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Solving Geometrical Puzzles by the True Slime Mold and Its Intracellular Computational Algorithm

Research Project

Project/Area Number 15300098
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionHokkaido University

Principal Investigator

UEDA Tetsuo (2004-2006)  Hokkaido University, Research Institute for Electronic Science., Professor, 電子科学研究所, 教授 (20113524)

中垣 俊之 (2003)  北海道大学, 電子科学研究所, 助教授 (70300887)

Co-Investigator(Kenkyū-buntansha) NAKAGAKI Toshiyuki  Hokkaido University, Research Institute for Electronic Science, Associate Professor, 電子科学研究所, 助教授 (70300887)
TAKAGI Seiji  Hokkaido University, Research Institute for Electronic Science, Assistant Professor, 電子科学研究所, 助手 (80372259)
NISHIURA Yasumasa  Hokkaido University, Research Institute for Electronic Science, Professor, 電子科学研究所, 教授 (00131277)
KOBAYASHI Ryo  Hiroshima University, Graduate School of Science, Professor, 大学院理学研究科, 教授 (60153657)
上田 哲男  北海道大学, 電子科学研究所, 教授 (20113524)
高橋 健吾  北海道大学, 電子科学研究所, 研究機関研究員
Project Period (FY) 2003 – 2006
Project Status Completed (Fiscal Year 2006)
Budget Amount *help
¥16,600,000 (Direct Cost: ¥16,600,000)
Fiscal Year 2006: ¥4,100,000 (Direct Cost: ¥4,100,000)
Fiscal Year 2005: ¥4,100,000 (Direct Cost: ¥4,100,000)
Fiscal Year 2004: ¥4,100,000 (Direct Cost: ¥4,100,000)
Fiscal Year 2003: ¥4,300,000 (Direct Cost: ¥4,300,000)
KeywordsTrue slime mold / coupled oscillators / cellular intelligence / mathematical modeling / intracellular computation / self-organization / cellular algorithm / cell behavior / 粘膜 / 真正粘菌 / Physarum / 細胞行動 / 細胞リズム / アメーバ運動 / 結合振動子系 / 細胞インテリジェンス / アメーバ行動 / スモールワールドネットワーク / ネットワーク最適化 / パターン形成 / 動物行動学
Research Abstract

With use of the single giant amoeboid cell of the Physarum plasmodium, we performed unconventional experiments concerning cellular intelligence and also constructed mathematical models based on nonlinear intracellular dynamics for clarifying computational algorithm. (1) The organism solved such geometrical puzzles as maze problems, Steiner problems, Fermart problems. (2) The formation of vein networks was governed by the trade-off among minimum path-length, assurance for not-breaking apart, and minimum danger, etc. (3) Mathematical models were constructed based on a coupled oscillators where the conservation of mass and the regional difference of the visco-elastic properties were taken into account. The model simulated synchronous oscillation patterns observed in the Physarum. (4) A mathematical model was constructed by taking into adaptive mechanism for the formation of veins. The model simulated maze solving by the Physarum, Steiner problems and Fermart problems.

Report

(5 results)
  • 2006 Annual Research Report   Final Research Report Summary
  • 2005 Annual Research Report
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • Research Products

    (57 results)

All 2007 2006 2005 2004 2003 Other

All Journal Article (40 results) Book (11 results) Publications (6 results)

  • [Journal Article] Mathematical model for adaptive transport network in path finding by true slime mold2007

    • Author(s)
      Tero, A., Kobayashi, R., Nakagaki, T.
    • Journal Title

      Journal of Theoretical Biology 244

      Pages: 553-564

    • NAID

      120000875271

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Indecisive behavior of amoeba crossing an environmental barrier2007

    • Author(s)
      Takagi, S., Nishiura, Y., Nakagaki, T., Ueda, T., K.-I.Ueda
    • Journal Title

      WSPC-Proceedings (in press)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Dispersion relation in oscillatory reaction-diffusion systems with self-consistent flow in true slime mold2007

    • Author(s)
      Yamada, H., Nakagaki, T., Ruth E.Baker, Philip K.Maini
    • Journal Title

      Journal of Mathematical Biology (to be published)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Indecisive behavior of amoeba crossing an environmental barrier2007

    • Author(s)
      Takagi, S., Nishiura, Y., Nakagaki, T., Ueda, T., K.-I.Ueda
    • Journal Title

      Proceeding of Topological Aspects of Critical Systems and Networks (to be published)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Effects of amount of food on pathselection in the transport network of an amoeboid organsim2007

    • Author(s)
      Nakagaki, T, Saigusa, T., Tero, A., Kobayashi, R.
    • Journal Title

