Publications

2021

[37] Ikki Yasuda, Katsuhiro Endo, Eiji Yamamoto, Yoshinori Hirano, Kenji Yasuoka,
“Ligand-induced protein dynamics differences correlate with protein-ligand binding affinities: An unsupervised deep learning approach”,
arXiv:2109.01339.

[36] Winarto, Eiji Yamamoto, and Kenji Yasuoka,
“Water molecules in CNT–Si3N4 membrane: Properties and the separation effect for water–alcohol solution”,
J. Chem Phys. 155, 104701 (2021).

[35] Eiji Yamamoto, Takuma Akimoto, Ayori Mitsutake, and Ralf Metzler,
“Universal Relation between Instantaneous Diffusivity and Radius of Gyration of Proteins in Aqueous Solution”,
Phys. Rev. Lett. 126, 128101 (2021). Featured in Physics (Synopsis).
arXiv:2009.06829.
プレスリリース

2020

[34] Ryo Soma, Bokusui Nakayama, Masashi Kuwahara, Eiji Yamamoto, and Toshiharu Saiki,
“Phase-change Janus particles with switchable dual properties”,
Appl. Phys. Lett. 117, 221601 (2020).

[33] Wresti L. Anggayasti, Kenta Ogino, Eiji Yamamoto, Erik Helmerhorst, Kenji Yasuoka, Ricardo L. Mancera,
“The Acidic Tail of HMGB1 Regulates its Secondary Structure and Conformational Flexibility: A Circular Dichroism and Molecular Dynamics Simulation Study”,
Comp. Struct. Biotechnol. J. 18, 1160-1172 (2020).

[32] Eiji Yamamoto, Jan Domański, Fiona B. Naughton, Robert B. Best, Antreas C. Kalli, Phillip J. Stansfeld, and Mark S. P. Sansom,
“Multiple Lipid Binding Sites Determine the Affinity of PH Domains for Phosphoinositide-Containing Membranes”,
Science Adv. 6, eaay5736 (2020).
プレスリリース

2019

[31] Winarto, Eiji Yamamoto, and Kenji Yasuoka,
“Separation of Water–Alcohol Mixtures using Carbon Nanotubes under an Electric Field”,
Phys. Chem. Chem. Phys. 21, 15431 (2019).

[30] Kei Yamaguchi, Eiji Yamamoto, Ryo Soma, Bokusui Nakayama, Masashi Kuwahara, and Toshiharu Saiki,
“Rapid Assembly of Colloidal Crystals under Laser Illumination on a GeSbTe Substrate”,
Langmuir 35, 6403 (2019).

la-2019-00176y_0006

[29] Ryo Nishihara, Ramasamy Paulmurugan, Takahiro Nakajima, Eiji Yamamoto, Arutselvan Natarajan, Rayhaneh Afjei, Yuki Hiruta, Naoko Iwasawa, Shigeru Nishiyama, Daniel Citterio, Moritoshi Sato, Sung Bae Kim, and Koji Suzuki,
“Highly bright and stable NIR-BRET with blue-shifted coelenterazine derivatives for deep-tissue imaging of molecular events in vivo”,
Theranostics 9, 2646 (2019).

BRET

2018

[28] Katsufumi Tomobe, Eiji Yamamoto, and Kenji Yasuoka,
“Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs”, Methods in Molecular Biology “G Protein-Coupled Receptor Signaling: Methods and Protocols”, DOI:10.1007/978-1-4939-9121-1.

[27] Makoto Naruse, Eiji Yamamoto, Takashi Nakao, Takuma Akimoto, Hayato Saigo, Kazuya Okamura, Izumi Ojima, Georg Northoff, and Hirokazu Hori,
“Why is the environment important for decision making? Local reservoir model for choice-based learning”,
PLoS ONE 13, e0205161 (2018).

2017

[26] Katsufumi Tomobe, Eiji Yamamoto, Dušan Kojić, Yohei Sato, Masato Yasui, and Kenji Yasuoka,
“Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds”,
Science Adv. 3, e1701400 (2017).
プレスリリース, Academist Journal

water-blueshift

[25] Takuma Akimoto and Eiji Yamamoto,
“Detection of transition times from single-particle-tracking trajectories”,
Phys. Rev. E 14, 052138 (2017).

detect

[24] Eiji Yamamoto,
“Computational and theoretical approaches for studies of a lipid recognition protein on biological membranes”,
Biophys. Physicobiol. 14, 153 (2017).

