SHINODA WATARU 篠田渉

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SHINODA Wataru 篠田渉

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Researcher Number	70357193
Other IDs	https://orcid.org/0000-0002-3388-9227
Affiliation (Current)	2026: 岡山大学, 先鋭研究領域, 教授
Affiliation (based on the past Project Information) *help	2025 – 2026: 岡山大学, 先鋭研究領域, 教授 2021 – 2024: 岡山大学, 異分野基礎科学研究所, 教授 2016 – 2021: 名古屋大学, 工学研究科, 准教授 2015: 名古屋大学, 大学院工学研究科, 准教授 2013 – 2014: 名古屋大学, 工学(系)研究科(研究院), 准教授 2012: 独立行政法人産業技術総合研究所, 健康工学研究部門, 主任研究員 2011: 独立行政法人産業技術総合研究所, ナノシステム研究部門, 研究グループ長
Review Section/Research Field	Principal Investigator Transformative Research Areas, Section (II) / Basic Section 32010:Fundamental physical chemistry-related / Physical chemistry Except Principal Investigator Transformative Research Areas, Section (II) / Medium-sized Section 37:Biomolecular chemistry and related fields / Broad Section D / Biomolecular chemistry / Mathematical physics/Fundamental condensed matter physics
Keywords	Principal Investigator 分子動力学シミュレーション / 分子シミュレーション / 膜融合 / 抗菌ペプチド / 物質透過 / 非対称膜 / ペプチド / 核酸医薬 / 機能性ペプチド / 光応答性機能分子 … More / 核酸輸送 / 膜透過 / 膜モジュレータ / 自由エネルギー解析 / 粗視化分子動力学シミュレーション / 粗視化 / 粗視化力場 / エンドソーム脱出 / 核酸送達 / トランスフェクション / 脂質ナノ粒子 / 脂質混合効果 / ベシクル間相互作用 / 膜弾性 / ストレス / ストーク / 生物物理 / 生体膜融合 / 粗視化モデル / 自由エネルギー … More Except Principal Investigator 脂質二重膜 / 核酸医薬 / 分子マシン / 中分子医薬 / ペプチド / オリゴ核酸 / 細胞膜透過 / 膜モジュレータ / 平均配向 / 固体NMR / 立体配座 / 脂肪鎖 / ウイルス様脂質ナノ粒子 / 人工エクソソーム / マイクロ流体デバイス / 脂質粒子 / 動的配座 / 古細菌脂質 / ドメイン構造 / スフィンゴミエリン / 脂質ラフト / イオンチャネル / 計算手法、プログラム開発 / 計算物理 / 生物物理 / 第一原理分子動力学 / プログラム開発 / 大規模第一原理計算 Less

Exploration of the Molecular Mechanisms of Transport Regulation Induced by Asymmetry and Heterogeneity in BiomembranesPrincipal Investigator
- Principal Investigator
  
  篠田渉
- Project Period (FY)
  2025 – 2027
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 32010:Fundamental physical chemistry-related
- Research Institution
  Okayama University
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Principal Investigator
- Principal Investigator
  
  篠田渉
- Project Period (FY)
  2025 – 2026
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (B)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  Okayama University
Development of Applications of Engineered Lipid Particles
- Principal Investigator
  
  渡慶次学
- Project Period (FY)
  2024 – 2028
- Research Category
  
  Grant-in-Aid for Scientific Research (S)
- Review Section
  
  Broad Section D
- Research Institution
  Hokkaido University
Molecular Dynamics of Intracellular Transport of Lipid Nanoparticles: Molecular Mechanism of Nucleic Acid Endosomal EscapePrincipal Investigator
- Principal Investigator
  
  SHINODA Wataru
- Project Period (FY)
  2024
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 32010:Fundamental physical chemistry-related
- Research Institution
  Okayama University
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
- Principal Investigator
  
  大澤昂志
- Project Period (FY)
  2024 – 2026
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (B)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  The University of Osaka
Computational Science of Membrane Permeation: Elucidation of Membrane Modulator Action and Nucleic Acid Permeation MechanismPrincipal Investigator
- Principal Investigator
  
  篠田渉
- Project Period (FY)
  2024 – 2026
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (B)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  Okayama University
Average orientation of lipid acyl chains in the domain structure of model membranes
- Principal Investigator
  
  村田道雄
- Project Period (FY)
  2023 – 2025
- Research Category
  
  Grant-in-Aid for Challenging Research (Pioneering)
- Review Section
  
  Medium-sized Section 37:Biomolecular chemistry and related fields
- Research Institution
  Osaka University
Dynamic conformation and domain structure of lipid molecules in model biomembranes
- Principal Investigator
  
  MURATA Michio
- Project Period (FY)
  2016 – 2020
- Research Category
  
  Grant-in-Aid for Scientific Research (S)
- Research Field
  
  Biomolecular chemistry
- Research Institution
  Osaka University
Environment-dependent force fields for complex biological systems based on very large-scale first-principles calculations
- Principal Investigator
  
