微生物集団が示す特異な動的秩序形成機構の解明とその制御

• Project Area: Dynamical ordering of biomolecular systems for creation of integrated functions
• Project/Area Number: 16H00765
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Science and Engineering
• 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): 2016-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2017: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000); Fiscal Year 2016: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
• Keywords: シミュレーション / 微生物 / 細胞 / 集団運動

Outline of Annual Research Achievements

本研究は「微生物集団が示す特異なダイナミクスの解明とそのハンドリング機構の基礎付け」を目的とするものであり，平成29年度は以下の成果を得ることに成功した．
細胞の大規模な集団運動のメカニズムは大きな謎となっており，生物学・医学・物理学などの様々な分野において研究者の興味を引きつけている．一般的に，細胞はその内部で起こる複雑な生化学プロセスを利用して周りの状況に応答する．例えば，複数の細胞が接触するような状況が発生すると，お互いに避けるような運動が応答として得られる．この現象は「細胞遊走の接触阻害（Contact inhibition of locomotion）」と呼ばれ，細胞の集団運動の発現に重要な役割を果たしていると信じられている．本研究では，非常に簡単な細胞モデルを用いて，実際の細胞集団が示す種々の複雑な集団運動を再現することに成功した．このモデルでは，基板上を遊走する細胞をバネでつながった２つの円盤として表現し，細胞の伸びに依存した推進力を導入することで接触阻害の効果を取り入れている．このような簡単なモデルにも関わらず，細胞が他の細胞と接触すると減速することや，基板上の細胞数密度の増加とともに不動状態に陥ることを正しく再現し，細胞の形が集団運動に大きな影響を与えることを示した．さらに，前部の円盤が後部より大きい場合に多数の細胞が同じ方向に集団移動が出現しやすいことを見出し，実際の遊走細胞の形との類似性を指摘した．

