Direct numerical simulations of meso fluids at non-equilibrium conditions

• Project/Area Number: 20H00129
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Medium-sized Section 13:Condensed matter physics and related fields
• Research Institution: Kyoto University
• Principal Investigator: 山本 量一 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: ¥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 / マイクロスイマー

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 Annual Research Achievements

ソフトマターとは，柔らかく複雑な内部構造を持つ物質の総称である．本研究では，特にシミュレーションの難易度が高い「メソフルイド分散系」を対象に，これまで比較的単純な粒子分散系に対して構築してきたシミュレーション手法を大幅に改善することで，i)メソスケール(濃度分布，界面，流動など)のダイナミクスを物理的に矛盾しない基礎方程式に基づいて計算するための直接数値シミュレーション手法を構築し，ii)それを使用した強力で適用性の高い直接数値シミュレーションソフトウェアを開発することを目指している．これらの目標を達成するためには，注目するメソスケールの時間変化を捉えるための直接数値シミュレーション手法の開発が不可欠である．本研究では，手法の構築だけでなく，第三者が利用できるよう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した．研究スタッフ1名の雇用を継続し，これまでに導入した並列計算機やワークステーションを使用し，大規模シミュレーションのデータ解析と可視化を実施して，当該分野で評価の高い，Physics of Fluids，Physical Review E，Soft Matter，PLOS ONE，などの各誌に論文6報を出版すると同時に，対面型を含む多数の国際会議・国内会議において研究成果の発表を行った．2023年10月には，メソフルイド分散系の直接数値計算を実施するためのソフトウェアの最新版として「KAPSEL-5．10」のリリースを行った．第三者の利用を容易にするために，100ページを超える日本語と英語のユーザーマニュアルの更新版も同時に公開した．

