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Direct numerical simulations of meso fluids at non-equilibrium conditions

Research Project

Project/Area Number 20H00129
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Review Section Medium-sized Section 13:Condensed matter physics and related fields
Research InstitutionKyoto University

Principal Investigator

Ryoichi Yamamoto  京都大学, 工学研究科, 教授 (10263401)

Project Period (FY) 2020-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥44,330,000 (Direct Cost: ¥34,100,000、Indirect Cost: ¥10,230,000)
Fiscal Year 2023: ¥7,670,000 (Direct Cost: ¥5,900,000、Indirect Cost: ¥1,770,000)
Fiscal Year 2022: ¥11,830,000 (Direct Cost: ¥9,100,000、Indirect Cost: ¥2,730,000)
Fiscal Year 2021: ¥11,830,000 (Direct Cost: ¥9,100,000、Indirect Cost: ¥2,730,000)
Fiscal Year 2020: ¥13,000,000 (Direct Cost: ¥10,000,000、Indirect Cost: ¥3,000,000)
Keywordsソフトマター / シミュレーション / 流体力学 / 直接数値計算 / コロイド分散系 / 微粒子分散系 / マイクロスイマー / アクティブマター
Outline of Research at the Start

メソフルイド分散系とは、相分離流体や高分子流体などのメソスケールの構造を有する流体中に粒子が分散した状態を表す名称である。メソフルイド分散系の内部には非常に遅いダイナミクスが存在するため、ミクロな分子シミュレーションを用いることは現実的でない。また内部に非平衡状態が容易に出現するため、マクロな計算流体力学をそのまま適用することもできない。注目するメソスケールの時間変化を捉えられる直接数値シミュレーション手法の開発が必要である。本研究では手法の構築にとどまらず、第三者が利用可能なソフトウェアを開発・公開することで、ソフトマター分野における計算科学の社会実装を目指す。

Outline of Final Research Achievements

The research is aimed at designing practical soft matter materials and processes by simulation of three research topics: 1) Dynamics of nanoparticle dispersion systems, 2) Dynamics of colloidal glass systems, 2) Dynamics of colloidal glass systems, 3) Dynamics of active particle systems. Multiscale and multiphysics simulations were applied to the three research topics: 1) dynamics of nanoparticle dispersion systems, 2) dynamics of colloidal glass systems, and 3) dynamics of active particle systems. In particular, significant results were achieved in understanding the role of the cell cycle on the collective motion of cells, the mechanism of rotation of microswimmers in viscoelastic fluids and the change in swimming speed due to the swimming morphology, and the propulsion mechanism of catalytic micromotors that self-propel in aqueous solutions.

Academic Significance and Societal Importance of the Research Achievements

分子動力学法や計算流体力学法など,既存のシミュレーション法ではソフトマターの膨大な自由度のごく一部しか同時に扱うことが出来ず,異なるスケールの運動を同時にまるごとシミュレーションすることは不可能であった.我々は,この問題を解決するために粗視化モデリングとマルチスケール・マルチフィジックスモデリングの2つのアプローチを用いてこの分野の研究を牽引している. これまでは純粋に科学的・学術的な興味が主体であり,材料やプロセスを設計するためのツールとして使える段階に至っていなかったが,本研究の成果はその克服につながるものである.

Report

(6 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • 2020 Comments on the Screening Results   Annual Research Report
  • Research Products

    (71 results)

All 2024 2023 2022 2021 2020 Other

All Int'l Joint Research (5 results) Journal Article (16 results) (of which Int'l Joint Research: 10 results,  Peer Reviewed: 16 results,  Open Access: 8 results) Presentation (45 results) (of which Int'l Joint Research: 27 results,  Invited: 9 results) Remarks (5 results)

  • [Int'l Joint Research] University of Warwick(英国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Universite´de Montpellier(フランス)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] University of Warwick(英国)

    • Related Report
      2022 Annual Research Report
  • [Int'l Joint Research] University of Warwick(英国)

    • Related Report
      2021 Annual Research Report
  • [Int'l Joint Research] University of Warwick(英国)

    • Related Report
      2020 Annual Research Report
  • [Journal Article] Dynamics of microswimmers near a liquid?liquid interface with viscosity difference2023

    • Author(s)
      Feng Chao、Molina John J.、Turner Matthew S.、Yamamoto Ryoichi
    • Journal Title

      Physics of Fluids

      Volume: 35 Issue: 5

    • DOI

      10.1063/5.0148008

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Dynamics of a Model Microswimmer in the Vicinity of a Liquid Droplet2023

