Takashi Yoshidome

Profile Information

Affiliation: Associate Professor, Graduate School of Engineering Department of Applied Physics Applied Condensed Matter Physics Applied Mathematical Physics, Tohoku University

Degree: 博士（理学）(Kyushu University)

J-GLOBAL ID: 201501064712955612
researchmap Member ID: 7000010917

External link: http://web.tohoku.ac.jp/mathphys/en/

Research Interests

Research Areas

Committee Memberships

Jan, 2022 - Dec, 2022

日本生物物理学会 2022年分野別専門委員
Nov, 2019 - Nov, 2021

2021年度日本生物物理学会年会実行委員
Jan, 2020 - Dec, 2020

2020年分野別専門委員, 日本生物物理学会
May, 2018 - Apr, 2020

会計, 日本生物物理学会東北支部会委員
Jan, 2017 - Dec, 2017

2017年分野別専門委員, 日本生物物理学会

Awards

Papers

Four‐dimensional imaging for cryo‐electron microscopy experiments using molecular simulations and manifold learning

Takashi Yoshidome

Journal of Computational Chemistry, 45(11) 738-751, Dec 19, 2023 Peer-reviewedLead authorCorresponding author
Mechanism of a high free-energy transduction efficiency of Bacillus PS3 F1-ATPase from the perspective of solvent entropy

Takashi Yoshidome

Journal of Molecular Liquids, 123346(1)-123346(9), Oct, 2023 Peer-reviewedLead authorCorresponding author
Elucidating Conformational Dynamics and Thermostability of Designed Aromatic Clusters by Using Protein Cages

Yuki Hishikawa, Hiroki Noya, Satoru Nagatoishi, Takashi Yoshidome, Basudev Maity, Kouhei Tsumoto, Satoshi Abe, Takafumi Ueno

Chemistry – A European Journal, 29(34) e202300488, May 2, 2023 Peer-reviewed
gr Predictor: A Deep Learning Model for Predicting the Hydration Structures around Proteins

Kosuke Kawama, Yusaku Fukushima, Mitsunori Ikeguchi, Masateru Ohta, Takashi Yoshidome

Journal of Chemical Information and Modeling, 62 4460-4473, Sep 6, 2022 Peer-reviewedCorresponding author
Simple-Fluid Model for Accurate Reproduction of Hydration Entropy

Takashi Yoshidome

Journal of the Physical Society of Japan, 91(9) 094802-1-094802-6, Aug 31, 2022 Peer-reviewedLead authorCorresponding author
AlphaFold-predicted Protein Structure vs Experimentally Obtained Protein Structure: An Emphasis on The Side Chains

Daiki Shiono, Takashi Yoshidome

Journal of the Physical Society of Japan, 91(6) 064804-1-064804-4, Jun, 2022 Peer-reviewedCorresponding author
A Measure for the Identification of Preferred Particle Orientations in Cryo-Electron Microscopy Data: A Simulation Study

18 96-107, Mar, 2021 Peer-reviewedCorresponding author
F1-ATPase Rotation and Its Inhibition from the Viewpoint of Solvent Entropy

T. Yoshidome

Chem. Phys. Lett., 757 137886-1-137886-6, Aug, 2020 Peer-reviewedLead authorCorresponding author
Comprehensive 3D-RISM Analysis of the Hydration of Small Molecule Binding Sites in Ligand-Free Protein Structures

Takashi Yoshidome, Mitsunori Ikeguchi, Masateru Ohta

J. Comp. Chem., 41 2406-2419, Aug, 2020 Peer-reviewedLead authorCorresponding author
Effects of a Low-Pass Filter on the Classification of Protein Electron-Density Maps in terms of Structural Polymorphism using Manifold Learning: A Simulation Study for Cryo-Electron Microscopy Experiments

YOSHIDOME Takashi

Journal of the Physical Society of Japan, 88 094801-1-094801-11, Aug, 2019 Peer-reviewedCorresponding author
An Automatic Classification of Molecular Dynamics Simulation Data into States, and Its Application to the Construction of a Markov State Model