      Proceeding of Topological Aspects of Critical Systems and Networks (to be published)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Mathematical model for adaptive transport network in path finding by true slime mold2007

    • Author(s)
      Tero, A., Kobayashi, R., Nakagaki, T.
    • Journal Title

      Journal of Theoretical Biology, Vol. 244

      Pages: 553-564

    • NAID

      120000875271

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Indecisive behavior of amoeba crossing an environmental barrier2007

    • Author(s)
      Takagi, S., Nishiura, Y., Nakagaki, T., Ueda, T., K.-I.Ueda.
    • Journal Title

      WSPC-Proceedings (in press)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Mathematical model for adaptive transport network in path finding by true slime mold2007

    • Author(s)
      Atsushi Tero, Ryo Kobayashi, Toshiyuki Nakagaki
    • Journal Title

      Journal of Theoretical Biology 244

      Pages: 553-564

    • NAID

      120000875271

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Super water-repellent surfaces with fractal structures and their potential application to biological studies.2006

    • Author(s)
      Yan, H., Shiga, H., Ito, E., Nakagaki, T., Takagi, S., Ueda, T.
    • Journal Title

      Colloids and Surfaces A : Physicochem.Eng.Aspects 284-285

      Pages: 490-494

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Multiple Oscillations in Changing Cell Shape by the Plasmodium of Physarum polycephalum : general formula governing oscillatory phenomena by the Physarum plasmodium.2006

    • Author(s)
      Kakiuchi, Y., Ueda, T.
    • Journal Title

      Biological Rhythm 37

      Pages: 137-146

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Annual Research Report 2006 Final Research Report Summary
  • [Journal Article] Mathematical model for rhythmic amoeboid movement in the true slime mold2006

    • Author(s)
      Kobayashi, R., Tero, A., Nakagaki, T.
    • Journal Title

      Journal of Mathematical Biology 53

      Pages: 273-286

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Physarum solver-a biologically inspired method for road-network navigation-2006

    • Author(s)
      Tero, A., Kobayashi, R., Nakagaki, T.
    • Journal Title

      Physica A 363

      Pages: 115-119

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Super Water-Repellent Surfaces with Fractal Structures and their Potential Application to Biological Studies2006

    • Author(s)
      Yan, H., Shiga, H., Ito, E., Nakagaki, T., Takagi, S., Ueda, T., Tsujii, K.
    • Journal Title

      Colloid. Surf. A 284-285

      Pages: 115-119

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Super water-repellent surfaces with fractal structures and their potential application to biological studies."2006

    • Author(s)
      Yan, H., Shiga, H., Ito, E., Nakagaki, T., Takagi, S., Ueda, T., Tsujii, K.
    • Journal Title

      Colloids and Surfaces A : Physicochem.Eng.Aspects 284- 285

      Pages: 490-494

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Physarum solved -a biologically inspired method for road-network navigation-2006

    • Author(s)
      Tero, A., Kobayashi, R., Nakagaki, T.
    • Journal Title

      Physica A, Vol. 363

      Pages: 115-119

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Super Water-Repellent Surfaces with Fractal Structures and their Potential Application to Biological Studies2006

    • Author(s)
      Yan, H., Shiga, H., Ito, E., Nakagaki, T., Takagi, S., Ueda, T., Tsujii, K.
    • Journal Title

      Colloid. Surf. A, Vol. 284-285

      Pages: 115-119

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Super water-repellent surfaces with fractal structures and their potential application to biological studies.2006

    • Author(s)
      Yan, H., Shiga, H., Ito, E., Nakagaki, T., Takagi, S., Ueda, T., Tsujii, K.
    • Journal Title

      Colloids and Surfaces A : Physicochem.Eng.Aspects 284-285

      Pages: 490-494

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Mathematical model for rhythmic amoeboid movement in the true slime mold2006

    • Author(s)
      Ryo Kobayashi, Atsushi Tero, Toshiyuki Nakagaki
    • Journal Title

      Journal of Mathematical Biology 53

      Pages: 273-286

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Physarum solver-a biologically inspired method for road-network navigation2006

    • Author(s)
      Atsushi Tero, Ryo Kobayashi, Toshiyuki Nakagaki
    • Journal Title

      Physica A 363

      Pages: 115-119

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Super water-repellent surfaces with fractal structures and their potential application to biological studies2006

    • Author(s)
      H.Yan, H.Shigam, E.Ito, T.Nakagaki, S.Takagi, T.Ueda, K.Tsujii
    • Journal Title

      Colloids and Surfaces A : physicochemical and engineering aspects (印刷中)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Coupled oscillator model with a conservation law in rhythmic amoeboid movements of plasmodial slime mold2005