  Miyazaki Tsuyoshi
- Project Period (FY)
  2014 – 2015
- Research Category
  
  Grant-in-Aid for Challenging Exploratory Research
- Research Field
  
  Mathematical physics/Fundamental condensed matter physics
- Research Institution
  National Institute for Materials Science
Multiscale Molecular Modeling of Membrane FusionPrincipal Investigator
- Principal Investigator
  
  SHINODA Wataru
- Project Period (FY)
  2011 – 2014
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Research Field
  
  Physical chemistry
- Research Institution
  Nagoya University
  National Institute of Advanced Industrial Science and Technology

All 2025 2024 2023 2022 2021 2020 2019 2018 2015 2014 2013 2012 2011 Other

All Journal Article Presentation

[Journal Article] Fully atomistic molecular dynamics modeling of photoswitchable azo-PC lipid bilayers: structure, mechanical properties, and drug permeation2025
- Author(s)
  Alberto Kevin A.、Hasna Begam M. N.、Xiong Hejian、Shinoda Wataru、Slesinger Paul A.、Qin Zhenpeng、Nielsen Steven O.
- Journal Title
  
  Nanoscale
  
  Volume: 17 Issue: 4 Pages: 2032-2042
- DOI
  10.1039/d4nr02509a
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-24H00839, KAKENHI-PLANNED-24H00843
[Journal Article] NMR and molecular simulation studies on the structure elucidation of the amphotericin B ion channel using <sup>13</sup>C and <sup>19</sup>F labelling2025
- Author(s)
  Umegawa Yuichi、Tsuchikawa Hiroshi、Shinoda Wataru、Murata Michio
- Journal Title
  
  Organic & Biomolecular Chemistry
  
  Volume: 23 Issue: 6 Pages: 1233-1252
- DOI
  10.1039/d4ob01468e
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-ORGANIZER-24H00839, KAKENHI-PLANNED-24H00843
[Journal Article] 分子シミュレーションによる脂質ナノ粒子の構造とエンドソーム脱出機構の解析2024
- Author(s)
  篠田渉
- Journal Title
  
  Farumashia
  
  Volume: 60 Issue: 2 Pages: 101-105
- DOI
  10.14894/faruawpsj.60.2_101
- ISSN
  0014-8601, 2189-7026
- Language
  Japanese
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23K21096
[Journal Article] Light-controllable cell-membrane disturbance for intracellular delivery2024
- Author(s)
  Huo Wenting、Miki Koji、Mu Huiying、Osawa Takashi、Yamaguma Harumi、Kasahara Yuuya、Obika Satoshi、Kawaguchi Yoshimasa、Hirose Hisaaki、Futaki Shiroh、Miyazaki Yusuke、Shinoda Wataru、Akai Shuji、Ohe Kouichi
- Journal Title
  
  Journal of Materials Chemistry B
  
  Volume: in press Issue: 17 Pages: 4138-4147
- DOI
  10.1039/d3tb02956e
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K20530, KAKENHI-ORGANIZER-24H00839, KAKENHI-PLANNED-24H00840, KAKENHI-PLANNED-24H00843, KAKENHI-PROJECT-23KJ1297
[Journal Article] pSPICA Force Field Extended for Proteins and Peptides2024
- Author(s)
  Miyazaki Yusuke、Shinoda Wataru
- Journal Title
  
  Journal of Chemical Information and Modeling
  
  Volume: 64 Issue: 2 Pages: 532-542
- DOI
  10.1021/acs.jcim.3c01611
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23K21096
[Journal Article] Protein?lipid acyl chain interactions: Depth-dependent changes of segmental mobility of phospholipid in contact with bacteriorhodopsin2024
- Author(s)
  Umegawa Yuichi、Kato Sho、Seo Sangjae、Shinoda Wataru、Kawatake Satoshi、Matsuoka Shigeru、Murata Michio
- Journal Title
  
  Biophysical Chemistry
  
  Volume: 308 Pages: 107204-107204
- DOI
  10.1016/j.bpc.2024.107204
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23K04943, KAKENHI-PROJECT-21H04707, KAKENHI-PROJECT-23K17373
[Journal Article] Understanding the effects of ethanol on the liposome bilayer structure using microfluidic-based time-resolved small-angle X-ray scattering and molecular dynamics simulations2024
- Author(s)
  Maeki Masatoshi、Kimura Niko、Okada Yuto、Shimizu Kazuki、Shibata Kana、Miyazaki Yusuke、Ishida Akihiko、Yonezawa Kento、Shimizu Nobutaka、Shinoda Wataru、Tokeshi Manabu
- Journal Title
  
