Simulations of tumor grawth with cell division

• Project/Area Number: 26610131
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• 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(Renkei-kenkyūsha): MOLINA John 京都大学, 大学院工学研究科, 助教 (20727581)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2014: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
• Keywords: シミュレーション / アクティブマター / 細胞遊走 / 生体組織 / 細胞分裂 / 腫瘍

Outline of Final Research Achievements

We developed a cell model by connecting multiple particles with springs that can be applicable for crawling cells on a substrate by changing their shapes. The effects of cell contraction due to myosin and cell adhesion due to adhesive proteins against the substrate are implemented into the model. Furthermore, the spatio-temporal evolutions of the densities of myosin and PIP3 molecules have been resolved by using a reaction-diffusion equation on cell membrane. The present model allows us to bridge between different scales from molecules to shape change of cells.

Research Products

• [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
• [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] 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] 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] 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] 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] 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
  • 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] 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] Collective motion of active swimming particles analogous to acoustic wave propagation (2015)
  • Author(s): Ryoichi Yamamoto
  • Organizer: Pacifichem2015
  • Place of Presentation: Hawaii, USA
  • Year and Date: 2015-12-15
  • Int'l Joint Research
• [Presentation] Emergence of collective dynamics in active biological systems (2015)
  • Author(s): Ryoichi Yamamoto
  • Organizer: 26th CDB Meeting "Mechanistic Perspectives of Multicellular Organization"
  • Place of Presentation: Kobe, Japan
  • Year and Date: 2015-09-08
  • Int'l Joint Research
• [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] 化学工学会 (2017)
  • Author(s): 山本量一、大山倫弘、John J. Molina、Simon K. Schnyder
  • Publisher: ソフトマターのモデリング：非平衡系・生物系への挑戦
• [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