Reika Ito, YOSHIDOME Takashi

Journal of the Physical Society of Japan, 87 114802-1-114802-8, Nov, 2018 Peer-reviewedCorresponding author
Growth of cuprous oxide particles in liquid-phase synthesis investigated by X-ray laser diffraction

Tomotaka Oroguchi, Takashi Yoshidome, Takashi Yamamoto, Masayoshi Nakasako

Nano Letters, 18 5192-5197, Aug, 2018 Peer-reviewed
An accurate computational method for an order parameter with a Markov state model constructed using a manifold-learning technique

Reika Ito, Takashi Yoshidome

Chemical Physics Letters, 691 22-27, Jan 1, 2018 Peer-reviewedCorresponding author
Computational Methods for Configurational Entropy Using Internal and Cartesian Coordinates

Simon Hikiri, Takashi Yoshidome, Mitsunori Ikeguchi

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 12(12) 5990-6000, Dec, 2016 Peer-reviewed
Classification of projection images of proteins with structural polymorphism by manifold: A simulation study for x-ray free-electron laser diffraction imaging

Takashi Yoshidome, Tomotaka Oroguchi, Masayoshi Nakasako, Mitsunori Ikeguchi

PHYSICAL REVIEW E, 92(3) 032710-1-032710-13, Sep, 2015 Peer-reviewedLead authorCorresponding author
An accurate and efficient computation method of the hydration free energy of a large, complex molecule

Takashi Yoshidome, Toru Ekimoto, Nobuyuki Matubayasi, Yuichi Harano, Masahiro Kinoshita, Mitsunori Ikeguchi

JOURNAL OF CHEMICAL PHYSICS, 142(17) 175101-1-175101-11, May, 2015 Peer-reviewedLead author
A theoretical framework for calculations of the structural relaxation time on the basis of the free energy landscape theory

Toru Ekimoto, Akira Yoshimori, Takashi Odagaki, Takashi Yoshidome

CHEMICAL PHYSICS LETTERS, 577 58-61, Jul, 2013 Peer-reviewed
Molecular Dynamics Simulations of Yeast F-1-ATPase before and after 16 degrees Rotation of the gamma Subunit

Yuko Ito, Takashi Yoshidome, Nobuyuki Matubayasi, Masahiro Kinoshita, Mitsunori Ikeguchi

JOURNAL OF PHYSICAL CHEMISTRY B, 117(12) 3298-3307, Mar, 2013 Peer-reviewed
Characterization of Experimentally Determined Native-Structure Models of a Protein Using Energetic and Entropic Components of Free-Energy Function

Hirokazu Mishima, Satoshi Yasuda, Takashi Yoshidome, Hiraku Oshima, Yuichi Harano, Mitsunori Ikeguchi, Masahiro Kinoshita

JOURNAL OF PHYSICAL CHEMISTRY B, 116(27) 7776-7786, Jul, 2012 Peer-reviewed
Structural characteristics of yeast F-1-ATPase before and after 16-degree rotation of the gamma subunit: Theoretical analysis focused on the water-entropy effect

Takashi Yoshidome, Yuko Ito, Nobuyuki Matubayasi, Mitunori Ikeguchi, Masahiro Kinoshita

JOURNAL OF CHEMICAL PHYSICS, 137(3) 035102-1-035102-8, Jul, 2012 Peer-reviewedLead author

Misc.

タンパク質水和分布を高速に予測する深層学習モデル「gr Predictor」

吉留崇

日本シミュレーション学会誌「シミュレーション」, Sep, 2024 Peer-reviewedInvitedLead authorCorresponding author
Reconstruction of Three-Dimensional Structures of a Protein with Software ENMA and EMC Algorithm: A Simulation for XFEL-CXDI Experiment

Takashi Yoshidome, Yuki Sekiguchi, Tomotaka Oroguchi, Masayoshi Nakasako, Mitsunori Ikeguchi

BIOPHYSICAL JOURNAL, 112(3) 288A-288A, Feb, 2017
An Accurate and Efficient, Computational Method for the Hydration Free Energy of Large and Complex Molecules

Takashi Yoshidome, Toru Ekimoto, Nobuyuki Matubayasi, Yuichi Harano, Masahiro Kinoshita, Mitsunori Ikeguchi

BIOPHYSICAL JOURNAL, 110(3) 328A-329A, Feb, 2016
7aAM-5 Imaging analysis using a new classification protocol of projection images based on the manifold

Yoshidome T., Oroguchi T., Nakasako M., Ikeguchi M.