    • Author(s)
      Feng Chao、Molina John J.、Yamamoto Ryoichi
    • Journal Title

      Journal of the Physical Society of Japan

      Volume: 92 Issue: 7

    • DOI

      10.7566/jpsj.92.074802

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Direct numerical simulations of a microswimmer in a viscoelastic fluid2023

    • Author(s)
      Kobayashi Takuya、Jung Gerhard、Matsuoka Yuki、Nakayama Yasuya、Molina John J.、Yamamoto Ryoichi
    • Journal Title

      Soft Matter

      Volume: 19 Issue: 37 Pages: 7109-7121

    • DOI

      10.1039/d3sm00600j

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Learning to swim efficiently in a nonuniform flow field2023

    • Author(s)
      Sankaewtong Krongtum、Molina John J.、Turner Matthew S.、Yamamoto Ryoichi
    • Journal Title

      Physical Review E

      Volume: 107 Issue: 6

    • DOI

      10.1103/physreve.107.065102

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Rational social distancing in epidemics with uncertain vaccination timing2023

    • Author(s)
      Schnyder Simon K.、Molina John J.、Yamamoto Ryoichi、Turner Matthew S.
    • Journal Title

      PLOS ONE

      Volume: 18 Issue: 7 Pages: e0288963-e0288963

    • DOI

      10.1371/journal.pone.0288963

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Rational social distancing policy during epidemics with limited healthcare capacity2023

    • Author(s)
      Schnyder Simon K.、Molina John J.、Yamamoto Ryoichi、Turner Matthew S.
    • Journal Title

      PLOS Computational Biology

      Volume: 19 Issue: 10 Pages: e1011533-e1011533

    • DOI

      10.1371/journal.pcbi.1011533

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Direct numerical simulations of isolated rigid particles; Validation of smooth profile method2023

    • Author(s)
      Uzair Muhammad、Qasim M. Danyal、Bhatti M. Aashan、Zaidi Ali Abbas、Molina John J.、Yamamoto Ryoichi、Hamid Adnan
    • Journal Title

      Powder Technology

      Volume: 418 Pages: 118280-118280

    • DOI

      10.1016/j.powtec.2023.118280

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Collective Motion of Quincke Rollers with Fully Resolved Hydrodynamics2023

    • Author(s)
      Imamura Shun、Sawaki Kohei、Molina John J.、Turner Matthew S.、Yamamoto Ryoichi
    • Journal Title

      Advanced Theory and Simulations

      Volume: 6 Issue: 4 Pages: 2200683-2200683

    • DOI

      10.1002/adts.202200683

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Dynamics of microswimmers near a soft penetrable interface2022

    • Author(s)
      Feng Chao、Molina John J.、Turner Matthew S.、Yamamoto Ryoichi
    • Journal Title

      Physical Review Research

      Volume: 4 Issue: 4 Pages: 043202-043202

    • DOI

      10.1103/physrevresearch.4.043202

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Competition between cell types under cell cycle regulation with apoptosis2022

    • Author(s)
      Li Jintao、Schnyder Simon K.、Turner Matthew S.、Yamamoto Ryoichi
    • Journal Title

      Physical Review Research

      Volume: 4 Issue: 3 Pages: 033156-033156

    • DOI

      10.1103/physrevresearch.4.033156

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Mechanochemical subcellular-element model of crawling cells2022

    • Author(s)
      Mitsusuke Tarama, Kenji Mori, Ryoishi Yamamoto
    • Journal Title

      Frontiers in Cell and Developmental Biology

      Volume: 10 Pages: 1046053-1046053

    • DOI

      10.3389/fcell.2022.1046053

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Relation between dynamic heterogeneities observed in scattering experiments and four-body correlations2022

    • Author(s)
      Kanayama Kohsei、Hoshino Taiki、Yamamoto Ryoichi
    • Journal Title

      Physical Review Research

      Volume: 4 Issue: 2

    • DOI

      10.1103/physrevresearch.4.l022006

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Direct Numerical Simulations of Colloidal Dispersions2021

    • Author(s)
      山本 量一
    • Journal Title

      THE MICROMERITICS

      Volume: 65 Issue: 0 Pages: 11-17

    • DOI

      10.24611/micromeritics.2022006

    • NAID

      130008129283

    • ISSN
      0429-9051, 2432-2075
    • Year and Date
      2021-12-15
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Role of the Cell Cycle in Collective Cell Dynamics2021

    • Author(s)
      Li Jintao、Schnyder Simon K.、Turner Matthew S.、Yamamoto Ryoichi
    • Journal Title

      Physical Review X

      Volume: 11 Issue: 3 Pages: 031025-031025

    • DOI

      10.1103/physrevx.11.031025

    • NAID

      120007141956

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Smoothed profile method for direct numerical simulations of hydrodynamically interacting particles2021