[23] Winarto, Eiji Yamamoto, and Kenji Yasuoka,
“Water Molecules in a Carbon Nanotube under an Electric Field, at Varying Temperatures and Pressures”,
Water 9, 473 (2017).

[22] Katsufumi Tomobe, Eiji Yamamoto, Masato Yasui, and Kenji Yasuoka,
“Effects of temperature, concentration, and isomer on the hydration structure in monosaccharide solutions”,
Phys. Chem. Chem. Phys. 19, 15239 (2017).

[21] Katsufumi Tomobe, Eiji Yamamoto, Kholmirzo Kholmurodov, and Kenji Yasuoka,
“Water permeation through the internal water pathway in activated GPCR rhodopsin”,
PLoS ONE 12, e0176876 (2017).

journal.pone.0176876.g003

[20] Eiji Yamamoto, Takuma Akimoto, Antreas C. Kalli, Kenji Yasuoka, and Mark S. P. Sansom,
“Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity”,
Science Adv. 3, e1601871 (2017).
プレスリリース

PH_PIP_diffusion.png

2016

[19] Winarto, Daisuke Takaiwa, Eiji Yamamoto, and Kenji Yasuoka,
“Separation of Water–Ethanol Solution with Carbon Nanotubes and Electric Fields”,
Phys. Chem. Chem. Phys. 18, 33310 (2016).

[18] Takuma Akimoto and Eiji Yamamoto,
“Distributional Behavior of Diffusion Coefficients Obtained by Single Trajectories in Annealed Transit Time Model”,
J. Stat. Mech.: Theory Exp. 2016, 123201 (2016). arXiv:1605.01174.

[17] Eiji Yamamoto, Antreas C. Kalli, Kenji Yasuoka, and Mark S. P. Sansom,
“Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High Throughput Molecular Dynamics”,
Structure 24, 1421 (2016).

fx1

[16] Tomoshige Miyaguchi, Takuma Akimoto, and Eiji Yamamoto,
“Langevin equation with fluctuating diffusivity: a two-state model”,
Phys. Rev. E 94, 012109 (2016). arXiv:1605.00106.

[15] Katsufumi Tomobe, Eiji Yamamoto, Takuma Akimoto, Masato Yasui, and Kenji Yasuoka,
“Instability of buried hydration sites increases protein subdomains fluctuations in the human prion protein by the pathogenic mutation T188R”,
AIP Adv. 6, 055324 (2016).

[14] Takuma Akimoto and Eiji Yamamoto,
“Distributional Behaviors of Time-averaged Observables in Langevin Equation with Fluctuating Diffusivity: Normal Diffusion but Anomalous Fluctuations”,
Phys. Rev. E 93, 062109 (2016). arXiv:1602.07007.

スクリーンショット 2016-02-25 0.53.24

2015

[13] Eiji Yamamoto, Antreas C. Kalli, Takuma Akimoto, Kenji Yasuoka, and Mark S. P. Sansom,
“Anomalous Dynamics of a Lipid Recognition Protein on a Membrane Surface”,
Sci. Rep. 5, 18245 (2015).

srep18245-f1

[12] Winarto, Daisuke Takaiwa, Eiji Yamamoto, and Kenji Yasuoka,
“Water–methanol separation with carbon nanotubes and electric fields”,
Nanoscale 7, 12659 (2015).

スクリーンショット 2017-05-15 14.17.30

[11] Winarto, Daisuke Takaiwa, Eiji Yamamoto, and Kenji Yasuoka,
“Structures of water molecules in carbon nanotubes under electric fields”,
J. Chem. Phys. 142, 12470 (2015), [selected as a cover].

jcpsa6_142_12

[10] Eiji Yamamoto, Takuma Akimoto, Masato Yasui, and Kenji Yasuoka,
“Origin of 1/f noise in hydration dynamics on lipid membrane surfaces”,
Sci. Rep. 5, 8876 (2015).