  Nanoscale Advances
  
  Volume: ー Issue: 8 Pages: 2166-2176
- DOI
  10.1039/d3na01073b
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-19H05781, KAKENHI-PUBLICLY-23H04049, KAKENHI-PROJECT-23K28408, KAKENHI-PROJECT-23K21096
[Journal Article] Self-Assembly of Glycerol-Amphiphilic Janus Dendrimers Amplifies and Indicates Principles for the Selection of Stereochemistry by Biological Membranes2023
- Author(s)
  Zhang Dapeng、Xiao Qi、Rahimzadeh Mehrnoush、Liu Matthew、Rodriguez-Emmenegger Cesar、Miyazaki Yusuke、Shinoda Wataru、Percec Virgil
- Journal Title
  
  Journal of the American Chemical Society
  
  Volume: 145 Issue: 7 Pages: 4311-4323
- DOI
  10.1021/jacs.3c00389
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Journal Article] Improved Protein Model in SPICA Force Field2023
- Author(s)
  Yamada Teppei、Miyazaki Yusuke、Harada Shogo、Kumar Ashutosh、Vanni Stefano、Shinoda Wataru
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 19 Issue: 23 Pages: 8967-8977
- DOI
  10.1021/acs.jctc.3c01016
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Journal Article] Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study2022
- Author(s)
  Miyazaki Yusuke、Shinoda Wataru
- Journal Title
  
  Biochimica et Biophysica Acta (BBA) - Biomembranes
  
  Volume: 1864 Issue: 9 Pages: 183955-183955
- DOI
  10.1016/j.bbamem.2022.183955
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23K21096
[Journal Article] SPICA Force Field for Proteins and Peptides2022
- Author(s)
  Kawamoto Shuhei、Liu Huihui、Miyazaki Yusuke、Seo Sangjae、Dixit Mayank、DeVane Russell、MacDermaid Christopher、Fiorin Giacomo、Klein Michael L.、Shinoda Wataru
- Journal Title
  
  Journal of Chemical Theory and Computation
  
  Volume: 18 Issue: 5 Pages: 3204-3217
- DOI
  10.1021/acs.jctc.1c01207
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Journal Article] Conformation and Orientation of Branched Acyl Chains Responsible for the Physical Stability of Diphytanoylphosphatidylcholine.2020
- Author(s)
  Hiroshi Tsuchikawa, Takuya Ono, Masaki Yamagami, Yuichi Umegawa, Wataru Shinoda, Michio Murata
- Journal Title
  
  Biochemistry
  
  Volume: 59 Issue: 40 Pages: 3929-3938
- DOI
  10.1021/acs.biochem.0c00589
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-20K05730, KAKENHI-PLANNED-17H06406, KAKENHI-PROJECT-16H06315
[Journal Article] Average Conformation of Branched Chain Lipid PGP-Me That Accounts for the Thermal Stability and High-Salinity Resistance of Archaeal Membranes.2019
- Author(s)
  Yamagami, M., Tsuchikawa, H., Cui, J., Umegawa, Y., Miyazaki, Y., Seo, S., Shinoda, W., Murata, M.
- Journal Title
  
  Biochemistry
  
  Volume: 58 Issue: 37 Pages: 3869-3879
- DOI
  10.1021/acs.biochem.9b00469
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-17H06406, KAKENHI-PROJECT-16H06315
[Journal Article] SPICA Force Field for Lipid Membranes: Domain Formation Induced by Cholesterol.2019
- Author(s)
  Seo, S., Shinoda, W.
- Journal Title
  
  J. Chem. Theory Comput.
  
  Volume: 15 Issue: 1 Pages: 762-774
- DOI
  10.1021/acs.jctc.8b00987
- NAID
  120006623810
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06315
[Journal Article] Cholesterol-Induced Conformational Change in the Sphingomyelin Headgroup2019
- Author(s)
  Hanashima Shinya、Murakami Kazuhiro、Yura Michihiro、Yano Yo、Umegawa Yuichi、Tsuchikawa Hiroshi、Matsumori Nobuaki、Seo Sangjae、Shinoda Wataru、Murata Michio
- Journal Title
  
  Biophysical Journal
  
  Volume: 117 Issue: 2 Pages: 307-318
- DOI
  10.1016/j.bpj.2019.06.019
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19K05713, KAKENHI-PROJECT-16H06315, KAKENHI-PROJECT-18K19149
[Journal Article] Amphotericin B-Ergosterol Complex Spans a Lipid Bilayer as a Single-Length Assembly.2019
- Author(s)
  Tomoya Yamamoto, Yuichi Umegawa, Hiroshi Tsuchikawa, Shinya Hanashima, Nobuaki Matsumori, Kosuke Funahashi, Sangjae Seo, Wataru Shinoda, Michio Murata.
- Journal Title
  
  Biochemistry
  
  Volume: 58 Issue: 51 Pages: 5188-5196
- DOI
  10.1021/acs.biochem.9b00835
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-16H06315, KAKENHI-PROJECT-18K19149
[Journal Article] Precise Calculation of the Local Pressure Tensor in Cartesian and Spherical Coordinates in LAMMPS2015
- Author(s)
  中村壮伸、川本周平、篠田　渉
- Journal Title
  
