論文 - 山本　詠士

Large-Scale FMO-MP2 Calculations of the Spike Protein Droplet Model

Doi, H; Nakano, T; Sakakura, K; Akisawa, K; Okuwaki, K; Hirano, Y; Yamamoto, E; Yasuoka, K; Ohshima, S; Katagiri, T; Mochizuki, Y

JOURNAL OF COMPUTATIONAL CHEMISTRY 46 （ 4 ）  2025年02月

ISSN  0192-8651

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TDP-43 multidomains and RNA modulate interactions and viscoelasticity in biomolecular condensates

Y Matsushita, I Yasuda, F Watanabe, E Yamamoto

arXiv preprint arXiv:2504.19790 2025年

Large‐Scale FMO‐MP2 Calculations of the Spike Protein Droplet Model

H Doi, T Nakano, K Sakakura, K Akisawa, K Okuwaki, Y Hirano, ...

Journal of Computational Chemistry 46 (4), e70052 2025年

FMO-based interaction analysis on DEET/icaridin—AgamOBP1 complex

K Akisawa, Y Sakuma, A Tsukamoto, H Doi, K Okuwaki, Y Hirano, ...

Chemistry Letters 54 (2), upaf030 2025年

Discovery of Pseudo-Luciferase Activity in Immunoglobulin G (IgG) and Its Application to the Detection of IgG Denaturation

R Nishihara, Y Kihara, E Yamamoto, Y Hirano, R Kurita

Analytical Chemistry 2025年

Coarse-grained model of disordered RNA for simulations of biomolecular condensates

I Yasuda, S von Bülow, G Tesei, E Yamamoto, K Yasuoka, ...

Journal of chemical theory and computation 21 (5), 2766-2779 21 （ 5 ） 2766 - 2779 2025年

ISSN  1549-9618

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BPS2025-Reentrant phase behavior and selective partitioning in protein-RNA condensates using molecular dynamics simulation

I Yasuda, S Bülow, G Tesei, E Yamamoto, K Yasuoka, K Lindorff-Larsen

Biophysical Journal 124 (3), 29a-30a 2025年

Water structures in tip-charged carbon nanotubes

Y Ono, E Yamamoto, K Yasuoka

The Journal of Chemical Physics 161 (5) 161 （ 5 ）  2024年

ISSN  0021-9606

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Molecular dynamics study on the permeation directionality of water molecules through AQP4

N Kuribayashi, E Yamamoto, Y Hirano, K Yasuoka

Biophysical Journal 123 (3), 66a-67a 123 （ 3 ） 66A - 67A 2024年

ISSN  0006-3495

Statistical Interaction Analyses on AgamOBP1-DEET/Icaridin Complex

K Akisawa, Y Sakuma, A Tsukamoto, H Doi, K Okuwaki, Y Hirano, ...

2024年

Estimating relaxation times from a single trajectory

T Akimoto, E Yamamoto, T Uneyama

Journal of the Physical Society of Japan 92 (7), 074005 92 （ 7 ）  2023年

ISSN  0031-9015

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Tunable pheromone interactions among microswimmers

B Nakayama, H Nagase, H Takahashi, Y Saito, S Hatayama, K Makino, ...

Proceedings of the National Academy of Sciences 120 (9), e2213713120 120 （ 9 ）  2023年

ISSN  0027-8424

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Heterogeneous biological membranes regulate protein partitioning via fluctuating diffusivity

K Sakamoto, T Akimoto, M Muramatsu, MSP Sansom, R Metzler, ...

PNAS nexus 2 (8), pgad258 2 （ 8 ）  2023年

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Wetting hysteresis induces effective unidirectional water transport through a fluctuating nanochannel

N Arai, E Yamamoto, T Koishi, Y Hirano, K Yasuoka, T Ebisuzaki

arXiv preprint arXiv:2204.09251 8 （ 5 ） 652 - 661 2022年

ISSN  2055-6756

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Differences in ligand-induced protein dynamics extracted from an unsupervised deep learning approach correlate with protein–ligand binding affinities

I Yasuda, K Endo, E Yamamoto, Y Hirano, K Yasuoka

Communications Biology 5 (1), 1-9 2022年

Theoretical Design of a Janus-Nanoparticle-Based Sandwich Assay for Nucleic Acids

