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Effective active stress in collective behaviours of active matters

Research Project

Project/Area Number 20K03874
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 13040:Biophysics, chemical physics and soft matter physics-related
Research InstitutionTohoku University

Principal Investigator

Yoshinaga Natsuhiko  東北大学, 材料科学高等研究所, 准教授 (90548835)

Project Period (FY) 2020-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2022: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2021: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2020: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywordsアクティブマター / 非平衡物理 / 生物物理 / 自己駆動粒子 / 非線形ダイナミックス / 集団運動 / 流体力学 / ソフトマター / 拡散係数
Outline of Research at the Start

アクティブマターは、内部にエネルギー源を持った粒子が自己駆動するメカニズムや、多数の自己駆動粒子が示す集団運動の解明を目指す分野である。これらの現象は多岐にわたり、大腸菌の集団運動のような生命現象から、Janus粒子と呼ばれる異なった性質の表面を持つ粒子でも、自己駆動粒子の集団運動が観測されている。本研究では、アクティブマターの構成方程式はどのように表現されるか。マクロな方程式に現れる係数の計算手法、物理的意味、そして直感的な値の大小を推測するための枠組みを構築する。

Outline of Final Research Achievements

In this project, we have performed numerical simulations and theoretical analyses for collective behaviours of active matters. A particular focus is on how the microscopic dynamics of self-propelled particles are related to macroscopic quantities. We have performed numerical simulations and mean-field-type analyses for the collective motions of bacteria and computed effective diffusion constants and macroscopic responses to external fields. The results were compared with experiments, and we found a qualitative agreement. We have also studied, using machine-learning techniques, coarse-graining and estimation of parameters in macroscopic equations from the data of microscopic particle dynamics.

Academic Significance and Societal Importance of the Research Achievements

アクティブマターは、非平衡状態でエネルギーを消費し環境に散逸しながら秩序を持った集団運動を実現するシステムである。平衡系とは異なり、アクティブマターには自由エネルギーのような最小化するものが一般には存在しないため、自由エネルギーを積分することによってマクロな支配方程式を得ることは困難である。本研究では、ダイナミックスからどのようにマクロな方程式の係数を得ることができるのかについて理解を深めるために行った。本研究で行ったような機械学習の手法と組み合わせてマクロな方程式が系統的に導出できるようになれば、階層性のある現象についての理論的・計算科学的解析手法が広がるのではないかと考えている。

Report

(5 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • 2020 Research-status Report
  • Research Products

    (33 results)

All 2024 2023 2022 2021 2020 Other

All Int'l Joint Research (1 results) Journal Article (10 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 8 results,  Open Access: 7 results) Presentation (20 results) (of which Int'l Joint Research: 19 results,  Invited: 2 results) Remarks (2 results)

  • [Int'l Joint Research] ブリストル大学(英国)

    • Related Report
      2023 Annual Research Report
  • [Journal Article] Inverse problems of inhomogeneous fracture toughness using phase-field models2023

    • Author(s)
      Gao Yueyuan、Yoshinaga Natsuhiko
    • Journal Title

      Physica D: Nonlinear Phenomena

      Volume: 448 Pages: 133734-133734

    • DOI

      10.1016/j.physd.2023.133734

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell‐Size Space2023

    • Author(s)
      Nishikawa Saki、Sato Gaku、Takada Sakura、Kohyama Shunshi、Honda Gen、Yanagisawa Miho、Hori Yutaka、Doi Nobuhide、Yoshinaga Natsuhiko、Fujiwara Kei
    • Journal Title

      Advanced Science

      Volume: 11 Issue: 6 Pages: 2308030-2308030

    • DOI

      10.1002/advs.202308030

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Collective gradient sensing by swimming bacteria without clustering2022

    • Author(s)
      Kai Tatsuro、Abe Takahiro、Yoshinaga Natsuhiko、Nakamura Shuichi、Kudo Seishi、Toyabe Shoichi
    • Journal Title

      bioarxiv

      Volume: - Pages: 516991-516991

    • DOI

      10.1101/2022.11.17.516991

    • Related Report
      2022 Research-status Report
  • [Journal Article] Bayesian modeling of pattern formation from one snapshot of pattern2022