スクリーンショット 2015-03-06 21.43.25

[9] Katsufumi Tomobe, Eiji Yamamoto, Dusan Kojic, Masato Yasui, and Kenji Yasuoka,
“Velocity auto-correlation function of ions and water molecules in different concentrations, anions, and ion clusters”,
 Mol. Sim. 41, 840 (2015).

2014

[8] Eiji Yamamoto, Takuma Akimoto, Masato Yasui, and Kenji Yasuoka,
“Origin of subdiffusion of water molecules on cell membrane surfaces”,
Sci. Rep. 4, 4720 (2014), [Selected as a featured article in Nature Japan].

名称未設定

[7] Eiji Yamamoto, Takuma Akimoto, Yoshinori Hirano, Masato Yasui, and Kenji Yasuoka,
“1/f fluctuations of amino acids regulate water transportation in aquaporin 1″,
Phys. Rev. E 89, 022718 (2014).

aqp

[6] Noriyoshi Arai, Takuma Akimoto, Eiji Yamamoto, Masato Yasui, and Kenji Yasuoka,
“Poisson property of the occurrence of flip-flops in a model membrane”,
J. Chem. Phys. 140, 064901 (2014), [selected as a cover].

スクリーンショット(2015-02-20 16.50.09)

2013

[5] Francesco Giangreco, Eiji Yamamoto, Yoshinori Hirano, Milan Hodoscek, Volker Knecht, Matteo di Giosia, Matteo Calvaresi, Francesco Zerbetto, Kenji Yasuoka, Tetsu Narumi, Masato Yasui, and Siegfried Höefinger,
“Common Force Field Thermodynamics of Cholesterol”,
Sci. World J. 2013, 207287 (2013).

[4] Eiji Yamamoto, Takuma Akimoto, Yoshinori Hirano, Masato Yasui, and Kenji Yasuoka,
“Power-Law Trapping of Water Molecules on the Lipid-Membrane Surface Induces Water Retardation”,
Phys. Rev. E 87, 052715 (2013).

2012

[3] Eiji Yamamoto, Takuma Akimoto, Hiroyuki Shimizu, Yoshinori Hirano, Masato Yasui, and Kenji Yasuoka,
“Diffusive Nature of Xenon Anesthetic Changes Properties of a Lipid Bilayer: Molecular Dynamics Simulations”,
J. Phys. Chem. B 116, 8989 (2012).

jp-2012-03330c_0010

[2] Siegfried Höfinger, Eiji Yamamoto, Yoshinori Hirano, Francesco Zerbetto, Tetsu Narumi, Kenji Yasuoka, and Masato Yasui,
“Structural Features of Aquaporin 4 Supporting the Formation of Arrays and Junctions in Biomembranes”,
Biochim. Biophys. Acta 1818, 2234 (2012).

2011

[1] Takuma Akimoto, Eiji Yamamoto, Kenji  Yasuoka, Yoshinori Hirano, and Masato Yasui,
“Non-Gaussian Fluctuations Resulting from Power-Law Trapping in a Lipid Bilayer”,
Phys. Rev. Lett. 107, 178103 (2011).

Japanese reviews

[6] 山本詠士, “膜結合タンパク質とホスホイノシチド含有生体膜の相互作用”, 生物物理 61, 253-254 (2021).

[5] 佐々木雄彦, 山本詠士, 佐々木純子, “細胞膜での蛋白質―イノシトールリン脂質相互作用へのアシル基の関与”, 医学のあゆみ 269, 1068 (2019).

[4] 山本詠士, “博士論文紹介「脂質膜周りの水分子の温度依存性と1/fゆらぎ」”, アンサンブル 19, 48 (2017).

[3] 山本詠士, “脂質膜表面での水分子とタンパク質の異常拡散現象”, アンサンブル 18, 143 (2016).

[2] 山本詠士, 泰岡顕治, “アクアポリンの1/f ゆらぎと水分子透過”, 高分子 65, 175 (2016).

[1] 山本詠士, 秋元琢磨, 泰岡顕治, “分子動力学シミュレーションによる細胞膜表面での水分子の異常拡散の解明”, 生物物理 55, 242 (2015).

55-5