Publications

Google Scholar / ORCID profiles
  1. K. Obayashi, R. Zou, T. Mori, H. Tsukamoto*, “Molecular basis underlying specific interaction of mammalian melanopsins with an antagonist AA92593”, bioRxiv:2024.11.01.621458
  2. K. Sekine*, K. Fuji, K. Kawashima, T. Mori*, Y. Kuninobu*, “Gold-Catalyzed Synthesis of 5H-Benzo[b]indeno[2,1-d]silines by Insertion of Vinyl Carbocations into the Si−H Bond”, Chem. Eur. J. (in press)
  3. K. Kawashima, T. Sato, K. Okazaki*, K. Kim*, N. Matubayasi*, T. Mori*, “Investigating the hyperparameter space of deep neural network models for reaction coordinate optimization: Application to alanine dipeptide in water”, arXiv:2408.02132
  4. Y. Furuike, Y. Onoue, S. Saito, T. Mori*, S. Akiyama*, “The priming phosphorylation of KaiC is activated by the release of its autokinase autoinhibition”, bioRxiv:2024.03.21.584037
  5. S. Sittiwanichai, C. Archapraditkul, D. Japrung, Y. Shigeta, T. Mori*, P. Pongprayoon*, “Aggregation of Apo/Glycated Human Serum Albumins and Aptamer-Saturated Graphene Quantum Dot: A Simulation Study”, Biochemistry 63, 1697-1707 (2024)
  6. K. Kawashima*, X. Lu, Y. Kuninobu*, T. Mori*, “Mechanistic Insights into the Role of Cyclodextrin in the Regioselective Radical C–H Trifluoromethylation of Aromatic Compounds”, J. Comput. Chem. 45, 2112-2118 (2024)
  7. K. Okada, T. Kikutsuji, K. Okazaki*, T. Mori*, K. Kim*, N. Matubayasi*, “Unveiling interatomic distances influencing the reaction coordinates in alanine dipeptide isomerization: An explainable deep learning approach”, J. Chem. Phys. 160, 174110 (2024) [arXiv version]
  8. A. Shiozuka, D. Wu, K. Kawashima, T. Mori, K. Sekine*, Y. Kuninobu*, “Carbamoylarylation of Alkenes with N-Aryl Oxamic Acids Involving 1,4-Aryl Migration Via C(aryl)–N Bond Cleavage”, ACS Catal. 14, 5972–5977 (2024)
  9. J. Ono‡, Y. Matsumura‡, T. Mori‡, S. Saito*, “Conformational Dynamics in Proteins: Entangled Slow Fluctuations and Nonequilibrium Reaction Events”, J. Phys. Chem. B 128 (Perspective), 20-32 (2024) ‡contributed equally
  10. T. Mori*, N. Yoshida, “Tuning the ATP–ATP and ATP–disordered protein interactions in high ATP concentration by altering water models”, J. Chem. Phys. 159, 035102 (2023)
  11. S. Sittiwanichai, D. Japrung, T. Mori*, P. Pongprayoon*, “Structural and Dynamic Alteration of Glycated Human Serum Albumin in Schiff Base and Amadori Adducts: A Molecular Simulation Study”, J. Chem. Phys. B 127, 5230-5240 (2023)
  12. D. Wu, A. Shiozuka, K. Kawashima, T. Mori, K. Sekine*, Y. Kuninobu*, “Bifunctional 1-Hydroxypyrene Photocatalyst for Hydrodesulfurization via Reductive C(Aryl)–S Bond Cleavage”, Org. Lett. 25, 3293-3297 (2023)