  Computer Physics Communications
  
  Volume: 190 Pages: 120-128
- DOI
  10.1016/j.cpc.2014.11.017
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-23350014
[Journal Article] Free energy analysis along the stalk mechanism of membrane fusion2014
- Author(s)
  川本周平、篠田　渉
- Journal Title
  
  Soft Matter
  
  Volume: 10 Issue: 17 Pages: 3048-3054
- DOI
  10.1039/c3sm52344f
- Peer Reviewed / Acknowledgement Compliant
- Data Source
  KAKENHI-PROJECT-23350014
[Journal Article] 脂質膜透過現象の分子シミュレーションによる研究2014
- Author(s)
  篠田　渉
- Journal Title
  
  膜(MEMBRANE)
  
  Volume: 39 Pages: 372-378
- NAID
  130005069452
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23350014
[Journal Article] Effective interaction between small unilamellar vesicles as probed by coarse-grained molecular dynamics simulations2014
- Author(s)
  篠田　渉、Michael L Klein
- Journal Title
  
  Pure and Applied Chemistry
  
  Volume: 86 Issue: 2 Pages: 215-222
- DOI
  10.1515/pac-2014-5023
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23350014
[Journal Article] Probing the structure of PEGylated-lipid assemblies by coarse-grained molecular dynamics2013
- Author(s)
  篠田　渉、Dennis E. Discher、Michael L. Klein、Sharon M. Loverde
- Journal Title
  
  Soft Matter
  
  Volume: 9 Issue: 48 Pages: 11549-11556
- DOI
  10.1039/c3sm52290c
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23350014
[Journal Article] A guiding potential method for evaluating the bending rigidity of tensionless lipid membranes from molecular simulation2013
- Author(s)
  川本周平、中村壮伸、Steven O. Nilesen、篠田　渉
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 139 Issue: 3
- DOI
  10.1063/1.4811677
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23350014
[Journal Article] Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory2013
- Author(s)
  中村壮伸、篠田　渉
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 138 Issue: 12
- DOI
  10.1063/1.4795579
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23350014
[Journal Article] 脂質膜の粗視化分子シミュレーション2013
- Author(s)
  篠田　渉
- Journal Title
  
  Colloid & Interface Communication
  
  Volume: 12 Pages: 55-61
- NAID
  40020187316
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23350014
[Journal Article] Computer simulation studies of self-assembling macromolecules2012
- Author(s)
  篠田　渉、Russell DeVane、Michael L Klein
- Journal Title
  
  Current Opinions in Structural Biology
  
  Volume: 22 Issue: 2 Pages: 175-186
- DOI
  10.1016/j.sbi.2012.01.011
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23350014
[Journal Article] Cholesterol Effect on Water Permeability through DPPC and PSM Lipid Bilayers : A Molecular Dynamics Study2011
- Author(s)
  斎藤大明、篠田渉
- Journal Title
  
  Journal of Physical Chemistry B
  
  Volume: 115 Issue: 51 Pages: 15241-15250
- DOI
  10.1021/jp201611p
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23350014, KAKENHI-PROJECT-23750008
[Journal Article] Novel numerical method for calculating the pressure tensor in spherical coordinates for molecular systems2011
- Author(s)
  中村壮伸、篠田渉、池庄司民夫
- Journal Title
  
  Journal of Chemical Physics
  
  Volume: 135 Issue: 9
- DOI
  10.1063/1.3626410
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23350014
[Journal Article] Free energy analysis of vesicle-to-bicelle transformation2011
- Author(s)
  篠田渉、中村壮伸、Steven O.Nielsen
- Journal Title
  
