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Kinetic modeling and multiscale mechanism in collective behaviors of microorganisms

Research Project

Project/Area Number 15KT0110
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Mathematical Sciences in Search of New Cooperation
Research InstitutionUniversity of Hyogo

Principal Investigator

Yasuda Shugo  兵庫県立大学, シミュレーション学研究科, 准教授 (70456797)

Co-Investigator(Kenkyū-buntansha) 青木 一生  京都大学, 工学研究科, 名誉教授 (10115777)
西畑 伸也  東京工業大学, 情報理工学院, 教授 (80279299)
Co-Investigator(Renkei-kenkyūsha) YAMAMOTO Ryoichi  京都大学, 工学研究科, 教授 (10263401)
Project Period (FY) 2015-07-10 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2017: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywords自己組織化 / 走化性バクテリア / 運動論 / メゾスコピック / 計算生物学 / 計算科学 / 数理生物学 / マルチスケール / 数理科学 / 微生物
Outline of Final Research Achievements

We carried out numerical and theoretical studies on the traveling wave and aggregation of bacteria, which are fundamental problems in the cluster formation dynamics, based on a kinetic chemotaxis model.
In the traveling wave problem, we theoretically obtained a dispersion relation of the population traveling wave of bacteria and numerically uncovered the variety of traveling wave solutions. In the aggregation problem, we theoretically obtained a linear instability condition, under which the bacteria create patterns from a uniform constant state. We also developed a new mesoscopic simulation method, i.e., a Monte Carlo simulation for chemotactic bacteria. The accuracy and validity of the Monte Carlo method has been established throughout comparisons of theoretical and experimental results.
This study fundamentally contributes to establishing a new academic research field, i.e., the study of active fluids.

Report

(4 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (35 results)

All 2018 2017 2016 2015 Other

All Int'l Joint Research (4 results) Journal Article (6 results) (of which Int'l Joint Research: 2 results,  Open Access: 3 results,  Peer Reviewed: 4 results,  Acknowledgement Compliant: 1 results) Presentation (22 results) (of which Int'l Joint Research: 17 results,  Invited: 17 results) Remarks (3 results)

  • [Int'l Joint Research] Sorbonne University/Institut Camille Jordan/CNRS(フランス)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Kaiserslautern(ドイツ)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] Laboratoire Jacques-Louis Lions, UPMC(France)

    • Related Report
      2016 Research-status Report
  • [Int'l Joint Research] Pierre and Marie Curie University/CNRS, Lyon(フランス)

    • Related Report
      2015 Research-status Report
  • [Journal Article] Numerical analysis on the traveling pulse in a kinetic chemotaxis equation2018

    • Author(s)
      S. Yasuda
    • Journal Title

      RIMS Kokyuroku

      Volume: 2038 Pages: 130-139

    • Related Report
      2017 Annual Research Report
    • Open Access
  • [Journal Article] Traveling wave and aggregation in a flux-limited Keller-Segel model2018

    • Author(s)
      V. Calvez, B. Perthame, and S. Yasuda
    • Journal Title

      Kinet. Relat. Mod.

      Volume: 印刷中

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Solidification of a simple liquid near wall in high-speed shear flows2018

    • Author(s)
      S. Yasuda and R. Ookawa
    • Journal Title

      Journal of Physics: Conference Series

      Volume: 印刷中

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Stiff-response-induced instability for chemotactic bacteria and flux-limited Keller-Segel equation2018

    • Author(s)
      B. Perthame and S. Yasuda
    • Journal Title

      Nonlinearity

      Volume: 印刷中

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] パリ滞在記2018

    • Author(s)
      安田修悟
    • Journal Title

      分子シミュレーション研究会会誌アンサンブル

      Volume: 印刷中

    • Related Report
      2017 Annual Research Report
    • Open Access
  • [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 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] 走化性運動論モデルの不安定性とパターン形成2018

    • Author(s)
      安田修悟
    • Organizer
      第7回計算科学連携セミナー, 非平衡現象のダイナミクス
    • Related Report
      2017 Annual Research Report
  • [Presentation] 走化性運動論モデルの不安定性とパターン形成2018

    • Author(s)
      安田修悟
    • Organizer
      非線形現象の数値シミュレーションと解析 2018
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Traveling wave and aggregation in a flux-limited Keller-Segel model2018

    • Author(s)
      S. Yasuda
    • Organizer
      The 12th AIMS Conference on Dynamical Systems
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Pattern formation and instability in a kinetic chemotaxis model2018

    • Author(s)
      S. Yasuda
    • Organizer
      第15回 生物数学の理論とその応用 -次世代の数理科学への展開-
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Monte Carlo method for kinetic chemotaxis model and its applications on traveling pulse and pattern formation2017

    • Author(s)
      S. Yasuda
    • Organizer
      The IHP trimester "Stochastic Dynamics Out of equilibrium"
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Self-organized pattern formation of run-and-tumble chemotactic bacteria: Instability analysis and Monte Carlo simulation2017

