, 14316-14323 (2019).
12.	"tSPICA: Temperature-and Pressure-dependent Coarse-Grained Force Field for Organic Molecules", Mark Z Griffiths, Wataru Shinoda, J. Chem. Inf. Model. 59, 3829-3838 (2019).
11.	"All-atom Molecular Dynamics Study of Impact Fracture of Glassy Polymers. I: Molecular Mechanisms of Brittleness of PMMA and Ductility of PC", Kazushi Fujimoto, Zhiye Tang, Wataru Shinoda, and Susumu Okazaki, Polymer, 178, 121570 (2019)
10.	"Divining the Shape of Nascent Polymer Crystal Nuclei", Kyle Wm Hall, Timothy W Sirk, Simona Percec, Michael L Klein, Wataru Shinoda, J. Chem. Phys. 151, 144901 (2019).
9.	"A Coarse-Grain Model for Entangled Polyethylene Melts and Polyethylene Crystallization", Kyle Wm Hall, Timothy W Sirk, Michael L Klein, Wataru Shinoda, J. Chem. Phys. 150, 244901 (2019).
8.	"Hydrogen Permeation in Hydrated Perfluorosulfonic Acid Polymer Membranes: Effect of Polymer Crystallinity and Equivalent Weight", Kotono Takeuchi, An-Tsung Kuo, Takeshi Hirai, Tatsuya Miyajima, Shingo Urata, Shinji Terazono, Susumu Okazaki, and Wataru Shinoda, J. Phys. Chem. C, 123, 20628-20638 (2019).
7.	"Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup", Shinya Hanashima, Kazuhiro Murakami, Michihiro Yura, Yo Yano, Yuichi Umegawa, Hiroshi Tsuchikawa, Nobuaki Matsumori, Sangjae Seo, Wataru Shinoda, and Michio Murata, Biophys. J. 117, 307–318 (2019).
6.	"Molecular Behavior of Linear Alkylbenzene Sulfonate in Hydrated Crystal, Tilted Gel, and Liquid Crystal Phases Studied by Molecular Dynamics Simulation", Takeda, Kosuke; Andoh, Yoshimichi; Shinoda, Wataru; Okazaki, Susumu, Langmuir 35, 10877-10884 (2019).
5.	"Molecular mechanism of material deformation and failure in butadiene rubber: Insight from all-atom molecular dynamics simulation using a bond breaking potential model", Rajdeep Singh Payal, Kazushi Fujimoto, Changwoon Jang, Wataru Shinoda, Yuki Takei, Hiroshi Shima, Katsuhiko Tsunoda, Susumu Okazaki, Polymer, 170, 113-119 (2019).
4.	"Development of dissociative force field for all-atomistic molecular dynamics calculation of fracture of polymers", Kazushi Fujimoto, Rajadeep Singh Payal, Tomonori Hattori, Wataru Shinoda, Masayuki Nakagaki, Shigeyoshi Sakaki, Susumu Okazaki, J. Comput. Chem. 40, 2571-2576 (2019).
3.	"Free energy analysis of membrane pore formation process in the presence of multiple melittin peptides", Yusuke Miyazaki, Susumu Okazaki and Wataru Shinoda, BBA-Biomembranes, 1861, 1409-1419 (2019).
2.	"Structure of Hydrated Crystal (Lc), Tilted Gel (Lβ'), and Liquid Crystal (Lα) Phases of Linear Alkylbenzene Sulfonate (LAS) Studied byX-ray Diffraction and Molecular Dynamics Simulation", KosukeTakeda, Yoshimichi Andoh, Wataru Shinoda, Susumu Okazaki, Langumuir 35, 9011-9019 (2019).
1.	"SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol", Sangjae Seo, Wataru Shinoda, J. Chem. Theory Comput. 15, 762-774 (2019).

2018

2017

2016

2015

2014