T Sato, K Esashika, E Yamamoto, T Saiki, N Arai

International Journal of Molecular Sciences 23 (15), 8807 23 （ 15 ）  2022年

ISSN  1661-6596

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Ligand-induced protein dynamics differences correlate with protein-ligand binding affinities: An unsupervised deep learning approach

I Yasuda, K Endo, E Yamamoto, Y Hirano, K Yasuoka

arXiv preprint arXiv:2109.01339 2021年

Water molecules in CNT–Si3N4 membrane: Properties and the separation effect for water–alcohol solution

Winarto, E Yamamoto, K Yasuoka

The Journal of Chemical Physics 155 (10), 104701 2021年

The Acidic Tail of HMGB1 Regulates its Secondary Structure and Conformational Flexibility: A Circular Dichroism and Molecular Dynamics Simulation Study

WL Anggayasti, K Ogino, E Yamamoto, E Helmerhorst, K Yasuoka, ...

Computational and Structural Biotechnology Journal 18   1160 - 1172 2020年

ISSN  2001-0370

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Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes

E Yamamoto, J Domański, FB Naughton, RB Best, AC Kalli, PJ Stansfeld, ...

Science Advances 6 (8), eaay5736 6 （ 8 ）  2020年

ISSN  2375-2548

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Universal relation between instantaneous diffusivity and radius of gyration of proteins in aqueous solution

E Yamamoto, T Akimoto, A Mitsutake, R Metzler

arXiv preprint arXiv:2009.06829 126 （ 12 ）  2020年

ISSN  0031-9007

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Phase-change Janus particles with switchable dual properties

R Soma, B Nakayama, M Kuwahara, E Yamamoto, T Saiki

Applied Physics Letters 117 (22), 221601 117 （ 22 ）  2020年

ISSN  0003-6951

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Separation of water-alcohol mixtures using carbon nanotubes under an electric field

Winarto, Yamamoto Eiji, Yasuoka Kenji

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 21 （ 28 ） 15431 - 15438 2019年07月

ISSN  1463-9076

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Highly bright and stable NIR-BRET with blue-shifted coelenterazine derivatives for deep-tissue imaging of molecular events in vivo

R Nishihara, R Paulmurugan, T Nakajima, E Yamamoto, A Natarajan, ...

Theranostics 9 (9), 2646 9 （ 9 ） 2646 - 2661 2019年

ISSN  1838-7640

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Rapid Assembly of Colloidal Crystals under Laser Illumination on a GeSbTe Substrate

K Yamaguchi, E Yamamoto, R Soma, B Nakayama, M Kuwahara, T Saiki

Langmuir 35 （ 19 ） 6403 - 6408 2019年

ISSN  0743-7463

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Separation of water–alcohol mixtures using carbon nanotubes under an electric field

E Yamamoto, K Yasuoka

Physical Chemistry Chemical Physics 21 (28), 15431-15438 2019年

Molecular Dynamic Simulations to Probe Water Permeation Pathways of GPCRs

K Tomobe, E Yamamoto, K Yasuoka

G Protein-Coupled Receptor Signaling, 21-30 1947   21 - 30 2019年

ISSN  1064-3745

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Selectivity of Carbon Nanotubes under An Electric Field on Transferring Water–Alcohol Mixtures

E Yamamoto, K Yasuoka

IOP Conference Series: Materials Science and Engineering 494 (1), 012099 2019年

Why is the environment important for decision making? Local reservoir model for choice-based learning

Naruse M., Yamamoto E., Nakao T., Akimoto T., Saigo H., Okamura K., Ojima I., Northoff G., Hori H.