  13. T. Mori, K. Sekine, K. Kawashima, T. Mori, Y. Kuninobu*, “Near-Infrared and Dual Emissions of Diphenylamino Group-Substituted Malachite Green Derivatives”, Eur. J. Org. Chem. 2022, e202200873 (2022)
  14. T. Mori*, S. Saito*, “Molecular Insights into the Intrinsic Dynamics and their Roles During Catalysis in Pin1 Peptidyl-prolyl Isomerase”, J. Phys. Chem. B 126, 5185-5193 (2022)
  15. A. Shiozuka, K. Sekine*, T. Toki, K. Kawashima, T. Mori*, Y. Kuninobu*, “Photoinduced Divergent Deaminative Borylation and Hydrodeamination of Primary Aromatic Amines”, Org. Lett. 24, 4281-4285 (2022)
  16. T. Kikutsuji, Y. Mori, K. Okazaki*, T. Mori*, K. Kim*, N. Matubayasi*, “Explaining reaction coordinates of alanine dipeptide isomerization obtained from deep neural networks using Explainable Artificial Intelligence (XAI)”, J. Chem. Phys. 156, 154108 (2022)
  17. Y. Mori, K. Okazaki*, T. Mori*, K. Kim*, N. Matubayasi*, “Learning reaction coordinates via cross-entropy minimization: Application to alanine dipeptide”, J. Chem. Phys. 153, 054115 (2020)
  18. T. Mori*, S. Saito*, “Dissecting the dynamics during enzyme catalysis: A case study of Pin1 peptidyl-prolyl isomerase”, J. Chem. Theory Comput. 16, 3396-3407 (2020)
  19. T. Mori*, S. Saito*, “Conformational Excitation and Nonequilibrium Transition Facilitate Enzymatic Reactions: Application to Pin1 Peptidyl-Prolyl Isomerase”, J. Phys. Chem. Lett. 10, 474-480 (2019) Suppl. Cover
  20. W. J. Glover, T. Mori, M. Schuurman, A. Boguslavskiy, O. Schalk, A. Stolow, T. J. Martínez*, “Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. II. Ab initio multiple spawning simulations”, J. Chem. Phys. 148, 164303 (2018) Featured Article
  21. A. Boguslavskiy, O. Schalk, N. Gador, W. J. Glover, T. Mori, T. Schultz, M. Schuurman, T. J. Martínez, A. Stolow*, “Excited state non-adiabatic dynamics of the smallest polyene, trans 1,3-butadiene. I. Time-resolved photoelectron-photoion coincidence spectroscopy”, J. Chem. Phys. 148, 164302 (2018) Featured Article
  22. P. Pongprayoon*, T. Mori*, “Critical role of dimer formation in monosaccharide binding to human serum albumin”, Phys. Chem. Chem. Phys. 20, 3249-3257 (2018)
  23. M. Kalathingal, T. Sumikama, T. Mori, S. Oiki, S. Saito*, “Structure and dynamics of solvent molecules inside Polytheonamide B channel in different environments: A molecular dynamics study”, Phys. Chem. Chem. Phys. 20, 3334-3348 (2018)
  24. T. Mori*, S. Saito*, “Molecular Mechanism Behind the Fast Folding/Unfolding Transitions of Villin Headpiece Subdomain: Hierarchy and Heterogeneity”, J. Phys. Chem. B 120, 11683-11691 (2016)
