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Developments and applications of accurate simulation methods for micro particles and organisms

Research Project

Project/Area Number 26247069
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Biological physics/Chemical physics/Soft matter physics
Research InstitutionKyoto University

Principal Investigator

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

Co-Investigator(Kenkyū-buntansha) 安田 修悟  兵庫県立大学, その他の研究科, 准教授 (70456797)
Co-Investigator(Renkei-kenkyūsha) TANIGUCHI Takashi  京都大学, 大学院工学研究科, 准教授 (60293669)
MOLINA John  京都大学, 大学院工学研究科, 助教 (20727581)
Project Period (FY) 2014-06-27 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥40,430,000 (Direct Cost: ¥31,100,000、Indirect Cost: ¥9,330,000)
Fiscal Year 2016: ¥12,350,000 (Direct Cost: ¥9,500,000、Indirect Cost: ¥2,850,000)
Fiscal Year 2015: ¥13,910,000 (Direct Cost: ¥10,700,000、Indirect Cost: ¥3,210,000)
Fiscal Year 2014: ¥14,170,000 (Direct Cost: ¥10,900,000、Indirect Cost: ¥3,270,000)
Keywordsソフトマター / アクティブマター / シミュレーション / コロイド / 流体力学
Outline of Final Research Achievements

Unique nontrivial collective motions can occur in several biological systems such as swimming microorganisms and migrating cells. we investigated the dynamics of confined microswimmers in parallel plate confining walls. We found that puller swimmers exhibit wave-like modes leading to traveling density waves which bounce back and forth between the walls while pusher swimmers don’t.
We have developed also a simple particle-based minimal model for crawling cells on substrate. It mimics a real mechanics of migrating cells with the mechanisms of the contact inhibition of locomotion (CIL) in a straightforward way. The present model has been applied to simulate the collective motions of crawling cells. We found that some basic properties seen in real crawling cells have been successfully reproduced.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (33 results)

All 2017 2016 2015 2014 Other

All Int'l Joint Research (3 results) Journal Article (15 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 15 results,  Acknowledgement Compliant: 4 results,  Open Access: 1 results) Presentation (12 results) (of which Int'l Joint Research: 7 results,  Invited: 9 results) Book (1 results) Remarks (1 results) Funded Workshop (1 results)

  • [Int'l Joint Research] Helmholtz-Zentrum Dresden-Rossendorf(Germany)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] University of Mainz(Germany)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Institut Curie(France)

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Monte Carlo Simulation for kinetic chemotais model: An application to the traveling population wave2017

    • Author(s)
      Shugo Yasuda
    • Journal Title

      Journal of Computational Physics

      Volume: 330 Pages: 1022-1042

    • DOI

      10.1016/j.jcp.2016.10.066

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Simulations of model micro-swimmers with fully resolved hydrodynamics2017

    • Author(s)
      Norihiro Oyama, John J. Molina, and Ryoichi Yamamoto
    • Journal Title

      J. Phys. Soc. Jpn.

      Volume: -

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] ソフトマターのモデリング:非平衡系・生物系への挑戦2017

    • Author(s)
      山本量一、大山倫弘、John J. Molina、Simon K. Schnyder
    • Journal Title

      化学工学会誌第

      Volume: 81

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Direct numerical simulation of a single particle attachment on a stationary immersed bubble2016

    • 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

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Purely hydrodynamic origin for swarming of swimming particles2016

    • Author(s)
      Norihiro Oyama, John Jairo Molina, and Ryoichi Yamamoto
    • Journal Title

      Phys. Rev. E

      Volume: 93 Issue: 4

    • DOI

      10.1103/physreve.93.043114

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rheological evaluation of colloidal dispersions using the smooth profile method: formulation and applications2016

    • Author(s)
      John J. Molina, Kotaro Otomura, Hayato Shiba, Hideki Kobayashi, Masaki Sano, and Ryoichi Yamamoto
    • Journal Title

      J. Fluid Mech.

      Volume: 792 Pages: 590-619

    • DOI

      10.1017/jfm.2016.78

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Synchronized molecular-dynamics simulation for the thermal lubrication of a polymeric liquid between parallel plates2016

    • Author(s)
      Shugo Yasuda and Ryoichi Yamamoto
    • Journal Title

      Computers and Fluids

      Volume: 124 Pages: 185-189

    • DOI

      10.1016/j.compfluid.2015.05.018

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamic polarization of a charged colloid in an oscillating electric field2015

    • Author(s)
      Chunyu Shih, John J. Molina, and Ryoichi Yamamoto
    • Journal Title

      Molec. Phys.

      Volume: 113 Issue: 17-18 Pages: 2511-2522

    • DOI

      10.1080/00268976.2015.1059510

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Simulation studies of microstructure of colloids in sedimentation2015

    • Author(s)
      Adnan Hamid, John J. Molina, and Ryoichi Yamamoto
    • Journal Title

      Molec. Simulation

      Volume: 9 Issue: 10-12 Pages: 1-6

    • DOI

      10.1080/08927022.2014.929124

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Multiscale simulation for thermo-hydrodynamic lubrication of a polymeric liquid between parallel plate2015

    • Author(s)
      Shugo Yasuda and Ryoichi Yamamoto
    • Journal Title

      Molec. Simulation

      Volume: 9 Issue: 10-12 Pages: 1-4

    • DOI

      10.1080/08927022.2014.951639

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Attachment of solid elongated particles on the surface of a stationary gas bubble2015

    • Author(s)
      Gregory Lecrivain, Giacomo Petrucci, Uwe Hampel and Ryoichi Yamamoto
    • Journal Title

      Int. J. Multiphase Flow

      Volume: 71 Pages: 83-93

    • DOI

      10.1016/j.ijmultiphaseflow.2015.01.002

    • NAID

      120005567896

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mutual information reveals multiple structural relaxation mechanisms in a model glassformer2015

    • Author(s)
      Andrew J. Dunleavy, Karoline Wiesner, Ryoichi Yamamoto, and C. Patrick Royall
    • Journal Title

      Nature Comm.