    • Author(s)
      Yoshinaga Natsuhiko、Tokuda Satoru
    • Journal Title

      Physical Review E

      Volume: 106 Issue: 6 Pages: 065301-065301

    • DOI

      10.1103/physreve.106.065301

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Formation and fluctuation of two-dimensional dodecagonal quasicrystals2022

    • Author(s)
      Lieu Uyen Tu、Yoshinaga Natsuhiko
    • Journal Title

      Soft Matter

      Volume: 18 Issue: 39 Pages: 7497-7509

    • DOI

      10.1039/d2sm00798c

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Mode selection mechanism in traveling and standing waves revealed by Min wave reconstituted in artificial cells2022

    • Author(s)
      Takada Sakura、Yoshinaga Natsuhiko、Doi Nobuhide、Fujiwara Kei
    • Journal Title

      Science Advances

      Volume: 8 Issue: 23

    • DOI

      10.1126/sciadv.abm8460

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Inverse design of two-dimensional structure by self-assembly of patchy particles2022

    • Author(s)
      Uyen Tu Lieu and Natsuhiko Yoshinaga
    • Journal Title

      Journal of Chemcial Physics

      Volume: 156 Issue: 5 Pages: 054901-054901

    • DOI

      10.1063/5.0072234

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Bayesian Modelling of Pattern Formation from One Snapshot of Pattern2021

    • Author(s)
      Natsuhiko Yoshinaga and Satoru Tokuda
    • Journal Title

      arXiv

      Volume: -

    • Related Report
      2021 Research-status Report
  • [Journal Article] Topological defects of dipole patchy particles on a spherical surface2020

    • Author(s)
      Uyen Tu Lieu and Natsuhiko Yoshinaga
    • Journal Title

      Soft Matter

      Volume: 16 Issue: 33 Pages: 7667-7675

    • DOI

      10.1039/d0sm00103a

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Conformational equilibrium of MinE regulates the allowable concentration ranges of a protein wave for cell division2020

    • Author(s)
      Shunshi Kohyama, Kei Fujiwara, Natsuhiko Yoshinaga, Nobuhide Doi
    • Journal Title

      Nanoscale

      Volume: 12 Issue: 22 Pages: 11960-11970

    • DOI

      10.1039/d0nr00242a

    • Related Report
      2020 Research-status Report
    • Peer Reviewed
  • [Presentation] Reinforcement learning for dynamic control of self-assembly of quasicrystals from patchy particles2024

    • Author(s)
      Uyen Tu Lieu and Natsuhiko Yoshinaga
    • Organizer
      APS March Meeting 2024
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Estimation of continuum models for (active) soft materials and data-driven coarse-graining2023

    • Author(s)
      Natsuhiko Yoshinaga
    • Organizer
      New statistical physics in living matter: non equilibrium states under adaptive control at Isaac Newton Institute for Mathematical Sciences
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Bayesian Model Selection of PDEs for Pattern Formation2023

    • Author(s)
      Natsuhiko Yoshinaga and Satoru Tokuda
    • Organizer
      the 10th International Congress on Industrial and Applied Mathematics (ICIAM2023), Minisymposium "Multiscale Pattern Formation"
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Reaction-diffusion models for Min oscillations: wave instability in a confined space2023

    • Author(s)
      Natsuhiko Yoshinaga
    • Organizer
      Complex motile matter - from single agents to collective behaviors
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Estimation of continuum and discrete models for quasicrystal formation2023

    • Author(s)
      Natsuhiko Yoshinaga
    • Organizer
      the 15th International Confernce on Quasicrystals
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Inverse design of two-dimensional dodecagonal quasicrystal structure by patchy particles2023

    • Author(s)
      Uyen Tu Lieu and Natsuhiko Yoshinaga
    • Organizer
      STATPHYS28
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Learning hydrodynamic equations from microscopic Langevin simulations of self-propelled particles dynamics2023