  25. S. Aono, T. Mori, S. Sakaki*, “3D-RISM-MP2 Approach to Hydration Structure of Pt(II) and Pd(II) Complexes: Unusual H-Ahead Mode vs Usual O-Ahead One”, J. Chem. Theory Comput.  12, 1189-1206 (2016)
  26. J. Abe‡, T. Hiyama‡, A. Mukaiyama‡, S. Son‡, T. Mori‡, S. Saito, M. Osako, J. Wolanin, E. Yamashita, T. Kondo, S. Akiyama*, “Atomic-scale origins of slowness in the cyanobacterial circadian clock”, Science 349, 312-316 (2015) ‡contributed equally
  27. T. Mori*, S. Saito*, “Dynamic heterogeneity in the folding/unfolding transitions of FiP35”, J. Chem. Phys. 142, 135101 (7 pages) (2015) Selected as one of the “2015’s most read papers” in J. Chem. Phys.
  28. P. Goyal, H.-J. Qian, S. Irle, X. Lu, D. Roston, T. Mori, M. Elstner, Q. Cui*, “Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models”, J. Phys. Chem. B (Feature Article), 118, 11007-11027 (2014)
  29. B. Holland, T. Mori, T. J. Martínez*, A. G. Suits*, “Photochemical dynamics of Ethylene Cation C2H4+”, J. Phys. Chem. Lett. 5, 1467-1471 (2014)
  30. T. Mori*, R. J. Hamers, J. A. Pedersen, Q. Cui*, “Integrated Hamiltonian Sampling: A Simple and Versatile Method for Free Energy Simulations and Conformational Sampling”, J. Phys. Chem. B 118, 8210-8220 (2014)
  31. T. Mori, R. J. Hamers, J. A. Pedersen, Q. Cui*, “An explicit consideration of desolvation is critical to binding free energy calculations of charged molecules at ionic surfaces”, J. Chem. Theory Comput. 9, 5059-5069 (2013)
  32. T. Mori and T. J. Martínez*, “Exploring the Conical Intersection Seam: The Seam Space Nudged Elastic Band Method”, J. Chem. Theory Comput. 9, 1155-1163 (2013)
  33. T. Kuhlman, W. J. Glover, T. Mori, K. B. Møller, T. J. Martínez*, “Between Ethylene and Polyenes – The Non-adiabatic Dynamics of cis-dienes”, Faraday Discuss. 157, 193-212 (2012)
  34. T. Mori, W. J. Glover, M. Schuurman, T. J. Martínez*, “The role of Rydberg states in the photochemical dynamics of ethylene”, J. Phys. Chem. A 116, 2808-2818 (2012)
  35. T. Mori*, K. Nakano and S. Kato, “Conical intersections of free energy surfaces: Effect of electron correlation on a protonated Schiff base in methanol solution”, J. Chem. Phys. 133, 064107 (11 pages) (2010)
  36. T. Mori and S. Kato*, “Dynamic electron correlation effect on conical intersections in photochemical ring-opening reaction of cyclohexadiene: MS-CASPT2 study”, Chem. Phys. Lett. 476, 97-100 (2009)
  37. T. Mori and S. Kato*, “Grignard Reagents in Solution: Theoretical Study of the Equilibria and the Reaction with a Carbonyl Compound in Diethyl Ether Solvent”, J. Phys. Chem. A 113, 6158-6165 (2009)
  38. T. Mori and S. Kato*, “Analytical RISM-MP2 free energy gradient method: Application to the Schlenk equilibrium of Grignard reagent”, Chem. Phys. Lett. 437, 159-163 (2007)

