Publications

Papers (including reviews and proceedings)

• S. Arai, Y. Takayama, and T. Yoshidome (Corresponding author, ポスドク指導),
  "TBA"
  in preparation.

• Y. Fukushima and T. Yoshidome (Corresponding author, 学生指導),
  “TBA”
  in preparation.

• S. Arai, G. Kikugawa, and T. Yoshidome (Corresponding author, ポスドク指導),
  "Extraction of Molecular Information from Experimental Data of Liquids using Manifold Learning"
  Submitted.

• 吉留崇,
  "深層学習モデル「gr Predictor」を用いたタンパク質水和分布の高速予測" (invited),
  日本シミュレーション学会 学会誌「シミュレーション」, 掲載決定 (2024).

• T. Yoshidome and S. Arai,
  "Interface-Packing Analysis of F1-ATPase using Integral Equation Theory and Manifold Learning"
  Submitted to Physica A.
  This paper will belong to a virtual special issue “Effective Interactions between Molecules, Proteins, and Colloidal Particles in Liquids: Manifestation of Thermodynamic Stability in Chemical and Biological Systems”.

• T. Yoshidome,
  "Four-Dimensional Imaging for Cryo-Electron Microscopy Experiments Using Molecular Simulations and Manifold Learning",
  Journal of Computational Chemistry, Vol. 45, 738 (2024). [Open access]

• T. Yoshidome,
  "Mechanism of a High Free-energy Transduction Efficiency of Bacillus PS3 F1-ATPase from the Perspective of Solvent Entropy",
  Journal of Molecular Liquids, Vol. 391, 123346 (2023).

• Y. Hishikawa, H. Noya, S. Nagatoishi, T. Yoshidome, B. Maity, K. Tsumoto, S. Abe, and T. Ueno
  "Elucidating Conformational Dynamics and Thermostability of Designed Aromatic Clusters Using Protein Cages",
  Chemistry - A European Journal, Vol. 29, e202300488 (2023).

• K. Kawama, Y. Fukushima, M. Ikeguchi, M. Ohta, and T. Yoshidome (Corresponding author, 学生指導)
  "gr Predictor: A Deep-Learning Model For Predicting the Hydration Structure of Proteins",
  Journal of Chemical Information and Modeling, Vol. 62, 4460 (2022).
  プログラム"gr Predictor"：https://github.com/YoshidomeGroup-Hydration/gr-predictor

• T. Yoshidome,
  "Simple-Fluid Model for Accurate Reproduction of Hydration Entropy",
  Journal of the Physical Society of Japan, Vol. 91, 094802 (2022).

• D. Shiono and T. Yoshidome (Corresponding author, 学生指導),
  “AlphaFold-predicted Protein Structure vs Experimentally Obtained Protein Structure: An Emphasis on The Side Chains”,
  Journal of the Physical Society of Japan, 91, 064804 (2022).

• R. Kojima and T. Yoshidome (Corresponding author, 学生指導),
  "A Measure for the Identification of Preferred Particle Orientations in Cryo-Electron Microscopy Data: A Simulation Study",
  Biophysics and Physicobiology, 18, 96 (2021). [Open access]
  Biophysics and Physicobiology (BPPB) の9th Editors Choice Awards に選ばれました
  日本生物物理学会のホームページにおける紹介文

• T. Yoshidome,
  "F1-ATPase Rotation and Its Inhibition from the Viewpoint of Solvent Entropy",
  Chem. Phys. Lett., 757, 137886 (2020).

• T. Yoshidome (Corresponding author), M. Ikeguchi, and M. Ohta (Corresponding author),
  "Comprehensive 3D-RISM Analysis of the Hydration of Small Molecule Binding Sites in Ligand-Free Protein Structures",
  J. Comput. Chem., 41, 2406 (2020). [Open access]

• N. Takano and T. Yoshidome (Corresponding author, 学生指導),
  "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",
  J. Phys. Soc. Jpn., 88, 094801 (2019).

• R. Ito and T. Yoshidome (Corresponding author, 学生指導),
  "An Automatic Classification of Molecular Dynamics Simulation Data into States, and Its Application to the Construction of a Markov State Model",
  J. Phys. Soc. Jpn., 87, 114802 (2018).