Meeting abstracts of the Physical Society of Japan, 69(2) 188-188, Aug 22, 2014
30aPS-101 A novel classification protocol of projection images : Toward analysis of dynamics of targets with coherent x-ray diffraction imaging

Yoshidome T., Oroguchi T., Nakasako M., Ikeguchi M.

Meeting abstracts of the Physical Society of Japan, 69(1) 423-423, Mar 5, 2014
Classification Protocol of Projection Images by Manifold: Toward Analysis of Dynamics of Particles with Coherent X-Ray Diffraction Imaging

Takashi Yoshidome, Tomotaka Oroguchi, Masayoshi Nakasako, Mitsunori Ikeguchi

BIOPHYSICAL JOURNAL, 106(2) 384A-384A, Jan, 2014
A novel computation method of hydration free energy: A hybrid of the method of energy representation and the morphometric approach

T. Yoshidome, T. Ekimoto, N. Matubayasi, R. Roth, Y. Harano, M. Kinoshita, M. Ikeguchi

7th Mini-Symposium on Liquids, Jul, 2013
コヒーレントX線回折イメージング構造解析理論の開発と展望

中迫雅由, 苙口友隆, 高山裕貴, 小林周, 児玉渉, 坂本啓太, 吉留崇, 池口満徳

放射光, 26 11-25, Jan 30, 2013
Molecular Dynamics Simulations of Yeast F-1-ATPase Before and after 16-Degree Rotation of the Gamma Subunit

Yuko Ito, Takashi Yoshidome, Nobuyuki Matubayasi, Masahiro Kinoshita, Mitsunori Ikeguchi

BIOPHYSICAL JOURNAL, 104(2) 332A-332A, Jan, 2013
排除容積効果の観点から見たタンパク質研究の展望

吉留崇

生物物理, 52 100-101, Mar 30, 2012
白質複合体におけるホットスポットの理論的予測

尾嶋拓, 安田賢司, 吉留崇, 池口満徳, 木下正弘

新学術領域研究「水を主役としたATPエネルギー変換」第4回領域全体会議，岩沼屋，仙台，2012.3.7-9, 2012
サブユニットの16度回転前後におけるイーストF1-ATPase の構造特性：水のエントロピー効果に焦点をあてた理論解析

吉留崇, 伊藤祐子, 松林伸幸, 池口満徳, 木下正弘

新学術領域研究「水を主役としたATPエネルギー変換」第4回領域全体会議，岩沼屋，仙台，2012.3.7-9, 2012
F1-ATPaseの回転のメカニズムにおける水のエントロピーの重要性

吉留崇

生物物理, 51(5) 230-231, Sep 25, 2011
モーター蛋白質F1-ATPaseの回転における水の役割：水のエントロピーの重要性

吉留崇

アンサンブル, 13(2) 50-56, Apr, 2011
26pPSB-43 On the Microscopic Mechanism of Cold Denaturation of Protein for Simple Solvent and in Water

Yoshidome T., Kinoshita M.

Meeting abstracts of the Physical Society of Japan, 66(1) 404-404, Mar 3, 2011
On the Physical Mechanism of Rotation of F1-ATPase:Crucial Importance of the Water Entropy Effect

T. Yoshidome, Y. Ito, M. Ikeguchi, M. Kinoshita

8th Liquid Matter Conference，Universität Wien, Austria，2011.9.9, 2011
A Theoretical Analysis on Water-Entropy Change in Yeast F1-ATPase during 16 Degrees Rotation of Gamma Subunit

吉留崇, 池口満徳, 木下正弘

第49回日本生物物理学会年会，兵庫県立大学，2011.9.16, 2011
Theoretical Analysis for Hot Spots in Protein-Protein Complexes: Critical Importance of Water Entropy