Research Progress Status

令和5年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和5年度が最終年度であるため、記入しない。

Research Products

• [Int'l Joint Research] University of Warwick(英国)
• [Int'l Joint Research] Universite´de Montpellier(フランス)
• [Int'l Joint Research] University of Warwick(英国)
• [Int'l Joint Research] University of Warwick(英国)
• [Int'l Joint Research] University of Warwick(英国)
• [Journal Article] Dynamics of microswimmers near a liquid?liquid interface with viscosity difference (2023)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Dynamics of a Model Microswimmer in the Vicinity of a Liquid Droplet (2023)
  • 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
  • Peer Reviewed
• [Journal Article] Direct numerical simulations of a microswimmer in a viscoelastic fluid (2023)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Learning to swim efficiently in a nonuniform flow field (2023)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Rational social distancing in epidemics with uncertain vaccination timing (2023)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Rational social distancing policy during epidemics with limited healthcare capacity (2023)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Direct numerical simulations of isolated rigid particles; Validation of smooth profile method (2023)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Collective Motion of Quincke Rollers with Fully Resolved Hydrodynamics (2023)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Dynamics of microswimmers near a soft penetrable interface (2022)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Competition between cell types under cell cycle regulation with apoptosis (2022)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Mechanochemical subcellular-element model of crawling cells (2022)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Relation between dynamic heterogeneities observed in scattering experiments and four-body correlations (2022)
  • Author(s): Kanayama Kohsei、Hoshino Taiki、Yamamoto Ryoichi
  • Journal Title: Physical Review Research Volume: 4 Issue: 2
  • DOI: 10.1103/physrevresearch.4.l022006
  • Peer Reviewed / Open Access
• [Journal Article] Direct Numerical Simulations of Colloidal Dispersions (2021)
  • 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
  • Peer Reviewed
• [Journal Article] Role of the Cell Cycle in Collective Cell Dynamics (2021)
  • 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
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Smoothed profile method for direct numerical simulations of hydrodynamically interacting particles (2021)
  • Author(s): Yamamoto Ryoichi、Molina John Jairo、Nakayama Yasuya
  • Journal Title: Soft Matter Volume: - Issue: 16 Pages: 4226-4253
  • DOI: 10.1039/d0sm02210a
  • Peer Reviewed / Open Access
• [Journal Article] Dynamics of a chiral swimmer sedimenting on a flat plate (2020)
  • 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
  • Peer Reviewed
• [Presentation] Direct numerical simulations of active particles with fully resolved hydrodynamics (2024)
  • Author(s): Ryoichi Yamamoto
  • Organizer: Advanced core-to-core network for the physics of self-organizing active matter, workshop in Wenzhou
  • Int'l Joint Research / Invited
• [Presentation] Simulations of hydrodynamically interacting particles (2024)
  • Author(s): Ryoichi Yamamoto
  • Organizer: JNCASR - CECAM Conference - MD@60
  • Int'l Joint Research / Invited
• [Presentation] Direct Numerical Simulations (DNS)of active particles in complex environments (2023)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Dynamics of microswimmers in complex media: influence of interface or viscoelasticity (2023)
  • Author(s): Ryoichi Yamamoto
  • Organizer: StatPhysHK 2023: A Satellite Meeting of The XXVIII IUPAP International Conference on Statistical Physics
  • Int'l Joint Research / Invited
• [Presentation] Direct numerical simulations (DNS) of active particles with fully resolved hydrodynamics (2023)
  • Author(s): Ryoichi Yamamoto
  • Organizer: 28th International Conference on Statistical Physics, Statphys28
  • Int'l Joint Research
• [Presentation] Direct numerical simulations (DNS) of active particles with fully resolved hydrodynamics (2023)
  • Author(s): Kenta Ogawa
  • Organizer: 28th International Conference on Statistical Physics, Statphys28
  • 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
  • Invited
• [Presentation] Direct Numerical Simulations (DNS)of active particles with fully resolved hydrodynamics (2023)
  • Author(s): Ryoichi Yamamoto
  • Organizer: Active Matter in Complex Environments
  • Int'l Joint Research
• [Presentation] Direct numerical simulations of microswimmers in viscoelastic fluids (2023)
  • Author(s): Takuya Kobayashi
  • Organizer: The 16th International Workshop for East Asian Young Rheologist
  • Int'l Joint Research
• [Presentation] Direct Numerical Simulation of Metallodielectric Janus Particles (2023)
  • Author(s): John J. Molina
  • Organizer: APS March Meeting 2023
  • Int'l Joint Research
• [Presentation] Direct numerical simulations of a model microswimmer near a liquid-liquid interface (2023)
  • Author(s): Chao Feng
  • Organizer: Active Matter Workshop 2023
