Organization
Scheduled update Professor
Position
Professor
External link
Shinoda Wataru
Degree
Degree
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博士(理学) ( 東京工業大学 )
Research Interests
Research Interests
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Molecular simulation, multiscale modeling, lipid membrane, biological membrane, self-assembly, liposome, lipid nanoparticles, drug delivery carrier, virus capsid, polymer materials, polymer electrolytes
Research Areas
Research Areas
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Natural Science / Biophysics, chemical physics and soft matter physics
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Nanotechnology/Materials / Fundamental physical chemistry
Education
Education
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Tokyo Institute of Technology 総合理工学研究科 電子化学専攻 博士後期課程
1995.4 - 1998.3
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Country： Japan
Research History
Research History
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Okayama University The Research Institute for Interdisciplinary Science Professor
2021.10
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Nagoya University Graduate School of Engineering Associate Professor
2014.1 - 2021.9
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Country：Japan
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University of Pennsylvania Department of Chemistry Visiting Scholar
2005.4 - 2007.3
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Country：United States
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National Institute of Advanced Industrial Science and Technology
2001.4 - 2013.12
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National Institute of Materials and Chemical Research
2000.4 - 2001.3
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Mitsubishi Chemical Corporation
1998.4 - 2000.3
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Japan Society for the Promotion of Science Research fellow (DC1)
1995.4 - 1998.3
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Professional Memberships
Professional Memberships
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American Chemical Society
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理論化学会
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日本化学会
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分子シミュレーション学会
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THE BIOPHYSICAL SOCIETY OF JAPAN
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THE SOCIETY OF POLYMER SCIENCE, JAPAN
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JAPAN SOCIETY FOR MOLECULAR SCIENCE
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溶液化学研究会
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Papers
Papers
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Amphotericin B assembles into seven-molecule ion channels: An NMR and molecular dynamics study. Reviewed International journal
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
Science advances 8 ( 24 ) eabo2658 2022.6
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Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)
Amphotericin B, an antifungal drug with a long history of use, forms fungicidal ion-permeable channels across cell membranes. Using solid-state nuclear magnetic resonance spectroscopy and molecular dynamics simulations, we experimentally elucidated the three-dimensional structure of the molecular assemblies formed by this drug in membranes in the presence of the fungal sterol ergosterol. A stable assembly consisting of seven drug molecules was observed to form an ion conductive channel. The structure is somewhat similar to the upper half of the barrel-stave model proposed in the 1970s but substantially different in the number of molecules and in their arrangement. The present structure explains many previous findings, including structure-activity relationships of the drug, which will be useful for improving drug efficacy and reducing adverse effects.
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SPICA Force Field for Nucleic Acids and Its Application to Lipid Nanoparticles
Akhil Pratap Singh, Hiroki Tanaka, Yusuke Miyazaki, Wataru Shinoda
The Journal of Physical Chemistry B 2025.6
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In Silico Study of Ionizable Lipid Nanoparticles Using the SPICA Force Field
Akhil Pratap Singh, Hiroki Tanaka, Yusuke Miyazaki, Shusaku Nagano, Wataru Shinoda
Journal of Chemical Theory and Computation 2025.6
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Unraveling the Molecular Mechanism of Transient Multilamellar Formation in Ethanol-Modified Vesicle Solutions Reviewed
Kana Shibata, Masatoshi Maeki, Manabu Tokeshi, Wataru Shinoda
Langmuir 2025.6
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Authorship：Last author, Corresponding author Publishing type：Research paper (scientific journal)
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Selective adsorption of unmethylated DNA on ZnO nanowires for separation of methylated DNA Reviewed
Marina Musa, Zetao Zhu, Hiromi Takahashi, Wataru Shinoda, Yoshinobu Baba, Takao Yasui
Lab on a Chip 25 ( 7 ) 1637 - 1646 2025.4
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Asymmetry and Heterogeneity in the Plasma Membrane
Teppei Yamada, Wataru Shinoda
2025.3
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Publisher：Cold Spring Harbor Laboratory
Plasma membranes (PMs) exhibit asymmetry between their two leaflets in terms of phospholipid headgroups, unsaturation, and resulting membrane properties such as packing and fluidity. Lateral heterogeneity, including the formation of lipid domains, is another crucial aspect of PMs with significant biological implications. However, the nature and even the existence of lipid domains in the two leaflets of PMs remain elusive, hindering a complete understanding of the significance of lipid asymmetry. Using coarse-grained molecular dynamics simulation of the asymmetric PM, we find that the outer leaflet predominantly adopts a liquid-ordered state, whereas the inner leaflet separates into nanoscale (≈10 nm) liquid-ordered and liquid-disordered domains, exhibiting highly dynamic fusion and fission events. This structural asymmetry is further reinforced by asymmetric lateral stress resulting from a cholesterol bias toward the outer leaflet. These findings suggest distinct functional roles for the two leaflets, modulated by asymmetric lateral stress. Additionally, comparing the phase behavior of asymmetric and fully scrambled PMs reveals a key determinant of domain size: intact PMs maintain nanoscale domains, while cell-derived giant PM vesicles, which have lost the strict lipid asymmetry, exhibit microscale domains.
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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
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Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/D4OB01468E
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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
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Discrepant lithium transference numbers due to heterogeneous speciation
Frederik Philippi, Yuna Matsuyama, Simon Buyting, Taku Sudoh, Keisuke Shigenobu, Wataru Shinoda, Monika Schönhoff, Masayoshi Watanabe, Kazuhide Ueno
Physical Chemistry Chemical Physics 2025
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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
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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
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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
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Publishing type：Research paper (scientific journal) Publisher：Elsevier BV
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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
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Language：English Publishing type：Research paper (scientific journal)
Highly polar and charged molecules, such as oligonucleotides, face significant barriers in crossing the cell membrane to access the cytoplasm. To address this problem, we developed a light-triggered twistable tetraphenylethene (TPE) derivative, TPE-C-N, to facilitate the intracellular delivery of charged molecules through an endocytosis-independent pathway. The central double bond of TPE in TPE-C-N is planar in the ground state but becomes twisted in the excited state. Under light irradiation, this planar-to-twisted structural change induces continuous cell membrane disturbances. Such disturbance does not lead to permanent damage to the cell membrane. TPE-C-N significantly enhanced the intracellular delivery of negatively charged molecules under light irradiation when endocytosis was inhibited through low-temperature treatment, confirming the endocytosis-independent nature of this delivery method. We have successfully demonstrated that the TPE-C-N-mediated light-controllable method can efficiently promote the intracellular delivery of charged molecules, such as peptides and oligonucleotides, with molecular weights ranging from 1000 to 5000 Da.
DOI： 10.1039/d3tb02956e
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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
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Language：English Publishing type：Research paper (scientific journal)
Boundary lipids surrounding membrane proteins play an essential role in protein function and structure. These protein-lipid interactions are mainly divided into electrostatic interactions between the polar amino acids of proteins and polar heads of phospholipids, and hydrophobic interactions between protein transmembrane sites and phospholipid acyl chains. Our previous report (Kawatake et al., Biochim. Biophys. Acta 1858 [2016] 2106-2115) covered a method for selectively analyzing boundary lipid interactions and showed differences in membrane protein-peripheral lipid interactions due to differences in their head group. Interactions in the hydrophobic acyl chains of phospholipids are relatively consistent among proteins, but the details of these interactions have not been elucidated. In this study, we reconstituted bacteriorhodopsin as a model protein into phospholipid membranes labeled with 2H and 13C for solid-state NMR measurement to investigate the depth-dependent effect of the head group structure on the lipid bilayer. The results showed that the position of the phospholipid near the carbonyl carbon was affected by the head group in terms of selectivity for protein surfaces, whereas in the deep interior of the bilayer near the leaflet interface, there was little difference between the head groups, indicating that the dependence of their interactions on the head group was much reduced.
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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
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)
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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
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Publishing type：Research paper (scientific journal) Publisher：Royal Society of Chemistry (RSC)
We investigated ethanol-induced structural changes in liposomes on a time scale from microseconds to tens of seconds using a microfluidic-based small-angle X-ray scattering (SAXS) measurement system coupled with molecular dynamics (MD) simulations.