  Soft Matter
  
  Volume: 7 Issue: 19 Pages: 9012-9020
- DOI
  10.1039/c1sm05404j
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Heterogeneity of Multicomponent Lipid Membranes2025
- Author(s)
  Wataru Shinoda
- Organizer
  Conference on Frontiers in Computational and Experimental Research on Membranes and Interfaces
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-24H00839
[Presentation] Simulating Lipid Nanopartiles2025
- Author(s)
  Wataru Shinoda
- Organizer
  Understanding Surfaces and Interfaces: A Symposium Celebrating 7 Decades of Service
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-24H00843
[Presentation] Simulating Lipid Nanopartiles2025
- Author(s)
  Wataru Shinoda
- Organizer
  Understanding Surfaces and Interfaces: A Symposium Celebrating 7 Decades of Service
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] Heterogeneity of Multicomponent Lipid Membranes2025
- Author(s)
  Wataru Shinoda
- Organizer
  Conference on Frontiers in Computational and Experimental Research on Membranes and Interfaces
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] Heterogeneity of Multicomponent Lipid Membranes2025
- Author(s)
  Wataru Shinoda
- Organizer
  Conference on Frontiers in Computational and Experimental Research on Membranes and Interfaces
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-24H00843
[Presentation] Simulating Lipid Nanopartiles2025
- Author(s)
  Wataru Shinoda
- Organizer
  Understanding Surfaces and Interfaces: A Symposium Celebrating 7 Decades of Service
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-24H00839
[Presentation] 膜モジュレータ分子を用いた核酸の膜透過機構の解明2024
- Author(s)
  門脇怜央, Wenting Huo, 三木康嗣, 大江浩一, 篠田渉
- Organizer
  第38回分子シミュレーション討論会
- Data Source
  KAKENHI-PLANNED-24H00843
[Presentation] Recent development of the SPICA force field and its application studies2024
- Author(s)
  Wataru Shinoda
- Organizer
  CECAM Flagship Workshop "From New Developments to Modeling Dynamics, Assemblies, and Macromolecular Machines"
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] Coarse-grained molecular dynamics of lipid membranes: Effects of cholesterols on various events in membranes2024
- Author(s)
  Wataru Shinoda
- Organizer
  A Symposium Celebrating 60 Years of Molecular Dynamics
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 膜モジュレータ分子を用いた核酸の膜透過機構の解明2024
- Author(s)
  門脇怜央, Wenting Huo, 三木康嗣, 大江浩一, 篠田渉
- Organizer
  第38回分子シミュレーション討論会
- Data Source
  KAKENHI-ORGANIZER-24H00839
[Presentation] Coarse-grained molecular dynamics of lipid membranes: Effects of cholesterols on various events in membranes2024
- Author(s)
  Wataru Shinoda
- Organizer
  A Symposium Celebrating 60 Years of Molecular Dynamics - Computer Simulation in Physical and Life Sciences
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PLANNED-24H00843
[Presentation] Coarse-grained molecular modeling of plasma membrane using SPICA force field: Properties and composition of lipid nanodomains2024
- Author(s)
  Teppei Yamada, Wataru Shinoda
- Organizer
  日本生物物理学会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 脂質膜・脂質ナノ粒子の分子シミュレーション　ー細胞内動態の解析に向けてー2024
- Author(s)
  篠田　渉
- Organizer
  日本薬学会-構造活性フォーラム
- Invited
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] Coarse-grained molecular dynamics of lipid membranes: Effects of cholesterol on various events in membranes2024
- Author(s)
  Wataru Shinoda
- Organizer
  Symposium Celebrating 60 Years of Molecular Dynamics - Computer Simulation in Physical and Life Sciences
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-ORGANIZER-24H00839
[Presentation] 濃厚電解液中のLiイオン伝導機構2023
- Author(s)
  篠田　渉
- Organizer
  分子研研究会「イオン液体インフォマティクスの発展にむけて」
- Invited
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] Coarse-Grained Molecular Dynamics Study on Endosomal Escape of Lipid Nanoparticles using SPICA Force Field2023
- Author(s)
  篠田　渉
- Organizer
  CECAM workshop "Macromolecular complexes: from ab initio and integrative modelling to functional dynamics"
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 脂質ナノ粒子のエンドソーム脱出の分子機構：分子シミュレーションによるアプローチ2023
- Author(s)
  篠田　渉
- Organizer
  第454回 CBI学会研究講演会
- Invited
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] Exploring the Mechanism of Endosomal Escape of Lipid Nanoparticles: A Coarse-Grained Molecular Dynamics Study2023
- Author(s)
  Wataru Shinoda
- Organizer
  The 10th edition of the conference of the Asia Pacific Association of Theoretical and Computational Chemistry (APATCC-10)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 分子シミュレーションによる脂質ナノ粒子の構造解析とエンドソーム脱出機構の解明2023
- Author(s)
  篠田　渉
- Organizer
  第58回薬剤学懇談会研究討論会
- Invited
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] Selective action of antimicrobial peptides on lipid membranes: Coarse-grained molecular dynamics study2023
- Author(s)
  篠田　渉
- Organizer
  第61回日本生物物理学会年会
- Invited
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] Coarse-grained molecular dynamics of lipid self-assembly2022
- Author(s)
  Wataru Shinoda
- Organizer
  CECAM workshop: IONS, MEMBRANE AND CHANNELS: MULTISCALE SIMULATIONS FROM QUANTUM TO COARSE-GRAIN. A SYMPOSIUM IN HONOR OF MICHAEL L. KLEIN, FRS
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 脂質ナノ粒子を用いた核酸エンドソーム脱出の分子動力学2022
- Author(s)
  柴田果奈，Akhil Pratap Singh，宮崎裕介，篠田渉
- Organizer
  第44回溶液化学シンポジウム
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 分子動力学計算による抗菌ペプチドの膜選択性解析2022
- Author(s)
  川端一正，宮崎裕介，篠田　渉
- Organizer
  第44回溶液化学シンポジウム
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 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2022
- Author(s)
