Automatic Synthesis of Process Calculus Using Abstraction

• Project/Area Number: 23650066
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Intelligent informatics
• Research Institution: The University of Tokyo
• Principal Investigator: HAGIYA Masami 東京大学, 大学院情報理工学系研究科, 教授 (30156252)
• Project Period (FY): 2011 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000); Fiscal Year 2011: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 探索 / 論理 / 推論アルゴリズム / プロセス計算 / DNA デバイス / グラフ書き換え系 / 抽象化 / 進化計算 / 自動合成 / DNAデバイス / 分子ロボティクス / 合成生物学

Research Abstract

We developed a method to construct a coarse-grained abstract model of DNA devices in which a graph or a set of graphs that represents DNA structures is approximated by a set of local structures (called abstract nodes). Using the method, we conducted evolutionary search of abstract systems and automatically synthesized DNA devices that implement various circuits and automata. We also applied the abstraction method to simulation of RNAi, and succeeded in simulating complex cases with more than twenty segments, and reproducing distribution of concentrations of siRNA by simulation.

Research Products

• [Journal Article] Towards Co-evolution of Information, Life and Artificial Life, Natural Computing and Beyond (2013)
  • Author(s): Masami Hagiy a and Ibuki Kawamata
  • Journal Title: Proceedings in Information and Communications Technology Volume: Vol.6 Pages: 39-48
• [Journal Article] Towards Co-evolution of Information, Life and Artificial Life, Natural Computing and Beyond (2013)
  • Author(s): Masami Hagiya, Ibuki Kawamata
  • Journal Title: Proceedings in Information and Communications Volume: 6 Pages: 39-48
  • DOI: 10.1007/978-4-431-54394-7_4
  • ISBN: 9784431543930, 9784431543947
  • Peer Reviewed
• [Journal Article] Abstraction of Graph-Based Models of Bio-Molecular Reaction Systems for Efficient Simulation (2012)
  • Author(s): Ibuki Kawamata, Nathanael Aubert, Masahiro Hamano and Masami Hagiya
  • Journal Title: Computational Methods in Systems Biology, 10th International Conference CMSB 2012,Lecture Notes in Bioinformatics, Volume: Vol.7605 Pages: 187-206
• [Journal Article] In Silico Design Control of the Trade-Off Balance in Robustness and Fragility of Logical Circuits Using DNA Nanostructures, (2012)
  • Author(s): Miki Hirabayashi, Ibuki Kawamata, Masami Hagiya, Hiroaki Kojima, and Kazuhiro Oiwa
  • Journal Title: IEEE NANO 2012 Pages: 1-6
• [Journal Article] Abstraction of Graph-Based Models of Bio-Molecular Reaction Systems for Efficient Simulation (2012)
  • Author(s): Ibuki Kawamata, Nathanael Aubert, Masahiro Hamano, Masami Hagiya
  • Journal Title: Lecture Notes in Bioinformatics Volume: 7605 Pages: 187-206
  • DOI: 10.1007/978-3-642-33636-2_12
  • ISBN: 9783642336355, 9783642336362
  • Peer Reviewed
• [Journal Article] In Silico Design Control of the Trade-Off Balance in Robustness and Fragility of Logical Circuits Using DNA Nanostructures (2012)
  • Author(s): Miki Hirabayashi, Ibuki Kawamata, Masami Hagiya, Hiroaki Kojima, and Kazuhiro Oiwa
  • Journal Title: Nanotechnology (IEEE-NANO), 2012 12th IEEE Conference on Volume: 1 Pages: 1-6
  • DOI: 10.1109/nano.2012.6321946
  • Peer Reviewed
• [Journal Article] Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling (2011)
  • Author(s): Ryoji Sekine, Masayuki Yamamura, Shotaro Ayukawa, Kana Ishimatsu,Satoru Akama, Masahiro Takinoue,Masami Hagiya, and Daisuke Kiga:
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America Volume: Vol.108 Pages: 17969-17973
• [Journal Article] Design of Molecular-Based Network Robots -Toward the Environmental Control (2011)
  • Author(s): Miki Hirabayashi, Akio Nishikawa, Fumiaki Tanaka, Masami Hagiya, Hiroaki Kojima, and Kazuhiro Oiwa
  • Journal Title: IEEE NANO 2011 Pages: 313-318
• [Journal Article] Abstraction of DNA Graph Structures for Efficient Enumeration and Simulation (2011)
  • Author(s): Ibuki Kawamata, Fumiaki Tanaka, and Masami Hagiya
  • Journal Title: The 2011 International Conference on Parallel and Distributed Processing,Techniques and Applications (PDPTA'11), Technical Session on Mathematical Modeling and Problem Solving Pages: 800-806
• [Journal Article] Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling (2011)
  • Author(s): Sekine, R., Yamamura, M., Ayukawa, S., Ishimatsu, K., Akama, S., Takinoue, M., Hagiya, M., Kiga, D.
  • Journal Title: Proc.Natl.Acad.Sci.U.S.A. Volume: 108 Issue: 44 Pages: 17969-17973
  • DOI: 10.1073/pnas.1105901108
  • Peer Reviewed
• [Journal Article] Design of Molecular-Based Network Robots - Toward the Environmental Control (2011)
  • Author(s): Miki Hirabayashi, Akio Nishikawa, Fumiaki Tanaka, Masami Hagiya, Hiroaki Kojima, and Kazuhiro Oiwa
  • Journal Title: IEEE NANO 2011 Volume: 2011 Pages: 313-318
  • DOI: 10.1109/nano.2011.6144361