DOI： 10.1039/d3na01073b
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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
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal)
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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
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)
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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
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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
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Language：English Publishing type：Research paper (scientific journal)
Boron neutron capture therapy (BNCT) is a promising modality for cancer treatment because of its minimal invasiveness. To maximize the therapeutic benefits of BNCT, the development of efficient platforms for the delivery of boron agents is indispensable. Here, we prepared carborane-integrated immunoliposomes via an exchanging reaction to achieve HER-2-targeted BNCT. The conjugation of an anti-HER-2 antibody to carborane-integrated liposomes successfully endowed these liposome with targeting properties toward HER-2-overexpressing human ovarian cancer cells (SK-OV3); the resulting BNCT activity toward SK-OV3 cells obtained using the current immunoliposomal system was 14-fold that of the l-BPA/fructose complex, which is a clinically available boron agent. Moreover, the growth of spheroids treated with our system followed by thermal neutron irradiation was significantly suppressed compared with treatment with the l-BPA/fructose complex.
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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
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Publishing type：Research paper (scientific journal) Publisher：Japan Society for Bioscience, Biotechnology, and Agrochemistry
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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
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Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)
DOI： 10.1021/jacs.3c04285
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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
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Language：English Publishing type：Research paper (scientific journal)
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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
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal)
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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
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Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal)
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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
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Publishing type：Research paper (scientific journal) Publisher：Elsevier BV
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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
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Language：English Publishing type：Research paper (scientific journal) Publisher：Wiley
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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
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Publishing type：Research paper (scientific journal) Publisher：American Chemical Society (ACS)
DOI： 10.1021/jacs.3c00389
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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
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Authorship：Last author Language：English Publishing type：Research paper (scientific journal)
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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
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Language：English Publishing type：Research paper (scientific journal)
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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
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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
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal)
We conducted a series of coarse-grained molecular dynamics (CG-MD) simulations to investigate the complicated actions of melittin, which is an antimicrobial peptide (AMP) derived from honey bee venom, on a lipid membrane. To accurately simulate the AMP action, we developed and used a protein CG model as an extension of the pSPICA force field (FF), which was designed to reproduce several thermodynamic quantities and structural properties. At a low peptide-to-lipid (P/L) ratio (1/102), no defect was detected. At P/L = 1/51, toroidal pore formation was observed due to collective insertion of multiple melittin peptides from the N-termini. The pore formation was initiated by a local increase in membrane curvature in the vicinity of the peptide aggregate. At a higher P/L ratio (1/26), two more modes were detected, seemingly not controlled by the P/L ratio but by a local arrangement of melittin peptides: 1. Pore formation accompanied by lipid extraction by melittin peptides:a detergent-like mechanism. 2. A rapidly formed large pore in a significantly curved membrane: bursting. Thus, we observed three pore formation modes (toroidal pore formation, lipid extraction, and bursting) depending on the peptide concentration and local arrangement. These observations were consistent with experimental observations and hypothesized melittin modes. Through this study, we found that the local arrangements and population of melittin peptides and the area expansion rate by membrane deformation were key to the initiation of and competition among the multiple pore formation mechanisms.
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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
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Royal Society of Chemistry ({RSC})
DOI： 10.1039/D2CP01348G
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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
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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
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Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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Authorship：Last author, Corresponding author Publishing type：Research paper (scientific journal) Publisher：Informa {UK} Limited
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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
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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
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Authorship：Last author, Corresponding author Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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Publishing type：Research paper (scientific journal) Publisher：Royal Society of Chemistry ({RSC})
DOI： 10.1039/D0CP04898D
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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
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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
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Language：English Publishing type：Research paper (scientific journal)
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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
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Publishing type：Research paper (scientific journal) Publisher：Proceedings of the National Academy of Sciences
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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
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Authorship：Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
Diphytanoylphosphatidylcholine (DPhPC) is a synthetic phospholipid in which two methyl-branched acyl chains are introduced into the glycerol moiety, mimicking phospholipids of eukaryotic and eubacterial origins. The lipid bilayers of DPhPC reproduce the outstanding physical properties of methyl-branched lipids that occur in archaeal membranes. DPhPC is commonly used as the base lipid in biophysical experiments, particularly for recording ion-channel currents. However, the dynamics of lipid molecules that induces their useful physical properties is still unclear. In this study, we examined the conformation and orientation of the methyl-branched acyl chain of DPhPC in a membrane using 2H nuclear magnetic resonance (NMR) measurements of the synthetic lipid with a high stereochemical purity and molecular dynamics (MD) simulations. Deuterium-labeled 3',3'-CD3,D-DPhPC (2) and 7',7'-CD3,D-DPhPC (3) showed the characteristic quadrupole splitting width in the 2H NMR spectra, which corresponded to the bent orientation reported for the archaeal lipid PGP-Me [Yamagami, M., et al. (2019) Biochemistry58, 3869-3879]. However, MD simulations, which reproduced the 2H NMR results well, unveiled the unknown features of DPhPC in the membrane; DPhPC has a chain-specific average orientation, where two bent orientations with upward and downward methyl groups occur at positions C3 and C7 of the sn-1 and sn-2 chains of DPhPC, respectively. These MD and NMR results reveal that these two bent orientations define the average orientation of DPhPC for the shallow part of the acyl chains, which is considered to be an important factor in the stability of DPhPC membranes.
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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
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Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
The asymmetric lipid composition in plasma membranes within the inner leaflet is not typically suitable for domain formation. Thus elucidation of the likelihood of the formation or stability of a raft-like domain in the inner leaflet is necessary. Herein we investigated the phase behavior of asymmetric membranes using coarse-grained molecular dynamics simulations. The lipid leaflet comprising dioleoylphosphatidylcholine (DOPC) and cholesterol (Chol) does not typically show well-developed domains in symmetric bilayer membranes; however, it does separate into liquid ordered (Lo) and liquid disordered (Ld) phases when the opposing leaflet containing sphingomyelin (SM), DOPC, and Chol demonstrates domain formation. We determine that interdigitated acyl chains modulated the partitioning of Chol in the opposing leaflet, resulting in phase separation. Similarly, the acyl chain length of SM within the opposing leaflet affected the phase behavior of the leaflet. Our results reveal the crucial role of interdigitation in determining the phase status in asymmetric membranes.
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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
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Other Link： https://onlinelibrary.wiley.com/doi/full-xml/10.1002/batt.201900197
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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
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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
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Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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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
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Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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Molecular simulation of the shape deformation of a polymersome Reviewed
Kaushik Chakraborty, Wataru Shinoda, Sharon M. Loverde
Soft Matter 16 ( 13 ) 3234 - 3244 2020
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Publishing type：Research paper (scientific journal) Publisher：Royal Society of Chemistry ({RSC})
DOI： 10.1039/C9SM02165E
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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
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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
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Authorship：Last author, Corresponding author Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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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
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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
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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
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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
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Kazushi Fujimoto, Zhiye Tang, Wataru Shinoda, Susumu Okazaki
Polymer 178 121570 - 121570 2019.9
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Publishing type：Research paper (scientific journal) Publisher：Elsevier {BV}
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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
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Kosuke Takeda, Yoshimichi Andoh, Wataru Shinoda, Susumu Okazaki
Langmuir 35 ( 33 ) 10877 - 10884 2019.8
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Kosuke Takeda, Yoshimichi Andoh, Wataru Shinoda, Susumu Okazaki
Langmuir 35 ( 27 ) 9011 - 9019 2019.7
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Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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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
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Publishing type：Research paper (scientific journal) Publisher：Elsevier {BV}
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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
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Publishing type：Research paper (scientific journal) Publisher：{AIP} Publishing
DOI： 10.1063/1.5092229
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Rajdeep Singh Payal, Kazushi Fujimoto, Changwoon Jang, Wataru Shinoda, Yuki Takei, Hiroshi Shima, Katsuhiko Tsunoda, Susumu Okazaki
Polymer 170 113 - 119 2019.4
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Publishing type：Research paper (scientific journal) Publisher：Elsevier {BV}
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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
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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
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Publishing type：Research paper (scientific journal) Publisher：American Chemical Society ({ACS})
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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
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Publishing type：Research paper (scientific journal) Publisher：{AIP} Publishing
DOI： 10.1063/1.5009814
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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
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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
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Language：English Publishing type：Research paper (scientific journal) Publisher：American Chemical Society
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Kuo, A.-T., Takeuchi, K., Tanaka, A., Urata, S., Okazaki, S., Shinoda, W.