  柴田果奈, Akhil Pratap Singh, 篠田渉
- Organizer
  第60回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 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2022
- Author(s)
  安田貴也、梅川雄一、篠田渉、村田道雄
- Organizer
  日本化学会第102春季年会
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] 生体膜・脂質膜の分子シミュレーション2022
- Author(s)
  篠田　渉
- Organizer
  高分子計算機科学研究会
- Invited
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 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2022
- Author(s)
  宮崎裕介, 篠田渉
- Organizer
  第60回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 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2022
- Author(s)
  山田哲平, 篠田渉
- Organizer
  第60回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 環境依存の構造変化を取り入れた粗視化タンパク質モデルの開発2022
- Author(s)
  山田哲平, 篠田渉
- Organizer
  第16回分子科学会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 粗視化分子力場SPICAのタンパク質系への拡張と応用2022
- Author(s)
  宮崎裕介, 篠田渉
- Organizer
  第16回分子科学会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 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2022
- Author(s)
  山田哲平, 篠田渉
- Organizer
  第36回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 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2022
- Author(s)
  柴田果奈, Akhil Pratap Singh, 宮崎裕介, 篠田渉
- Organizer
  第36回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 抗菌ペプチドによる膜細孔形成の分子シミュレーション研究2022
- Author(s)
  川端一正, 宮﨑裕介, 篠田渉
- Organizer
  第60回生物物理学会年会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 抗菌ペプチドがもつ膜選択性の分子論的研究2022
- Author(s)
  川端一正, 宮崎裕介, 山田哲平, 篠田渉
- Organizer
  第36回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 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2022
- Author(s)
  柴田果奈, Pratap Singh Akhil, 宮崎裕介, 篠田渉
- Organizer
  第 73 回コロイドおよび界面化学討論会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] Elucidation of inter-leaflet coupling in asymmetric membranes induced by very long chain sphingomyelin based on solid-state NMR2021
- Author(s)
  Keeratisakulsith, T., Umegawa, Y., Tsuchikawa, H., Hanashima, S., Murata, M., Shinoda, W.
- Organizer
  日本化学会第101春季年会
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] 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2021
- Author(s)
  川端一正、宮﨑裕介、篠田渉
- Organizer
  第35回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] Coarse-Grained Molecular Dynamics of Biomolecular Self-Assembly: Membranes, Vesicles, Lipid Nanoparticles, Virus Capsids2021
- Author(s)
  篠田　渉
- Organizer
  Pacifichem2021
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 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2021
- Author(s)
  柴田果奈、真栄城正寿、渡慶次学、篠田渉
- Organizer
  第35回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 生体高分子集合系の分子シミュレーション2021
- Author(s)
  篠田　渉
- Organizer
  第16回複雑生命系秩序懇談会
- Invited
- Data Source
  KAKENHI-PROJECT-23K21096
[Presentation] 固体リンNMRを用いたバクテリオロドプシンと周辺脂質の相互作用解析2019
- Author(s)
  加藤翔、梅川雄一、村田道雄、Seo Sangjae、篠田渉
- Organizer
  日本化学会第99春季年会
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] Synthesis of novel 13C, 2H-labeled Amphotericin B and the conformational analysis of glycosidic linkage in lipid bilayers.2019
- Author(s)
  Yamamoto, T., Umegawa, Y., Suzuki, T., Tsuchikawa, H., Hanashima, S., Murata, M., Matsumori, N., Seo, S., Funahashi, K., Shinoda, W.
- Organizer
  日本化学会第99春季年会
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] メチル分岐アシル基含有リン脂質DPhPCが示す二重膜の安定性を担う分子配向・配座の解析2019
- Author(s)
  斧拓冶、土川博史、山上正輝、梅川雄一、村田道雄、篠田渉
- Organizer
  日本化学会第99春季年会
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] 混合モデル二重膜における極長鎖スフィンゴミエリンの内葉・外葉間相互作用の解明2019
- Author(s)
  足立美和子、森内舞、土川博史・Seo Sangjae、篠田渉、村田道雄
- Organizer
  日本化学会第99春季年会
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] Molecular Dynamics Study of Stability of Amphotericin B Channel.2018
- Author(s)
  Funahashi, K., Seo, S., Okazaki, S., Umegawa, Y., Murata, M., Shinoda. W.
- Organizer
  Conference of EMLG/JMLG Meeting 2018 and 41st Symposium on Solution Chemistry of Japan
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] Molecular orientation and conformation of archaeal membrane lipid PGP-Me by solid-state NMR and its interaction with bacteriorhodopsin2018
- Author(s)
  Yamagami Masaki、Tsuchikawa Hiroshi、Cui Jin、Kawatake Satoshi、Sato Fuminori、Umegawa Yuichi、Murata Michio、Seo Sangjar、Shinoda Wataru
- Organizer
  日本化学会第98春季年会
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] アンフォテリシンBとステロールが形成するチャネル複合体の構造研究2018
- Author(s)
  山本智也、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、松森信明、Seo Sangjaed、篠田渉
- Organizer
  第60回天然有機化合物討論会
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] Amphotericin B チャネルの構造安定性と疎水性ミスマッチによるチャネル間相互作用解析2018
- Author(s)
  舟橋康佑, Sangjae Seo、岡崎進、梅川雄一、村田道雄、篠田渉
- Organizer
  第32回分子シミュレーション討論会
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] Coarse-grained modeling of sphingomyelin and domain formation simulation.2018
- Author(s)
  Seo, S., Shinoda, W.
- Organizer
  Joint Conference of EMLG/JMLG Meeting 2018 and 41st Symposium on Solution Chemistry of Japan
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] Molecular dynamics simulations of domain formation in mixed lipid bilayers.2018
- Author(s)
  Seo, S., Shinoda, W.
- Organizer
  第56回日本生物物理学会年会
- Data Source
  KAKENHI-PROJECT-16H06315
[Presentation] 膜の粗視化分子シミュレーション2015
- Author(s)
  篠田　渉
- Organizer
  第359回CBI学会講演会「粗視化による生体分子系のシミュレーション」
- Place of Presentation
  東大、東京
- Year and Date
  2015-02-24
- Invited
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] 膜構造形成の分子シミュレーション2014
- Author(s)
  篠田　渉
- Organizer
  日本物理学会第69回年次大会
- Place of Presentation
  神奈川
- Invited
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] 膜の柔らかさと機能：分子シミュレーションによるアプローチ2014