PLoS ONE （PLoS ONE）  13 （ 10 ）  2018年10月

ISSN  1932-6203

　概要を見る

© 2018 Naruse et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Decision making based on behavioral and neural observations of living systems has been extensively studied in brain science, psychology, neuroeconomics, and other disciplines. Decision-making mechanisms have also been experimentally implemented in physical processes, such as single photons and chaotic lasers. The findings of these experiments suggest that there is a certain common basis in describing decision making, regardless of its physical realizations. In this study, we propose a local reservoir model to account for choicebased learning (CBL). CBL describes decision consistency as a phenomenon where making a certain decision increases the possibility of making that same decision again later. This phenomenon has been intensively investigated in neuroscience, psychology, and other related fields. Our proposed model is inspired by the viewpoint that a decision is affected by its local environment, which is referred to as a local reservoir. If the size of the local reservoir is large enough, consecutive decision making will not be affected by previous decisions, thus showing lower degrees of decision consistency in CBL. In contrast, if the size of the local reservoir decreases, a biased distribution occurs within it, which leads to higher degrees of decision consistency in CBL. In this study, an analytical approach for characterizing local reservoirs is presented, as well as several numerical demonstrations. Furthermore, a physical architecture for CBL based on single photons is discussed, and the effects of local reservoirs are numerically demonstrated. Decision consistency in human decisionmaking tasks and in recruiting empirical data is evaluated based on the local reservoir. This foundation based on a local reservoir offers further insights into the understanding and design of decision making.

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Water permeation through the internal water pathway in activated GPCR rhodopsin.

K Tomobe, E Yamamoto, K Kholmurodov, K Yasuoka

PloS one 12 (5), e0176876 12 （ 5 ）  2017年

ISSN  1932-6203

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Effects of temperature, concentration, and isomer on the hydration structure in monosaccharide solutions

K Tomobe, E Yamamoto, M Yasui, K Yasuoka

Physical Chemistry Chemical Physics 19 (23), 15239-15246 19 （ 23 ） 15239 - 15246 2017年

ISSN  1463-9076

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Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity

E Yamamoto, T Akimoto, AC Kalli, K Yasuoka, MSP Sansom

Science Advances 3, e1601871 3 （ 1 ）  2017年

ISSN  2375-2548

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Detection of transition times from single-particle-tracking trajectories

T Akimoto, E Yamamoto

Physical Review E 96 (5), 052138 96 （ 5 ）  2017年

ISSN  2470-0045

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Computational and theoretical approaches for studies of a lipid recognition protein on biological membranes

E Yamamoto

Biophysics and Physicobiology 14, 153-160 14   153 - 160 2017年

ISSN  2189-4779

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Origin of the blueshift of water molecules at interfaces of hydrophilic cyclic compounds

K Tomobe, E Yamamoto, D Kojić, Y Sato, M Yasui, K Yasuoka

Science Advances 3 (12), e1701400 3 （ 12 ）  2017年

ISSN  2375-2548

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Water Molecules in a Carbon Nanotube under an Applied Electric Field at Various Temperatures and Pressures

E Yamamoto, K Yasuoka

Water 9 (7), 473 9 （ 7 ）  2017年

ISSN  2073-4441

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1/f fluctuation and water permeation of aquaporins

E Yamamoto, K Yasuoka

Kobunshi 65 (4), 175-176 2016年

Distributional behaviors of time-averaged observables in the Langevin equation with fluctuating diffusivity: Normal diffusion but anomalous fluctuations

T Akimoto, E Yamamoto

Physical Review E 93 (6), 062109 93 （ 6 ）  2016年

ISSN  2470-0045

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Distributional behavior of diffusion coefficients obtained by single trajectories in annealed transit time model

T Akimoto, E Yamamoto

Journal of Statistical Mechanics: Theory and Experiment 2016 (12), 123201 2016年

ISSN  1742-5468

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Instability of buried hydration sites increases protein subdomains fluctuations in the human prion protein by the pathogenic mutation T188R

K Tomobe, E Yamamoto, T Akimoto, M Yasui, K Yasuoka

AIP Advances 6 (5), 055324 6 （ 5 ）  2016年

ISSN  2158-3226

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Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High-Throughput Molecular Dynamics

E Yamamoto, AC Kalli, K Yasuoka, MSP Sansom

Structure 24 （ 8 ） 1421 - 1431 2016年

ISSN  0969-2126

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Langevin equation with fluctuating diffusivity: A two-state model

T Miyaguchi, T Akimoto, E Yamamoto

Physical Review E 94 (1), 012109 94 （ 1 ）  2016年

ISSN  2470-0045

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Separation of water-ethanol solutions with carbon nanotubes and electric fields

