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

• Project/Area Number: 26247069
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biological physics/Chemical physics/Soft matter physics
• Research Institution: Kyoto 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: ¥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.

Research Products

• [Int'l Joint Research] Helmholtz-Zentrum Dresden-Rossendorf(Germany)
• [Int'l Joint Research] University of Mainz(Germany)
• [Int'l Joint Research] Institut Curie(France)
• [Journal Article] Monte Carlo Simulation for kinetic chemotais model: An application to the traveling population wave (2017)
  • Author(s): Shugo Yasuda
  • Journal Title: Journal of Computational Physics Volume: 330 Pages: 1022-1042
  • DOI: 10.1016/j.jcp.2016.10.066
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Simulations of model micro-swimmers with fully resolved hydrodynamics (2017)
  • Author(s): Norihiro Oyama, John J. Molina, and Ryoichi Yamamoto
  • Journal Title: J. Phys. Soc. Jpn. Volume: -
  • 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
  • Peer Reviewed
• [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
• [Journal Article] Purely hydrodynamic origin for swarming of swimming particles (2016)
  • 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
  • Peer Reviewed
• [Journal Article] Rheological evaluation of colloidal dispersions using the smooth profile method: formulation and applications (2016)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Synchronized molecular-dynamics simulation for the thermal lubrication of a polymeric liquid between parallel plates (2016)
  • 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
  • Peer Reviewed
• [Journal Article] Dynamic polarization of a charged colloid in an oscillating electric field (2015)
  • 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
  • Peer Reviewed
• [Journal Article] Simulation studies of microstructure of colloids in sedimentation (2015)
  • 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
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Multiscale simulation for thermo-hydrodynamic lubrication of a polymeric liquid between parallel plate (2015)
  • 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
  • Peer Reviewed
• [Journal Article] Attachment of solid elongated particles on the surface of a stationary gas bubble (2015)
  • 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
  • Peer Reviewed
• [Journal Article] Mutual information reveals multiple structural relaxation mechanisms in a model glassformer (2015)
  • 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
  • Peer Reviewed
• [Journal Article] Dynamic Electrophoresis of Charged Colloids in an Alternating Electric Field (2014)
  • Author(s): Chunyu Shih and Ryoichi Yamamoto
  • Journal Title: Phys. Rev. E Volume: 89 Issue: 6
  • DOI: 10.1103/physreve.89.062317
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Direct Numerical Simulations of Sedimenting Spherical Particles at Finite Reynolds Number (2014)
  • 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
  • Peer Reviewed
• [Journal Article] Synchronized molecular dynamics simulation via macroscopic heat and momentum transfer: an application to polymer lubrication (2014)
  • Author(s): Shugo Yasuda and Ryoichi Yamamoto
  • Journal Title: Phys. Rev. X Volume: 4 Issue: 4
  • DOI: 10.1103/physrevx.4.041011
  • NAID: 120005555514
  • Peer Reviewed / Open Access
• [Presentation] Collective Motion of Cells Crawling on a Substrate (2016)
  • Author(s): Ryoichi Yamamoto
  • Organizer: The 4th International Conference on Molecular Simulation (ICMS2016)
  • Place of Presentation: Shanghai, China
  • Year and Date: 2016-10-23
  • Int'l Joint Research / Invited
• [Presentation] A particle-based minimal model for crawling and dividing cells on substrate (2016)
  • Author(s): Ryoichi Yamamoto
  • Organizer: The 4th International Soft Matter Conference
  • Place of Presentation: Grenoble, France
  • Year and Date: 2016-09-12
  • Int'l Joint Research
• [Presentation] A dynamical phase transition of crawling cells from coherent motion to clustering driven by the shape of the cells (2016)
  • Author(s): Simon Schnyder
  • Organizer: Summer School 2016 Active Complex Matter
  • Place of Presentation: Cargese, France
  • Year and Date: 2016-07-12
  • 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
  • Invited
• [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
  • Place of Presentation: Kyoto, Japan
  • 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
  • Invited
• [Presentation] Collective motion of active swimming particles analogous to acoustic wave propagation (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Emergence of collective dynamics in active biological systems (2015)
  • 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
  • Int'l Joint Research
• [Presentation] Anomalous wave-propagation in an active swimmer dispersion (2015)
  • 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
  • Int'l Joint Research / Invited
• [Presentation] Simulating Particles Moving through Fluids (2015)
  • 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
  • Invited
• [Presentation] DNS of colloidal dispersions using the smoothed profile method: formulation and applications (2015)
  • 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
  • Invited
• [Presentation] Direct Numerical Simulations (DNS) of Swimming Particles (2014)
  • 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
  • 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
• [Remarks] KAPSEL HomePage
  • URL: http://www-tph.cheme.kyoto-u.ac.jp/kapsel/
• [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