Polymer 146 53 - 62 2018
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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
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Publishing type：Research paper (scientific journal)
DOI： 10.1016/j.cplett.2018.07.011
Other Link： http://orcid.org/0000-0002-3388-9227
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An-Tsung Kuo, Atsushi Tanaka, Jun Irisawa, Wataru Shinoda, Susumu Okazaki
JOURNAL OF PHYSICAL CHEMISTRY C 121 ( 39 ) 21374 - 21382 2017.10
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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
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DOI： 10.1063/1.4986287
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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
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c7cp02779f
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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
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Language：English Publishing type：Research paper (scientific journal)
Other Link： http://orcid.org/0000-0002-3388-9227
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Permeability across lipid membranes Invited Reviewed
Wataru Shinoda
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 1858 ( 10 ) 2254 - 2265 2016.10
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Authorship：Lead author, Corresponding author Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1016/j.bbamem.2016.03.032
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Shuhei Kawamoto, Michael L. Klein, Wataru Shinoda
JOURNAL OF CHEMICAL PHYSICS 143 ( 24 ) 2015.12
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1063/1.4933087
Other Link： http://orcid.org/0000-0002-3388-9227
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1063/1.4937153
Other Link： http://orcid.org/0000-0002-3388-9227
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1016/j.cpc.2014.11.017
Other Link： http://orcid.org/0000-0002-3388-9227
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c4cp04718d
Other Link： http://orcid.org/0000-0002-3388-9227
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[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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1021/la503732q
Other Link： http://orcid.org/0000-0002-3388-9227
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Shunsuke Mieda, Atsushi Ikeda, Yasushi Shigeri, Wataru Shinoda
JOURNAL OF PHYSICAL CHEMISTRY C 118 ( 23 ) 12555 - 12561 2014.6
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1021/jp5029905
Other Link： http://orcid.org/0000-0002-3388-9227
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Wataru Shinoda, Michael L. Klein
PURE AND APPLIED CHEMISTRY 86 ( 2 ) 215 - 222 2014.2
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Language：English Publishing type：Research paper (scientific journal)
Other Link： http://orcid.org/0000-0002-3388-9227
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Free energy analysis along the stalk mechanism of membrane fusion Reviewed
Shuhei Kawamoto, Wataru Shinoda
SOFT MATTER 10 ( 17 ) 3048 - 3054 2014
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c3sm52344f
Other Link： http://orcid.org/0000-0002-3388-9227
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Atsushi Ikeda, Akiko Hirata, Michiko Ishikawa, Jun-Ichi Kikuchi, Shunsuke Mieda, Wataru Shinoda
Organic and Biomolecular Chemistry 11 ( 45 ) 7843 - 7851 2013.12
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c3ob41513a
Other Link： http://orcid.org/0000-0002-3388-9227
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1063/1.4827519
Other Link： http://orcid.org/0000-0002-3388-9227
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Seiji Tsuzuki, Wataru Shinoda, Shiro Seki, Yasuhiro Umebayashi, Kazuki Yoshida, Kaoru Dokko, Masayoshi Watanabe
ChemPhysChem 14 ( 9 ) 1993 - 2001 2013.6
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Language：English Publishing type：Research paper (scientific journal)
Other Link： http://orcid.org/0000-0002-3388-9227
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1021/jo3027609
Other Link： http://orcid.org/0000-0002-3388-9227
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Takenobu Nakamura, Wataru Shinoda
JOURNAL OF CHEMICAL PHYSICS 138 ( 12 ) 124903 2013.3
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1063/1.4795579
Other Link： http://orcid.org/0000-0002-3388-9227
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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
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Language：English Publishing type：Part of collection (book)
DOI： 10.1007/12_2013_262
Other Link： http://orcid.org/0000-0002-3388-9227
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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
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Authorship：Lead author Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c3sm52290c
Other Link： http://orcid.org/0000-0002-3388-9227
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Shuhei Kawamoto, Takenobu Nakamura, Steven O. Nielsen, Wataru Shinoda
Journal of Chemical Physics 139 ( 3 ) 2013
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1063/1.4811677
Other Link： http://orcid.org/0000-0002-3388-9227
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1021/jp307545m
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An-Tsung Kuo, Chien-Hsiang Chang, Wataru Shinoda
LANGMUIR 28 ( 21 ) 8156 - 8164 2012.5
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Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1021/la300651u
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1016/j.sbi.2012.01.011
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David N. LeBard, Benjamin G. Levine, Russell DeVane, Wataru Shinoda, Michael L. Klein
CHEMICAL PHYSICS LETTERS 522 38 - 42 2012.1
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1016/j.cplett.2011.11.075
Other Link： http://orcid.org/0000-0002-3388-9227
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Chi-cheng Chiu, Wataru Shinoda, Russell H. DeVane, Steven O. Nielsen
SOFT MATTER 8 ( 37 ) 9610 - 9616 2012
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c2sm26357b
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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
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1021/ct2005193
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Hiroaki Saito, Wataru Shinoda
JOURNAL OF PHYSICAL CHEMISTRY B 115 ( 51 ) 15241 - 15250 2011.12
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1021/jp201611p
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Takenobu Nakamura, Wataru Shinoda, Tamio Ikeshoji
JOURNAL OF CHEMICAL PHYSICS 135 ( 9 ) 2011.9
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1063/1.3626410
Other Link： http://orcid.org/0000-0002-3388-9227
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Molecular Simulation of Lipid Membranes and Liposomes : A Coarse-Grained Molecular Modeling Approach
SHINODA Wataru
MEMBRANE 36 ( 1 ) 31 - 37 2011.1
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Language：Japanese Publisher：THE MEMBRANE SOCIETY OF JAPAN
We developed a coarse-grained (CG) molecular model, which is useful to investigate a self-assembling process of lipids and surfactants in an aqueous solution or a phase transition process at the molecular resolution. The CG model is designed to reproduce the interfacial properties, solvation free energy, as well as molecular distribution functions obtained from simulations with the all-atomic detail. The systematic CG modeling enabled us to investigate large molecular assemblies such as liposomes with chemical characterization of molecule, which is not accessible by previous phenomenological models. Several application studies given in this paper will elucidate the power of CG molecular dynamics simulation to shed light on molecular processes in lipid membranes happening on the scale of ‹ 100 nm.
Other Link： https://jlc.jst.go.jp/DN/JALC/00363326984?from=CiNii
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Coarse-grained force field for ionic surfactants Reviewed
Wataru Shinoda, Russell DeVane, Michael L. Klein
SOFT MATTER 7 ( 13 ) 6178 - 6186 2011
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c1sm05173c
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c1sm05145h
Other Link： http://orcid.org/0000-0002-3388-9227
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Free energy analysis of vesicle-to-bicelle transformation Reviewed
Wataru Shinoda, Takenobu Nakamura, Steven O. Nielsen
SOFT MATTER 7 ( 19 ) 9012 - 9020 2011
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c1sm05404j
Other Link： http://orcid.org/0000-0002-3388-9227
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Nakamura O, Ohana T, Tazawa M, Yokota S, Shinoda W, Nakamura O, Itoh J
Synthesiology 4 ( 2 ) 111 - 114 2011
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c0sm00963f
Other Link： http://orcid.org/0000-0002-3388-9227
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Seiji Tsuzuki, Hajime Matsumoto, Wataru Shinoda, Masuhiro Mikami
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13 ( 13 ) 5987 - 5993 2011
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1039/c0cp02087g
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R. J. K. Udayana Ranatunga, Chuong T. Nguyen, Chi-cheng Chiu, Wataru Shinoda, Steven O. Nielsen
AMPHIPHILES: MOLECULAR ASSEMBLY AND APPLICATIONS 1070 295 - + 2011
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Language：English Publishing type：Research paper (international conference proceedings)
DOI： 10.1021/bk-2011-1070.ch018
Other Link： http://orcid.org/0000-0002-3388-9227
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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
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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
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1021/jp1070264
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Wataru Shinoda, Masakatsu Hato
Self-Organized Surfactant Structures 175 - 194 2010.11
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Language：English Publishing type：Part of collection (book) Publisher：Wiley-VCH
DOI： 10.1002/9783527632633.ch9
Other Link： http://orcid.org/0000-0002-3388-9227
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Self-assembled Structure of Amphiphiles by Coarse-grained Molecular Model
SHINODA Wataru
Seibutsu Butsuri 50 ( 5 ) 232 - 235 2010.9
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Language：Japanese Publisher：The Biophysical Society of Japan General Incorporated Association
The recently developed coarse-grained (CG) molecular model enables us to investigate meso-scopic morphologies of self-assembly of amphiphilic molecules at the molecular level. The present CG model is designed to well reproduce the interfacial properties, solvation free energy, as well as molecular distribution obtained from simulations at the all-atomic detail. The transferability and versatility is demonstrated by applying the model to the bulk aqueous solution as well as to the air/water interfacial system.<br>
Other Link： https://jlc.jst.go.jp/DN/JALC/00356578628?from=CiNii
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Seiji Tsuzuki, Tatsuya Umecky, Hajime Matsumoto, Wataru Shinoda, Masuhiro Mikami
JOURNAL OF PHYSICAL CHEMISTRY B 114 ( 35 ) 11390 - 11396 2010.9
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Language：English Publishing type：Research paper (scientific journal)
DOI： 10.1021/jp104380s
Other Link： http://orcid.org/0000-0002-3388-9227
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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
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DOI： 10.1021/jp9117369
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Wataru Shinoda, Russell DeVane, Michael L. Klein
JOURNAL OF PHYSICAL CHEMISTRY B 114 ( 20 ) 6836 - 6849 2010.5
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DOI： 10.1021/jp9107206
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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
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DOI： 10.1021/jp9117375
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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
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DOI： 10.1063/1.3308625
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Xibing He, Wataru Shinoda, Russell DeVane, Kelly L. Anderson, Michael L. Klein
CHEMICAL PHYSICS LETTERS 487 ( 1-3 ) 71 - 76 2010.2
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DOI： 10.1016/j.cplett.2010.01.029
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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
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DOI： 10.1016/j.chemphys.2009.10.009
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Xibing He, Wataru Shinoda, Russell DeVane, Michael L. Klein
MOLECULAR PHYSICS 108 ( 15 ) 2007 - 2020 2010
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DOI： 10.1080/00268976.2010.503197
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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
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DOI： 10.1063/1.3276915
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Seiji Tsuzuki, Wataru Shinoda, Hiroaki Saito, Masuhiro Mikami, Hiroyuki Tokuda, Masayoshi Watanabe
JOURNAL OF PHYSICAL CHEMISTRY B 113 ( 31 ) 10641 - 10649 2009.8
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DOI： 10.1021/jp811128b
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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
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DOI： 10.1021/ct800441u
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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
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DOI： 10.1021/jp900645z
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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
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DOI： 10.1021/la8032918
