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2016 Fiscal Year Annual Research Report

Design and Implementation of Chemical Reaction Circuits for Molecular Robots with Intelligence

Planned Research

Project AreaDevelopment of Molecular Robots equipped with sensors and intelligence
Project/Area Number 24104003
Research InstitutionThe University of Electro-Communications

Principal Investigator

小林 聡  電気通信大学, 大学院情報理工学研究科, 教授 (50251707)

Co-Investigator(Kenkyū-buntansha) 山下 雅史  九州大学, システム情報科学研究院, 教授 (00135419)
小宮 健  東京工業大学, 情報理工学院, 助教 (20396790)
鈴木 泰博  名古屋大学, 情報科学研究科, 准教授 (50292983)
藤本 健造  北陸先端科学技術大学院大学, 先端科学技術研究科, 教授 (90293894)
Project Period (FY) 2012-06-28 – 2017-03-31
Keywords分子ロボット / DNAコンピュータ / 自己組織化 / 知能ロボティクス / 生体生命情報学
Outline of Annual Research Achievements

化学反応回路の設計論と高性能化に関する成果,分子ロボットプロトタイプの構築に関する成果,新しい計算モデルに関する成果を収めた.
化学反応回路の設計論については,Time Responsiveなアナログ回路の設計論を理論的に確立した.関数の標準形という概念を導入し,目的の関数を近似的に化学反応で実装する手法を考案した.テイラー近似可能な任意の関数を用いた分類タスクを,提案した手法により近似的に設計できることを示した.回路の高性能化については,光架橋反応におけるピリミジン5位の置換基の影響を調べることにより,これまで報告したDNA鎖置換反応の速度を制御できることを見出した.また,DNA鎖置換反応を用いた新規光開裂反応を開発し、配列選択的に室温条件下での光開裂を実現した.さらに,高次構造を形成し、検出が困難な標的rRNAに対して有効な新規RNA FISH法の開発に成功した.
分子ロボットのプロトタイプ構築に関しては,機能要素間の「分子濃度ギャップ」を克服するDNAシグナル増幅回路の性能を向上させて,ベシクル内で機能させることに成功した.さらに,前年度の感覚班との連携による設計を発展させ,アメーバ班とも連携して全機能要素を統合したアメーバ型分子ロボットの構築に取り組み,動作の検証を行った.
新しい計算モデルについては,分子ロボットシステムを分散システムの観点からモデル化し,分子ロボットの持つべき特性を明らかにする研究を進展させた.これまでは,2次元空間を移動するロボットを想定してきたが,本年度は,3次元空間を移動するロボットを対象として,重要な進展が得られた.環境に適応する化学反応による計算モデルについては,抽象化学系でニューラルネットワークを構築し音声入出力を介し環境変動に適応的に動作する系を構築した.また自己維持的なDNA反応系を用いて環境変動に適応して反応を維持する系を実現した.

Research Progress Status

28年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

28年度が最終年度であるため、記入しない。

  • Research Products

    (42 results)

All 2017 2016 Other

All Int'l Joint Research (1 results) Journal Article (19 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 18 results,  Acknowledgement Compliant: 18 results,  Open Access: 1 results) Presentation (19 results) (of which Int'l Joint Research: 8 results,  Invited: 5 results) Book (2 results) Patent(Industrial Property Rights) (1 results)

  • [Int'l Joint Research] University of Ottawa/Carleton University(Canada)

    • Country Name
      Canada
    • Counterpart Institution
      University of Ottawa/Carleton University
  • [Journal Article] Plane Formation by Synchronous Mobile Robots in the Three Dimensional Euclidean Space2017

    • Author(s)
      Yukiko Yamauchi, Taichi Uehara, Shuji Kijima, and Masafumi Yamashita
    • Journal Title

      Journal of the ACM

      Volume: - Pages: 印刷中

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Molecular Artificial Intelligence by using DNA reactions2017

    • Author(s)
      Yasuhiro Suzuki, Rie Taniguchi
    • Journal Title

      Proceedings of International Conference on Artificial Life and Robotics 2017

      Volume: - Pages: 591-594

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Neural Networks by using Self-Reinfocement Reactions2017

    • Author(s)
      Yasuhiro Suzuki
    • Journal Title

      Proc. of International Conference on Artificial Life and Robotics 2017

      Volume: - Pages: 595-598

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Artificial Chemistry by Sound Waves2017

    • Author(s)
      Yasuhiro Suzuki
    • Journal Title

      International Conference on Artificial Life and Robotics 2017

      Volume: - Pages: 599-602

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] RNA fluorescence in situ hybridization using 3-cyanovinylcarbazole modified oligodeoxyribonucleotides as photo-cross-linkable probes2016

    • Author(s)
      Kenzo Fujimoto, Kei Toyosato, Shigetaka Nakamura; Takashi Sakamoto
    • Journal Title

      Bioorg. Med. Chem. Lett.

