篠田　渉　（しのだ　わたる）

岡山大学
異分野基礎科学研究所
理学部化学科兼担
教授



略歴：
1998年3月　東京工業大学総合理工学研究科　博士課程修了　（理学博士）
1998年4月　三菱化学(株)　横浜総合研究所
2000年4月　通産省　工業技術院　物質工学工業研究所
2001年4月　独立行政法人 産業技術総合研究所
（2005年4月-2007年3月　ペンシルバニア大学化学科　客員研究員）
2014年1月　名古屋大学　大学院工学研究科
2021年10月　岡山大学　異分野基礎科学研究所（理学部化学科兼担）

受賞：
平成20年度 分子シミュレーション研究会　学術賞 「両親媒性分子の自己集合構造の分子シミュレーション」
平成23年度 日本油化学会　オレオサイエンス賞 「分子シミュレーションによる界面活性剤・脂質分子自己集合体構造の研究」

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Last updated:　December 25, 2023

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以上，すべてGnu GPLで無償公開．

発表論文等

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2025

162. M. Musa, Z. Zhu, H. Takahashi, W. Shinoda, Y. Baba, and T. Yasui, "Selective adsorption of unmethylated DNA on ZnO nanowires for separation of methylated DNA", Lab Chip 25, 1637-1646(2025).
161. K. A. Alberto, H. B. M. Nazar, H. Xiong, W. Shinoda, P. A. Slesinger, Z. Qin, and S. O. Nielsen, "Fully atomistic molecular dynamics modeling of photoswitchable azo-PC lipid bilayers: structure, mechanical properties, and drug permeation", Nanoscale 17, 2032-2042 (2025).
160. Y. Umegawa, H. Tsuchikawa, W. Shinoda, and M. Murata, "NMR and molecular simulation studies on structure elucidation of the Amphotericin B ion-channel using 13C and 19F-labelling", Org. Biomol. Chem. 23, 1233-1252 (2025).
Front Cover from Organic and Biomolecular Chemistry, Vol. 23 Number 6, Feb. 14, 2025.

2024

159. 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, "Discrimination of extracellular miRNA sources for the identification of tumor-related functions based on nanowire thermofluidics", Device, 2, 100363 (2024).
158. 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, "Evolving Better Solvate Electrolytes for Lithium Secondary Batteries", Chem. Sci. 15, 7342-7358 (2024).
157. T. Ishikawa , S. Haga , K. Shigenobu , T. Sudoh , S. Tsuzuki , W. Shinoda , K. Dokko , M. Watanabe, and K. Ueno, "Linear ether-based highly concentrated electrolytes for Li-sulfur batteries", Faraday Discuss., 253, 385-406 (2024).
156. W. Huo, K. Miki, H. Mu, T. Osawa, H. Yamaguma, Y. Kasahara, S. Obika, Y. Kawaguchi, H. Hirose, S. Futaki, Y. Miyazaki, W. Shinoda, S. Akai, and K. Ohe, "Light-controllable cell-membrane disturbance for intracellular delivery", J. Mater. Chem. B, 12, 4138-4147 (2024).
Front Cover from Journal of Materials Chemistry B, Vol. 12 Number 17, May. 7, 2024.
155. M. Maeki, N. Kimura, Y. Okada, K. Shimizu, K. Shibata, Y. Miyazaki, A. Ishida, K. Yonezawa, N. Shimizu, W. Shinoda, and M. Tokeshi, "Understanding the effects of ethanol on structural changes in liposomes using microfluidic-based time-resolved small-angle X-ray scattering and MD simulations", Nanoscale Adv., 6, 2166-2176 (2024).
154. Y. Umegawa, S. Kato, S. Seo, W. Shinoda, S. Kawatake, S. Matsuoka, and M. Murata, "Protein–lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin", Biophys. Chem., 308, 107204 (2024).
J21. 篠田 渉, "分子シミュレーションによる脂質ナノ粒子の構造とエンドソーム脱出機構の解析", ファルマシア, 60 (2), 101-105 (2024).
153. Y. Miyazaki and W. Shinoda, "pSPICA Force Field Extended for Proteins and Peptides", J. Chem. Inf. Model., 64, 532-542 (2024).

2023

152. K. Shigenobu, S. Tsuzuki, F. Philippi, T. Sudoh, Y. Ugata, K. Dokko, M. Watanabe, K. Ueno, and W. Shinoda, "The molecular level origin of ion dynamics in highly concentrated electrolytes", J. Phys. Chem. B, 127, 10422-10433 (2023).
151. T. Yamada, Y. Miyazaki, S. Harada, A. Kumar, S. Vanni, and W. Shinoda, "Improved Protein Model in SPICA Force Field", J. Chem. Theory Comput., 19, 8967-8977(2023).
Supplementary Cover from Journal of Chemical Theory and Computation, Vol. 19 issue 23, Dec. 12, 2023.
150. R. Kawasaki, A. Oshige, K. Yamana, H. Hirano, K. Nishimura, Y. Miura, R. Yorioka, Y. Sanada, K. Bando, A. Tabata, K. Yasuhara, Y. Miyazaki, W. Shinoda, T. Nishimura, H. Azuma, T. Takata, Y. Sakurai, H. Tanaka, M. Suzuki, T. Nagasaki, and A. Ikeda "HER-2-targeted Boron Neutron Capture Therapy with Carborane-integrated Immunoliposomes Prepared via an Exchanging Reaction", Chem. Eur. J., 29 e202302486(2023).
149. 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, "Pragmatic Coarse-Graining of Proteins: Models and Applications", J. Chem. Theory Comput. 19 7112-7135 (2023).
J20. 梅川 雄一, 篠田 渉, 村田 道雄, "抗真菌剤アンフォテリシンBのイオンチャネル構造と作用機構:固体NMRと計算科学による天然有機化合物の会合体の研究", 化学と生物, 61, 419-431 (2023).
J19. 篠田 渉, "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農耕リチウム塩電解液中のイオン伝導機構", 電池技術, 35, 167-177 (2023).
148. J. Luan, D. Wang, S. Zhang, Y. Miyazaki, W. Shinoda, and D. Wilson, "Complex Energy Landscapes of Self-Assembled Vesicles", J. Am. Chem. Soc. 145 15496-15506 (2023).
147. S. Tsuzuki, S. Ikeda, W. Shinoda, K. Shigenobu, K. Ueno, K. Dokko, and M. Watanabe, "Molecular dynamics simulations of high-concentration Li[TFSA] sulfone solution: Effect of easy conformation change of sulfolane on fast diffusion of Li ion, J. Phys. Chem. B, 127, 6333-6341(2023).
146. S. Ikeda, S. Tsuzuki, T. Sudoh, K. Shigenobu, K. Ueno, K. Dokko, M. Watanabe, and W. Shinoda "Lithium-Ion Dynamics in Sulfolane-based Highly Concentrated Electrolyte", J. Phys. Chem. C, 127, 13837-13845(2023).
145. T. Sudoh, S. Ikeda, K. Shigenobu, S. Tsuzuki, K. Dokko, M. Watanabe, W. Shinoda, and K. Ueno "Li-Ion Transport and Solution Structure in Sulfolane-Based Localized High-Concentration Electrolytes", J. Phys. Chem. C, 127 12295-12303 (2023).
144. H. Takahashi, T. Yasui, M. Hirano, K. Shinjo, Y. Miyazaki, W. Shinoda, T. Hasegawa, A. Natsume, Y. Kitano, M. Ida, M. Zhang, T. Shimada, P. Paisrisarn, Z. Zhu, F. Ohka, K. Aoki, S. Rahong, K. Nagashima, T. Yanagida, Y. Baba, "Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy", Biosens. Bioelectron. 234, 115318 (2023).
143. S. Tsuzuki and W. Shinoda, "Liquid Structures and Ion Dynamics of Ionic Liquids viewed from Intermolecular Interactions ", Chem. Rec. 23, e202200272 (2023).
142. D. Zhang, Q. Xiao, M. Rahimzadeh, M. Liu, C. Rodriguez-Emmenegger, Y. Miyazaki, W. Shinoda, and V. Percec, "Self-Assembly of Glycerol-Amphiphilic Janus Dendrimers Amplifies and Indicates Principles for the Selection of Stereochemistry by Biological Membranes ", J. Am. Chem. Soc. 145, 4311-4323 (2023).
141. K. Masuda, R. Omokawa, R. Kawasaki, Y. Mise, Y. Ooyama, S. Harada, W. Shinoda, and A. Ikeda, "Fluorescence Turn-on of Tetraphenylethylene Derivative by Transfer from Cyclodextrin to Liposome, HeLa cells, and E. coli ", Chem. Eur. J. 29, e202203071 (2023).