  • Peer Reviewed
• [Journal Article] Abstraction of DNA Graph Structures for Efficient Enumeration and Simulation (2011)
  • Author(s): Ibuki Kawamata, Fumiaki Tanaka, and Masami Hagiya
  • Journal Title: The 2011 International Conference on Parallel and Distributed Processing, Techniques and Applications Volume: 2011 Pages: 800-806
  • Peer Reviewed
• [Presentation] 化学反応系の複雑さと分子ロボットの知能 (2012)
  • Author(s): 川又生吹, 萩谷昌己
  • Organizer: 人工知能学会合同研究会第 51回分子生物情報研究会
  • Place of Presentation: 慶應義塾大学日吉キャンパス來往舎.
  • Year and Date: 2012-11-15
• [Presentation] Abstraction of Graph-Based Models of Bio-Molecular Reaction Systems for Efficient Simulation (2012)
  • Author(s): Ibuki Kawamata, Nathanael Aubert, Masahiro Hamano, and Masami Hagiya
  • Place of Presentation: The Royal Society, London, UK.
  • Year and Date: 2012-10-04
• [Presentation] In Silico Design Control of the Trade-Off Balance in Robustness and Fragility of Logical Circuits Using DNA Nanostructures, (2012)
  • Author(s): Miki Hirabayashi, Ibuki Kawamata, Masami Hagiya, Hiroaki Kojima, andKazuhiro Oiwa
  • Organizer: 12th IEEE Conference on Nanotechnology(IEEE-NANO) 2012
  • Place of Presentation: International Convention Centre,Birmingham, UK.
  • Year and Date: 2012-08-22
• [Presentation] Enforcing Delays in DNA Computing Systems (2012)
  • Author(s): Nathanael Aubert, Yannick Rondelez,Teruo Fujii, and Masami Hagiya
  • Organizer: The 18th International Conference on DNA Computing and Molecular Programming
  • Place of Presentation: Aarhus University, Aarhus, Denmark.
  • Year and Date: 2012-08-16
• [Presentation] Towards Co-evolution of Information, Life and Artificial Life (2012)
  • Author(s): Masami Hagiya and Ibuki Kawamata
  • Organizer: 6th International Workshop on Natural Computing
  • Place of Presentation: University of Tokyo, Tokyo, Japan.
  • Year and Date: 2012-03-29
• [Presentation] Efficiency and Exactness of Simulations by Abstracting Graph Models for DNA and RNA Reaction Systems, (2012)
  • Author(s): Ibuki Kawamata, Nathanael Aubert, Masahiro Hamano, and Masami Hagiya
  • Organizer: The 18th International Conference on DNA Computing and Molecular Programming
  • Place of Presentation: Aarhus University, Aarhus, Denmark.
• [Presentation] Efficiency and Exactness of Simulations by Abstracting Graph Models for DNA and RNA Reaction Systems (2012)
  • Author(s): Ibuki Kawamata, Nathanael Aubert, Masahiro Hamano, and Masami Hagiya
  • Organizer: The 18th International Conference on DNA Computing and Molecular Programming
  • Place of Presentation: Aarhus University, Aarhus, Denmark
• [Presentation] The 2011 International Conference on Parallel and Distributed Processing (2011)
  • Author(s): Ibuki Kawamata, Fumiaki Tanaka, and Masami Hagiya
  • Organizer: Techniques and Applications
  • Place of Presentation: Las Vegas,USA.
  • Year and Date: 2011-07-18
• [Presentation] Experimental Validation of Automatically Designed DNA Automaton (2011)
  • Author(s): Ibuki Kawamata and M a sa mi H ag i ya
  • Organizer: The 17th International Conference on DNA Computing and Molecular Programming
  • Place of Presentation: Pasadena, USA.
• [Presentation] Abstraction of DNA Graph Structures for Efficient Enumeration and Simulation (2011)
  • Author(s): Ibuki Kawamata
  • Organizer: The 2011 International Conference on Parallel and Distributed Processing, Techniques and Applications
  • Place of Presentation: Las Vegas, USA
• [Presentation] Experimental Validation of Automatically Designed DNA Automaton (2011)
  • Author(s): Ibuki Kawamata
  • Organizer: The 17th International Meeting on DNA Computing and Molecular Programming
  • Place of Presentation: Pasadena, USA
• [Presentation] Abstraction of Graph-Based Models of Bio-Molecular Reaction Systems for Efficient Simulation
  • Author(s): Ibuki Kawamata, Nathanael Aubert, Masahiro Hamano, and Masami Hagiya
  • Organizer: The 10th Conference on Computational Methods in Systems Biology (CMSB2012)
  • Place of Presentation: The Royal Society, London, UK
• [Presentation] Enforcing Delays in DNA Computing Systems
  • Author(s): Nathanael Aubert, Yannick Rondelez, Teruo Fujii, and Masami Hagiya
  • Organizer: The 18th International Conference on DNA Computing and Molecular Programming
  • Place of Presentation: Aarhus University, Aarhus, Denmark
• [Presentation] In Silico Design Control of the Trade-Off Balance in Robustness and Fragility of Logical Circuits Using DNA Nanostructures
  • Author(s): Miki Hirabayashi, Ibuki Kawamata, Masami Hagiya, Hiroaki Kojima, and Kazuhiro Oiwa
  • Organizer: 12th IEEE Conference on Nanotechnology (IEEE-NANO) 2012
  • Place of Presentation: International Convention Centre, Birmingham, UK
• [Presentation] 化学反応系の複雑さと分子ロボットの知能
  • Author(s): 川又生吹, 萩谷昌己
  • Organizer: 人工知能学会合同研究会 第51回分子生物情報研究会
  • Place of Presentation: 慶應義塾大学 日吉キャンパス來往舎