H. Oshima, S. Yasuda, T. Yoshidome, M. Ikeguchi, M. Kinoshita

8th Liquid Matter Conference，Universität Wien, Austria，2011.9.9, 2011
実験で得られた蛋白質天然構造モデルのキャラクタリゼーション

三嶋浩和, 安田哲司, 吉留崇, 池口満徳, 木下正弘

第34 回溶液化学シンポジウム，名古屋大学ES総合館ESホール，2011.11.15-17, 2011
Importance of water entropy in rotation mechanism of F1-ATPase

Takashi Yoshidome

Biophysics, 7 113-122, 2011

Books and Other Publications

Fundamentals of Condensed Matter Physics

(Role: Joint translator) (Original Author(s): M. L. Cohen, S. G. Louie)

Sep, 2021

Presentations

112

リガンド結合に伴う水分子置換を予測する深層学習モデルの開発

伊藤祐希, 大田雅照, 池口満徳, 吉留崇

第52回構造活性相関シンポジウム, Dec 12, 2024
Deep-Learning Model for Predicting the Replacement of Water Molecule upon Ligand Binding

伊藤祐希, 大田雅照, 池口満徳, 吉留崇

CBI学会2024年大会, Oct 29, 2024
創薬におけるリード最適化への応用に向けたタンパク質水和熱力学量分布の包括的解析

吉留崇

第11回「富岳」を中核とするHPCIシステム利用研究課題成果報告会, Oct 25, 2024
深層学習に基づく高速水和自由エネルギー計算法の提案

吉留崇

R6年度学術変革A「学習物理学」領域会議, Sep 27, 2024
Deep-Learning Model For Fast And Accurate Computation Of Hydration Structures Around Proteins

Takashi Yoshidome, Kosuke Kawama, Yusaku Fukushima, Mitsunori Ikeguchi, Masateru Ohta

Biomolecular Horizons 2024, Sep 26, 2024 Invited
Manifold-Learning Approach to Material Data: Application to Experimental Data of Liquid Substances and Porous Structural Data

Shota Arai, Gota Kikugawa, Yuki Takayama, Takashi Yoshidome

12th Liquid Matter Conference, Sep 24, 2024
深層学習に基づくリガンド結合に伴う水分子置換の予測

伊藤祐希, 大田雅照, 池口満徳, 吉留崇

日本物理学会第79回年次大会, Sep 18, 2024
深層学習を用いたタンパク質水和自由エネルギー計算の高速化

伊藤太一, 吉留崇

日本物理学会第79回年次大会, Sep 18, 2024
分子動力学法を用いたタンパク質アンフォールドにおける遷移状態解析

門脇颯汰, 吉留崇

日本物理学会第79回年次大会, Sep 18, 2024
マニフォールドラーニングによる多孔質構造と物理的特性の関係の構築

荒井翔太, 高山裕貴, 吉留崇

日本物理学会第79回年次大会, Sep 17, 2024
低温電子顕微鏡4次元イメージング法の構築

吉留崇

第14回SPring-8データ科学研究会, Sep 9, 2024 Invited
マニフォールドラーニングを用いたタンパク質構造変化データの解析

加藤智世, 吉留崇

2024年度電気関係学会東北支部連合大会, Aug 30, 2024
深層学習を用いた水和自由エネルギー計算の高速化

吉留崇

第3回学術変革領域「学習物理」物性関係討論会, Aug 1, 2024
Manifold-Learning Approach for Extracting Molecular Information and Predicting of Physical Properties

Shota Arai, Gota Kikugawa, Yuki Takayama, Takashi Yoshidome

17th Mini-Symposium on Liquids (MSL2024), Jul 6, 2024
Deep Learning-Based Water Molecule Displacement Prediction Method for Improving the Accuracy of Drug Discovery Docking Software

Yuki Ito, Masateru Ohta, Mitsunori Ikeguchi, Takashi Yoshidome

IUPAB2024, Jun 28, 2024
Molecular Dynamics Study of the Unfolding Processes of Proteins with Highly Similar Native Structure