2022

140. H. O. S. Yadav, A. Kuo, S. Urata, K. Funahashi, Y. Imamura, and W. Shinoda, "Adsorption Characteristics of Peptides on the ω-Functionalized Self-assembled Monolayers: A Molecular Dynamics Study", Phys. Chem. Chem. Phys. 24, 14805-14815 (2022).
selected as 2022 PCCP HOT Articles
139. Y. Umegawa, T. Yamamoto, M. Dixit, K. Funahashi, S. Seo, Y. Nakagawa, T. Suzuki, S. Matsuoka, H. Tsuchikawa, S. Hanashima, T. Oishi, N. Matsumori, W. Shinoda, M. Murata, "Amphotericin B Assembles into Seven-Molecule Ion Channels: An NMR and Molecular Dynamics Study", Sci. Adv. 8, eabo2658 (2022).
138. Y. Miyazaki and W. Shinoda, "Cooperative Antimicrobial Action of Melittin on Lipid Membranes: A Coarse-Grained Molecular Dynamics Study", Biochem. Biophys. Acta- Biomembranes,1864, 183955 (2022).
137. S. Kawamoto, H. Liu, Y. Miyazaki, S. Seo, M. Dixit, R. DeVane, C. MacDermaid, G. Fiorin, M. L. Klein, W. Shinoda, "The SPICA Coarse-Grained Force Field for Proteins and Peptides", J. Chem. Theory Comput. 18, 3204-3217 (2022).

2021

136. K. Shigenobu, T. Sudoh, M. Tabuchi, S. Tsuzuki, W. Shinoda, K. Dokko, M. Watanabe, and K. Ueno, "Effects of Li ion-solvent interaction on ionic transport and electrochemical properties in highly concentrated cyclic carbonate electrolytes", J. Non-Cryst. Solids X, 11-12, 100071(2021).
135. K. Chakraborty, P. Khatua, W. Shinoda, S. M. Loverde, "Domain Formation in Charged Polymer Vesicles", Macromolecules 54, 9258–9267(2021).
134. K. Fujimoto, Y. Yamaguchi, R. Urano, W. Shinoda, T. Ishikawa, K. Omagari, Y. Tanaka, A. Nakagawa, S. Okazaki, "All-atom molecular dynamics study of hepatitis B virus containing pregenome RNA in solution", J. Chem. Phys. 155, 145101(2021).
133. M. Griffiths and W. Shinoda, "Analyzing the Role of Surfactants on the Colloidal Stability of Nanoparticles in Oil Through Coarse-Grained Molecular Dynamics Simulations", J. Phys. Chem. B 125, 6315-6321 (2021).
Cover from Journal of Physical Chemistry B, Vol. 125 issue 23, June 17, 2021.
132. H. O. S. Yadav, S. Harada, A. Kuo, S. Urata, and W. Shinoda, "Hemimicelle Formation of Semi-fluorocarbon Chains at Air–Water Interface: Coarse-Grained Molecular Dynamics Study with an Extension of the SPICA Force Field", Mol. Phys. e1910355 (2021).
131. S. Tsuzuki, T. Kaneko, K. Sodeyama, Y. Umebayashi, W. Shinoda, S. Seki, K. Ueno, K. Dokko, M. Watanabe, "Thermodynamic aspect of sulfur, polysulfide anion and lithium polysulfide: Plausible reaction path during discharge of lithium-sulfur battery", Phys. Chem. Chem. Phys. 23 6832-6840 (2021).
130. V. Zoni, R. Khaddaj, I. Lukmantara, W Shinoda, H. Yang, R. Schneiter, and S. Vanni, "Seipin accumulates and traps diacylglycerols and triglycerides in its ring-like structure", Proc. Natl. Acad. Sci. U.S.A. 118 e2017205118 (2021).
129. K. W. Hall, S. Percec, W. Shinoda, M. L. Klein, "Chain-End Modification: A Starting Point for Controlling Polymer Crystal Nucleation", Macromolecules, 54, 1599-1610 (2021).
Supplementary Cover from Macromolecules Vol 54 issue 4, Feb 23, 2021.

2020

128. T. Nagai, S. Tsurumaki, R. Urano, K. Fujimoto, W. Shinoda, and S. Okazaki, "Position-Dependent Diffusion Constant of Molecules in Heterogeneous Systems as Evaluated by the Local Mean Squared Displacement", J. Chem. Theory Comput. 16, 7239-7254 (2020).
127. H. Tsuchikawa, T. Ono, M. Yamagami, Y. Umegawa, W. Shinoda, and M. Murata, "Conformation and orientation of branched acyl chains responsible for the physical stability of diphytanoylphosphatidylcholine", Biochemistry, 59, 3929-3938 (2020).
126. S. Seo, M. Murata, W. Shinoda, "Pivotal Role of Interdigitation in Interleaflet Interactions: Implications from Molecular Dynamics Simulations", J. Phys. Chem. Lett. 11, 5171-5176 (2020).
125. R. Urano, W. Shinoda, N. Yoshii, S. Okazaki, "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", J. Chem. Phys. 152, 244115 (2020).
124.

H. Yadav, A. Kuo, S. Urata, W. Shinoda, "Effect of Packing Density on the Surface Hydrophobicity of ω-Functionalized (–CF3, –CH3, –OCH3, and –OH) Self-assembled Monolayers: A Molecular Dynamics Study", J. Phys. Chem. C, 124, 14237-14244 (2020).
Supplementary Cover from J. Phys. Chem. C Vol 124 issue 26, July 2, 2020.
123. K. W. Hall, S. Percec, W. Shinoda, M. L Klein, "Property Decoupling across the Embryonic Nucleus-Melt Interface during Polymer Crystal Nucleation", J. Phys. Chem. B, 124, 4793-4804 (2020).
Supplementary Cover from J. Phys. Chem. B Vol 124 issue 23, June 11, 2020.
122. K. Fujimoto, M. Fukai, R. Urano, W. Shinoda, T. Ishikawa, K. Omagari, Y. Tanaka, A. Nakagawa, S. Okazaki, "Free energy profile of permeation of Entecavir through Hepatitis B virus capsid studied by molecular dynamics calculation", Pure Appl. Chem. 92, 1585-1594 (2020).
121. S. Tsuzuki, T. Nakamura, T. Morishita, W. Shinoda, S. Seki, Y. Umebayashi, K. Ueno, K. Dokko, M. Watanabe, "Effects of anion on liquid structures of ionic liquids at graphene electrode interface analyzed by molecular dynamics simulations", Batteries & Supercaps, 3, 658-667 (2020).
120. K. Chakraborty, W. Shinoda, S. M. Loverde, "Molecular Simulation of the Shape Deformation of a Polymersome" Soft Matter, 16, 3234-3244 (2020).
119. K. W. Hall, T. W. Sirk, S. Percec, M. L. Klein, W. Shinoda, "Monodisperse polymer melts crystallize via structurally polydisper nanoscale clusters: Insights from polyethylene" Polymers, 12, 447 (2020).  
118.  Y. Miyazaki, S. Okazaki, and W. Shinoda, "pSPICA: A coarse-grained force field for lipid membranes based on a polar water model" J. Chem. Theory Comput. 16, 782-793 (2020).
Supplementary Cover from J. Chem. Theory Comput. Vol 16 issue 1, January 14, 2020
J18 篠田　渉，"脂質膜系の粗視化力場SPICAの開発とその展望"，生物物理, 60, 157-161 (2020).
生物物理, Vol 60, 表紙、2020年6月