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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
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DOI： 10.1016/j.cplett.2008.12.001
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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
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DOI： 10.1007/s10910-008-9374-7
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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
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DOI： 10.1109/ULIS.2009.4897539
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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
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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
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DOI： 10.1002/jcc.20956
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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
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DOI： 10.1021/jp801057k
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Large-scale molecular dynamics simulations of self-assembling systems Reviewed
Michael L. Klein, Wataru Shinoda
SCIENCE 321 ( 5890 ) 798 - 800 2008.8
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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
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DOI： 10.1021/jp800687p
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Nobuyuki Matubayasi, Wataru Shinoda, Masaru Nakahara
JOURNAL OF CHEMICAL PHYSICS 128 ( 19 ) 2008.5
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DOI： 10.1063/1.2919117
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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
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DOI： 10.1103/PhysRevB.77.075431
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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
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DOI： 10.1039/b808701f
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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
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DOI： 10.1080/08927020601054050
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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
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DOI： 10.1039/b611543h
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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
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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
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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
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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
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DOI： 10.1063/1.1878693
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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
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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
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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
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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
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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
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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
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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
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W Shinoda, M Mikami, T Baba, M Hato
SLOW DYNAMICS IN COMPLEX SYSTEMS 708 352 - 353 2004
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DOI： 10.1063/1.1764171
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1P108 MD Simulation of Halorhodopsin in Lipid bilayer
Hayashi M., Miyagawa Y., Shinoda W., Sakurai M.
Seibutsu Butsuri 44 S56 2004
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W Shinoda, M Mikami, T Baba, M Hato
JOURNAL OF PHYSICAL CHEMISTRY B 107 ( 50 ) 14030 - 14035 2003.12
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DOI： 10.1021/jp035493j
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W Shinoda, M Mikami, T Baba, M Hato
NANOTECH 2003, VOL 3 3 512 - 515 2003
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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
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Self-guided molecular dynamics in the isothermal-isobaric ensemble Reviewed
W Shinoda, M Mikami
CHEMICAL PHYSICS LETTERS 335 ( 3-4 ) 265 - 272 2001.2
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DOI： 10.1016/S0009-2614(01)00054-9
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W Shinoda, S Okazaki
JOURNAL OF MOLECULAR LIQUIDS 90 ( 1-3 ) 95 - 103 2001.2
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DOI： 10.1016/S0167-7322(01)00111-8
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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
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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
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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
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W Shinoda, M Shimizu, S Okazaki
JOURNAL OF PHYSICAL CHEMISTRY B 102 ( 34 ) 6647 - 6654 1998.8
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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
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DOI： 10.1063/1.476702
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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
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W SHINODA, T FUKADA, S OKAZAKI, OKADA, I
CHEMICAL PHYSICS LETTERS 232 ( 3 ) 308 - 312 1995.1
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DOI： 10.1016/0009-2614(94)01352-V
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MISC
MISC
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Elucidation of inter-leaflet coupling in asymmetric membranes induced by very long chain sphingomyelin based on solid-state NMR
KEERATISAKULSITH Tanatchphong, UMEGAWA Yuichi, TSUCHIKAWA Hiroshi, HANASHIMA Shinya, MURATA Michio, SHINODA Wataru
日本化学会春季年会講演予稿集(Web) 101st 2021
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B型肝炎ウイルス(HBV)への逆転写阻害薬剤分子の自由エネルギー計算によるカプシド内部への吸収・透過機構の解明
浦野諒, 藤本和士, 安藤嘉倫, 吉井範行, 篠田渉, 岡崎進
分子シミュレーション討論会講演要旨集 33rd 2019
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B型肝炎ウイルス(HBV)への逆転写阻害薬剤分子のカプシド内部の自由エネルギー計算
浦野諒, 藤本和士, 安藤嘉倫, 吉井範行, 篠田渉, 岡崎進
分子科学討論会講演プログラム&要旨(Web) 13th 2019
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分子動力学計算による界面活性剤含水ラメラの構造決定および分子挙動に関する研究
武田康助, 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 33rd 2019
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Structure Elucidation of Ion Channel Assembly Formed by Amphotericin B and Sterol
山本智也, 山本智也, 梅川雄一, 梅川雄一, 中川泰男, 鈴木大河, 山上正輝, 土川博史, 花島慎弥, 村田道雄, 村田道雄, 松森信明, 松森信明, SEO Sangjae, 篠田渉
天然有機化合物討論会講演要旨集(Web) 60th 2018
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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Language：English Publishing type：Research paper, summary (international conference)
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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
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Language：English Publishing type：Research paper, summary (international conference)
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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
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Language：English Publishing type：Research paper, summary (international conference)
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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
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Language：Japanese Publisher：The Physical Society of Japan (JPS)
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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
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Language：Japanese Publisher：The Physical Society of Japan (JPS)
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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
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Language：English Publishing type：Research paper, summary (international conference)
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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
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Language：English Publishing type：Research paper, summary (international conference)
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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
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Language：Japanese Publishing type：Article, review, commentary, editorial, etc. (scientific journal) Publisher：分子シミュレーション研究会
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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
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Language：English Publishing type：Research paper, summary (international conference)
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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
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Language：English Publishing type：Research paper, summary (international conference)
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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
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Language：English Publishing type：Research paper, summary (international conference)
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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
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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
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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
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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
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Language：Japanese Publisher：The Physical Society of Japan (JPS)
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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
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Language：Japanese Publisher：The Physical Society of Japan (JPS)
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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
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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
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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
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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
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Language：Japanese Publisher：The Physical Society of Japan (JPS)
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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
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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
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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
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Language：Japanese Publisher：The Physical Society of Japan (JPS)
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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
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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
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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
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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
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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
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Language：Japanese Publisher：The Physical Society of Japan (JPS)
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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
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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
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Language：Japanese Publisher：The Physical Society of Japan (JPS)
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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
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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
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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
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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
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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
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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
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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
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Publisher：公益社団法人 日本化学会・情報化学部会
The TACPACK2000 system consists of general purpose molecular dynamics simulators for large scale system of complicated materials such as biopolymer, organic crystal, liquid crystal, polymers, semiconductor, metal and alloy and ceramics and integration system for the simulators. In this presentation, the systematization technologies of the integration system are described. In the database management technology, we have developed the new technology using XML(eXtensible Markup Language) to control uniformly the data composed of molecular structure, crystal structure , potential and pseudopotential function etc. Also in the plug-in function, we have developed the software technologies for program restoration / deletion function to this system, compilation linkage functions of the program and automatic generation function of parameters input screen.