•  T. Oroguchi, T. Yoshidome, T. Yamamoto, and M. Nakasako,
  "Growth of Cuprous Oxide Particles in Liquid-Phase Synthesis Investigated by X-Ray Laser Diffraction",
  Nano Lett., 18, 5192 (2018).
  Press release (RIKEN)：SACLAにより銅キューブ粒子の内部構造変化を可視化（理化学研究所、2018年7月31日）

• R. Ito and T. Yoshidome (Corresponding author, 学生指導),
  "An Accurate Computation of an Order Parameter with a Markov State Model Constructed using a Manifold-Learning Technique",
  Chem. Phys. Lett., 691, 22 (2018).

• S. Hikiri, T. Yoshidome, and M. Ikeguchi,
  "Computational Methods for Configurational Entropy using Internal and Cartesian Coordinates",
  J. Chem. Theory Compt., 12, 5990 (2016). 

• T. Yoshidome (Corresponding author), T. Oroguchi, M. Nakasako, and M. Ikeguchi (Corresponding author),
  "Classification of Projection Images of Proteins with Structural Polymorphism by Manifold: A Simulation Study for X-Ray Free-Electron Laser Diffraction Imaging",
  Phys. Rev. E, 92, 032710 (2015).

• T. Yoshidome, T. Ekimoto, N. Matubayasi, Y. Harano, M. Kinoshita, and M. Ikeguchi,
  "An Accurate and Efficient Computation Method of the Hydration Free Energy of a Large, Complex Molecule", 
  J. Chem. Phys., 142, 175101 (2015).

• T. Ekimoto, A. Yoshimori, T. Odagaki, and T. Yoshidome,
  "A Theoretical Framework for Calculations of the Structural Relaxation Time on the Basis of the Free Energy Landscape Theory",
  Chem. Phys. Lett., 577, 58 (2013).

• Y. Ito, T. Yoshidome, N. Matsubayasi, M. Kinoshita, and M. Ikeguchi,
  "Molecular Dynamics Simulations of Yeast F1-ATPase before and after 16-degree Rotation of Gamma Subunit", 
  J. Phys. Chem. B, 117, 3298 (2013).

• 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,
  "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",
  放射光学会誌, 26, 11 (2013).

• T. Yoshidome and M. Kinoshita,
  "Physical Origin of Hydrophobicity Studied in terms of Cold Denaturation of Proteins: Comparison between Water and Simple Fluids",
  Phys. Chem. Chem. Phys., 14, 14554 (2012).  

•  T. Yoshidome, Y. Ito, N. Matubayasi, M. Ikeguchi, and M. Kinoshita,
  "Structural Characteristics of Yeast F1-ATPase before and after 16-degree Rotation of the Gamma Subunit: Theoretical Analysis Focused on the Water-Entropy Effect", 
  J. Chem. Phys., 137, 035102 (2012).

• H. Mishima, S. Yasuda, T. Yoshidome, H. Oshima, Y. Harano, M. Ikeguchi, and M. Kinoshita,
  "Characterization of Experimentally Determined Native-Structure Models of a Protein Using Entropic and Energetic Components of Free-Energy Function",
  J. Phys. Chem. B., 116, 7776 (2012).

• 吉留崇,
  "排除容積効果の観点から見たタンパク質研究の展望" (invited),
  生物物理, 300号記念特集号, 52, 100 (2012).

• T. Yoshidome,
  "Importance of Water Entropy in Rotation Mechanism of F1-ATPase" (invited mini review),
  BIOPHYSICS, 7, 113 (2011).

• 吉留崇,
  "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" (invited),
  「生物物理」トピックス（新進気鋭シリーズ）, 51, 230 (2011).

• H. Oshima, S. Yasuda, T. Yoshidome, M. Ikeguchi, and M. Kinoshita,
  "Crucial Importance of Water-Entropy Effect for Predicting Hot Spots in Protein-Protein Complexes",
  Phys. Chem. Chem. Phys., 13, 16236 (2011). 

• 吉留崇,
  "モーター蛋白質F1-ATPaseの回転のメカニズム：水のエントロピーの重要性" (invited),
  分子シミュレーション研究会会誌「アンサンブル」, 13, 50 (2011).

•  S. Yasuda, T. Yoshidome, Y. Harano, R. Roth, H. Oshima, K. Oda, Y. Sugita, M. Ikeguchi, and M. Kinoshita,
  "Free-Energy Function for Discriminating the Native Fold of a Protein from Misfolded Decoys",
  Proteins: Structure, Function, and Bioinformatics, 79, 2161 (2011).