2019

117. T. Yamamoto, Y. Umegawa, H. Tsuchikawa, S. Hanashima, N. Matsumori, K. Funahashi, S. Seo, W. Shinoda, and M. Murata, "Amphotericin B-Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly" Biochemistry, 58, 5188-5196 (2019)..
116.  H. Liu, S. Okazaki, and W. Shinoda, "Heteroaryldihydropyrimidines Alter Capsid Assembly by Adjusting the Binding Affinity and Pattern of the Hepatitis B Virus Core Protein" J. Chem. Inf. Model., 59, 5104-5110 (2019).
Cover from J. Chem. Inf. Model. Vol 59 issue 12, December 23, 2019.
115. H. Yadav, A. Kuo, S. Urata, and W. 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, 35, 14316-14323 (2019).
114.  K. W. Hall, T. W. Sirk, S. Percec, M. L. Klein, and W. Shinoda, "Divining the Shape of Nascent Polymer Crystal Nuclei" J. Chem. Phys. 151, 144901 (2019).
113. A. Kuo, Y. Miyazaki, C. Jang, T. Miyajima, S. Urata, S. O. Nielsen, S. Okazaki, and W. Shinoda, "Large-scale Molecular Dynamics Simulation of Perfluorosulfonic Acid Membranes: Remapping Coarse-Grained to All-Atomistic Simulations" Polymer, 181, 121766 (2019). 
112. M. Yamagami, H. Tsuchikawa, J. Cui, Y. Umegawa, Y. Miyazaki, S. Seo, W. Shinoda, M. Murata, "Average Conformation of Branched-Chain Lipid PGP-Me that Accounts for the Thermal Stability and High-Salinity Registance of Archaeal Membranes" Biochemistry, 58, 3869-3879 (2019).
Cover from Biochemistry Vol 58 issue 41, October 15, 2019.
111. M. E. Griffiths and W. Shinoda, "tSPICA: Temperature- and Pressure-dependent Coarse-Grained Force Field for Organic Molecules" , J. Chem. Info. Model. 59, 3829-3838 (2019).
110.

K. Takeuchi, A. Kuo, T. Hirai, T. Miyajima, S. Urata, S. Okazaki, and W. Shinoda, "Hydrogen Permeation in Hydrated Perfluorosulfonic Acid Polymer Membranes: Effect of Polymer Crystallinity and Equivalent Weight", J. Phys. Chem. C, 123, 20628-20638 (2019).

109.

K. Takeda, Y. Andoh, W. Shinoda, and S. Okazaki, "Molecular Behavior of Linear Alkylbenzene Sulfonate in Hydrated Crystal, Tilted Gel, and Liquid Crystal Phases Studied by Molecular Dynamics Simulation", Langmuir, 35, 10877-10884 (2019).
Cover from Langmuir, Vol 35, issue 33, August 20, 2019.
108, S. Hanashima, K. Murakami, M. Yura, Y. Yano, Y. Umegawa, H. Tsuchikawa, N. Matsumori, S. Seo, W. Shinoda, and M. Murata, "Cholesterol-induced Conformational Change in the Sphingomyelin Headgroup", Biophys. J. 117, 307-318 (2019).
107. K. Fujimoto, Z. Tang, W. Shinoda, and S. Okazaki, "All-atom Molecular Dynamics Study of Impact Fracture of Glassy Polymers. I: Molecular Mechanisms of Brittleness of PMMA and Ductility of PC." Polymer, 178, 121570 (2019).
106. K. Takeda, Y. Andoh, W. Shinoda, and S. 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, 35, 9011-9019(2019).
105. K. Fujimoto, R. Payal, T. Hattori, W. Shinoda, M. Nakagaki, S. Sakaki, and S. Okazaki, "Development of Dissociative Force Field for All-Atomistic Molecular Dynamics Calculation of Fracture of Polymers", J. Comput. Chem. 40, 2571-2576 (2019).
104.

K. Hall, T. Sirk, M. L. Klein, and W. Shinoda, "A Coarse-Grain Model for Entanbled Polyethylene Melts and Polyethylene Crystallization", J. Chem. Phys. 150, 244901 (2019).
103.

Y. Miyazaki, S. Okazaki, and W. Shinoda, "Free Energy Analysis of Membrane Pore Formation Process in the Presence of Multiple Melittin Peptides ", BBA - Biomembranes, 1861, 1409-1419 (2019).
102.

R. S. Payal, K. Fujimoto, C. Jang, W. Shinoda, Y. Takei, H. Shima, K. Tsunoda, and S. Okazaki, "Molecular Mechanism of Material Deformation and Failure in Butadiene Rubber: Insight from All-Atom Molecular Dynamics Simulation Using a Bond Breaking Potential Model", Polymer, 170, 113-119 (2019).
101. S. Seo and W. Shinoda, "SPICA force field for Lipid Membranes: Doamin Formation Induced by Cholesterol" J. Chem. Theory Comput. 15, 762-774 (2019).
Cover from J. Chem. Theory Comput. Vol. 15 Issue 1, January 8, 2019.

2018

100. K. Dokko, D. Watanabe, Y. Ugata, M. L Thomas, S. Tsuzuki, W. Shinoda, K. Hashimoto, K. Ueno, Y. Umebayashi, M. Watanabe, "Direct Evidence for Li Ion Hopping Conduction in Highly Concentrated Sulfolane-Based Liquid Electrolytes", J. Phys. Chem. B, 122, 10736-10745(2018).
(引用数>200)
99. T. Morishita, T. Nakamura, W. Shinoda, A. M. Ito, "Isokinetic approach in logarithmic mean-force dynamics for on-the-fly free energy reconstruction", Chem. Phys. Lett. 706, 633-640 (2018).
98. S. Seo and W. Shinoda, "Molecular Dynamics Simulations", Elsevir Reference Module in Chemistry, Molecular Sciences and Chemical Engineering, edited by J. Reedijk, 2018, DOI: 10.1016/B978-0-12-409547-2.14274-X
97. A. Kuo, K. Takeuchi, A. Tanaka, S. Urata, S. Okazaki, and W. Shinoda, "Exploring the Effect of Pendent Side Chain Length on the Structural and Mechanical Properties of Hydrated Perfluorosulfonic Acid Polymer Membranes by Molecular Dynamics Simulation" Polymer, 146, 53-62 (2018).
96. S. Rath, H. Liu, S. Okazaki, and W. Shinoda, "Identification of Factors Promoting HBV Capsid Self-Assembly by Assembly-Promoting Antivirals" J. Chem. Info. Model. 58, 328-337 (2018).
95. W. Shinoda, Y. Hatanaka, M. Hirakawa, S. Okazaki, S. Tsuzuki, K. Ueno, M. Watanabe, "Molecular Dynamics Study of Thermodynamic Stability and Dynamics of [Li(Glyme)]+ Complex in Lithium-Glyme Solvate Ionic Liquids" J. Chem. Phys. 148, 193809 (2018). 
94. Y. Kitazawa, K. Iwata, R. Kido, S. Imaizumi, S. Tsuzuki, W. Shinoda, K. Ueno, T. Mandai, H. Kokubo, K. Dokko, and M. Watanabe, "Polymer Electrolytes Containing Solvate Ionic Liquids: A New Approach To Achieve High Ionic Conductivity, Thermal Stability, and a Wide Potential Window" Chem. Mater. 30, 252-261(2018).