- Author(s)
  篠田　渉
- Organizer
  日本化学会第94春期年会
- Place of Presentation
  名古屋
- Invited
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Coarse-Grained molecular Dynamics Study of Self-assembled Macromolecules2013
- Author(s)
  篠田　渉
- Organizer
  International Conference on Biomolecular Simulations & Dynamics
- Place of Presentation
  Chennai, India
- Invited
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Coarse-Grained Molecular Simulation of Lipid Self-Assembly2013
- Author(s)
  篠田　渉
- Organizer
  APS March Meeting 2013
- Place of Presentation
  Baltimore, MD, USA
- Invited
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Coarse-grained molecular dynamics study on stability of liposome and effect of carbon nanoparticles2013
- Author(s)
  篠田　渉
- Organizer
  246th ACS National Meeting
- Place of Presentation
  Indianapolis, IN, USA
- Invited
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Free Energy Analysis of Topological and Morphological Changes in Lipid Membranes: Molecular Dynamics Study2013
- Author(s)
  篠田　渉、川本周平
- Organizer
  3rd International Conference on Molecular Simulation 2013 (ICMS2013)
- Place of Presentation
  神戸
- Invited
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Molecular Dynamics Study of Lipid Self-Assembly2013
- Author(s)
  篠田　渉
- Organizer
  33rd International Conference on Solution Chemistry
- Place of Presentation
  京都
- Invited
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Effect of lipid components on the stability of stalk of membrane fusion2012
- Author(s)
  川本周平、篠田　渉
- Organizer
  IACIS2012 (International Association of Colloid and Interface Scientists, Conference)
- Place of Presentation
  仙台
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] 生体膜融合における融合細孔の形成過程のシミュレーション2012
- Author(s)
  川本周平、篠田　渉
- Organizer
  日本物理学会2012秋季大会
- Place of Presentation
  横浜
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] 階層的分子シミュレーションによる脂質膜・ベシクルの研究2012
- Author(s)
  篠田　渉
- Organizer
  第16回ペプチドフォーラム
- Place of Presentation
  京都
- Invited
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Morphology change of fusion stalk of lipid bilayer membrane studied by molecular dynamics simulation2012
- Author(s)
  川本周平、篠田　渉
- Organizer
  第50回日本物理学会年会
- Place of Presentation
  名古屋
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Molecular Dynamics Study of Self-Assembly of Amphiphiles2012
- Author(s)
  篠田渉
- Organizer
  International Workshop : Mathematical approach to emerging topics in Material Science 2012
- Place of Presentation
  東北大学(宮城)(招待講演)
- Year and Date
  2012-02-19
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] 曲げ応力による膜の曲げ弾性係数の解析手法2012
- Author(s)
  川本周平、篠田　渉
- Organizer
  第26回分子シミュレーション討論会
- Place of Presentation
  福岡
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] 膜融合の分子メカニズムの解析2012
- Author(s)
  川本周平、篠田渉
- Organizer
  第67回日本物理学会
- Place of Presentation
  関西学院大学(大阪)
- Year and Date
  2012-03-24
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] 膜融合過程の自由エネルギー解析2012
- Author(s)
  川本周平、篠田　渉
- Organizer
  第26回分子シミュレーション討論会
- Place of Presentation
  福岡
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Coarse Grained Molecular Simulations of Lipid Self-Assembly2012
- Author(s)
  篠田　渉
- Organizer
  Bridging Scales in Computational Polymer Chemistry
- Place of Presentation
  Providence, RI, USA
- Invited
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Molecular Dynamics Study of Effective Interaction Between Liposomes2012
- Author(s)
  篠田　渉
- Organizer
  IACIS2012 (International Association of Colloid and Interface Scientists, Conference)
- Place of Presentation
  仙台
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Stability of Liposome : Free Energy Analysis of Vesicle-to-Bicelle Transformation2011
- Author(s)
  篠田渉、中村壮伸、Steven O Nielsen
- Organizer
  Conference on Computational Physics 2011
- Place of Presentation
  Gatlinburg, Tennessee
- Year and Date
  2011-11-02
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Molecular Simulation of Liposomal Membranes2011
- Author(s)
  篠田渉
- Organizer
  The 2nd international symposium on "Multi-scale Simulations of Biological and Soft Materials" (MSBSM 2011)
- Place of Presentation
  京都大学芝蘭会館稲盛ホール(京都)(招待講演)
- Year and Date
  2011-09-10
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Membrane Fusion: Free Energy Analysis
- Author(s)
  篠田　渉、川本周平、Michael L. Klein
- Organizer
  International Symposium on Extended Molecular Dynamics and Enhanced Sampling: Nosé Dynamics 30 Years (NOSE30)
- Place of Presentation
  慶應大、東京
- Year and Date
  2014-11-10 – 2014-11-11
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Coarse-grained model of membrane protein
- Author(s)
  川本周平, Giacomo Fiorin, Chris MacDermaid, Russell DeVane, 篠田渉, Michael L. Klein
- Organizer
  International Symposium on Extended Molecular Dynamics and Enhanced Sampling: Nosé Dynamics 30 Years (NOSE30)
- Place of Presentation
  慶應大、東京
- Year and Date
  2014-11-10 – 2014-11-11
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] Free Energy Analysis of Membrane Fusion
- Author(s)
  川本周平、篠田渉、Michael L Klein
- Organizer
  XXVI IUPAP Conference on Computational Physics, CCP2014
- Place of Presentation
  Boston, USA
- Year and Date
  2014-08-11 – 2014-08-14
- Data Source
  KAKENHI-PROJECT-23350014
[Presentation] 膜タンパクの粗視化モデル
- Author(s)
  川本周平, Giacomo Fiorin, Chris MacDermaid, Russell DeVane, 篠田渉, Michael L. Klein
- Organizer
  第28回分子シミュレーション討論会
- Place of Presentation
  仙台
- Year and Date
  2014-11-12 – 2014-11-14
- Data Source
  KAKENHI-PROJECT-23350014

