Developing Shape Language and Building a Special Purpose Computer for Simulating Abstract Chemical Systems

• Project/Area Number: 19300104
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Bioinformatics/Life informatics
• Research Institution: The University of Tokyo
• Principal Investigator: IKEGAMI Takashi The University of Tokyo, 大学院・総合文化研究科, 教授 (10211715)
• Co-Investigator(Renkei-kenkyūsha): TAIJI Makoto 理化学研究所, ゲノム科学総合研究センター, チームリーダー (10242025)
• Project Period (FY): 2007 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000); Fiscal Year 2009: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000); Fiscal Year 2008: ¥6,370,000 (Direct Cost: ¥4,900,000、Indirect Cost: ¥1,470,000); Fiscal Year 2007: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000)
• Keywords: 専用計算機 / 人工生命 / オートマトン / FPGA / タイルプロセッサー / 抽象科学 / ライフゲーム / 専用計算 / セルラオ-トマトン / 整数演算 / セルラオートマトン

Research Abstract

Based on Cellular automaton modeling, we studied artificial cell system and designed a high-speed tile integer processing circuit. As results, we reported simulations of proto-cell systems on 2 and 3 dimensions and argued robustness of living systems. As for the main result, we completed the logical design of the integer processor and emulated its performance on FPGA systems.