2017

93. A. Kuo, S. Okazaki, and W. Shinoda, "Transferable Coarse-Grained Model for Perfluorosulfonic Acid Polymer Membranes" J. Chem. Phys. 147, 094904 (2017).
92. A. Kuo, A. Tanaka, J. Irisawa, W. Shinoda, and S. Okazaki, "Molecular Dynamics Study on the Mechanical Deformation of Hydrated Perfluorosulfonic Acid Polymer Membranes." J. Phys. Chem. C, 121, 21374 (2017).
91. Q. Xiao, S. E. Sharman, S. E. Wilner, X. Zhou, C. Dazen, T. Baumgart, E. H. Reed, D. A. Hammer, W. Shinoda, M. L. Klein, and V. Percec, "Janus Dendrimersomes Coassembled from Fluorinated, Hydrogenated, and Hybrid Janus Dendrimers as Models for Cell Fusion and Fission." Proc. Natl. Acad. Sci. U.S.A., 114, E7045 (2017).
90. S. Tsuzuki, T. Mandai, S. Suzuki, W. Shinoda,T. Nakamura, T. Morishita, K. Ueno, S. Seki, Y. Umebayashi, K. Dokko, and M. Watanabe,"Effect of the cation on the stability of cation-glyme complexes and their interactions with the [TFSA]- anion" Phys. Chem. Chem. Phys. 19, 18262 (2017).

2016

89. A. Kuo, W. Shinoda, and S. Okazaki, "Molecular Dynamics Study of the Morphology of Hydrated Perfluorosulfonic Acid Polymer Membranes. " J. Phys. Chem. C, 120, 25832–25842(2016).
88. W. Shinoda, "Permeability Across Lipid Membranes", Biochim. Biophys. Acta (BBA) - Biomembranes, 1858, 2254-2265 (2016).
膜透過に関する総説論文．脂質膜の受動輸送に関する現在までの研究の総括と今後の発展について述べた．
(引用数>270)
J17. 都築　誠二、篠田　渉、「第5章　計算化学を用いたイオン液体の物性予測」，イオン液体研究最前線と社会実装，渡邉正義監修，pp. 49-56, 2016.

2015

87. C. M. MacDermaid, H. K. Kashyap, R. DeVane, W. Shinoda, J. B. Klauda, M. L. Klein, and G. Fiorin, "Molecular Dynamics Simulations of Cholesterol-Rich Membranes Using a Coarse-Grained Force Field for Cyclic Alkanes." J. Chem. Phys. 143, 243144 (2015).
コレステロールの粗視化モデルを導入．
86. S. Kawamoto, M. L. Klein, and W. Shinoda, "Coarse-Grained Molecular Dynamics Study of Membrane Fusion: Curvature Effects on Free Energy Barriers along the Stalk Mechanism." J. Chem. Phys. 143, 243112 (2015).
膜融合における自由エネルギー障壁を曲率を持つ/持たない膜面間で比較した．曲率の影響は大きく，曲がった膜の融合は平面膜よりも遙かに起こりやすい．また、脂質種依存性も非常に大きく、自由エネルギー障壁はPEの存在によって非常に小さくなることが示された．
85. T. Nakamura, S. Kawamoto, and W. Shinoda, "Precise Calculation of the Local Pressure Tensor in Cartesian and Spherical Coordinates in LAMMPS." Comput. Phys. Comm. 190, 120-128 (2015).
84. S. Tsuzuki, W. Shinoda, M. Matsugami, Y. Umebayashi, K. Ueno, T. Mandai, S Seki, K. Dokko, M. Watanabe, "Structures of [Li(glyme)]+ complexes and their interactions with anions in equimolar mixtures of glymes and Li[TFSA]: Analysis by molecular dynamics simulations", Phys. Chem. Chem. Phys. 17, 126 (2015).
(引用数>100)

2014

83. A. Ikeda, K. Kiguchi, T. Hida, K. Yasuhara, K. Nobusawa, M. Akiyama, W. Shinoda, "[70]Fullerenes Assists the Formation of Phospholipid Bicelles at Low Lipid Concentrations" Langmuir, 30, 12315-12320 (2014)..
C70の導入によってバイセルが安定化することが実験的に示された．→C70が膜中で凝集し膜の曲げ弾性率を上げるため剛直となって，バイセルが優位になると考えられる．
82. S. Mieda, A. Ikeda, Y. Shigeri, and W. Shinoda, "Thermodynamic Stability of [60]Fullerene and γ-Cyclodextrin Complex in Aqueous Solution: Free Energy Simulation", J Phys. Chem. C, 118, 12555-12561 (2014).
C60を水溶液に可溶化するためにγ-シクロデキストリンによる包摂が使われる．このシクロデキストリンによる包摂の安定性を分子動力学シミュレーションに基づく自由エネルギー計算を行い評価した．また包摂構造の安定性とDMSO溶媒の関係を調べている．ABFを用いた距離と回転を含む2次元での自由エネルギー計算により，シクロデキストリンの乖離過程について議論した．
81. S. Kawamoto and W. Shinoda, "Free energy analysis along the stalk mechanism of membrane fusion" Soft Matter, 10, 3048 (2014).
ストークを経由する膜融合の自由エネルギー変化を定量的に評価する手法の提案．2つの独立した膜の状態からストーク形成，融合ポア形成までの自由エネルギー計算を可能とした．平面膜だけでなくベシクルにも適用可能な手法である．
80. W. Shinoda and M. L. Klein, "Effective Interaction Between Small Unilamellar Vesicles as Probed by Coarse-Grained Molecular Dynamic Simulations" Pure Appl. Chem. 86, 215-222 (2014).
ベシクル間に働く相互作用を自由エネルギー解析を用いて評価．混合膜ではlipid sortingによって膜変形の自由エネルギーが低下することが明確に示された．
J16. 篠田　渉，"脂質膜透過現象の分子シミュレーションによる研究"，膜(MEMBRANE)，39(6), 372-378 (2014)..