      Volume: 6 Issue: 1

    • DOI

      10.1038/ncomms7089

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamic Electrophoresis of Charged Colloids in an Alternating Electric Field2014

    • Author(s)
      Chunyu Shih and Ryoichi Yamamoto
    • Journal Title

      Phys. Rev. E

      Volume: 89 Issue: 6

    • DOI

      10.1103/physreve.89.062317

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Direct Numerical Simulations of Sedimenting Spherical Particles at Finite Reynolds Number2014

    • Author(s)
      Adnan Hamid, John J. Molina, and Ryoichi Yamamoto
    • Journal Title

      RSC Advances

      Volume: 4 Issue: 96 Pages: 53681-53693

    • DOI

      10.1039/c4ra11025k

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Synchronized molecular dynamics simulation via macroscopic heat and momentum transfer: an application to polymer lubrication2014

    • Author(s)
      Shugo Yasuda and Ryoichi Yamamoto
    • Journal Title

      Phys. Rev. X

      Volume: 4 Issue: 4

    • DOI

      10.1103/physrevx.4.041011

    • NAID

      120005555514

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Collective Motion of Cells Crawling on a Substrate2016

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      The 4th International Conference on Molecular Simulation (ICMS2016)
    • Place of Presentation
      Shanghai, China
    • Year and Date
      2016-10-23
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A particle-based minimal model for crawling and dividing cells on substrate2016

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      The 4th International Soft Matter Conference
    • Place of Presentation
      Grenoble, France
    • Year and Date
      2016-09-12
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A dynamical phase transition of crawling cells from coherent motion to clustering driven by the shape of the cells2016

    • Author(s)
      Simon Schnyder
    • Organizer
      Summer School 2016 Active Complex Matter
    • Place of Presentation
      Cargese, France
    • Year and Date
      2016-07-12
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 自発的に運動する細胞集団の物理学的モデリング2016

    • Author(s)
      山本量一
    • Organizer
      基生研研究会「物理学は生物現象の謎を解けるか」
    • Place of Presentation
      岡崎市
    • Year and Date
      2016-01-05
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] The emergence of collective motion: from glass to biological systems2016

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      CerSJ-GOMD Joint Symposium on Glass Science and Technologies
    • Place of Presentation
      Kyoto, Japan
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ガラス転移のメカニズムを考える2016

    • Author(s)
      山本量一
    • Organizer
      第142回ニューガラス研究会
    • Place of Presentation
      大阪市
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Collective motion of active swimming particles analogous to acoustic wave propagation2015

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      The 2015 International Chemical Congress of Pacific Basin Societies (PACIFICHEM 2015)
    • Place of Presentation
      Honolulu, USA
    • Year and Date
      2015-12-12
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Emergence of collective dynamics in active biological systems2015

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      The 26th CDB Meeting "Mechanistic Perspectives of Multicellular Organization"
    • Place of Presentation
      Kobe, Japan
    • Year and Date
      2015-09-08
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Anomalous wave-propagation in an active swimmer dispersion2015

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      Japan-France Joint Seminar "New Frontiers in Non-equilibrium Physics of Glassy Materials"
    • Place of Presentation
      Kyoto, Japan
    • Year and Date
      2015-08-11
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Simulating Particles Moving through Fluids2015

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      Physics of Structural and Dynamical Hierarchy in Soft Matter
    • Place of Presentation
      Tokyo, Japan
    • Year and Date
      2015-03-16 – 2015-03-18
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] DNS of colloidal dispersions using the smoothed profile method: formulation and applications2015

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      High Performance and Parallel Computing for Materials Defects and Multiphase Flows
    • Place of Presentation
      Singapore
    • Year and Date
      2015-03-02 – 2015-03-06
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Direct Numerical Simulations (DNS) of Swimming Particles2014

    • Author(s)
      Ryoichi Yamamoto
    • Organizer
      International symposium and workshop on Computational condensed matter: advances and challenges (CompMat2014)
    • Place of Presentation
      Whitehaven, UK
    • Year and Date
      2014-09-07 – 2014-09-09
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Book] Chapter 8 of "Computer Simulation of Polymeric Materials: Applications of the OCTA System"2016

    • Author(s)
      John. J. Molina, Ryoichi Yamamoto
    • Total Pages
      18
    • Publisher
      Springer
    • Related Report
      2016 Annual Research Report
  • [Remarks] KAPSEL HomePage

    • URL

      http://www-tph.cheme.kyoto-u.ac.jp/kapsel/

    • Related Report
      2016 Annual Research Report 2015 Annual Research Report 2014 Annual Research Report
  • [Funded Workshop] Lorentz Center Workshop on "Structured Soft Interfaces: Caught Between Multi-Scale Simulation and Application"2017

    • Place of Presentation
      Letden, the Neitherlands
    • Year and Date
      2017-01-23
    • Related Report
      2016 Annual Research Report

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Published: 2014-11-20   Modified: 2018-03-22  

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