Winarto, Takaiwa Daisuke, Yamamoto Eiji, Yasuoka Kenji

PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18 （ 48 ） 33310 - 33319 2016年

ISSN  1463-9076

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Separation of water–ethanol solutions with carbon nanotubes and electric fields

D Takaiwa, E Yamamoto, K Yasuoka

Physical Chemistry Chemical Physics 18 (48), 33310-33319 2016年

Structures of water molecules in carbon nanotubes induced with electric fields and its application for water-methanol separation

W Winarto, D Takaiwa, E Yamamoto, K Yasuoka

Applied Mechanics and Materials 842, 453-456 2016年

Water-methanol separation with carbon nanotubes and electric fields

Winarto, D Takaiwa, E Yamamoto, K Yasuoka

Nanoscale 7 （ 29 ） 12659 - 12665 2015年

ISSN  2040-3364

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Anomalous dynamics of a lipid recognition protein on a membrane surface

E Yamamoto, AC Kalli, T Akimoto, K Yasuoka, MSP Sansom

Scientific reports 5, 18245 5 2015年

ISSN  2045-2322

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Origin of 1/f noise in hydration dynamics on lipid membrane surfaces

E Yamamoto, T Akimoto, M Yasui, K Yasuoka

Scientific reports 5, 8876 5 2015年

ISSN  2045-2322

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Structures of water molecules in carbon nanotubes under electric fields

Winarto, D Takaiwa, E Yamamoto, K Yasuoka

The Journal of chemical physics 142 (12), 124701 142 （ 12 ）  2015年

ISSN  0021-9606

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Velocity auto-correlation function of ions and water molecules in different concentrations, anions and ion clusters

K Tomobe, E Yamamoto, D Kojic, M Yasui, K Yasuoka

Molecular Simulation 41 (10-12), 840-844 41 （ 10-12 ） 840 - 844 2015年

ISSN  0892-7022

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Poisson property of the occurrence of flip-flops in a model membrane

N Arai, T Akimoto, E Yamamoto, M Yasui, K Yasuoka

The Journal of chemical physics 140 (6), 064901 140 （ 6 ）  2014年

ISSN  0021-9606

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1/f fluctuations of amino acids regulate water transportation in aquaporin 1

E Yamamoto, T Akimoto, Y Hirano, M Yasui, K Yasuoka

Physical Review E 89 (2), 022718 89 （ 2 ）  2014年

ISSN  1539-3755

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Origin of subdiffusion of water molecules on cell membrane surfaces

E Yamamoto, T Akimoto, M Yasui, K Yasuoka

Scientific Reports 4, 4720 4 2014年

ISSN  2045-2322

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Power-law trapping of water molecules on the lipid-membrane surface induces water retardation

E Yamamoto, T Akimoto, Y Hirano, M Yasui, K Yasuoka

Physical Review E 87 (5), 052715 87 （ 5 ）  2013年

ISSN  1539-3755

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Common Force Field Thermodynamics of Cholesterol

F Giangreco, E Yamamoto, Y Hirano, M Hodoscek, V Knecht, M di Giosia, ...

The Scientific World Journal 2013 2013年

ISSN  1537-744X

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Structural features of aquaporin 4 supporting the formation of arrays and junctions in biomembranes

S Höfinger, E Yamamoto, Y Hirano, F Zerbetto, T Narumi, K Yasuoka, ...

Biochimica et Biophysica Acta (BBA)-Biomembranes 1818 (9), 2234-2243 1818 （ 9 ） 2234 - 2243 2012年

ISSN  0005-2736

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Diffusive nature of xenon anesthetic changes properties of a lipid bilayer: molecular dynamics simulations

E Yamamoto, T Akimoto, H Shimizu, Y Hirano, M Yasui, K Yasuoka

The Journal of Physical Chemistry B 116 (30), 8989-8995 116 （ 30 ） 8989 - 8995 2012年

ISSN  1520-6106

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Non-gaussian fluctuations resulting from power-law trapping in a lipid bilayer

T Akimoto, E Yamamoto, K Yasuoka, Y Hirano, M Yasui

Physical review letters 107 (17), 178103 107 （ 17 ）  2011年

ISSN  0031-9007

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