    • Author(s)
      Bappaditya Roy and Natsuhiko Yoshinaga
    • Organizer
      STATPHYS28
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Inverse Design of Two-dimensional Dodecagonal Quasicrystal Structure by Patchy Particles2023

    • Author(s)
      Uyen Tu Lieu and Natsuhiko Yoshinaga
    • Organizer
      ISMC2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Learning hydrodynamic equations from microscopic Langevin simulations of self-propelled particles dynamics2023

    • Author(s)
      Bappaditya Roy and Natsuhiko Yoshinaga
    • Organizer
      CCP2023 - 34th IUPAP Conference on Computational Physics
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Model Selection of Nonlinear PDEs for Pattern Formation2022

    • Author(s)
      Natsuhiko Yoshinaga
    • Organizer
      SIAM Conference on Mathematics of Data Science (MDS22)
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Bayesian Model Selection of Partial Differential Equations for Pattern Formation2022

    • Author(s)
      Natsuhiko Yoshinaga
    • Organizer
      WCCM-APCOM 2022
    • Related Report
      2022 Research-status Report
    • Int'l Joint Research
  • [Presentation] Bayesian Modelling of Phase-Field Crystal Models for Targeted Crystalline Patterns2022

    • Author(s)
      Natsuhiko Yoshinaga and Satoru Tokuda
    • Organizer
      American Physical Society March Meeting 2022, Chicago, USA (hybrid)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Inverse Design of Two-dimensional Self-assembly of Patchy Particles2022

    • Author(s)
      Uyen T Lieu and Natsuhiko Yoshinaga
    • Organizer
      American Physical Society March Meeting 2022, Chicago, USA (hybrid)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Model Selection of Phase-Field Crystal Models for Targeted Crystalline Patterns2021

    • Author(s)
      Natsuhiko Yoshinaga and Satoru Tokuda
    • Organizer
      Materials Research Meeting 2021, Yokohama, Japan (hybrid meeting)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Inverse design of two-dimensional self-assembly of patchy particles2021

    • Author(s)
      Uyen T Lieu and Natsuhiko Yoshinaga
    • Organizer
      Materials Research Meeting 2021, Yokohama, Japan (hybrid meeting)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Bayesian Inference of Phase-Field Crystal Models for Target Crystalline Patterns2021

    • Author(s)
      Natsuhiko Yoshinaga and Satoru Tokuda
    • Organizer
      Meeting of the International Research Network: Open space between aperiodic order and physics & chemistry of materials
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Model Selection of PDE for Pattern Formation2021

    • Author(s)
      Natsuhiko Yoshinaga and Satoru Tokuda
    • Organizer
      25th International Congress of Theoretical and Applied Mechanics (ICTAM 2020+1), Milano, Italy (online)
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Model Selection of Phase-Field Crystal Models for Targeted Crystalline Patterns2021

    • Author(s)
      Natsuhiko Yoshinaga and Satoru Tokuda
    • Organizer
      E-MRS 2021 Spring, Virtual Conference
    • Related Report
      2021 Research-status Report 2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] Model Selection of PDE for Pattern Formation2021

    • Author(s)
      Natsuhiko Yoshinaga and Satoru Tokuda
    • Organizer
      25th International Congress of Theoretical and Applied Mechanics (ICTAM 2020+1), Milano, Italy
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] ベイズ推定を用いた目的の相分離パターンの支配方程式の推定2021

    • Author(s)
      義永那津人、徳田悟
    • Organizer
      日本物理学会第76回年次大会
    • Related Report
      2020 Research-status Report
  • [Remarks] ホームページ

    • URL

      http://www.wpi-aimr.tohoku.ac.jp/~yoshinaga/index.html

    • Related Report
      2023 Annual Research Report 2020 Research-status Report
  • [Remarks] 研究代表者による研究内容に関するwebページ

    • URL

      http://www.wpi-aimr.tohoku.ac.jp/~yoshinaga/

    • Related Report
      2022 Research-status Report 2021 Research-status Report

URL: 

Published: 2020-04-28   Modified: 2025-01-30  

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