    • Author(s)
      Tero, A., Kobayashi, R., Nakagaki, T
    • Journal Title

      Physica D 205

      Pages: 125-135

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] 粘菌のインテリジェンス : 巨大アメーバ細胞を活用した計算原理と情報統合機構の研究2005

    • Author(s)
      上田哲男
    • Journal Title

      化学と生物 43

      Pages: 445-446

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] あるアメーバ様生物の行動に見る賢さ-粘菌変形体のリズム性運動と編目体形-2005

    • Author(s)
      中垣 俊之
    • Journal Title

      科学 75

      Pages: 1393-1395

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] How does an amoeba tackle some geometrical puzzles?2005

    • Author(s)
      Nakagaki, T
    • Journal Title

      Proc. SICE Ann. Conf.

      Pages: 3537-3542

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Coupled oscillator model with a conservation law in rhythmic amoeboid movements of plasmodial slime mold2005

    • Author(s)
      Tero, A., Kobayashi, R., Nakagaki, T.
    • Journal Title

      Physica D. 205

      Pages: 125-135

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] How does an amoeba tackle some geometrical puzzles?2005

    • Author(s)
      Nakagaki, T.
    • Journal Title

      Proc. SICE Ann. Conf.

      Pages: 3537-3542

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] A coupled-oscillator model with a conservation law for the rhythmic amoeboid movements of plasmodial slime molds2005

    • Author(s)
      A.Tero, R.Kobayashi, T.Nakagaki
    • Journal Title

      Physica D 205

      Pages: 125-135

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Collective movement of epithelial cells on a collagen gel substrate2005

    • Author(s)
      H.Haga, C.Irahara, R.Kobayashi, T.Nakagaki, K.Kawabata
    • Journal Title

      Biophysical Journal 88

      Pages: 1-7

    • Related Report
      2005 Annual Research Report
  • [Journal Article] How does an amoeba tackle some geometrical puzzles?2005

    • Author(s)
      T.Nakagaki
    • Journal Title

      Proc.SICE Ann.Conf.

      Pages: 3537-3542

    • Related Report
      2005 Annual Research Report
  • [Journal Article] あるアメーバ様細胞の行動に見る賢さ-粘菌変形体のリズム性運動と編目体形-2005

    • Author(s)
      中垣俊之
    • Journal Title

      科学 75巻12号

      Pages: 1393-1395

    • Related Report
      2005 Annual Research Report
  • [Journal Article] 粘菌のインテリジェンス:巨大アメーバ細胞を活用した計算原理と情報統合機構の研究2005

    • Author(s)
      上田哲男
    • Journal Title

      化学と生物 43

      Pages: 445-446

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Obtaining multiple separate food sources : behavioral intelligence in the Physarum2004

    • Author(s)
      Nakagaki, T., Kobayashi, R., Nishiura, Y., Ueda, T.
    • Journal Title

      Proc. R. Soc. Lond. B 271

      Pages: 2305-2310

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Coupled oscillator model with a conservation law in rhythmic amoeboid movements of plasmodial slime mold2004

    • Author(s)
      Nakagaki, T., Yamada, H., Hara, M
    • Journal Title

      Biophys. Chem. 107

      Pages: 125-135

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Obtaining multiple separate food sources : behavioral intelligence in the Physarum.2004

    • Author(s)
      Nakagaki, T., Kobayashi, R., Nishiura, Y., Ueda, T.
    • Journal Title

      Proc. R. Soc. Lond B 271

      Pages: 2305-2310

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Smart network solutions in an amoeboid organism2004

    • Author(s)
      Nakagaki, T., Yamada, H., Hara, M.
    • Journal Title

      Biophys. Chem 107

      Pages: 1-5

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Obtaining multiple separate food sources : behavioural intelligence in the Physarum plasmodium2004

    • Author(s)
      Nakagaki, T., Kobayashi, R., Nishiura, Y., Ueda, T.
    • Journal Title

      Proceedings of The Royal Society B : Biological Sciences 271,1554

      Pages: 2305-2310

    • NAID

      120001720435

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Dispersion relation in oscillatory re action-diffusion systems with self-consistent flow in true slime mold

    • Author(s)
      Yamada, H., Nakagaki, T, Ruth E.Baker, Philip K.Maini
    • Journal Title

      Journal of Mathematical Biology (to be published)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Indecisive behavior of amoeba crossing an environmental barrier

    • Author(s)
      Takagi, S., Nishiura, Y., Nakagaki, T., Ueda, T., K.-I.Ueda
    • Journal Title

      Proceeding of Topological Aspects of Critical Systems and Networks (to be published)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] Effects of amount of food on pathselection in the transport network of an amoeboid organism

    • Author(s)
      Nakagaki, T, Saigusa, T., Tero, A., Kobayashi, R.
    • Journal Title

      Proceeding of Topological Aspects of Critical Systems and Networks, to be published (to be published)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Journal Article] A coupled-oscillator model with a conservation law for the rhythmic amoeboid movements of plasmodial slime mold.