Souta Kadowaki, Takashi Yoshidome

IUPAB2024, Jun 27, 2024
Fast Computational Method for the Hydration Free Energy

Taichi Ito, Takashi Yoshidome

IUPAB2024, Jun 26, 2024
Hybrid of Manifold Learning and Molecular Simulation to Reconstruct the Protein Conformational Change using Cryo-Electron Microscopy Experiment

Takashi Yoshidome

IUPAB2024, Jun 26, 2024
Four-Dimensional Imaging Technique To Reconstruct Protein Conformational Change Using Cryo-Electron Microscopy Experiment

Feb 13, 2024
タンパク質水和分布を予測する深層学習モデル

吉留崇

第2回学術変革領域「学習物理」物性関係討論会, Jan 5, 2024

Teaching Experience

Apr, 2024 - Present

Statistical Physics (Tohoku University)
Oct, 2023 - Present

Statistical Mechanics B (Tohoku University)
Apr, 2023 - Present

統計力学A (東北大学)
Apr, 2024 - Mar, 2025

応用物理学研修 (東北大学)
Oct, 2015 - Mar, 2023

統計力学演習 (東北大学)
Apr, 2015 - Mar, 2023

プログラミング演習A (東北大学)
Apr, 2021 - Sep, 2022

基礎物理学 (東北文化学園大学)
Jan, 2021 - Jan, 2021

物理学特論III (新潟大学)
Mar, 2018 - Mar, 2018

学外見学 (東北大学)
May, 2016 - May, 2017

基礎ゼミ (東北大学)

Professional Memberships

Research Projects

次世代放射光X線ナノCT計測の確立と展開

CREST, JST, Oct, 2022 - Mar, 2028

高山裕貴
「高速・高精度な水和理論」を用いたリガンド結合予測の精度向上

基盤研究(C), Apr, 2024 - Mar, 2027
タンパク質水和の「深層学習モデル」の展開：水和熱力学量の高速計算

学術変革領域研究(A) (公募研究), Apr, 2023 - Mar, 2025

吉留崇
生体分子ダイナミクスの高解像度解析を実現する「4次元イメージング法」の確立

2022年度学術・研究助成, 公益財団法人住友電工グループ社会貢献基金, Oct, 2022 - Mar, 2024

吉留崇
A Construction of Drug Design Theory based on the Hydration of Proteins

Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, Apr, 2021 - Mar, 2024
Development of a Theory for Controlling the Motions of Biomolecular Machines Based on Amino Acid Mutations

Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area), Japan Society for the Promotion of Science, Apr, 2021 - Mar, 2023
革新的4次元イメージング法：生体分子構造変化の高解像度解析への挑戦

令和２年度学術研究助成, 公益財団法人山口育英奨学会, Jul, 2020 - Mar, 2021

吉留崇
溶液理論計算と人工知能の融合によるタンパク質リガンド結合予測法の開発

理化学研究所共同研究, Jun, 2018 - Mar, 2021

池口満徳
低温電子顕微鏡を用いた革新的4次元イメージング法の確立

基礎科学研究助成, 公益財団法人住友財団, Nov, 2018 - Mar, 2020

吉留崇
F1-ATPase の回転機構に関わる基本相互作用の解明：非平衡統計力学の応用

基盤研究(C), 日本学術振興会, Apr, 2017 - Mar, 2020

佐々木一夫
マニフォールド理論と単粒子解析実験データを用いた革新的4次元イメージング法の構築

若手研究(B), 日本学術振興会, Apr, 2016 - Mar, 2018

吉留崇
Statistical Physics of ionic liquids

Grants-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (C), Japan Society for the Promotion of Science, 2006 - 2008

YOSHIMORI Akira, ODAGAGI Takashi, SUMI Tomonari, YOSHIDOME Takashi

Profile Information

Research Interests

Research Areas

Committee Memberships

Awards

Papers

Misc.

Books and Other Publications

Presentations

Teaching Experience

Professional Memberships

Research Projects

Menu

Coauthors