    • Author(s)
      Yamamoto Ryoichi、Molina John Jairo、Nakayama Yasuya
    • Journal Title

      Soft Matter

      Volume: - Issue: 16 Pages: 4226-4253

    • DOI

      10.1039/d0sm02210a

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Dynamics of a chiral swimmer sedimenting on a flat plate2020

    • Author(s)
      Fadda Federico、Molina John Jairo、Yamamoto Ryoichi
    • Journal Title

      Physical Review E

      Volume: 101 Issue: 5 Pages: 52608-52608

    • DOI

      10.1103/physreve.101.052608

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Presentation] Direct numerical simulations of active particles with fully resolved hydrodynamics2024

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      Advanced core-to-core network for the physics of self-organizing active matter, workshop in Wenzhou
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Simulations of hydrodynamically interacting particles2024

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      JNCASR - CECAM Conference - MD@60
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Direct Numerical Simulations (DNS)of active particles in complex environments2023

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      New statistical physics in living matter: non equilibrium states under adaptive control, Workshop at the Isaac Newton Institute for Mathematical Sciences
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dynamics of microswimmers in complex media: influence of interface or viscoelasticity2023

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      StatPhysHK 2023: A Satellite Meeting of The XXVIII IUPAP International Conference on Statistical Physics
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Direct numerical simulations (DNS) of active particles with fully resolved hydrodynamics2023

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      28th International Conference on Statistical Physics, Statphys28
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Direct numerical simulations (DNS) of active particles with fully resolved hydrodynamics2023

    • Author(s)
      Kenta Ogawa
    • Organizer
      28th International Conference on Statistical Physics, Statphys28
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] KAPSELによる粒子分散系の直接数値シミュレーション2023

    • Author(s)
      山本量一
    • Organizer
      OCTA20周年記念講演会
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Direct Numerical Simulations (DNS)of active particles with fully resolved hydrodynamics2023

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      Active Matter in Complex Environments
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Direct numerical simulations of microswimmers in viscoelastic fluids2023

    • Author(s)
      Takuya Kobayashi
    • Organizer
      The 16th International Workshop for East Asian Young Rheologist
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Direct Numerical Simulation of Metallodielectric Janus Particles2023

    • Author(s)
      John J. Molina
    • Organizer
      APS March Meeting 2023
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Direct numerical simulations of a model microswimmer near a liquid-liquid interface2023

    • Author(s)
      Chao Feng
    • Organizer
      Active Matter Workshop 2023
    • Related Report
      2022 Annual Research Report
  • [Presentation] 直接数値計算による自己推進粒子のダイナミクス2023

    • Author(s)
      山本量一
    • Organizer
      生物とソフトマターに関する理論とシミュレーションについての研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Dynamics of micro-swimmers near deformable and penetrable interfaces2022

    • Author(s)
      Chao Feng
    • Organizer
      APPC15: The 15th Asia Pacific Physics Conference
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Microswimmers in viscoelastic fluids2022

    • Author(s)
      Takuya Kobayashi
    • Organizer
      APPC15: The 15th Asia Pacific Physics Conference
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Learning to swim efficiently in a nonuniform flow field2022

    • Author(s)
      Krongtum Sankaewtong
    • Organizer
      The International Soft Matter Conference (ISMC 2022)
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] DNS of active particles with fully resolved hydrodynamics2022

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      The International Soft Matter Conference (ISMC 2022)
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Direct numerical simulations of active particles with fully resolved hydrodynamics2022

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      25th Anniversary Symposium of German-japanese Joint Research Project on Nonequilibrium Statistical Physics Perspective for Future Collaboration
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Direct numerical simulations of active particles with fully resolved hydrodynamics2022

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      KPS 70th Anniversary and 2022 Fall Meeting
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Direct Numerical Simulations (DNS)of active particleswith fully resolved hydrodynamics2022

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      The 31st International Toki Conference on Plasma and Fusion Research (ITC31)Expanding academic world emerging from fusion science
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 粘弾性流体中を泳動するマイクロスイマー:回転運動による速度上昇2022

    • Author(s)
      小林巧弥
    • Organizer
      日本物理学会 2022年秋季大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] コロイド分散系の直接数値計算2022

    • Author(s)
      山本量一
    • Organizer
      ホソカワ粉体工学シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] 直接数値計算による粘弾性流体中を泳動するマイクロスイマーのダイナミクス2022

    • Author(s)
      小林巧弥
    • Organizer
      第70回レオロジー討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 粘弾性流体中を泳動するモデル微生物の直接数値計算2022

    • Author(s)
      小林巧弥
    • Organizer
      第10回ソフトマター研究会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 粒子分散系の直接数値シミュレーターKAPSELの紹介2022