    • Author(s)
      A.Tero, R.Kobayashi, T.Nakagaki
    • Journal Title

      Physica D (印刷中)

    • Related Report
      2004 Annual Research Report
  • [Book] 「生物物理学ハンドブック」生物のパターン形成と情報機能 : 反応拡散カップリング2007

    • Author(s)
      上田哲男
    • Total Pages
      3
    • Publisher
      朝倉書店
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Book] 「プラントミメティックスー-植物に学ぶ」粘菌の行動と形態形成 : パターンダイナミクスと情報創発2006

    • Author(s)
      上田哲男
    • Total Pages
      8
    • Publisher
      株式会社 エヌ・ティー・エス
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Book] 粘菌の行動と形態形成 : パターンダイナミクスと情報創発(「プラントミメティックス--植物に学ぶ」監修、甲斐 昌一、森川 弘道)2006

    • Author(s)
      上田哲男, 高木清二
    • Total Pages
      8
    • Publisher
      株式会社 エヌ・ティー・エス
    • Related Report
      2006 Annual Research Report
  • [Book] An intelligent slime mold : a self-organizing system of cell shape and information. In "Networks of Interacting Machines : production organization in complex industrial systems and biological cells"2005

    • Author(s)
      Ueda, T
    • Total Pages
      26
    • Publisher
      World Scientific Publishing Co.
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Book] An intelligent slime mold : a self-organizing system of cell shape and information, Networks of Interacting machines : production organization in complex industrial systems and biological cells2005

    • Author(s)
      T.Ueda
    • Total Pages
      267
    • Publisher
      World Scientific Publishing Company
    • Related Report
      2005 Annual Research Report
  • [Book] 数理生理学2005

    • Author(s)
      中垣俊之, 高木清二 他7名 訳
    • Total Pages
      827
    • Publisher
      日本評論社
    • Related Report
      2004 Annual Research Report
  • [Book] 「形の科学事典」粘菌細胞の変形 : サイズ制御とリズム発現に伴う細胞骨格の構築2004

    • Author(s)
      上田哲男
    • Total Pages
      3
    • Publisher
      朝倉書店
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Book] 脳のフィジックス(脳機能と力学系)(長谷川建治・吉岡亨編集)2004

    • Author(s)
      上田哲男
    • Total Pages
      38
    • Publisher
      共立出版
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Book] 形の科学百科事典(粘菌変形体の形と機能)(アメーバの形と機能)(形の科学会編集)2004

    • Author(s)
      中垣俊之
    • Total Pages
      4
    • Publisher
      朝倉書店
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Book] かたちの事典(真正粘菌)(高木隆司編著)2003

    • Author(s)
      中垣俊之
    • Total Pages
      2
    • Publisher
      丸善
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Book] Traffic and Granular Flow '01 "Oscillation patterns in cytoplasmic networks of the Physarum plasmodium" (edited by M. Fukui, Y. Sugiyama,M. Schreckenberg, D. E. Wolf)2003

    • Author(s)
      Yamada, H.
    • Total Pages
      6
    • Publisher
      Springer-Verlag
    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2006 Final Research Report Summary
  • [Publications] T.Nakagaki, H.Yamada, M.Hara: "Smart network solutions in an amoeboid organism"Biophys.Chem.. 107. 1-5 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] H.Yamada, R.Tanaka, T.Nakagaki: "Sequences of symmetry-breaking in phyllotactic transitions"Bullet.Math.Biol.. (in press). (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] 小林 亮, 中垣 俊之: "真性粘菌変形体の運動の数理モデル"京都大学 数理解析研究所講究録. 1305. 8-14 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 中垣 俊之, 小林 亮: "粘菌変形体の流路ネットワークの形態形成"京都大学 数理解析研究所講究録. 1305. 1-7 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] H.Yamada, T.Nakagaki: "Oscillation patterns in cytoplasmic networks of the Physarum plasmodium"Traffic and Granular Flow '01 (Springer-Verlag). 536-568 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 田中 玲子, 山田 裕康, 高松 敦子, 中垣 俊之 訳: "ゴルビツキー/スチュアート 対称性の破れとパターン形成の数理"丸善. 562 (2003)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2016-04-21  

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