Research Products

• [Journal Article] Robustness in Artificial Life (2010)
  • Author(s): Silverman, E, Ikegami, T.
  • Journal Title: Int' 1 J. Bio-Inspired Computation Vol. 2 No. 3 Pages: 197-203
• [Journal Article] Mater thesis (2010)
  • Author(s): Kei Kobayashi, Self-Movement of Oil Droplets sustained by Convection Flow
  • Journal Title: University of Tokyo
• [Journal Article] Robustness in Artificial Life (2010)
  • Author(s): E.Silverman, T.Ikegami
  • Journal Title: Int.J.Bio-Inspired Computation Vol.2, No.3 Pages: 197-203
  • Peer Reviewed
• [Journal Article] Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations to periodic biomolecular systems (2009)
  • Author(s): Kikugawa, G., Apostolov, R., Kamiya, N., Taiji, M., Himeno, R., Nakamura, H., Yonezawa, Y.
  • Journal Title: J. Comput. Chem 30 Pages: 110-118
• [Journal Article] Current performance gains from utilizing the GPU or the ASIC MDGRAPE-3 within an enhanced Poisson Boltzmann approach (2009)
  • Author(s): Narumi, T., Yasuoka, K., Taiji, M., Hoefinger, S.
  • Journal Title: J. Comput. Chem 30(14) Pages: 2351-2357
• [Journal Article] Shapes and Self-Movements in Proto-Cell Systems (2009)
  • Author(s): Suzuki, T., Ikegami, T
  • Journal Title: Artificial Life 15 Pages: 59-70
• [Journal Article] Computer Architecture for Compute-Limited Scientific Models, Ph. D. Thesis (2009)
  • Author(s): Madina, D
  • Journal Title: University of Tokyo
• [Journal Article] Re Rehabilitating Biology as a Natural History (2009)
  • Author(s): Ikegami, T
  • Journal Title: Adaptive Behavior vol.17 Pages: 325-328
• [Journal Article] A novel mutliple-walk parallel algorithm for the Barnes-Hut Treecode on GPUs -towards cost effective (2009)
  • Author(s): Hamada, T., Nitadori, K., Benkrid, K., Ohno, Y., Morimoto, G., Masada, T., Shibata, Y., Oguri, K., Taiji, M.
  • Journal Title: high performance N-Body simulation, Computer Science-Research and Development 24(1-2) Pages: 21-31
• [Journal Article] Protocells as smart agents for architectural design (2009)
  • Author(s): Hanczyc, M., Ikegami, T.
  • Journal Title: Technoetic Arts 7(2) Pages: 117-120
• [Journal Article] The search for a first cell under the maximalism design principle (2009)
  • Author(s): Ikegami, T., Hanczyc, M
  • Journal Title: Journal of Technoetic Arts 70 Pages: 153-164
• [Journal Article] The Illusion of Agency (2009)
  • Author(s): Aucouturier, J. J., Ikegami, T
  • Journal Title: Two Engineering Approaches to Compromise Autonomy and Reactivity in an Artificial System Adaptive Behavior 17 Pages: 402-420
• [Journal Article] Computer Architecture for Compute-Limited Scientific Models (2009)
  • Author(s): D.Madina
  • Journal Title: PhD thesis, University of Tokyo
  • Peer Reviewed
• [Journal Article] Rehabilitating Biology as a Natural History (2009)
  • Author(s): Ikegami, T
  • Journal Title: Adaptive Behavior 17 Pages: 325-328
  • Peer Reviewed
• [Journal Article] Origin of Life and Lattice Artificial Chemistry (2009)
  • Author(s): Ono, N., Madina, D. and Ikegami
  • Journal Title: ProtoCells edby S.Rasumussen, et.al , MIT Press Pages: 197-212
  • Peer Reviewed
• [Journal Article] Shapes and Self-movements in Proto-Cell Systems , (2009)
  • Author(s): Suzuki, K., Ikegami, T.,
  • Journal Title: Artificial Life 15 Pages: 59-70
  • Peer Reviewed
• [Journal Article] Accelerating molecular dynamics simulations on PlayStation 3 platform using virtual-GRAPE programming model (2008)
  • Author(s): Narumi, T., Kameoka, S., Taiji, M., Yasuoka, K.
  • Journal Title: SIAM J. Sci. Comput 30 Pages: 3108-3125
• [Journal Article] Circuit and Physical Design of the MDGRAPE-4 on-chip network links (2008)
  • Author(s): Madina, D., Taiji, M.
  • Journal Title: the proceedings of the SLIP' 08 Pages: 59-63
• [Journal Article] From Homeostatic to Homeodynamic Self (2008)
  • Author(s): Ikegami, T, Suzuki, K
  • Journal Title: BioSystems 9 Pages: 1388-400
• [Journal Article] Circuit and physical design of the MDGRAPE-4 on-chip network links (2008)
  • Author(s): Duraid Madina and Makoto Taiji
  • Journal Title: Proceedings of the SLIP'08 Pages: 59-63
  • Peer Reviewed
• [Journal Article] Self-maintained Movements of Droplets with Convection Flow (2007)
  • Author(s): Matsuno, H., Hanczyc, M. M., Ikegami, T.
  • Journal Title: ACAL Pages: 179-188
• [Journal Article] Formal Model of Embodiment on Abstract Systems : From Hierarchy to Heterarchy. in the proceedings of ECAL (2007)
  • Author(s): Nakajima, K, Shinkai, S., Ikegami, T.
  • Journal Title: Springer-Verlag New York I Pages: 1110-1119
• [Journal Article] Self-maintained Movements of Droplets with Convection Flow. : 179-188 (2007)
  • Author(s): Hiroki Matsuno, Martin M. Hanczyc, Takashi Ikegami
  • Journal Title: the proceedings of ACAL 2007 Pages: 179-188
  • Peer Reviewed
• [Journal Article] Formal Model of Embodiment on Abstract Systems : From Hierarchy to Heterarchy (2007)
  • Author(s): Kohei Nakajima, Soya Shinkai, Takashi Ikegami
  • Journal Title: the proceedings of ECAL 2007 Pages: 1110-1119
  • Peer Reviewed
• [Journal Article] Basis for Minimal Cognition
  • Author(s): Hanczyc, M., Ikegami, T. Chemical
  • Journal Title: Artificial Life (in press)
• [Presentation] 生命とは何か、人とは何か (2009)
  • Author(s): 池上高志
  • Organizer: ダーウィン生誕200年記念ワークショップ
  • Place of Presentation: 奈良女子大
  • Year and Date: 2009-06-21
• [Presentation] Homeodynamics, Shape and Motion dynamics in Self-Moving Oil Droplets (2009)
  • Author(s): Ikegami, T
  • Organizer: "What is Evolution?" (Organized by Murase)
  • Place of Presentation: Kyoto, Japan
• [Presentation] Is Life an Emergent property? (2009)
  • Author(s): Ikegami, T.
  • Organizer: "The Origin of Life"conference (organized by Luisi Luigi)
  • Place of Presentation: San Sebastian, Spain
• [Presentation] 生命とは何か、人とは何か (2009)
  • Author(s): 池上高志
  • Organizer: ダーウィン生誕200年記念ワークショプ
  • Place of Presentation: 奈良
• [Presentation] Artificial Life is Dead (2008)
  • Author(s): Ikegami, T.
  • Organizer: Artificial Life XI
  • Place of Presentation: Winchester, UK
• [Presentation] Circuit and Physical Design of the MDGRAPE-4 on chip network links (2008)
  • Author(s): Madina, D.
  • Organizer: At the International Workshop on System level Interconnect Prediction
  • Place of Presentation: New Castle, UK
• [Presentation] Circuit and physical design of the MDGRAPE-4 on-chip network links (2008)
  • Author(s): Duraid Madina
  • Organizer: International Workshop on bystem'Level Interconnect Prediction
  • Place of Presentation: UK, NewCastle
• [Presentation] Membrane as an Interface in a Simple Metabolic Cell (2007)
  • Author(s): Suzuki, K., Ikegami, T.
  • Organizer: International Conference on Morphological Computation
  • Place of Presentation: Venezia, Italy
• [Presentation] International Conference on Morphological Computation (2007)
  • Author(s): Ikegami, T.
  • Organizer: Venezia, Italy
  • Place of Presentation: Ikegami, T. From Chaos to Cosmos
• [Presentation] From Chaos to Cosmos (2007)
  • Author(s): Ikegami, T.
  • Organizer: Integration in Biological Systems : Yamada Science Foundation 3
  • Place of Presentation: Shouna, Japan
• [Book] Rasumussen et al, rigin of Life and Lattice Artificial Chemistry, Tin Proto Cells, ed. By S (2009)
  • Author(s): Ono, N. Madina, D., Ikegarni
  • Publisher: MIT pressO