2013

79. G. Fiorin, M. L. Klein, R. DeVane, and W. Shinoda, "Computer Simulation of Self-Assembling Macromolecules" Adv. Polym. Sci. 262, 93 (2013).
粗視化分子モデルを用いたマクロ分子の自己組織化に関する研究の総説論文
78. S. Tsuzuki, W. Shinoda, M. S. Miran, H. Kinoshita, T. Yasuda, and M. Watanabe, "Interactions in ion pairs of protic ionic liquids: Comparison with aprotic ionic liquids", J. Chem. Phys. 139, 174504 (2013).
77. W. Shinoda, D. Discher, M. Klein, S. Loverde, "Probing the Structure of PEGylated-lipid Assemblies by Coarse-grained Molecular Dynamics" Soft Matter, 9, 11549 (2013).
PEG修飾された脂質集合体の振る舞いについての考察．
76. A. Ikeda, A. Hirata, M. Ishikawa, J. Kikuchi, S. Mieda, and W. Shinoda,"Effect of substituents in the water-solubilities and stabilities of [60]fullerene derivative・gamma-cyclodextrin 1:2 complexes.", Org. Biomol. Chem. 11, 7843 (2013).[Cover title]
Front cover from Org. Biomol. Chem. Vol. 45 Number 45, 7 December 2013.
75. S. Kawamoto, T. Nakamura, S. O. Nielsen, and W. Shinoda, "A Guiding Potential Method for Evaluating the Bending Rigidity of Tensionless Lipid Membranes from Molecular Simulation" J. Chem. Phys. 139, 034108 (2013).
膜の曲げ弾性係数をMDで求める手法の提案．2つのシリンダー型外部ポテンシャルを用いて膜を曲げ，必要な力との関係から弾性係数を導出した．
74. S. Tsuzuki, W. Shinoda, S. Seki, Y. Umebayashi, K. Yoshida, K. Dokko, and M. Watanabe, "Intermolecular Interactions in Li+-glyme and Li+-glyme-TFSA- complexes: Relationship with Physicochemical Properties of [Li(glyme)][TFSA] Ionic Liquids" ChemPhysChem, 14, 1993(2013).
73. T. Nakamura and W. Shinoda, "Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory", J. Chem. Phys. 138, 124903 (2013).
曲率を持った脂質膜の弾性係数を計算し，弾性係数の曲率依存性を議論した．Helfrich／Fromherz理論の枠組みにおいて曲率依存の弾性係数を考慮することで，20nm程度の小さなベシクルの開口自由エネルギーを定量的に予測する可能性を議論した．
72. A. Ikeda, M. Ishikawa, R. Aono, J. Kikuchi, M. Akiyama, and W. Shinoda, "Regioselective Recognition of a [60]Fullerene-Bisadduct by Cyclodextrin" J. Org. Chem. 78, 2534 (2013).
J15. 篠田　渉，"脂質膜の粗視化分子シミュレーション"，Colloid & Interface Communication, 38 (2013).

2012

71. C. -C. Chiu, R. H. DeVane, M. L. Klein, W. Shinoda, P. B. Moore, S. O. Nielsen, "Effect of Carboxylation on Carbon Nanotube Aqueous Dispersibility: A Predictive Coarse-Grained Molecular Dynamics Approach", J. Phys. Chem. C, 116, 23102 (2012).
70. C. -C. Chiu, W. Shinoda, R. DeVane, S. O. Nielsen, "Effects of spherical fullerene nanoparticles on a dipalmitoyl phosphatidylcholine lipid monolayer: a coarse grain molecular dynamics approach.", Soft Matter, 8, 9610 (2012).
69. A. Kuo, C.-H. Chang, W. Shinoda, "Molecular Dynamics Study of Cationic Vesicle Bilayers Composed of Ion Pair Amphiphiles with Double-tailed Cationic Surfactants", Langmuir, 28, 8156 (2012).
68. S. Kawamoto, M. Takasu, T. Miyakawa, R. Akiyama, T. Oda, H. Saito, S. Futaki, H. Nagao, W. Shinoda, "Free Energy of Cell-Penetrating Peptide through Lipid Bilayer Membrane: Coarse-Grained Model Simulation." Prog. Theo. Chem. Phys. 26, 503 (2012).
67. W. Shinoda, R. DeVane, M. L. Klein, "Computer Simulation Studies of Self-Assembling Macromolecules" Curr. Opin. Struct. Biol. 22, 175 (2012).
(引用数>120)
66. D. LeBard, B. Levine, R. DeVane, W. Shinoda, M. L. Klein, "Premicelles In Aqueous Surfactant Solutions Above and Below the Critical Micelle Concentration" Chem. Phys. Lett. 552, 38 (2012).
J14. 篠田　渉，"分子シミュレーションによる界面活性剤・脂質分子自己集合体構造の研究"，オレオサイエンス，12(2), 55-61 (2012).
J13. 篠田　渉，"粗視化分子モデリング 4:分子集合体の形態変化の自由エネルギー解析"，アンサンブル，14(1), 51-55 (2012).

2011

65. H. Saito and W. Shinoda, "Cholesterol Effect on Water Permeability Through DPPC and PSM Lipid Bilayers: A Molecular Dynamics Study" J. Phys. Chem. B 115, 15241 (2011).
脂質二重層膜を横切る水分子の透過係数に対するコレステロール濃度の影響を調べた．飽和グリセロ脂質のジパルミトイルホスファチジルコリンDPPCと飽和スフィンゴ脂質のパルミトイルスフィンゴミエリンPSMの作る脂質二重層膜について分子動力学シミュレーションを行った．コレステロール濃度の上昇とともにいずれの膜でも水の透過係数は低くなっていく．コレステロール濃度の低いところではPSM膜の透過係数がより低いが，高濃度ではPSMとDPPC膜の差が小さくなることが判明した．
(引用数>130)
64. B. Levine, D. LeBard, R. DeVane, W. Shinoda, A. Kohlmeyer, M. L. Klein, "Micellization studied by GPU-accelerated coarse-grained molecular dynamics", J. Chem. Theory Comput. 7, 4135 (2011).
GPU上で動作するMDソフトウェアHOOMD-Blueに粗視化モデルを組み込み，ミセル形成のMD計算をシステマティックに行った．高効率のシミュレーションにより，長時間MDを多数繰り返すことが可能となった．
63. R. J. K. U. Ranatunga, C. T. Nguen, C. C. Chiu, W. Shinoda, S. O. Nielsen, "Molecular Dynamics Simulations of Nanoparticles and Surfactants at Oil/Water Interfaces- A Qualitative Overview", Chapter 18, pp 295-314, in Amphiphiles: Molecular Assembly and Applications, ACS Synposium Series, Vol 1070, Ed. R. Nagarajan, 2011.
62. T. Nakamura, W. Shinoda, T. Ikeshoji, "Novel Numerical Method for Calculating the Pressure Tensor in Spherical Coordinates for Molecular Systems" J. Chem. Phys. 135, 094106 (2011).
球座標における局所ストレスの精密な測定方法を提案した論文．ミセルやリポソーム系への適用を念頭に開発した．
61. W. Shinoda, T. Nakamura, S. O. Nielsen, "Free Energy Analysis of Vesicle-to-Bicelle Transformation" Soft Matter, 7, 9012 (2011).
球状ベシクルからバイセル（ディスク）への構造転移に関する自由エネルギー障壁を測定し，連続体現象理論との比較を行った．同自由エネルギー手法は膜の線張力の精密な測定にも使用できる．膜面の高さのスペクトル解析からの曲げ弾性係数，ストレスプロファイルからのガウス弾性係数などすべてをMDシミュレーションから見積もり，現象論との比較を行った最初の論文である．100nm程度の小さなベシクルを記述する理論の形成に役立てられればと考えている．
60. R. J. K. U. Ranatunga, C. T. Nguyen, B. A. Wilson, W. Shinoda, S. O. Nielsen, "Molecular Dynamics Study of Nanoparticles and Nonionic Surfactant at an Oil/Water Interface", Soft Matter, 7, 6942 (2011).
59. W. Shinoda, R. DeVane, M. L. Klein, "Coarse-Grianed Force Field for Ionic Surfactants" Soft Matter, 7, 6178 (2011).
イオン性界面活性剤の粗視化モデル．SDSなどの分子モデルを作成し，希薄系から高濃度系にわたってイオン性界面活性剤の挙動がリーズナブルに再現できることを示した．また，塩の添加により気液界面への吸着挙動や凝集構造が変化する様子を調べ，実験事実と符合する結果を得た．クーロン相互作用の取り扱いについても議論．
58. S. Tsuzuki, H. Matsumoto, W. Shinoda, M. Mikami, "Effects of conformational flexibility of alkyl chain of cations on diffusion of ions in ionic liquids" Phys. Chem. Chem. Phys. 13, 5987 (2011).
57. A. Jusufi, R. DeVane, W. Shinoda, M. L. Klein, "Nanoscale Carbon Particles and the Stability of Lipid Bilayers", Soft Matter, 7, 1139 (2011).
フラーレン(C60,C180,C540)の脂質二重層膜との相互作用解析として自由エネルギー計算を行い，膜へのフラーレンの吸着性を全原子モデルで調べた．さらに，自由エネルギーを再現する粗視化モデルの構築を行い，膜内部でのフラーレンの凝集挙動を調べた．フラーレンのサイズによって，凝集によってもたらされる膜物性の変化は全く異なることがわかった．
J12. 篠田　渉，"粗視化分子モデリングによる脂質膜の分子シミュレーション"，シミュレーション，30(4),217-223(2011).
J11. 篠田　渉，"粗視化分子モデリング 3:固液界面"，アンサンブル，13(3)，125 (2011).
J10. 篠田　渉，"オープンソースコードを用いた粗視化分子動力学シミュレーションの取り組み"，CMD Newsletter，46，25 (2011).
J9. 篠田　渉，"脂質膜・リポソームの分子シミュレーション-粗視化分子モデリングによる研究-"，膜(MEMBRANE)，36(1)，31-37 (2011).