Research Progress Status

29年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

29年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] Modeling of Cells which Migrate and Proliferate on a Substrate (2018)
  • Author(s): 山本 量一、Molina John J.、Schneider Simon K.
  • Journal Title: Journal of Computer Chemistry, Japan Volume: 17 Issue: 1 Pages: 14-19
  • DOI: 10.2477/jccj.2018-0003
  • NAID: 130006528633
  • ISSN: 1347-1767, 1347-3824
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Mechanics of Cell Crawling by Means of Force-free Cyclic Motion (2018)
  • Author(s): Tarama Mitsusuke、Yamamoto Ryoichi
  • Journal Title: Journal of the Physical Society of Japan Volume: 87 Issue: 4 Pages: 044803-044803
  • DOI: 10.7566/jpsj.87.044803
  • NAID: 210000134796
  • Peer Reviewed
• [Journal Article] Collective motion of cells crawling on a substrate: roles of cell shape and contact inhibition (2017)
  • Author(s): Schnyder Simon K.、Molina John J.、Tanaka Yuki、Yamamoto Ryoichi
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 5163-5163
  • DOI: 10.1038/s41598-017-05321-0
  • Peer Reviewed / Open Access
• [Journal Article] Simulations of Model Microswimmers with Fully Resolved Hydrodynamics (2017)
  • Author(s): Oyama Norihiro、Molina John J.、Yamamoto Ryoichi
  • Journal Title: Journal of the Physical Society of Japan Volume: 86 Issue: 10 Pages: 101008-101008
  • DOI: 10.7566/jpsj.86.101008
  • Peer Reviewed
• [Journal Article] Do hydrodynamically assisted binary collisions lead to orientational ordering of microswimmers? (2017)
  • Author(s): Oyama Norihiro、Molina John Jairo、Yamamoto Ryoichi
  • Journal Title: The European Physical Journal E Volume: 40 Issue: 11 Pages: 95-95
  • DOI: 10.1140/epje/i2017-11586-4
  • Peer Reviewed
• [Journal Article] Microstructure of rod like sedimenting particles: Direct numerical simulations (2017)
  • Author(s): Mehdi Samia、Hamid Adnan、Ullah Atta、Yamamoto Ryoichi
  • Journal Title: Proc. 14th International Bhurban Conference on Applied Sciences and Technology Volume: 1 Pages: 622-626
  • DOI: 10.1109/ibcast.2017.7868115
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Direct numerical simulation of a single particle attachment on a stationary immersed bubble (2016)
  • Author(s): G. Lecrivain, R. Yamamoto, U. Hampel, and T. Taniguchi
  • Journal Title: Physics of Fluids Volume: 28 Issue: 8 Pages: 083301-083301
  • DOI: 10.1063/1.4960627
  • Peer Reviewed / Int'l Joint Research
• [Presentation] Particle-based model for crawling and proliferating cells with contact inhibitions (2018)
  • Author(s): Ryoichi Yamamoto
  • Organizer: 2018 Aspen Winter Conference on Fundamental Problems in Active Matter
  • Int'l Joint Research
• [Presentation] Colony growth of cells on a substrate (2018)
  • Author(s): Simon Schnyder
  • Organizer: Active Matter Workshop
• [Presentation] Mechanosensitivity of crawling cells (2018)
  • Author(s): John Molina
  • Organizer: Active Matter Workshop
• [Presentation] 基盤上を運動する細胞の力学モデル (2018)
  • Author(s): 多羅間充輔
  • Organizer: 研究会「凝縮系の理論化学」
  • Invited
• [Presentation] 細胞分裂を考慮した自発運動粒子モデルによる創傷治癒のシミュレーション (2018)
  • Author(s): 松田拓也
  • Organizer: 研究会「凝縮系の理論化学」
  • Invited
• [Presentation] Particle-based Model for Crawling and Proliferating Cells with Contact Inhibitions (2018)
  • Author(s): 山本量一
  • Organizer: 新学術領域研究「動的秩序と機能」第6回国際シンポジウム
• [Presentation] Mechanosensitivity of Crawling Cells (2017)
  • Author(s): John Molina
  • Organizer: Complex Motion in Fluids
  • Int'l Joint Research
• [Presentation] Mechanosensitivity of Crawling Cells (2017)
  • Author(s): John Molina
  • Organizer: International Symposium on Fluctuation and Structure out of Equilibrium
  • Int'l Joint Research
• [Presentation] 微生物集団が示す特異な動的秩序形成機構の解明とその制御 (2017)
  • Author(s): 山本量一
  • Organizer: 科研費新学術領域研究「動的秩序と機能」2017全体班会議
• [Presentation] A par-cle-based minimal model for crawling and prolifera-ng cells on substrate (2017)
  • Author(s): 山本量一
  • Organizer: 日本生物物理学会第55回年会
  • Invited
• [Presentation] 微生物集団が示す特異な動的秩序形成機構の解明とその制御 (2016)
  • Author(s): 山本量一
  • Organizer: 科研費新学術「動的秩序と機能」2016全体班会議
• [Presentation] Understanding hydrodynamic polar ordering in swimmer dispersio by binary collisions (2016)
  • Author(s): Norihiro Oyama
  • Organizer: Microswimmers international conference 2016
  • Int'l Joint Research
• [Presentation] The emergence of collective motion: from glass to biological systems (2016)
  • Author(s): Ryoichi Yamamoto
  • Organizer: CerSJ-GOMD Joint Symposium on Glass Science and Technologies
  • Int'l Joint Research / Invited
• [Presentation] Collective Motion of Cells Crawling on a Substrate (2016)
  • Author(s): Ryoichi Yamamoto
  • Organizer: The 4th International Conference on Molecular Simulation (ICMS2016)
  • Int'l Joint Research / Invited
• [Presentation] 自己組織化する細胞集団のモデリングとシミュレーション (2016)
  • Author(s): 山本量一
  • Organizer: 化学工学会 第48回秋季大会特別シンポジウム「SP-3 新時代に向けたバイオプロセスイノベーション」
  • Invited
• [Book] Chapter 8 of "Computer Simulation of Polymeric Materials: Applications of the OCTA System" (2016)
  • Author(s): John. J. Molina and Ryoichi Yamamoto
  • Total Pages: 18
  • Publisher: Springer
  • ISBN: 9811008140
• [Remarks] KAPSEL HomePage
  • URL: http://www-tph.cheme.kyoto-u.ac.jp/kapsel/
• [Remarks] KAPSEL Home Page
  • URL: http://www-tph.cheme.kyoto-u.ac.jp/kapsel/
• [Funded Workshop] Structured Soft Interfaces: Caught Between Multi-Scale Simulation and Application (2017)