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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
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Presentations
Presentations
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Simulating Endosomal Escape of Lipid Nanoparticles Invited
Wataru Shinoda
The 6th International Conference on Molecular Simulation (ICMS2023) 2023.10.7
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Event date： 2023.10.6 - 2023.10.9
Language：English Presentation type：Oral presentation (keynote)
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Coarse Grained Molecular Dynamics Study on Endosomal Escape of dsDNA Encapsulated in Lipid Nanoparticles using the SPICA Force Field Invited
Wataru Shinoda
CECAM workshop: Macromolecular complexes: from ab initio and integrative modelling to functional dynamics 2023.9.7
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Event date： 2023.9.5 - 2023.9.8
Language：English Presentation type：Oral presentation (invited, special)
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梅川雄、齋藤宣樹、花島慎弥、篠田渉、村田道雄
ケミカルバイオロジー学会 第17回年会 2023.5.29 日本ケミカルバイオロジー学会
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Event date： 2023.5.29 - 2023.5.31
Language：Japanese Presentation type：Poster presentation
Venue：⼤阪⼤学会館（⼤阪⼤学 豊中キャンパス） Country：Japan
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Exploring the Mechanism of Endosomal Escape of Lipid Nanoparticles: A Coarse-Grained Molecular Dynamics Study Invited International conference
Wataru Shinoda
Asia Pacific Conference of Theoretical and Computational Chemistry APATCC-10 2023.2.19
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Event date： 2023.2.19 - 2023.2.23
Language：English Presentation type：Oral presentation (invited, special)
Venue：The International Centre for Interdisciplinary Science and Education (ICISE) Country：Viet Nam
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分子動力学計算による Li 伝導機構解明に立脚した高 Li 輸率のための 電解液設計と最適化
篠田 渉
JST-ALCA SPRING Li-S電池チームミーティング 2023.1.8 JST
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Event date： 2023.1.8 - 2023.1.9
Language：Japanese Presentation type：Oral presentation (general)
Venue：静岡県 Country：Japan
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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
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Event date： 2022.12.5 - 2022.12.7
Language：Japanese Presentation type：Oral presentation (general)
Venue：東京工業大学 Country：Japan
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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
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Event date： 2022.12.5 - 2022.12.7
Language：Japanese Presentation type：Oral presentation (general)
Venue：東京工業大学 Country：Japan
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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
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Event date： 2022.12.5 - 2022.12.7
Language：Japanese Presentation type：Poster presentation
Venue：東京工業大学 Country：Japan
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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
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Event date： 2022.12.5 - 2022.12.7
Language：Japanese Presentation type：Poster presentation
Venue：東京工業大学 Country：Japan
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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
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Event date： 2022.12.5 - 2022.12.7
Language：Japanese Presentation type：Poster presentation
Venue：東京工業大学 Country：Japan
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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
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Event date： 2022.11.8 - 2022.11.10
Presentation type：Oral presentation (general)
Venue：福岡国際会議場 Country：Japan
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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
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Event date： 2022.11.8 - 2022.11.10
Presentation type：Oral presentation (general)
Venue：福岡国際会議場 Country：Japan
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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
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Event date： 2022.11.8 - 2022.11.10
Presentation type：Oral presentation (general)
Venue：福岡国際会議場 Country：Japan
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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
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Event date： 2022.10.27 - 2022.10.29
Language：English Presentation type：Oral presentation (general)
Venue：Rome, Italy Country：Italy
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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
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Event date： 2022.10.27 - 2022.10.29
Presentation type：Poster presentation
Venue：鹿児島大学 Country：Japan
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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
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Event date： 2022.10.27 - 2022.10.29
Presentation type：Poster presentation
Venue：鹿児島大学 Country：Japan
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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
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Event date： 2022.10.27 - 2022.10.29
Presentation type：Poster presentation
Venue：鹿児島大学 Country：Japan
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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
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Event date： 2022.10.5 - 2023.2.1
Presentation type：Public lecture, seminar, tutorial, course, or other speech
Venue：オンライン開催 Country：Japan
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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
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Event date： 2022.9.28 - 2022.9.30
Presentation type：Poster presentation
Venue：北海道函館市 Country：Japan
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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
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Event date： 2022.9.28 - 2022.9.30
Presentation type：Oral presentation (general)
Venue：北海道函館市 Country：Japan
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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
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Event date： 2022.9.28 - 2022.9.30
Presentation type：Poster presentation
Venue：北海道函館市 Country：Japan
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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
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Event date： 2022.9.28 - 2022.9.30
Presentation type：Poster presentation
Venue：北海道函館市 Country：Japan
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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
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Event date： 2022.9.28 - 2022.9.30
Presentation type：Poster presentation
Venue：北海道函館市 Country：Japan
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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
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Event date： 2022.9.20 - 2022.9.22
Presentation type：Oral presentation (general)
Venue：広島大学 Country：Japan
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山田 哲平，篠田 渉
第16回分子科学会 2022.9.21 分子科学会
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Event date： 2022.9.19 - 2022.9.22
Presentation type：Poster presentation
Venue：慶應義塾大学矢上キャンパス Country：Japan
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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
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Event date： 2022.9.19 - 2022.9.22
Presentation type：Oral presentation (general)
Venue：慶應義塾大学矢上キャンパス Country：Japan
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宮崎 裕介，篠田 渉
第16回分子科学会 2022.9.19 分子科学会
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Event date： 2022.9.19 - 2022.9.22
Presentation type：Oral presentation (general)
Venue：慶應義塾大学矢上キャンパス Country：Japan
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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
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Event date： 2022.9.8 - 2022.9.9
Presentation type：Oral presentation (general)
Venue：神奈川大学 みなとみらいキャンパス Country：Japan
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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
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Event date： 2022.9.7 - 2022.9.9
Venue：静岡市清水文化会館マリナート Country：Japan
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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
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Event date： 2022.9.5 - 2022.9.7
Language：Japanese Presentation type：Public lecture, seminar, tutorial, course, or other speech
Venue：岡崎コンファレンスセンター Country：Japan
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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
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Event date： 2022.3.23 - 2022.3.26
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
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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
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Event date： 2022.3.23 - 2022.3.26
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
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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
