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Computational study on thermal relaxation processes in biomolecular systems

Research Project

Project/Area Number 21K06098
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 43040:Biophysics-related
Research InstitutionKobe University

Principal Investigator

Tanaka Shigenori  神戸大学, システム情報学研究科, 教授 (10379480)

Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2023: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2022: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2021: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords温度生物学 / 生体高分子 / 熱伝導度 / 分子動力学法 / 細胞内夾雑環境 / 非線形振動 / エネルギー移動 / エネルギー等分配
Outline of Research at the Start

細胞内の夾雑環境中の生体高分子系における熱緩和現象の理論的および計算機シミュレーション手法による解明を行う。まず、球対称あるいは円筒対称形状のタンパク質内部の熱伝導度ならびに周囲の水との界面における熱伝達率を非平衡全原子分子動力学シミュレーションによる温度緩和の結果を熱拡散方程式にマッピングすることで算出する。さらに、非平衡解離過程にあるタンパク質複合体における原子の速度分布の相関を調べることで、運動エネルギーとそれに付随した熱エネルギー・温度の「質」に関して議論する。さらに、生体高分子系に対する熱平衡ならびに非平衡状態における温度制御・熱浴設定の最適プロトコルを再検討する。

Outline of Final Research Achievements

First, we developed and established a theoretical method to quantitatively evaluate the thermal conductivity of a protein placed in an aqueous solution and the thermal conductance at the interface with the surrounding water based on molecular dynamics (MD) simulations, and verified its validity through actual calculations. It is particularly important that we are now able to accurately describe anisotropic heat conduction in the protein systems. Furthermore, we used the MD method to investigate in detail how energy generated by chemical reactions and other events is transferred in protein complexes, using all-atom and nonlinearly coupled oscillator models. Through this research, we elucidated the role of nonlinear mode coupling; we also derived a general analytic expression for the thermodynamic distribution function of quantum-mechanical harmonic oscillator systems.

Academic Significance and Societal Importance of the Research Achievements

近年、ダイヤモンドNVセンターなどを用いた量子ナノセンサーの技術的進展が目覚ましく、細胞内の局所的な温度計測が可能となりつつある。このような技術の延長上には、がんや脳神経疾患などの早期診断への応用が考えられ、また学術的にも分子生物学における局所温度変動の重要性を主張する温度生物学への適用が考えられる。本計画研究において、細胞環境中の生体分子周辺の温度変化や熱伝導を微視的に解析できる理論・シミュレーション手法が開発されたことは、これらの実験・計測を通じて得られた結果を解釈したり、新たな実験デザインを行ったりする上での貴重な基礎的知見を与えることになると言える。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • Research Products

    (46 results)

All 2024 2023 2022 2021 Other

All Int'l Joint Research (2 results) Journal Article (27 results) (of which Int'l Joint Research: 8 results,  Peer Reviewed: 27 results,  Open Access: 14 results) Presentation (14 results) (of which Int'l Joint Research: 6 results,  Invited: 5 results) Remarks (3 results)

  • [Int'l Joint Research] アルバータ大学(カナダ)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] アルバータ大学(カナダ)

    • Related Report
      2022 Research-status Report
  • [Journal Article] Manipulation of photosynthetic energy transfer by vibrational strong coupling2024

    • Author(s)
      Jun-Yu Dong, Yasutaka Kitahama, Takatoshi Fujita, Motoyasu Adachi, Yasuteru Shigeta, Akihito Ishizaki, Shigenori Tanaka, Ting-Hui Xiao, Keisuke Goda
    • Journal Title

      The Journal of Chemical Physics

      Volume: 160 Issue: 4 Pages: 045101-045101

    • DOI

      10.1063/5.0183383

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Prediction of Binding Pose and Affinity of Nelfinavir, a SARS-CoV-2 Main Protease Repositioned Drug, by Combining Docking, Molecular Dynamics, and Fragment Molecular Orbital Calculations2024

    • Author(s)
      Handa Yuma、Okuwaki Koji、Kawashima Yusuke、Hatada Ryo、Mochizuki Yuji、Komeiji Yuto、Tanaka Shigenori、Furuishi Takayuki、Yonemochi Etsuo、Honma Teruki、Fukuzawa Kaori
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 128 Issue: 10 Pages: 2249-2265

    • DOI

      10.1021/acs.jpcb.3c05564

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Holographic Brain Theory: Super-Radiance, Memory Capacity and Control Theory2024

    • Author(s)
      Nishiyama Akihiro、Tanaka Shigenori、Tuszynski Jack A.、Tsenkova Roumiana
    • Journal Title