1. MURATA Michio (40183652)

# of Collaborated Projects: 2 results

# of Collaborated Products: 12 results
2. 花島慎弥 (50373353)

# of Collaborated Projects: 2 results

# of Collaborated Products: 5 results
3. TSUZUKI Seiji (10357527)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. Miyazaki Tsuyoshi (50354147)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
5. OTSUKA Takao (30465968)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
6. 梅川雄一 (20587779)

# of Collaborated Projects: 1 results

# of Collaborated Products: 11 results
7. 土川博史 (30460992)

# of Collaborated Projects: 1 results

# of Collaborated Products: 9 results
8. 三浦薫 (90353515)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. 櫻井香里 (50447512)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
10. 渡慶次学 (60311437)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
11. 真栄城正寿 (40744248)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
12. 浦野諒 (00836976)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
13. 宮崎裕介 (10963324)

# of Collaborated Projects: 1 results

# of Collaborated Products: 7 results
14. 北條裕信 (00209214)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
15. 下山敦史 (90625055)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
16. 杉山成 (90615428)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
17. 大澤昂志 (00783226)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
18. 三木康嗣 (60422979)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
19. 川口祥正 (90936808)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
20. KLEIN Michael

# of Collaborated Projects: 1 results

# of Collaborated Products: 7 results
21. SHIMIZU Nobutaka

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
22. MU Huiying

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
23. 篠田恵子

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

SHINODA WATARU 篠田 渉

SHINODA Wataru 篠田 渉

Research Projects

Research Products

Co-Researchers

Exploration of the Molecular Mechanisms of Transport Regulation Induced by Asymmetry and Heterogeneity in BiomembranesPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

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Principal Investigator

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Development of Applications of Engineered Lipid Particles

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Molecular Dynamics of Intracellular Transport of Lipid Nanoparticles: Molecular Mechanism of Nucleic Acid Endosomal EscapePrincipal Investigator

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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

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Computational Science of Membrane Permeation: Elucidation of Membrane Modulator Action and Nucleic Acid Permeation MechanismPrincipal Investigator

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Average orientation of lipid acyl chains in the domain structure of model membranes

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Dynamic conformation and domain structure of lipid molecules in model biomembranes

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Environment-dependent force fields for complex biological systems based on very large-scale first-principles calculations

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Multiscale Molecular Modeling of Membrane FusionPrincipal Investigator

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[Journal Article] Fully atomistic molecular dynamics modeling of photoswitchable azo-PC lipid bilayers: structure, mechanical properties, and drug permeation2025

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[Journal Article] NMR and molecular simulation studies on the structure elucidation of the amphotericin B ion channel using <sup>13</sup>C and <sup>19</sup>F labelling2025

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[Journal Article] 分子シミュレーションによる脂質ナノ粒子の構造とエンドソーム脱出機構の解析2024

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SHINODA WATARU 篠田渉

SHINODA Wataru 篠田渉