• T. Yoshidome, Y. Ito, M. Ikeguchi, and M. Kinoshita,
  "Rotation Mechanism of F1-ATPase: Crucial Importance of Water-Entropy Effect", 
  J. Am. Chem. Soc. 133, 4030 (2011).

• K. Oda, R. Kodama, T. Yoshidome, M. Yamanaka, Y. Sambongi, and M. Kinoshita,
  "Effects of heme on the thermal stability of four cytochromes c: Theoretical analyses",
  J. Chem. Phys. 134, 025101 (2011). 

• K. Amano, T. Yoshidome, M. Iwaki, M. Suzuki, and M. Kinoshita,
  "Entropic potential field formed for a linear-motor protein near a filament: Statistical-mechanical analyses using simple models",
  J. Chem. Phys, 133, 045103 (2010). 

• T. Yoshidome,
  "General framework of pressure effects on structures formed by the entropically driven self-assembly'' (invited review), 
  Journal Entropy, 12, 1632 (2010).
  This paper belongs to a special issue "Configurational Entropy." 

• 吉留崇,
  "アポプラストシアニン折り畳みの熱力学：理論と実験との定量的比較" (invited),
  「生物物理」トピックス(新進気鋭シリーズ), 50, 90 (2010).

• S. Yasuda, T. Yoshidome, H. Oshima, R. Kodama, Y. Harano, and M. Kinoshita,
  "Effects of side-chain packing on the formation of secondary structures in protein folding",
  J. Chem. Phys. 132, 065105 (2010).
  This paper was selected in research highlight featured on the journal website home page of Journal of Chemical Physics".

• H. Oshima, T. Yoshidome, K. Amano, and M. Kinoshita,
  "A Theoretical Analysis on Characteristics of Protein Structures Induced by Cold Denaturation",
  J. Chem. Phys. 131, 205102 (2009). 

• T. Yoshidome, K. Oda, Y. Harano, R. Roth, Y. Sugita, M. Ikeguchi, and M. Kinoshita,
  "Free-energy Function Based on an All-atom Model for Proteins",
  Proteins: Structure, Function, and Bioinformatics, 77, 950 (2009).

• T. Yoshidome and M. Kinoshita,
  "Pressure effect on helix-coil transition of an alanine-based peptide: Theoretical study",
  Chem. Phys. Lett, 477, 211 (2009). 
  This paper was selected in Faculty of 1000 Biology (2009).

• K. Amano, T. Yoshidome, Y. Harano, K. Oda, and M. Kinoshita,
  "Theoretical Analysis on thermal stability of a protein focused on water entropy", 
  Chem. Phys. Lett, 474, 190 (2009).

• M. Kinoshita and T. Yoshidome,
  "Molecular origin of the negative heat capacity of hydrophilic hydration",
  J. Chem. Phys. 130, 144705 (2009). 

• T. Yoshidome and M. Kinoshita,
  "Hydrophobicity at low temperatures and cold denaturation of a protein",
  Phys. Rev. E (Rapid Communication), 79, 030905 (2009). 

• T. Yoshidome, Y. Harano, and M. Kinoshita,
  "Pressure effects on structures formed by the entropically driven self-assembly: Illustration for denaturation of proteins",
  Phys. Rev. E, 79, 011912 (2009). 

• Y. Harano, T. Yoshidome, and M. Kinoshita,
  "Molecular mechanism of pressure denaturation of proteins",
  J. Chem. Phys, 129, 145103 (2008). 

•  T. Yoshidome, M. Kinoshita, S. Hirota, N. Baden, and M. Terazima,
  "Thermodynamics of apoplastocyanin folding: comparison between experimental and theoretical results",
  J. Chem. Phys, 128, 225104 (2008). 

• T. Yoshidome, T. Odagaki, and A. Yoshimori,
  "Free energy landscape for a tagged particle in a dense hard sphere fluid",
  Phys. Rev. E. 77 061503 (2008). 

• T. Yoshidome, A. Yoshimori, and T. Odagaki,
  "Free energy landscape and cooperatively rearranging region in a hard sphere glass",
  Phys. Rev. E. 76, 021506 (2007).