2010

56. R. DeVane, A. Jusufi, W. Shinoda, C. C. Chiu, S. O. Nielsen, P. B. Moore, M. L. Klein, "Parameterization and application of a coarse grained forcefield for benzene/fullerene interactions with lipids" J. Phys. Chem. B, 114, 16364 (2010).
55. W. Shinoda, M. Hato, "Molecular Dynamics Study of Isoprenoid-Chained Lipids: Salient Features of Isoprenoid Chains As Compared with Ordinal Alkyl Chains", in "Self-Organized Surfactant Structures", T. F. Tedros Ed., Wiley-Vch, 2010.
54. S. Tsuzuki, T. Umecky, H. Matsumoto, W. Shinoda, M. Mikami, "Interactions of perfluoroalkyltrifluoroborate anions with Li ion and imidazolium cation: Effects of perfluoroalkyl chain on motion of ions in ionic liquids" J. Phys. Chem. B 114, 11390 (2010).
53. X. He, W. Shinoda, R. DeVane, M. L. Klein, "Exploring the utility of coarse-grained water models for computational studies of interfacial systems" Mol. Phys. 108, 2007 (2010).
水分子の粗視化モデルを密度，表面張力，弾性率を再現するように組み立てるときに生ずる粗視化解像度への制限や限界について，さまざまな相互作用関数や粗視化レベルを用いて系統的に調べた
52. W. Shinoda, R. DeVane, M. L. Klein, "Zwitterionic lipid assemblies: Molecular dynamics studies of monolayers, bilayers, and vesicles using a new coarse grain force field." J. Phys. Chem. B, 114, 6836 (2010).(引用数>280)
脂質分子の新しい粗視化モデルの提案．双極性ヘッドグループを持つ脂質について粗視化モデルの構築・評価を行い，気液界面における単分子層膜，二重層膜，ベシクル（形成）の分子動力学シミュレーションを適用研究として紹介した．
51. C. C. Chiu, R. DeVane, M. L. Klein, W. Shinoda, P. B. Moore, and S. O. Nielsen, "Coarse Grained Molecular Dynamics of Phenyl Based Molecules: II. Application to Fullerenes" J. Phys. Chem. B, 114, 6394 (2010).
50. R. DeVane, C. C. Chiu, S. O. Nielsen, W. Shinoda, P. B. Moore, and M. L. Klein, "Coarse Grained Molecular Dynamics of Phenyl Based Molecules: I. Parametrization" J. Phys. Chem. B, 114, 6386 (2010).
49. X. He, W. Shinoda, R. DeVane, K. Andersen, M. L. Klein, "Paramaterization of a Coarse-Grained Model for Linear Alkylbenzene Sulfonate Surfactants and Molecular Dynamics Studies of Their Selfassembly in Aqueous Solution" Chem. Phys. Lett. 487, 71(2010).
イオン性界面活性剤，Linera Alkylbenzene Sulfonate(LAS)の粗視化モデルにより相挙動をシミュレートした．疎水鎖とベンゼン環のリンク位置の変更に伴って生じるisomer間の分子構造変化が相挙動に変化をもたらすことが再現された．
48. C. C. Chiu, R. J. K. U. Ranatunga, D. T. Flores, D. V. Perez, P. B. Moore, W. Shinoda, and S. O. Nielsen, "A mean field approach for computing solid-liquid surface tension for nanoscale interfaces", J. Chem. Phys. 132,054706 (2010).
表面張力は巨視的には界面自由エネルギーの面積の微分で定義されるが，ナノスケールではこの限りでない．ナノスケールでの固液表面張力の計算手法について述べた論文．
47. T. Nakamura, W. Shinoda, M. Mikami, "The shear hysteresis in lamellar structure of surfactant-water binary system", Chem. Phys. 367, 20 (2010).
シア流動場における両親媒性分子のラメラ相の構造変化についてのDPDによる観察
J8. 篠田　渉，"粗視化分子モデリング2:脂質膜・ベシクル"，アンサンブル，12(4)，12 (2010).
J7. 篠田　渉，"粗視化モデルによる両親媒性分子の自己組織化構造解析"，生物物理，50，232 (2010).
J6. 篠田　渉，"粗視化分子モデリング1:リン脂質モデル"，アンサンブル，12(3)，26 (2010).