    • Author(s)
      山本量一
    • Organizer
      先端化学・材料技術部会 CC分科会 高分子WG勉強会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Competition between two cell types under cell cycle regulation with apoptosis2022

    • Author(s)
      Jintao Li
    • Organizer
      American Physical Society (APS) March Meeting 2022
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Collective Dynamics of Quincke Rollers with Fully Resolved Hydrodynamics2022

    • Author(s)
      Shun Imamura
    • Organizer
      American Physical Society (APS) March Meeting 2022
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Rational policy design for epidemics2022

    • Author(s)
      Simon K. Schnyder
    • Organizer
      American Physical Society (APS) March Meeting 2022
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Nash Neural Networks2022

    • Author(s)
      John J. Molina
    • Organizer
      American Physical Society (APS) March Meeting 2022
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Rational policy design for epidemics2021

    • Author(s)
      Simon K. Schnyder
    • Organizer
      27th International Conference on Computing in Economics and Finance
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] DNS of self-propelled particles2021

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      RIMS Workshop Mathematical Mechanobiology
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Direct numerical simulation of Quincke rollers2021

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      11th Liquid Matter Conference
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Cell migration and colony growth in a monolayer of model cells2021

    • Author(s)
      Simon K. Schnyder
    • Organizer
      11th Liquid Matter Conference
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] The role of the cell cycle in collective cell dynamics2021

    • Author(s)
      Jintao Li
    • Organizer
      Physics meets Biology 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Rational policy design for epidemics2021

    • Author(s)
      Simon K. Schnyder
    • Organizer
      24.5th Workshop on Economics with Heterogeneous Interacting Agents 2021
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Role of the Cell Cycle in Collective Cell Dynamics2021

    • Author(s)
      Simon K. Schnyder
    • Organizer
      RIMS Workshop on Mathematical Mechanobiology
    • Related Report
      2021 Annual Research Report
  • [Presentation] X 線散乱実験と分子シミュレーションの連携による過冷却液体の動 的構造の解明2021

    • Author(s)
      金山昂生
    • Organizer
      日本物理学会2021年秋季大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 直接数値計算による液滴乾燥過程のダイナミクス2021

    • Author(s)
      小林巧弥
    • Organizer
      第69回レオロジー討論会
    • Related Report
      2021 Annual Research Report
  • [Presentation] X線散乱実験と分子シミュレーションの連携による過冷却液体の動的構造の解明2021

    • Author(s)
      金山昂生
    • Organizer
      第35回分子シミュレーション討論会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Role of the Cell Cycle in Collective Cell Dynamics2021

    • Author(s)
      Simon K. Schnyder
    • Organizer
      Active Matter Workshop 2022
    • Related Report
      2021 Annual Research Report
  • [Presentation] Mechanical competition between different cell types2021

    • Author(s)
      Jintao Li
    • Organizer
      Active Matter Workshop 2022
    • Related Report
      2021 Annual Research Report
  • [Presentation] A mechano-chemical cell cycle for growing cell colonies2021

    • Author(s)
      Simon Schnyder
    • Organizer
      American Physical Society (APS) March Meeting
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] MDシミュレーションによるせん断流下での過冷却液体の解析2021

    • Author(s)
      金山 昂生
    • Organizer
      化学工学会第86年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 直接数値計算による二成分流体コロイド分散系の粘弾性の評価2020

    • Author(s)
      金山 昂生
    • Organizer
      第68回レオロジー討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 直接数値計算によるヤヌス粒子の誘起電荷電気泳動2020

    • Author(s)
      江里口 拓哉
    • Organizer
      第68回レオロジー討論会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 直接数値計算によるクインケローラーの挙動解析2020

    • Author(s)
      佐脇 航平
    • Organizer
      第68回レオロジー討論会
    • Related Report
      2020 Annual Research Report
  • [Remarks] Soft Matter Engineering Lab.

    • URL

      https://sm.cheme.kyoto-u.ac.jp/

    • Related Report
      2023 Annual Research Report
  • [Remarks] KAPSEL-5 HP

    • URL

      https://kapsel-dns.com/v5/

    • Related Report
      2023 Annual Research Report
  • [Remarks] Welcome to KAPSEL-5 HP

    • URL

      https://kapsel-dns.com/v5/

    • Related Report
      2022 Annual Research Report
  • [Remarks] Welcome to KAPSEL-4 HP

    • URL

      https://kapsel-dns.com/v4/

    • Related Report
      2021 Annual Research Report
  • [Remarks] KAPSEL HP

    • URL

      https://kapsel-dns.com/

    • Related Report
      2020 Annual Research Report

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

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