• T. Odagaki, T. Yoshidome, A. Koyama, and A. Yoshimori,
  "Free energy landscape approach to glass transition",
  J. Non-Crys. Solids. 352, 4843 (2006).
  Proceedings of the 5th International Discussion Meeting on Relaxation in Complex Systems (IDMRCS)

• T. Yoshidome, A. Yoshimori, and T. Odagaki,
  "Construction of the free energy landscape by the density functional approach",
  J. Phys. Soc. Jpn 75, 054005 (2006).

• T. Yoshidome, A. Yoshimori, and T. Odagaki, 
  "Free energy landscape and CRR of glass-forming substance", AIP Conference Proceedings 832, 188 (2006).
  Proceedings of the 3rd International Conference on Flow Dynamics

• T. Odagaki, T. Yoshidome, T. Tao, and A. Yoshimori,
  "Specific heat anomaly at the glass transition",
  J. Chem. Phys. 117, 10151 (2002).

著書・訳書

• 小田垣 孝、吉留 崇、大久保 毅、
  「現代の物性物理学」(M. L. Cohen and S. G. Louie: Fundamentals of Condensed Matter Physics)
  吉岡書店、2021年9月出版 Amazonのページ

Other publications

• T. Yoshidome,
  "A Theoretical Study for Thermal Unfolding of Proteins with Quite Similar Native Structure ",
  Activity Report 2020 (Supercomputer Center, Institute for Solid State Physics, The University of Tokyo), page 276 (2021).

• T. Yoshidome,
  "A Method for Analyzing Protein Dynamics: A Hybrid of Cryo-Electron Microscopy Experiment and Molecular Simulation",
  Activity Report 2020 (Supercomputer Center, Institute for Solid State Physics, The University of Tokyo), page 277 (2021).

• T. Yoshidome,
  "Investigation of Dynamics of a Supercooled Liquid and Proteins using the Free-Energy Landscape",
  Activity Report 2019 (Supercomputer Center, Institute for Solid State Physics, The University of Tokyo), page 325 (2020).

• T. Yoshidome,
  "Quantitative computation of the dissociation rate of a protein- ligand complex using a manifold-learning technique",
  Activity Report 2018 (Supercomputer Center, Institute for Solid State Physics, The University of Tokyo), page 263 (2019).

• T. Yoshidome,
  "Accurate computation of the free-energy change of apoplastocyanin using the end-points method”,
  Activity Report 2017 (Supercomputer Center, Institute for Solid State Physics, The University of Tokyo), page 235 (2018).

• T. Yoshidome,
  "Elucidation of binding and unbinding processes of a ligand to a protein using a hybrid of the manifold theory and the Markov state model”,
  Activity Report 2017 (Supercomputer Center, Institute for Solid State Physics, The University of Tokyo), page 234 (2018).

• T. Yoshidome,
  "A construction of the Markov state model of protein folding using the manifold theory",
  Activity Report 2016 (Supercomputer Center, Institute for Solid State Physics, The University of Tokyo), page235 (2017).

• 吉留崇，関安孝, 佐々木 一夫,
  「支部だより～東北支部からのお知らせ～」,
  生物物理、56, 239 (2016).

• 吉留崇，
  "Entropic effect arising from complex solute-solvent correlations",
  2nd Mini-Symposium on Liquids"報告書, 物性研究, 44, pp716 (2009年3月号).

• 吉留崇、吉森明、小田垣孝,
  "密度汎関数理論による自由エネルギーランドスケープの決定" ,
  東京大学物性研究所短期研究会 「極端非平衡系の物性とエネルギーランドスケープ」報告書, 物性研だより, 44, 30 (2005).

• 小田垣 孝、吉留崇、吉森 明、松井 淳、田尾聡明、田川文隆、
  "CRR、SRR，FELとガラス転移",
  東京大学物性研究所短期研究会 「極端非平衡系の物性とエネルギーランドスケープ」報告書, 物性研だより, 44, 22 (2005).

• 吉森 明、吉留崇、小田垣 孝,
  "構造ガラスにおける自由エネルギーランドスケープとは何か",
  東京大学物性研究所短期研究会 「極端非平衡系の物性とエネルギーランドスケープ」報告書, 物性研だより, 44, 22 (2005).

Thesis

博士論文："Theoretical Study on Free Energy Landscape for Glass Forming Materials" (2007).

修士論文："密度汎関数理論によるランドスケープの決定とガラス転移" (2004).

卒業論文："ガラス転移における比熱の振る舞い" (2002).