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Event date： 2022.3.23 - 2022.3.26
Language：Japanese Presentation type：Poster presentation
Venue：オンライン Country：Japan
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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
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Event date： 2022.2.4
Language：Japanese Presentation type：Oral presentation (invited, special)
Venue：オンライン開催 Country：Japan
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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
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Event date： 2022.1.13
Language：Japanese Presentation type：Oral presentation (invited, special)
Venue：オンライン Country：Japan
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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
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Event date： 2022.1.11 - 2022.1.12
Presentation type：Oral presentation (invited, special)
Venue：オンライン開催 Country：Japan
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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
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Event date： 2021.12.22 - 2021.12.23
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
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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
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Event date： 2021.12.22 - 2021.12.23
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
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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
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Event date： 2021.12.22 - 2021.12.23
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
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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
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Event date： 2021.12.22 - 2021.12.23
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
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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
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Event date： 2021.12.16 - 2021.12.21
Language：English Presentation type：Oral presentation (invited, special)
Venue：online
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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
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Event date： 2021.12.9
Language：Japanese Presentation type：Oral presentation (invited, special)
Venue：オンライン Country：Japan
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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
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Event date： 2021.11.29 - 2021.12.1
Language：Japanese Presentation type：Poster presentation
Venue：岡山 Country：Japan
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B型肝炎ウイルスのカプシド含有エンベロープの分子モデリングとシミュレーション
浦野諒、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
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Event date： 2021.11.29 - 2021.12.1
Language：Japanese Presentation type：Poster presentation
Venue：岡山
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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、藤本和士
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
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Event date： 2021.11.29 - 2021.12.1
Language：Japanese Presentation type：Poster presentation
Venue：岡山 Country：Japan
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エタノール混合によるベシクル構造転移:マルチラメラ形成機構
柴田果奈、真栄城正寿、渡慶次学、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
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Event date： 2021.11.29 - 2021.12.1
Language：Japanese Presentation type：Poster presentation
Venue：岡山 Country：Japan
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分子シミュレーションを用いた抗菌ペプチドの膜選択性の解明
川端一正、宮﨑裕介、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
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Event date： 2021.11.29 - 2021.12.1
Language：Japanese Presentation type：Poster presentation
Venue：岡山 Country：Japan
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B型肝炎ウイルスのエンベロープのモデリングとシミュレーション
浦野諒、篠田渉
第59回日本生物物理学会年会 2021.11 日本生物物理学会
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Event date： 2021.11.25 - 2021.11.27
Language：English Presentation type：Oral presentation (general)
Venue：オンライン Country：Japan
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スルホラン系高濃度Li塩電解液におけるLiイオン拡散機構
池田周平、都築誠二、上野和英、渡邉正義、篠田渉
第43回溶液化学シンポジウム 2021.10 溶液化学研究会
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Event date： 2021.10.28 - 2021.10.29
Language：Japanese Presentation type：Poster presentation
Venue：オンライン Country：Japan
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分子シミュレーションによる界面活性剤/脂質の自己集合構造と安定性評価 Invited
篠田 渉
日本油化学会2021年若手の会交流会 2021.10.8 日本油化学会若手の会
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Event date： 2021.10.8
Language：Japanese Presentation type：Public lecture, seminar, tutorial, course, or other speech
Venue：オンライン Country：Japan
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全原子分子動力学計算によるPMMAの溶剤破壊シミュレーション
下岡稔、篠田渉、三宅大輝、原光生、藤本和士
第15回分子科学討論会 2021.9 分子科学会
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Event date： 2021.9.18 - 2021.9.21
Language：Japanese Presentation type：Poster presentation
Venue：オンライン Country：Japan
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2H,13C-二重標識POPCを用いた脂質二重膜における不飽和アシル鎖の配座・配向の固体NMR解析
安田 貴也、梅川 雄一、今井 茅希、村田 道雄、篠田 渉
日本化学会第101春季大会 2021.3.21 日本化学会
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Event date： 2021.3.19 - 2021.3.22
Language：Japanese Presentation type：Poster presentation
Venue：オンライン Country：Japan
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Elucidation of inter-leaflet coupling in asymmetric membranes induced by very long chain sphingomyelin based on solid-state NMR
Tanatchphong Keeratisakulsith, Yuichi Umegawa, Hiroshi Tsuchikawa, Shinya Hanashima, Michio Murata, Wataru Shinoda
2021.3.19
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Event date： 2021.3.19 - 2021.3.22
Language：English Presentation type：Oral presentation (general)
Country：Japan
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Seipin Accumulates and Traps Diacylglycerols and Tryglycerides in Its Ring-Like Structure International coauthorship International conference
Valeria Zoni, Wataru Shinoda, Stefano Vanni
65th Biophysical Society Annual Meeting 2021.2 Biophysical Society
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Event date： 2021.2.22 - 2021.2.26
Language：English Presentation type：Poster presentation
Venue：online
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Computer simulations of biomacromolecular self-assembly using the SPICA coarse-grained model Invited International conference
Wataru Shinoda
The 1st Fugaku Bio-supercomputing Workshop on Cellular-scale Molecular Dynamics Simulations 2021.1.6
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Event date： 2021.1.6 - 2021.1.7
Language：English Presentation type：Oral presentation (invited, special)
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粗視化分⼦動⼒学法による脂質膜相分離、抗菌ペプチド作⽤の研究 Invited
篠田 渉、宮﨑 裕介、Sangjae Seo
物性研究所スパコン共同利用・CCMS合同研究会「計算物質科学の新展開2020」 2020.12 東大物性研
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Event date： 2020.12.21 - 2020.12.22
Language：Japanese Presentation type：Oral presentation (invited, special)
Venue：オンライン Country：Japan
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気液界面における半フッ化炭素のヘミミセル形成
原田 昌吾、Hari O. S. Yadav、篠田 渉
第34回分子シミュレーション討論会 2020.12.5 分子シミュレーション学会
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Event date： 2020.12.5
Language：Japanese Presentation type：Poster presentation
Venue：オンライン
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薬剤分子の B 型肝炎ウイルスへの透過機構の探索
弦巻 周平、浦野 諒、藤本 和士、篠田 渉、岡崎 進
第34回分子シミュレーション討論会 2020.12.5 分子シミュレーション学会
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Event date： 2020.12.5
Language：Japanese Presentation type：Poster presentation
Venue：オンライン Country：Japan
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定量的粗視化力場SPICA のDNA モデルヘの拡張: 脂質ナノ粒子の構造予測
田中 裕貴、宮崎 裕介、Akhil Pratap Singh、篠田 渉
第34回分子シミュレーション討論会 2020.12.5 分子シミュレーション学会
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Event date： 2020.12.5
Language：Japanese Presentation type：Poster presentation
Venue：オンライン Country：Japan
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不均一系における位置に依存した拡散係数の新規手法の提案
永井 哲郎、弦巻 周平、浦野 諒、藤本 和士、篠田 渉、岡崎 進
第34回分子シミュレーション討論会 2019.12 分子シミュレーション学会
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Event date： 2020.12.5
Language：Japanese Presentation type：Poster presentation
Venue：オンライン
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高精度量子化学計算を用いた電極中の硫黄の還元反応の解析
都築 誠二，金子 智昭，袖山 慶太郎，梅林 泰宏，篠田 渉，関 志朗，上野 和英，獨古 薫，渡邉 正義
第61回電池討論会 2020.11 電気化学会
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Event date： 2020.11.18 - 2020.11.20
Language：Japanese Presentation type：Oral presentation (general)
Venue：オンライン
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濃厚電解質溶液中のイオンダイナミクス：分子動力学法による検討
篠田 渉
2020年度イオン液体研究会 2020.7.16 イオン液体研究会
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Event date： 2020.7.16
Language：Japanese Presentation type：Oral presentation (invited, special)
Venue：オンライン
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All-Atomistic Molecular Dynamics Study of Impact Fracture of Glassy Polymers:Molecular Mechanism of Brittleness and Ductility International conference