    • Author(s)
      S. Yasuda
    • Organizer
      Seminar at Kaiserslautern University
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Solidification of a simple liquid near wall in high-speed lubrication flows2017

    • Author(s)
      S. Yasuda and R. Ookawa
    • Organizer
      Conference on Computational Physics (CCP) 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Monte Carlo simulation for pattern formation of run-and-tumble bacteria2017

    • Author(s)
      S. Yasuda
    • Organizer
      Conference on Computational Physics (CCP) 2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Self-organized pattern formation of run-and-tumble chemotactic bacteria: Instability analysis and Monte Carlo simulation2017

    • Author(s)
      S. Yasuda
    • Organizer
      Seminar at RWTH Aachen University
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Synchronized Molecular-Dynamics simulation via global heat and momentum transport2017

    • Author(s)
      S. Yasuda
    • Organizer
      Seminar at Karlsruher Institut of Technology
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Stiff-response-induced instability of chemotactic bacteria2017

    • Author(s)
      S. Yasuda
    • Organizer
      Recent advances in kinetic equations and applications
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Self-organized pattern formation in run-and-tumble chemotactic bacteria with stiff response2017

    • Author(s)
      S. Yasuda
    • Organizer
      Seminar at Penn State University
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Self-organized pattern formation in a kinetic transport equation for chemotactic bacteria2017

    • Author(s)
      S. Yasuda
    • Organizer
      SIAM Conference on Analysis of PDE
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Self-organized pattern formation of run-and-tumble chemotactic bacteria2017

    • Author(s)
      安田修悟
    • Organizer
      日本航空宇宙学会関西支部分科会「運動論方程式、流体力学とその周辺」
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] Turing instability of kinetic chemotaxis equation2017

    • Author(s)
      Shugo YASUDA
    • Organizer
      Journee de Biologie Mathematique Laboratoire de Mathematiques Analyse Numerique et EDP Universite Paris-sud Paris-Saclay
    • Place of Presentation
      Orsay, France
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Linear instability and pattern formation in a kinetic chemotaxis equation2017

    • Author(s)
      Shugo YASUDA
    • Organizer
      Seminaire du Laboratoire Jacques-Louis Lions
    • Place of Presentation
      Paris, France
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Numerical analysis of the traveling wave on the kinetic chemotaxis model2016

    • Author(s)
      Shugo YASUDA
    • Organizer
      RIMS Workshop on Mathematical Analysis in Fluid and Gas Dynamics
    • Place of Presentation
      京都大学・数理解析研究所(京都府京都市)
    • Year and Date
      2016-07-06
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Monte Carlo simulation for kinetic chemotaxis model of bacteria2016

    • Author(s)
      Shugo YASUDA
    • Organizer
      8th Summer School “Methods & Models of Kinetic Theory” Hotel Don Pedro
    • Place of Presentation
      Porto Ercole, Italy
    • Year and Date
      2016-06-05
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Monte Carlo simulation for kinetic chemotaxis model of bacteria2016

    • Author(s)
      Shugo YASUDA
    • Organizer
      8th Edition of the Summer Schoool on "methods and models of kinetic theory"
    • Place of Presentation
      Porto Ercole(Grosseto, Italy)
    • Year and Date
      2016-06-05
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Monte Carlo simulation for kinetic chemotaxis model of bacteria2016

    • Author(s)
      Shugo YASUDA
    • Organizer
      Workshop on Kinetic Theory and Fluid Dynamics: From micro to macroscopic modeling
    • Place of Presentation
      京都大学・楽友会館(京都府京都市)
    • Year and Date
      2016-05-26
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Monte Carlo simulation for kinetic chemotaxis model of bacteria2015

    • Author(s)
      Shugo YASUDA
    • Organizer
      Workshop on "Aspects of motions in biofluid problems"
    • Place of Presentation
      京都大学(京都府京都市左京区)
    • Year and Date
      2015-10-26
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] 走化性運動論モデルに基づくバクテリアの集団移動のモンテカルロシミュレーション2015

    • Author(s)
      安田修悟
    • Organizer
      日本流体力学会 年会2015
    • Place of Presentation
      東京工業大学(東京都目黒区)
    • Year and Date
      2015-09-26
    • Related Report
      2015 Research-status Report
  • [Remarks] ORCID

    • URL

      http://orcid.org/0000-0002-1824-0032

    • Related Report
      2017 Annual Research Report 2016 Research-status Report 2015 Research-status Report
  • [Remarks] Researcher ID

    • URL

      http://www.researcherid.com/rid/C-3670-2009

    • Related Report
      2016 Research-status Report
  • [Remarks] ResercherID Tomson Reuters

    • URL

      http://www.researcherid.com/rid/C-3670-2009

    • Related Report
      2015 Research-status Report

URL: 

Published: 2015-07-14   Modified: 2019-03-29  

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