      International Journal of Molecular Sciences

      Volume: 25 Issue: 4 Pages: 2399-2399

    • DOI

      10.3390/ijms25042399

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] 量子場と脳、その歴史と新展開2024

    • Author(s)
      西山陽大、田中成典
    • Journal Title

      科学基礎論研究

      Volume: 51 Pages: 57-73

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Thermal Conductivity and Conductance of Protein in Aqueous Solution: Effects of Geometrical Shape2023

    • Author(s)
      I. Kurisaki, S. Tanaka, I. Mori, T. Umegaki, Y. Mori, and S. Tanaka
    • Journal Title

      J. Comput. Chem.

      Volume: 44 Issue: 7 Pages: 857-868

    • DOI

      10.1002/jcc.27048

    • Related Report
      2023 Annual Research Report 2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Non-Equilibrium Phi4 Theory in a Hierarchy: Towards Manipulating Holograms in Quantum Brain Dynamics2023

    • Author(s)
      Nishiyama Akihiro、Tanaka Shigenori、Tuszynski Jack A.
    • Journal Title

      Dynamics

      Volume: 3 Issue: 1 Pages: 1-17

    • DOI

      10.3390/dynamics3010001

    • Related Report
      2023 Annual Research Report 2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Quantum Chemical Interaction Analysis between SARS-CoV-2 Main Protease and Ensitrelvir Compared with Its Initial Screening Hit2023

    • Author(s)
      Watanabe Chiduru、Tanaka Shigenori、Okiyama Yoshio、Yuki Hitomi、Ohyama Tatsuya、Kamisaka Kikuko、Takaya Daisuke、Fukuzawa Kaori、Honma Teruki
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 14 Issue: 15 Pages: 3609-3620

    • DOI

      10.1021/acs.jpclett.2c03768

    • Related Report
      2023 Annual Research Report 2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] End-to-end protein-ligand complex structure generation with diffusion-based generative models2023

    • Author(s)
      Shuya Nakata, Yoshiharu Mori, and Shigenori Tanaka
    • Journal Title

      BMC Bioinformatics

      Volume: 24 Issue: 1 Pages: 233-233

    • DOI

      10.1186/s12859-023-05354-5

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Renormalization in Quantum Brain Dynamics2023

    • Author(s)
      Nishiyama Akihiro、Tanaka Shigenori、Tuszynski Jack A.
    • Journal Title

      AppliedMath

      Volume: 3 Issue: 1 Pages: 117-146

    • DOI

      10.3390/appliedmath3010009

    • Related Report
      2023 Annual Research Report 2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Anesthetic Binding Induced Motion of GABAA Receptors Revealed by Coarse-Grained Molecular Dynamics Simulations2023

    • Author(s)
      Shuya Nakata, Yoshiharu Mori, and Shigenori Tanaka
    • Journal Title

      The Journal of Physical Chemistry B

      Volume: 127 Issue: 28 Pages: 6306-6315

    • DOI

      10.1021/acs.jpcb.3c01684

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Deciphering the Potential of Multidimensional Carbon Materials for Surface-Enhanced Raman Spectroscopy through Density Functional Theory2023

    • Author(s)
      Tang Xuke、Kishimoto Naoki、Kitahama Yasutaka、You Ting-Ting、Adachi Motoyasu、Shigeta Yasuteru、Tanaka Shigenori、Xiao Ting-Hui、Goda Keisuke
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 14 Issue: 45 Pages: 10208-10218

    • DOI

      10.1021/acs.jpclett.3c02962

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] 量子開放系に対する準古典マッピング動力学シミュレーション2023

    • Author(s)
      鬼頭宏任、梅垣俊仁、西山陽大、田中成典
    • Journal Title

      理論化学会誌「フロンティア」

      Volume: 5 Pages: 261-269

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fragment molecular orbital calculations containing Mg<sup>2+</sup> ions: PPlase domain of Cyclophilin G2022

    • Author(s)
      M. Fujii, C. Watanabe, K. Fukuzawa, and S. Tanaka
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: 22 Issue: 0 Pages: 55-62

    • DOI

      10.1273/cbij.22.55

    • ISSN
      1347-0442, 1347-6297
    • Year and Date
      2022-09-16
    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Protein-ligand binding affinity prediction of cyclin‐dependent kinase‐2 inhibitors by dynamically averaged fragment molecular orbital‐based interaction energy2022

    • Author(s)
      Takaba Kenichiro、Watanabe Chiduru、Tokuhisa Atsushi、Akinaga Yoshinobu、Ma Biao、Kanada Ryo、Araki Mitsugu、Okuno Yasushi、Kawashima Yusuke、Moriwaki Hirotomo、Kawashita Norihito、Honma Teruki、Fukuzawa Kaori、Tanaka Shigenori
    • Journal Title

      Journal of Computational Chemistry

      Volume: 43 Issue: 20 Pages: 1362-1371

    • DOI

      10.1002/jcc.26940

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Quantum Brain Dynamics in 2 + 1 Dimensions: Non-Equilibrium Analysis towards Memory Formations2022