Z. Tang, K. Fujimoto, W. Shinoda, S. Okazaki
Materials Research Meeting 2019 2019.12 MRM2019
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Event date： 2019.12.10 - 2019.12.14
Language：English Presentation type：Poster presentation
Venue：Yokohama Country：Japan
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粗視化分子力場pSPICAを用いたペプチドによる細孔形成過程の解析
宮﨑裕介、岡崎進、 篠田渉
第33回分子シミュレーション討論会 2019.12 分子シミュレーション学会
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Event date： 2019.12.9 - 2019.12.11
Language：Japanese Presentation type：Poster presentation
Venue：名古屋 Country：Japan
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Molecular view of lipid-based nanoparticles as drug delivery system revealed by coarse grained simulation
A. P. Singh, H. Tanaka, Y. Miyazaki, W. Shinoda
2019.12
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Event date： 2019.12.9 - 2019.12.11
Language：English Presentation type：Poster presentation
Country：Japan
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分子動力学シミュレーションによるAm-photericinB チャネルの構造安定性の解析
舟橋康佑、 Sang-jae Seo、 岡崎進、 梅川雄一、 村田道雄、篠田渉
第33回分子シミュレーション討論会 2019.12 分子シミュレーション学会
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Event date： 2019.12.9 - 2019.12.11
Language：Japanese Presentation type：Poster presentation
Venue：名古屋 Country：Japan
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定量的粗視化力場SPICAのDNA/RNAモデルへの拡張
田中裕貴、 宮崎裕介、 Akhil Pratap Singh、岡崎進、 篠田渉
第33回分子シミュレーション討論会 2019.12 分子シミュレーション学会
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Event date： 2019.12.9 - 2019.12.11
Language：Japanese Presentation type：Poster presentation
Venue：名古屋 Country：Japan
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B 型肝炎ウイルス(HBV) への逆転写阻害薬剤分子の自由エネルギー計算によるカプシド内部への吸収・透過機構の解明
浦野諒、藤本和士、 安藤嘉倫、吉井範行、 篠田渉、岡崎進
第33回分子シミュレーション討論会 2019.12 分子シミュレーション学会
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Event date： 2019.12.9 - 2019.12.11
Language：Japanese Presentation type：Oral presentation (general)
Venue：名古屋 Country：Japan
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分子動力学計算による界面活性剤含水ラメラの構造決定および分子挙動に関する研究
武田康助、 安藤嘉倫、 篠田渉、 岡崎進
第33回分子シミュレーション討論会 2019.12 分子シミュレーション学会
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Event date： 2019.12.9 - 2019.12.11
Language：Japanese Presentation type：Oral presentation (general)
Venue：名古屋 Country：Japan
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不均一系での物質輸送を評価の際に利用する位置に依存した拡散係数の新規評価方法
永井哲郎、弦巻周平、 浦野諒、 藤本和士、 篠田渉、 岡崎進
第33回分子シミュレーション討論会 2019.12 分子シミュレーション学会
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Event date： 2019.12.9 - 2019.12.11
Language：Japanese Presentation type：Oral presentation (general)
Venue：名古屋 Country：Japan
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tSPICA: Introducing Temperature- and Pressure- Dependence for the SPICA Coarse-Grained Force Field
M. Griffiths，W. Shinoda
2019.12
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Event date： 2019.12.9 - 2019.12.11
Language：English Presentation type：Poster presentation
Country：Japan
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Coarse-Grained MD Study of Entecavir Drug Insertion into Hepatitis B Virus (HBV) Capsid
M. Dixit,H. Liu, Y. Miyazaki, R. Urano,S. Okazaki, W. Shinoda
2019.12
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Event date： 2019.12.9 - 2019.12.11
Language：English Presentation type：Poster presentation
Country：Japan
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Effects of Packing Density and Chain Length on the Surface Hydrophobicity of Thin Films Composed of Perfluoroalkyl Acrylate Chains: A Molecular Dynamics Study
H. Yadav,An-Tsung Kuo, S. Urata, W.Shinoda
2019.12
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Event date： 2019.12.9 - 2019.12.11
Language：English Presentation type：Poster presentation
Country：Japan
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電荷を置いたグラフェン近傍のイオンの配向
都築誠二、森下徹也、中村壮伸、篠田渉、関志朗、梅林泰宏、上野和英、獨古薫、渡邉正義
第10回イオン溶液討論会 2019.11 イオン液体研究会
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Event date： 2019.11.21 - 2019.11.22
Language：Japanese Presentation type：Oral presentation (general)
Venue：大阪 Country：Japan
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ポリスルフィドアニオン、多硫化リチウムの構造と安定性
都築誠二、森下徹也、篠田渉、袖山慶太朗、梅林泰宏、関志朗、上野和英、獨古薫、渡邉正義
第60回電池討論会 2019.11 電気化学会
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Event date： 2019.11.13 - 2019.11.15
Language：Japanese Presentation type：Oral presentation (general)
Venue：京都 Country：Japan
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A new coarse-grained force field to perform molecular dynamics simulations for lipid bilayer systems using a polar water model International conference
Y. Miyazaki, S. Okazaki, W. Shinoda
The 5th International Conference on Molecular Simulation 2019.11
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Event date： 2019.11.3 - 2019.11.6
Language：English Presentation type：Poster presentation
Venue：Jeju Country：Korea, Republic of
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Coarse-Grained Molecular Dynamics Study of Lipid-Protein Complex Invited International conference
W. Shinoda, S. Seo, K. Funahashi
The 5th International Conference on Molecular Simulation 2019.11
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Event date： 2019.11.3 - 2019.11.6
Language：English Presentation type：Oral presentation (invited, special)
Venue：Jeju Country：Korea, Republic of
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Introducing Temperature- and Pressure- Dependence to a Coarse-Grained Model for Organic Molecules: The tSPICA Force Field International conference
Mark Z. Griffiths, Wataru Shinoda
The 5th International Conference on Molecular Simulation 2019.11
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Event date： 2019.11.3 - 2019.11.6
Language：English Presentation type：Poster presentation
Venue：Jeju Country：Korea, Republic of
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膜透過・相分離の分子シミュレーションによる研究 Invited
篠田渉、徐相宰、田村美侑
第42回溶液化学シンポジウム プレシンポジウム 2019.10.29 溶液化学研究会
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Event date： 2019.10.29
Language：Japanese Presentation type：Oral presentation (invited, special)
Venue：仙台 Country：Japan
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非晶高分子の衝撃破壊に関する分子論的研究:ミクロの視点における降伏現象の解明
湯 之也、藤本 和士、篠田 渉、岡崎 進
第68回高分子討論会 2019.9 高分子学会
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Event date： 2019.9.25 - 2019.9.27
Language：Japanese Presentation type：Oral presentation (general)
Venue：福井 Country：Japan
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P-SPICA: A coarse-grained force field for biological systems with a polar coarse-grained water model
Y.Miyazaki, S.Okazaki, W.Shinoda
2019.9
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Event date： 2019.9.24 - 2019.9.26
Language：English Presentation type：Poster presentation
Country：Japan
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Calculation of free energy of transfer of a reverse transcription inhibitor to the inside of HepatitisB Virus (HBV) capsid
R.Urano, K. Fujimoto, Y. Andoh, N. Yoshii, W. Shinoda, S. Okazaki
2019.9
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Event date： 2019.9.24 - 2019.9.26
Language：English Presentation type：Poster presentation
Country：Japan
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B型肝炎ウイルス(HBV)への逆転写阻害薬剤分子のカプシド内部の自由エネルギー計算
浦野諒、藤本和士、安藤嘉倫、吉井範行、篠田渉、岡崎進
第13回分子科学討論会 2019.9 分子科学会
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Event date： 2019.9.17 - 2019.9.20
Language：Japanese Presentation type：Oral presentation (general)
Venue：名古屋 Country：Japan
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分子動力学シミュレーションによるAmphotericin Bチャネルの構造安定性の解析
舟橋康佑、サンジェ セオ、岡崎進、 梅川雄一、村田道雄、 篠田渉
第13回分子科学討論会 2019.9 分子科学会
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Event date： 2019.9.17 - 2019.9.20
Language：Japanese Presentation type：Poster presentation
Venue：名古屋 Country：Japan
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極性を持つ粗視化水モデルを基礎とした生体分子系のための新規粗視化分子力場の開発
宮崎裕介、岡崎進、篠田渉
第13回分子科学討論会 2019.9 分子科学会
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Event date： 2019.9.17 - 2019.9.20
Language：Japanese Presentation type：Poster presentation
Venue：名古屋 Country：Japan
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Molecular study of hepatitis B virus with pgRNA in the solution by all-atom molecular dynamics calculation International conference
K. Fujimoto,Y. Yamaguchi,R. Urano, W. Shinoda,T. Ishikawa, K. Omagari, Y. Tanaka,A. Nakagawa,S. Okazaki
Joint EMLG/JMLG conference 2019 2019.9 European Molecular Liquids Group(EMLG)
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Event date： 2019.9.8 - 2019.9.13
Language：English Presentation type：Poster presentation
Venue：Kutna Hora Country：Czech Republic
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Molecular study of hepatitis B virus with pgRNA in the solution
K. Fujimoto, Y. Yamaguchi, R. Urano, W. Shinoda, T.Ishikawa, K. Omagari, Y. Tanaka, A. Nakagawa, S. Okazaki
the 36th International Conference on Solution Chemistry (ICSC2019) 2019.8
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Event date： 2019.8.4 - 2019.8.8
Language：English Presentation type：Poster presentation
Country：China
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Novel method to evaluate position-dependent diffusion constant of small molecules in heterogeneous systems International conference
T. Nagai, S. Tsurumaki, R. Urano, K. Fujimoto, W. Shinoda, S. Okazaki
the 36th International Conference on Solution Chemistry (ICSC2019) 2019.8
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Event date： 2019.8.4 - 2019.8.8