2009

46. S. Tsuzuki, W. Shinoda, H. Saito, M. Mikami, H. Tokuda, and M. Watanabe, "Molecular dynamics simulations of ionic liquids: cation annd anion depenndece of self-diffusion coefficients of ions." J. Phys. Chem. B 113, 10641 (2009).(引用数>280)
45. J. Henin, W. Shinoda, and M. L. Klein, "Models for phospatidylglycerol lipids put to structural test." J. Phys. Chem. B, 113, 6958 (2009).
ホスファチジルグリセロール(PG)をヘッドグループに持つ脂質モデルについて，力場を比較．脂質膜構造の評価によって，CHARMM27Rのunited atom版を用いた場合に最も良好な結果を得た．
44. H. Saito, W. Shinoda, M. Mikami, "Fluorination Effects on Structure and Dynamics of Phospholipid Bilayer: A Molecular Dynamics Study" Chem. Phys. Lett. 468, 260 (2009).
フッ素化された炭素鎖を持つ合成脂質の分子構造特性とダイナミクスの解析
43. C. C. Chiu, P. B. Moore, W. Shinoda, S. O. Nielsen, "Size-dependent hydrophobic to hydrophilic transition for nanoparticles: a molecular dynamics study", J. Chem. Phys. 131, 244706 (2009).
ナノ粒子のサイズの変更によって溶媒和自由エネルギーが正から負に変わる現象の報告
42. R. DeVane, W. Shinoda, P. B. Moore, M. L. Klein, "Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids" J. Chem. Theory Comput. 5, 2115 (2009).(引用数>140)
アミノ酸の粗視化モデルの提案
41. R. J. B. Kalescky, W. Shinoda, P. B. Moore, S. O. Nielsen, "Area per ligand as a function of nanoparticle radius: a theoretical and computer simulation approach", Langmuir, 25, 1352 (2009).
ナノコロイド上に化学的に吸着した界面活性剤分子数とコロイド分散安定性の相関について評価した論文．コロイドの粗視化モデリングの研究としても意味がある．溶媒和自由エネルギー，有限サイズのコロイド上の界面における表面張力の評価法として新規アプローチを提案．
40. U. O. M. Vazquez, W. Shinoda, P. B. Moore, C. C. Chiu, S. O. Nielsen, "Calculating the surface tension between a flat solid and a liquid: a theoretical and computer simulation study of three topologically different methods." J. Math. Chem. 45 161(2009)..
固液界面の表面張力評価法について新しいアプローチを提案
J5. 齋藤大明，篠田　渉，"合成脂質膜の分子シミュレーション－フッ素化脂質"，アンサンブル，11(4)，22 (2009).
J4. 篠田　渉，"学術賞受賞寄稿:両親媒性分子自己集合構造の分子シミュレーション"，アンサンブル，11(2)，2 (2009).

2008

39. M. L. Klein and W. Shinoda, "Large-Scale Molecular Dynamics Simulations of Self-Assembling Systems" Science, 321, 798 (2008)[Cover title](引用数>510)
Full cover from Science Vol. 321, no. 5890, 8 August 2008. Reprinted with permission from AAAS
大規模系のMD，特に分子自己集合構造の計算についてのPerspective．表紙を飾る
38. W. Shinoda, R. DeVane, M. L. Klein, "Coarse-grained molecular modeling of nonionic surfactant self-assembly" Soft Matter, 4, 2454 (2008).(引用数>270)
ポリエチレングリコール界面活性剤の粗視化モデルの汎用性を示した論文．自己集合構造の形成，ヘキサゴナルからラメラへの転移，気液・液液界面での単分子層膜のシミュレーションなど．
37. W. Shinoda, R. DeVane, M. L. Klein, "Self-assembly of Surfactants in Bulk Phases and at Interfaces using Coarse-grain Models", Chapter 22 of the book "Coarse-Graining of Condensed Phase and Biomolecular Systems", G. A. Voth Ed., CRC Press, 2008.
ノニオン性界面活性剤の粗視化モデルの概要と応用計算例について紹介
36. K. Shinoda, W. Shinoda, M. Mikami, "Efficient free energy calculation of water across lipid membranes." J. Comput. Chem. 29, 1912 (2008).
水分子の脂質二重層膜を横切る際の自由エネルギープロフィールを高速に高精度に見積もるための方法について提案．Cavity Insertion法とOverlapping distribution法を組み合わせることにより，低分子であれば，熱力学的積分法を用いた場合に比べ2桁程度の高速化が望める．さらに積分誤差がないため精度がより高い．
35. J. Hénin, W. Shinoda, and M. L. Klein, "United-atom acyl chains for CHARMM phospholipids." J. Phys. Chem. B 112, 7008 (2008)
CHARMM力場のunited atomバージョンを開発．CHARMM27Rに基づいたunited atom版．
34. N. Matubayasi, W. Shinoda, M. Nakahara, "Free-energy analysis of the binding into membrane with the method of energy representation." J. Chem. Phys. 128, 195107 (2008).
エネルギー表示法を用いた脂質膜への分子の透過に対する自由エネルギー解析．エチルベンゼンなどのやや大きな分子についても非常に収束性のよい結果を得ている
33. H. Saito, W. Shinoda, M. Mikami, "Enhanced Hydrophobicity of Fluorinated Lipid Bilayer: A Molecular Dynamics Study" J. Phys. Chem. B 112, 11305 (2008).
フッ素化合成脂質の疎水性について分子論的な解析．自由エネルギープロフィールの計算とフッ素化膜の水分子の低透過性についての分子シミュレーション．
32. K. Nishio, T. Ozaki, T. Morishita, W. Shinoda, M. Mikami, "Effects of encapsulating sodium and iodine atoms on the electronic and optical properties of polyicosahedral Si nanostructures: a first-principles study" Phys. Rev. B 77 075431(2008).

2007

31. K. Shinoda, W. Shinoda, M. Mikami, "Molecular dynamics simulation of archaeal lipid bilayer with sodium chloride." Phys. Chem. Chem. Phys. 9 643 (2007). [Cover title]
Front cover from PCCP Vol. 9 No. 5, 7 Feb. 2007.
古細菌型脂質膜への塩化ナトリウム添加による影響を解析．通常の脂質膜に比べ，塩濃度上昇による構造変化は非常に小さい．表紙を飾る．
30. W. Shinoda, R. DeVane, M. L. Klein, "Multi-property Fitting and Parameterization of a Coarse Grained Model for Aqueous Surfactants", Mol. Simul. 33 27(2007).(引用数>500)
新しい粗視化モデルの構築方法とポリエチレングリコール界面活性剤への適用について詳説

2006

29. K. Nishio, T. Morishita, W. Shinoda and M. Mikami, "Molecular dynamics simulations of self-organized polyicosahedral Si nanowire." J. Chem. Phys. 125 074712 (2006).

2005

28 S. Urata, J. Irisawa, A. Takada, S. Tsuzuki, W. Shinoda, and M. Mikami, "Intermolecular interaction between the pendant chain of perfluorinated ionomer and methanol." J. Fluorine Chem. 126 1312 (2005).
27. S. Urata, J. Irisawa, A. Takada, W. Shinoda, S. Tsuzuki, and M. Mikami, "Molecular Dynamics Study of the Methanol Effect on the Membrane Morphology of Perfluorosulfonic Ionomer" J. Phys. Chem. B 109 17274 (2005).
26. S. Urata, J. Irisawa, A. Takada, W. Shinoda, S. Tsuzuki, and M. Mikami, "Molecular Dynamics Simulation of Swollen Membrane of Perfluorinated Ionomer." J. Phys. Chem. B 109, 4269 (2005).(引用数>240)
25. K. Nishio, W. Shinoda, T. Morishita, and M. Mikami, "Spatial Confinement Effect on the Atomic Structure of Solid Argon." J. Chem. Phys. 112 124715 (2005).
空間的に小さなポアに閉じこめられたアルゴンの低温における構造．空間閉じこめにより結晶化が妨げられていることを示した
24. K. Nishio, T. Morishita, W. Shinoda , and M. Mikami, "Formation of Icosahedral Si Quantum Dots from Liquid Droplets." Phys. Rev. B 72 245321 (2005).
Siの液滴の急冷による構造化のシミュレーション．特徴的なicosahedralな構造が観測された
23. M. Shiga and W. Shinoda, "Calculation of heat capacities of light and heavy water by path integral molecular dynamics." J. Chem. Phys. 123 134502 (2005).
比熱への同位体効果について解析．
22. W. Shinoda and M. Shiga, "Quantum simulation of the heat capacity of water." Phys. Rev. E 71 041204 (2005).
経路積分分子動力学シミュレーションを用いた水の比熱の計算．ガス，液体，固体の三態においてそれぞれ比熱を計算．核の量子効果が比熱に与える影響は常温においても気相以外では無視できない．
21. W. Shinoda, K. Shinoda, T. Baba, and M. Mikami, "Molecular dynamics study of bipolar tetraether membranes." Biophys. J. 89 3195 (2005).
テトラエーテル型脂質膜の構造やダイナミックスについて分子動力学シミュレーションで解析を行った最初の論文．