    • Author(s)
      A. Nishiyama, S. Tanaka, and J.A. Tuszynski
    • Journal Title

      Physica A

      Volume: 598 Pages: 127397-127397

    • DOI

      10.1016/j.physa.2022.127397

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Quantum Brain Dynamics and Holography2022

    • Author(s)
      A. Nishiyama, S. Tanaka, and J.A. Tuszynski
    • Journal Title

      Dynamics

      Volume: 2 Issue: 2 Pages: 187-218

    • DOI

      10.3390/dynamics2020010

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Interspecies Comparison of Interaction Energies between Photosynthetic Protein RuBisCO and 2CABP Ligand2022

    • Author(s)
      M. Fujii and S. Tanaka
    • Journal Title

      Int. J. Mol. Sci.

      Volume: 23 Issue: 19 Pages: 11347-11347

    • DOI

      10.3390/ijms231911347

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dynamical Free Energy Based Model for Quantum Decision Making2022

    • Author(s)
      S. Tanaka, T. Umegaki, A. Nishiyama, and H. Kitoh-Nishioka
    • Journal Title

      Physica A

      Volume: 605 Pages: 127979-127979

    • DOI

      10.1016/j.physa.2022.127979

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inhibition of Melittin Activity Using a Small Molecule with an Indole Ring2022

    • Author(s)
      S. Kanemitsu, K. Morita, Y. Tominaga, K. Nishimura, T. Yashiro, H. Sakurai, Y. Yamamoto, I. Kurisaki, S. Tanaka, M. Matsui, T. Ooya, A. Tamura, and T. Maruyama
    • Journal Title

      J. Phys. Chem. B

      Volume: 126 Issue: 31 Pages: 5793-5802

    • DOI

      10.1021/acs.jpcb.2c03595

    • Related Report
      2022 Research-status Report
    • Peer Reviewed
  • [Journal Article] Thermal and Quantum Fluctuations of Harmonic Oscillator2022

    • Author(s)
      S. Tanaka and Y. Komeiji
    • Journal Title

      J. Phys. Chem. Res.

      Volume: 4 Issue: 3 Pages: 151-151

    • DOI

      10.36266/jpcr/151

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Remarked suppression of Aβ42 protomer-protomer dissociation reaction elucidated by molecular dynamics simulation2022

    • Author(s)
      Kurisaki Ikuo、Tanaka Shigenori
    • Journal Title

      Proteins: Structure, Function, and Bioinformatics

      Volume: 2022 Issue: 7 Pages: 1-9

    • DOI

      10.1002/prot.26319

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Computational prediction of heteromeric protein complex disassembly order using hybrid Monte Carlo/molecular dynamics simulation2022

    • Author(s)
      Kurisaki Ikuo、Tanaka Shigenori
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 24 Issue: 17 Pages: 10575-10587

    • DOI

      10.1039/d2cp00267a

    • Related Report
      2021 Research-status Report
    • Peer Reviewed
  • [Journal Article] Appearance of Thermal Time2021

    • Author(s)
      Tanaka Shigenori
    • Journal Title

      Foundations of Physics

      Volume: 51 Issue: 2 Pages: 34-34

    • DOI

      10.1007/s10701-021-00445-w

    • NAID

      120007026363

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Non-equilibrium Quantum Brain Dynamics II: Formulation in 3+1 dimensions2021

    • Author(s)
      Nishiyama Akihiro、Tanaka Shigenori、Tuszynski Jack A.
    • Journal Title

      Physica A: Statistical Mechanics and its Applications

      Volume: 567 Pages: 125706-125706

    • DOI

      10.1016/j.physa.2020.125706

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Improvement of the Force Field for β-d-Glucose with Machine Learning2021

    • Author(s)
      Ikejo Makoto、Watanabe Hirofumi、Shimamura Kohei、Tanaka Shigenori
    • Journal Title

      Molecules

      Volume: 26 Issue: 21 Pages: 6691-6691

    • DOI

      10.3390/molecules26216691

    • NAID

      120007170798

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Elucidating microscopic events driven by GTP hydrolysis reaction in the Ras-GAP system with semi-reactive molecular dynamics simulations: the alternative role of a phosphate binding loop for mechanical energy storage2021

    • Author(s)
      Kurisaki Ikuo、Tanaka Shigenori
    • Journal Title

      Physical Chemistry Chemical Physics

      Volume: 23 Issue: 46 Pages: 26151-26164

    • DOI

      10.1039/d1cp04061h

    • NAID

      120007179185

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Collective residue interactions in trimer complexes of SARS-CoV-2 spike proteins analyzed by fragment molecular orbital method2021