Language：English Presentation type：Oral presentation (general)
Country：China
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Coarse-grained molecular dynamics study for protein-lipid complexes Invited International coauthorship International conference
S. Seo, H. Liu, W. Shinoda
2019.6
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Event date： 2019.6.24 - 2019.6.26
Language：English Presentation type：Oral presentation (invited, special)
Country：Japan
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非晶高分子の衝撃破壊に関する分子論的研究 I：延性と脆性
藤本和士、湯之也、篠田渉、岡崎進
第68回高分子学会年次大会 2019.5 高分子学会
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Event date： 2019.5.29 - 2019.5.31
Language：Japanese Presentation type：Oral presentation (general)
Venue：大阪 Country：Japan
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全原子分子動力学計算による純ブタジエンゴム破壊の分子機構の研究
パヤル ラジディープ 、藤本和士、ジャン チャンウーン、篠田渉、武井祐樹、島広志、角田克彦、岡崎進
第68回高分子学会年次大会 2019.5 高分子学会
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Event date： 2019.5.29 - 2019.5.31
Venue：大阪
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非晶高分子の衝撃破壊に関する分子論的研究 II：分子論的解釈
湯之也、藤本和士、篠田渉、岡崎進
第68回高分子学会年次大会 2019.5
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Event date： 2019.5.29 - 2019.5.31
Language：Japanese Presentation type：Oral presentation (general)
Venue：大阪 Country：Japan
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抗B型肝炎ウイルス(HBV)薬剤分子のカプシド内部への吸収の自由エネルギー
浦野諒、藤本和士、安藤嘉倫、吉井範行、篠田渉、岡崎進
第22回理論化学討論会 2019.5 理論化学会
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Event date： 2019.5.27 - 2019.5.29
Language：Japanese Presentation type：Oral presentation (general)
Venue：北海道
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不均一系の物質輸送の理解に向けた小分子の位置に依存する自己拡散係数評価方法の確立
弦巻周平、浦野諒、藤本和士、篠田渉、 岡崎進
第22回理論化学討論会 2019.5 理論化学会
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Event date： 2019.5.27 - 2019.5.29
Language：Japanese Presentation type：Poster presentation
Venue：北海道 Country：Japan
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ガラス状高分子の衝撃破壊に関する分子論的研究
藤本和士、湯之也、篠田渉、岡崎進
第22回理論化学討論会 2019.5 理論化学会
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Event date： 2019.5.27 - 2019.5.29
Language：Japanese Presentation type：Oral presentation (general)
Venue：北海道
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Multiscale Molecular Modeling for Polymer Electrolyte Membrane for Fuel Cell Invited International conference
Wataru Shinoda
235th ECS Meeting The Electrochemical Society
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Event date： 2019.5.26 - 2019.5.31
Language：English Presentation type：Oral presentation (invited, special)
Venue：Dallas Country：United States
Research Projects
Research Projects
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生体膜の非対称性と不均一性が引き起こす物質輸送制御の分子機構の探求
Grant number：25K01729 2025.04 - 2028.03
日本学術振興会 科学研究費助成事業 基盤研究(B)
篠田 渉
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Development of Applications of Engineered Lipid Particles
Grant number：24H00038 2024.04 - 2029.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (S)
渡慶次 学, 真栄城 正寿, 篠田 渉
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膜透過の計算科学：膜モジュレータの作用と核酸透過機構の解明
Grant number：24H00843 2024.04 - 2027.03
日本学術振興会 科学研究費助成事業 学術変革領域研究(B)
篠田 渉
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細胞膜をゆらす核酸医薬の膜透過機構の総合理解と膜透過学の創成
Grant number：24H00839 2024.04 - 2027.03
日本学術振興会 科学研究費助成事業 学術変革領域研究(B)
大澤 昂志, 三木 康嗣, 篠田 渉, 川口 祥正
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Average orientation of lipid acyl chains in the domain structure of model membranes
Grant number：23K17373 2023.06 - 2026.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Research (Pioneering)
村田 道雄, 篠田 渉, 花島 慎弥, 杉山 成
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Molecular Dynamics of Intracellular Transport of Lipid Nanoparticles: Molecular mechanism of endosomal escape of nucleic acids
Grant number：21H01880 2021.04 - 2025.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B)
篠田 渉, 浦野 諒
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Grant amount：\17420000 （ Direct expense: \13400000 、 Indirect expense：\4020000 ）
脂質ナノ粒子(LNP)のエンドソーム脱出を分子動力学(MD)シミュレーションで解析し、その分子機構を明らかにすることを目的としており、当該年度においては、まず、核酸と脂質の複合構造であるLNPとエンドソーム膜の分子モデリングを中心に行った。dsDNAに標準系の脂質(1,2-dilinoleyloxy-3-dimethylaminopropane (DLin-MC3-DMA),コレステロール(Chol), ホスファチジルコリン(PC)脂質)を混合してできたLNPのMD計算を行った。カチオン性脂質(DLin-MC3-DMA)のpH変化に伴うイオン化状態の変化を考慮した粗視化(SPICA)力場を作成し、約30nmの直径のLNPのMD計算を実行した。DLin-MC3-DMAのイオン化状態の変化は、LNP構造を大きく変化させ、特にdsDNAのLNP内包状態が変化することがわかった。また、エンドソーム膜のモデリングを行い、実験情報に合わせた脂質組成を持つエンドソーム膜モデルをSPICA力場で作成した。コレステロールを含む5種の異なる脂質の混合膜としてモデルを作成し、大きなドメイン構造を持たないことを確認した。さらに、LNPとエンドソーム膜の相互作用を確認する分子動力学(MD)シミュレーションを行った。LNPは中性条件ではエンドソーム膜と積極的な相互作用を示さなかったが、酸性条件においては静電相互作用によってエンドソーム膜に強く吸着することがわかった。吸着後の融合プロセスは非常に長時間を要するため、律速段階であるLNPとエンドソーム膜間の吸着表面の脱水和を人工的にさせ、その後の融合の進展を観測した。現在、融合シミュレーションの途中であるが、数µs以上かけて構造緩和をしながら融合が進む様子が見られた。次年度以降にも継続して融合MD計算を実行する必要がある。
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全原子・粗視化分子動力学による細胞内分子動態の解明
Grant number：JPMXP102020010 2020.04 - 2023.03
文部科学省 スーパーコンピュータ「富岳」成果創出加速プログラム 受託研究
篠田 渉
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Authorship：Coinvestigator(s) Grant type：Competitive
Grant amount：\21450000 （ Direct expense: \19500000 、 Indirect expense：\1950000 ）
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次世代高性能リチウム硫黄電池の開発
2018.04
国立研究開発法人科学技術振興機構 ALCA 先端的低炭素化技術開発 重点課題
篠田 渉
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Authorship：Coinvestigator(s) Grant type：Competitive
Grant amount：\32942000 （ Direct expense: \25340000 、 Indirect expense：\7602000 ）
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Dynamic conformation and domain structure of lipid molecules in model biomembranes
Grant number：16H06315 2016.05 - 2021.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (S) Grant-in-Aid for Scientific Research (S)
MURATA Michio
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Grant amount：\182780000 （ Direct expense: \140600000 、 Indirect expense：\42180000 ）
In this study, we aimed to elucidate the molecular mechanisms of domains formed on cell membranes at atomic resolution in order to bring biological membranes into the ring of structural biology. By chemically synthesizing stable isotope-conjugated membrane lipids and measuring solid-state NMR, they succeeded in elucidating the shape of membrane lipid molecules, the mechanism of their assembly, and the intermolecular interactions during assembly. For example, it was found that domain-forming lipids have a strong tendency to form nano-sized aggregates through intermolecular hydrogen bonds.
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生体分子システムの機能制御による革新的創薬基盤の構築
2014.04 - 2020.03
文部科学省 ポスト「京」重点課題アプリケーション開発重点課題(1) 委託研究
篠田 渉
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Authorship：Coinvestigator(s) Grant type：Competitive
Grant amount：\79577300 （ Direct expense: \72343000 、 Indirect expense：\7234300 ）
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Grant number：26610120 2014.04 - 2016.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Challenging Exploratory Research Grant-in-Aid for Challenging Exploratory Research
Miyazaki Tsuyoshi, SHINODA Wataru, OTSUKA Takao
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Grant amount：\3770000 （ Direct expense: \2900000 、 Indirect expense：\870000 ）
In this research project, using a large-scale first-principles calculation code we have been developing, we have succeeded to employ the self-consistent first-principles calculations for several snapshot structures of a complex biological system, an ion channel gramicidin A system embedded in lipid bilayers sandwiched by bulk water regions. By comparing the results with those by classical force fields, which are used in most theoretical studies of biological systems, we have clarified the accuracy and the problems of the classical force fields. We also developed a calculation method, which enables us to realize the molecular dynamics of complex biological systems containing several tens of thousands of atoms, based on the accurate first-principles calculations.
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Multiscale Molecular Modeling of Membrane Fusion
Grant number：23350014 2011.04 - 2015.03
Japan Society for the Promotion of Science Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (B) Grant-in-Aid for Scientific Research (B)
SHINODA Wataru, TSUZUKI Seiji, KLEIN Michael
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Grant amount：\19110000 （ Direct expense: \14700000 、 Indirect expense：\4410000 ）
In order to understand the molecular mechanism in the membrane fusion process, a series of molecular dynamics simulation of membrane systems including vesicles has been conducted using a newly developed (semi)-quantitative coarse-grained molecular model on the basis of all-atom molecular dynamics trajectories. Interaction between curved membranes such as vesicles and fusion process has been investigated in terms of free energy analysis. Effects of lipid components and the presence of the peptides have been analyzed in the free energy calculations. New methods to accurately evaluate the line tension and curvature moduli of membranes have been also developed. The calculated physical constants were used to compare a simple continuum model and molecular dynamics for the free energy barriers of membrane fusion, which elucidated that the elastic energy contribution explains the fusion energy barrier only qualitatively.
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