2004

20. S. Urata, J. Irisawa, A. Takada, S. Tsuzuki, W. Shinoda, and M. Mikami, "Intermolecular interaction between the pendant chain of perfluorinated ionomer and water." Phys. Chem. Chem. Phys. 6, 3325 (2004).
19. K. Shinoda, W. Shinoda, C. C. Liew, S. Tsuzuki, Y. Morikawa, and M. Mikami, "Mechanism of two-dimensional superstructure formation of self-assembled adenine molecules." Transactions of the Materials Research Society of Japan, 29, 3755 (2004).
18. K. Shinoda, W. Shinoda, C. C. Liew, S. Tsuzuki, Y. Morikawa, and M. Mikami, "Two-dimensional self-assembled structures of adenine molecules: Modeling and simulation." Surf. Sci. 556, 109 (2004).
アデニン分子の基盤上における自己集合構造に関するエネルギー解析．2次元の分子動力学シミュレーションも行った．
17. W. Shinoda, M. Mikami, T. Baba, and M. Hato, "Molecular dynamics study of the lipid bilayers: Effects of the chain branching on the structure and dynamics" AIP Conference series, 708, 352 (2004).
16. K. Shinoda, W. Shinoda, T. Baba, and M. Mikami, "Comparative molecular dynamics study of ether- and ester-linked phospholipid bilayers." J. Chem. Phys. 121 9648 (2004).
古細菌にみられるエーテル型脂質の特徴を解析．
15. W. Shinoda, M. Mikami, T. Baba, and M. Hato, "Dynamics of a highly branched lipid bilayer: A molecular dynamics study." Chem. Phys. Lett. 390, 35 (2004).
分岐型の脂質膜のダイナミクスに関する研究．隣接分子の疎水鎖間の絡み合いとそのダイナミクス（並進・回転）への影響を解析．
14. W. Shinoda, M. Mikami, T. Baba, and M. Hato, "Molecular dynamics study on the effects of chain branching on the physical properties of lipid bilayers: 2. Permeability." J. Phys. Chem. B 108 9346 (2004).
脂質二重層膜の分岐鎖による物性変化．特に低分子の透過性への影響について解析．膜を横切る自由エネルギー解析と易動度の評価により透過係数を見積もった．空隙分布などから実際の低分子透過のダイナミクスに関する考察を試みた．(引用数>150)
13. M. Shiga and W. Shinoda, "Stress-assisted grain boundary sliding and migration at finite temperature: A molecular dynamics study", Phys. Rev. B 70, 054102 (2004).
固体中の粒界移動についての分子動力学シミュレーション
12. W. Shinoda, M. Shiga, and M. Mikami, "Rapid estimation of elastic constants by molecular dynamics simulation under constant stress." Phys. Rev. B 69, 134103 (2004).
分子動力学シミュレーションを用いた固体弾性率の計算について熱浴との強力なカップリングにより収束性を改善した．ストレス一定のMDのrRESPAによるアルゴリズムの提示，Hybrid MCなどを試みている．後にLAMMPSに本アルゴリズムが採用された．(引用数>1200)
11. B. Hafskjold, C. C. Liew, and W. Shinoda, "Can such long time steps really be used in dissipative particle dynamics simulations?" Mol. Simul. 30, 879 (2004).
散逸粒子動力学法の数値的な安定性について，ポテンシャル関数や数値積分法による影響を解析した論文．
J3. 篠田　渉，"脂質膜の構造安定性と透過性の分子動力学シミュレーションによる予測"，膜(MEMBRANE), 29, 353 (2004).

2003

10. W. Shinoda and M. Mikami, "Rigid-body dynamics in the isothermal-isobaric ensemble: A test on the accuracy and computational efficiency." J. Comput. Chem. 24, 920 (2003).
部分剛体近似を用いた分子モデルの定温定圧での分子シミュレーション法についての論文(引用数>110)
9. W. Shinoda, M. Mikami, T. Baba, and M. Hato, "Molecular dynamics study on the effect of chain branching on the physical properties of lipid bilayers: Structural stability." J. Phys. Chem. B 107, 14030 (2003).
脂質疎水鎖の分岐による膜構造の変化について調べた最初の論文
8. W. Shinoda, M. Mikami, T. Baba, and M. Hato, "A comparison of straight- and branch-chained lipid bilayers for static and dynamic properties: A molecular dynamics study" Technical Proceedings of the 2003 Nanotechnology Conference and Trade Show，3，512 (2003).

2002

J2. 篠田　渉，三上益弘，"イオンチャンネル/受動輸送"，化学フロンティア ｢生体系のコンピュータ・シミュレーション」，pp. 196-208 (2002).

2001

7. W. Shinoda and M. Mikami, "Self-guided molecular dynamics in the isothermal-isobaric ensemble", Chem. Phys. Lett. 335 265 (2001).
自己誘導力分子動力学シミュレーション法のNPTアンサンブルを開発．ＬＪ流体の結晶化を例題としてサンプリング効率への効果を検証した．
6. W. Shinoda and S. Okazaki, "Molcular dynamics study of the dipalmitoyl phosphatidylcholine bilayer in the liquid crystal phase: An effect of potential force field on the membrane structure." J. Mol. Liq. 90 95 (2001).
脂質疎水鎖の力場モデルの変更により，膜面積の実験からのずれが改善．

-2000

J1. 篠田　渉，岡崎　進，"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"，電気化学 68, 129-133(2000).
5. Z. Fang, A. D. J. Haymet, W. Sihnoda, and S. Okazaki, "Parallel molecular dynamics simulation: implementation of PVM for a lipid membrane", Comput. Phys. Comm. 116, 295 (1999).
4. W. Shinoda, M. Shimizu, and S. Okazaki, "Molecular dynamics study on electrostatic properties of the lipid bilayer : Polarization, electrostatic potential, and the effects on structure and dynamics of water near the interface." J. Phys. Chem. B 102 6647 (1998).
脂質膜系の静電気学と水和構造・ダイナミクスの解析
3. W. Shinoda and S. Okazaki, "A Voronoi analysis of lipid area fluctuation in a bilayer." J. Chem. Phys. 109 1517 (1998).
2次元のボロノイ解析により膜面積を定義．膜面積揺らぎと脂質分子の構造・ダイナミクスの相関を調べた．(引用数>110)
2. W. Shinoda, N. Namiki, and S. Okazaki, "Molecular dynamics study of a lipid bilayer. Convergence, structure, and long-time dynamics." J. Chem. Phys. 106 5731(1997).
脂質二重層膜のMD計算における問題の解決と構造・ダイナミックス・膜面弾性の計算
1. W. Shinoda, T. Fukada, S. Okazaki, and I. Okada, "Molecular dynamics simulation of the dipalmitoylphosphatidylcholine(DPPC) lipid bilayer in the fluid phase using the Nose-Parrinello-Rahman NPT ensemble." Chem. Phys. Lett. 232 308 (1995).
Full flexible cellを用いたNPTアンサンブルを用いた初の脂質二重層膜のMD計算

MD覚え書き：研究室内のみ