    • Author(s)
      Okuwaki Koji、Akisawa Kazuki、Hatada Ryo、Mochizuki Yuji、Fukuzawa Kaori、Komeiji Yuto、Tanaka Shigenori
    • Journal Title

      Applied Physics Express

      Volume: 15 Issue: 1 Pages: 017001-017001

    • DOI

      10.35848/1882-0786/ac4300

    • NAID

      120007181729

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Non-Equilibrium Quantum Field Theory in a Hierarchy: Towards Manipulating Holograms in Quantum Brain Dynamics2023

    • Author(s)
      Akihiro Nishiyama, Shigenori Tanaka, Jack A. Tuszynski
    • Organizer
      The Science of Consciousness (Taormina, Italy)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 水溶液中タンパク質の熱伝導の理論解析2023

    • Author(s)
      田中成典、栗崎以久男、田中聖也、森一郎、梅垣俊仁、森義治
    • Organizer
      量子生命科学会第5回大会(大阪大学)
    • Related Report
      2023 Annual Research Report
  • [Presentation] 量子場脳理論:その背景2023

    • Author(s)
      田中成典、西山陽大
    • Organizer
      科学基礎論学会2023年度総会(東海大学)
    • Related Report
      2023 Annual Research Report
  • [Presentation] 量子場脳理論:新展開2023

    • Author(s)
      西山陽大、田中成典
    • Organizer
      科学基礎論学会2023年度総会(東海大学)
    • Related Report
      2023 Annual Research Report
  • [Presentation] Molecular Dynamics Study on the Stability of G-Quadruplexes2023

    • Author(s)
      S. Tanaka
    • Organizer
      Fiber International Summit for Nucleic Acids (FISNA2023)(Konan University, Kobe)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 量子による生命現象の理解2023

    • Author(s)
      田中成典
    • Organizer
      一般社団法人量子ICTフォーラム量子生命シンポジウム「量子技術の新展開-量子と生命の融合-」(赤坂インターシティコンファレンス、東京)
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] 翻訳の起源について2023

    • Author(s)
      田中成典
    • Organizer
      CBI学会2023年大会(東京)
    • Related Report
      2023 Annual Research Report
  • [Presentation] Holographic Brain Theory: Super-radiance, Memory Capacity and Control Theory2023

    • Author(s)
      Akihiro Nishiyama, Shigenori Tanaka, Jack A. Tuszynski, Roumiana Tsenkova
    • Organizer
      Quantum Innovation 2023 (Tokyo)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 量子散逸系に対する準古典マッピング動力学法の精度検証2023

    • Author(s)
      鬼頭宏任、梅垣俊仁、西山陽大、田中成典
    • Organizer
      日本物理学会2023年春季大会
    • Related Report
      2022 Research-status Report
  • [Presentation] 量子意思決定の自由エネルギーモデル2022

    • Author(s)
      田中成典、梅垣俊仁、西山陽大、鬼頭宏任
    • Organizer
      量子生命科学会第4回大会
    • Related Report
      2022 Research-status Report
  • [Presentation] 量子認知と意思決定の自由エネルギー理論2022

    • Author(s)
      田中成典
    • Organizer
      CBI学会2022年大会
    • Related Report
      2022 Research-status Report
    • Invited
  • [Presentation] Quantum Brain Dynamics and Holography2022

    • Author(s)
      Akihiro Nishiyama, Shigenori Tanaka, Jack A. Tuszynski
    • Organizer
      The Science of Consciousness 2022
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Non-equilibrium φ4 Theory in a Hierarchy: Towards Manipulating Holograms in Quantum Brain Dynamics2022

    • Author(s)
      Akihiro Nishiyama, Shigenori Tanaka, Jack A. Tuszynski
    • Organizer
      The 5th International Forum on Quantum Metrology and Sensing
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Dynamical Association/Dissociation Processes of Biomolecules in Crowding Conditions2022

    • Author(s)
      Shigenori Tanaka
    • Organizer
      2nd International Symposium on Chemistry for Multimolecular Crowding Biosystems (CMCB2022)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research / Invited
  • [Remarks] 神戸大学田中研究室ホームページ

    • URL

      https://www.edu.kobe-u.ac.jp/csi-eniac/index.html

    • Related Report
      2023 Annual Research Report
  • [Remarks] 神戸大学大学院システム情報学研究科田中研究室ホームページ

    • URL

      https://www.edu.kobe-u.ac.jp/csi-eniac/index.html

    • Related Report
      2022 Research-status Report
  • [Remarks] 神戸大学大学院システム情報学研究科計算科学専攻田中研究室ホームページ

    • URL

      http://eniac.scitec.kobe-u.ac.jp/tanaka/

    • Related Report
      2021 Research-status Report

URL: 

Published: 2021-04-28   Modified: 2025-01-30  

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