Review Articles

  1. T. Mori*, “酵素反応の静的・動的分子機構の解明に向けて”, アンサンブル (Ensemble) 23, 121-126 (2021)
  2. T. Mori*, “気相・凝縮系における反応ダイナミクスの理論研究 (Award Accounts)”, Molecular Science 13, A0106 (2019)
  3. T. Mori*, “酵素のダイナミクスは酵素反応の理解に重要か？(Are Conformational Dynamics of Enzymes Important for Enzyme Catalysis?)”, 生物物理 (Seibutsu Butsuri) 59, 271-272 (2019)
  4. T. Mori*, S. Saito*, “超長時間シミュレーションで見るタンパク質のフォールディング過程 (What We can Learn about Protein Folding from Ultra-long Molecular Dynamics Simulations) ”, 生物物理 (Seibutsu Butsuri) 57, 030-032 (2017)
  5. T. Mori*, “分子の光化学反応における非断熱遷移と時間分解光電子スペクトル (Theory of nonadiabatic dynamics and time resolved photoelectron spectrum for photochemistry of molecules)”, アンサンブル (Ensemble) 18, 240-243 (2016)

Invited Talks

2024

  • T. Mori, “酵素反応の階層的ダイナミクスと反応座標”, レア・イベントの計算科学第7回ワークショップ, 大阪, Dec. 1, 2024
  • T. Mori, “Elucidating the molecular mechanisms of protein functions from machine learning approaches”, Boston University Center for Computational Science Seminar, Boston, Oct. 16, 2024
  • T. Mori, “Revisiting enzyme catalysis from static and dynamic perspectives”, Greater Boston Area Theoretical Chemistry Seminar Series, Boston, Oct. 2, 2024
  • T. Mori, “Elucidating the hierarchical dynamics of proteins during folding and function from molecular simulations”, Boston University Physical Chemistry Seminar, Boston, Sep. September 4, 2024
  • T. Mori, “生体分子の構造ダイナミクスと機能発現機構”, 第17回分子集合系計算科学セミナー, 大阪, May 17, 2024
  • T. Mori, “Theoretical study on the role of dynamics during enzyme catalysis”, Pure and Applied Chemistry International Conference (PACCON2024), Bangkok, Jan. 26-27, 2024
  • T. Mori, “Elucidating the Dynamics of Proteins During Folding and Catalysis from Molecular Simulations”, Seminar at New York University – Shanghai, Shanghai, Jan. 19, 2024

2023

  • T. Mori, “Elucidating the conformational dynamics of proteins during enzyme catalysis from molecular simulations”, Computational Biophysics and Chemistry Symposium at Boston University, Boston, Sep. 22, 2023
  • T. Mori, “Theoretical study on the role of protein conformational dynamics during enzyme catalysis”, International Symposium for the 80th Anniversary of the 80th Anniversary of the Tohoku Branch of the Chemical Society of Japan and 2023 Joint Meeting of the Tohoku Area Chemistry Societies, Sendai, Sep. 8-10, 2023
  • T. Mori, “Elucidating the dynamics of proteins during folding and catalysis from molecular simulations”, Seminar at Kasetsart University, Bangkok, Aug. 30, 2023
  • T. Mori, “Bridging the Gap between Static and Dynamic Mechanisms in Enzyme Catalysis”, International Workshop on “Multi-scale Molecular Dynamics Simulation and Machine Learning of Biomolecular Systems”, Wako, Aug. 9-10, 2023
  • T. Mori, “Dissecting the heterogeneous dynamics of proteins during folding and catalysis”, Telluride Science Research Center 2023 Protein Dynamics Workshop, Telluride, Jul. 24-28, 2023
  • T. Mori, “タンパク質の変性状態に対する溶媒環境の影響の理論的解析”,「凝縮系の理論化学2023」研究会, 那覇, Mar. 9-11, 2023

2022

  • T. Mori, “Elucidating the Role of Dynamics During Enzyme Catalysis using Molecular Simulations”, 7th International Symposium of Quantum Beam Science at Ibaraki University (ISQBS2022), Mito (hybrid), Dec. 1-3, 2022
  • T. Mori, “タンパク質の変性状態における構造ダイナミクスと溶媒環境依存性の理論的解析”, 第60櫂日本生物物理学会年会（「動的溶液環境が駆動するタンパク質凝集」シンポジウム）, 函館, Sep. 28-30, 2022
  • T. Mori, “凝縮系反応の動的機構と反応座標の理論的解明”,「化学反応経路探索のニューフロンティア2022」シンポジウム, 横浜, Sep. 18, 2022
  • K. Kawashima, “シクロデキストリンを用いる位置選択的 C-H トリフルオロメチル化反応の機構解明”, 「凝縮系の理論化学2022」研究会, 那覇, Mar. 29, 2022
  • T. Mori, “生体分子の状態遷移と機能の動力学 (Role of dynamics in conformational transitions and functions of biomolecules)”, 日本化学会第102春季年会（アジア国際シンポジウム-物理化学ディビジョン）, オンライン, Mar. 23-26, 2022
  • T. Mori, “生体分子の動的構造と機能発現機構の理論的解明”, 京都大学福井謙一記念研究センターオンラインシンポジウム, 京都（オンライン）, Jan. 26, 2022