• [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
• [Presentation] Dynamics of micro-swimmers near deformable and penetrable interfaces (2022)
  • Author(s): Chao Feng
  • Organizer: APPC15: The 15th Asia Pacific Physics Conference
  • Int'l Joint Research
• [Presentation] Microswimmers in viscoelastic fluids (2022)
  • Author(s): Takuya Kobayashi
  • Organizer: APPC15: The 15th Asia Pacific Physics Conference
  • Int'l Joint Research
• [Presentation] Learning to swim efficiently in a nonuniform flow field (2022)
  • Author(s): Krongtum Sankaewtong
  • Organizer: The International Soft Matter Conference (ISMC 2022)
  • Int'l Joint Research
• [Presentation] DNS of active particles with fully resolved hydrodynamics (2022)
  • Author(s): Ryoichi Yamamoto
  • Organizer: The International Soft Matter Conference (ISMC 2022)
  • Int'l Joint Research
• [Presentation] Direct numerical simulations of active particles with fully resolved hydrodynamics (2022)
  • Author(s): Ryoichi Yamamoto
  • Organizer: 25th Anniversary Symposium of German-japanese Joint Research Project on Nonequilibrium Statistical Physics Perspective for Future Collaboration
  • Int'l Joint Research / Invited
• [Presentation] Direct numerical simulations of active particles with fully resolved hydrodynamics (2022)
  • Author(s): Ryoichi Yamamoto
  • Organizer: KPS 70th Anniversary and 2022 Fall Meeting
  • Int'l Joint Research / Invited
• [Presentation] Direct Numerical Simulations (DNS)of active particleswith fully resolved hydrodynamics (2022)
  • Author(s): Ryoichi Yamamoto
  • Organizer: The 31st International Toki Conference on Plasma and Fusion Research (ITC31)Expanding academic world emerging from fusion science
  • 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
• [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
• [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
• [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
• [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
• [Presentation] Competition between two cell types under cell cycle regulation with apoptosis (2022)
  • Author(s): Jintao Li
  • Organizer: American Physical Society (APS) March Meeting 2022
  • Int'l Joint Research
• [Presentation] Collective Dynamics of Quincke Rollers with Fully Resolved Hydrodynamics (2022)
  • Author(s): Shun Imamura
  • Organizer: American Physical Society (APS) March Meeting 2022
  • Int'l Joint Research
• [Presentation] Rational policy design for epidemics (2022)
  • Author(s): Simon K. Schnyder
  • Organizer: American Physical Society (APS) March Meeting 2022
  • Int'l Joint Research
• [Presentation] Nash Neural Networks (2022)
  • Author(s): John J. Molina
  • Organizer: American Physical Society (APS) March Meeting 2022
  • Int'l Joint Research
• [Presentation] Rational policy design for epidemics (2021)
  • Author(s): Simon K. Schnyder
  • Organizer: 27th International Conference on Computing in Economics and Finance
  • Int'l Joint Research
• [Presentation] DNS of self-propelled particles (2021)
  • Author(s): Ryoichi Yamamoto
  • Organizer: RIMS Workshop Mathematical Mechanobiology
  • Int'l Joint Research / Invited
• [Presentation] Direct numerical simulation of Quincke rollers (2021)
  • Author(s): Ryoichi Yamamoto
  • Organizer: 11th Liquid Matter Conference
  • Int'l Joint Research
• [Presentation] Cell migration and colony growth in a monolayer of model cells (2021)
  • Author(s): Simon K. Schnyder
  • Organizer: 11th Liquid Matter Conference
  • Int'l Joint Research
• [Presentation] The role of the cell cycle in collective cell dynamics (2021)
  • Author(s): Jintao Li
  • Organizer: Physics meets Biology 2021
  • Int'l Joint Research
• [Presentation] Rational policy design for epidemics (2021)
  • Author(s): Simon K. Schnyder
  • Organizer: 24.5th Workshop on Economics with Heterogeneous Interacting Agents 2021
  • Int'l Joint Research
• [Presentation] Role of the Cell Cycle in Collective Cell Dynamics (2021)
  • Author(s): Simon K. Schnyder
  • Organizer: RIMS Workshop on Mathematical Mechanobiology
• [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
• [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
• [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
• [Presentation] Role of the Cell Cycle in Collective Cell Dynamics (2021)
  • Author(s): Simon K. Schnyder
  • Organizer: Active Matter Workshop 2022
• [Presentation] Mechanical competition between different cell types (2021)
  • Author(s): Jintao Li
  • Organizer: Active Matter Workshop 2022
• [Presentation] A mechano-chemical cell cycle for growing cell colonies (2021)
  • Author(s): Simon Schnyder
  • Organizer: American Physical Society (APS) March Meeting
  • 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
• [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
• [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
• [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
• [Remarks] Soft Matter Engineering Lab.
  • URL: https://sm.cheme.kyoto-u.ac.jp/
• [Remarks] KAPSEL-5 HP
  • URL: https://kapsel-dns.com/v5/
• [Remarks] Welcome to KAPSEL-5 HP
  • URL: https://kapsel-dns.com/v5/
• [Remarks] Welcome to KAPSEL-4 HP
  • URL: https://kapsel-dns.com/v4/
• [Remarks] KAPSEL HP
  • URL: https://kapsel-dns.com/