      Volume: 26 Pages: 5312-5314

    • DOI

      10.1016/j.bmcl.2016.09.035

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Sequence-specific DNA photo-splitting of 3-cyanovinylcarbazole using DNA strand displacement2016

    • Author(s)
      Shigetaka Nakamura, Hayato Kawabata, Kenzo Fujimoto
    • Journal Title

      ChemBioChem

      Volume: 17 Pages: 1499 - 1503

    • DOI

      10.1002/cbic.201600236

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Effect of 5-substitution of uracil base in DNA photo-cross-linking using 3-cyanovinylcarbazole2016

    • Author(s)
      Shigetaka Nakamura, Hayato Kawabata, Hodaka Muramatsu, Kenzo Fujimoto
    • Journal Title

      Chem. Lett.

      Volume: 45 Pages: 887 - 889

    • DOI

      10.1246/cl.160382

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] UVA Responsive Anticancer Prodrugs Based on Photoinduced Electron Injection into Oligonucleotide Having 5-Halouracils2016

    • Author(s)
      Kenzo Fujimoto, Mirei Furusawa, Shigetaka Nakamura, Takashi Sakamoto
    • Journal Title

      Chem. Lett.

      Volume: 45 Pages: 1078-1080

    • DOI

      10.1246/cl.160492

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Reversible Gel-Sol Transition of Photo-Responsive DNA Gel2016

    • Author(s)
      Daisuke Kandatsu, Ibuki Kawamata, Shogo Hamada, Shin-ichiro M. Nomura, Kenzo Fujimoto, Satoshi Murata
    • Journal Title

      ChemBioChem

      Volume: 17 Pages: 1118-1121

    • DOI

      10.1002/cbic.201600088

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Autonomous mobile robots with lights2016

    • Author(s)
      Shantanu Das, Paola Flocchini, Giuseppe Prencipe, Nicola Santoro, Masafumi Yamashita
    • Journal Title

      Theor. Comput. Sci.

      Volume: 609 Pages: 171-184

    • DOI

      http://doi.org/10.1016/j.tcs.2015.09.018

    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Plane Formation by Semi-synchronous Robots in the Three Dimensional Euclidean Space2016

    • Author(s)
      Taichi Uehara, Yukiko Yamauchi, Shuji Kijima, and Masafumi Yamashita
    • Journal Title

      Proceedings of the 18th International Symposium on Stabilization, Safety, and Security of Distributed Systems

      Volume: - Pages: 383-398

    • DOI

      10.1007/978-3-319-49259-9_30

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Searching for an Evader in an Unknown Graph by an Optimal Number of Searchers2016

    • Author(s)
      Takahiro Yakami, Yukiko Yamauchi, Shuji Kijima, and Masafumi Yamashita
    • Journal Title

      Proceedings of the 18th International Symposium on Stabilization, Safety, and Security of Distributed Systems

      Volume: - Pages: 399-414

    • DOI

      10.1007/978-3-319-49259-9_31

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Brief Announcement: Symmetricity in 3D-space---Characterizing Formable Patterns by Synchronous Mobile Robots2016

    • Author(s)
      Yukiko Yamauchi, Taichi Uehara, and Masafumi Yamashita
    • Journal Title

      Proceedings of the 30th International Symposium on Distributed Computing

      Volume: - Pages: 471--473

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Brief Announcement: Pattern Formation Problem for Synchronous Mobile Robots in the Three Dimensional Euclidean Space2016

    • Author(s)
      Yukiko Yamauchi, Taichi Uehara, and Masafumi Yamashita
    • Journal Title

      Proceedings of the 35th ACM SIGACT-SIGOPS Symposium on Principles of Distributed Computing

      Volume: - Pages: 447-449

    • DOI

      DOI:http://dx.doi.org/10.1145/2933057.2933063

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Universal Systems of Oblivious Mobile Robots2016

    • Author(s)
      Paola Flocchini, Nicola Santoro, Giovanni Viglietta, and Masafumi Yamashita
    • Journal Title

      Proceedings of the 23rd International Colloquium on Structural Information and Communication Complexity

      Volume: - Pages: 242-257

    • DOI

      DOI: 10.1007/978-3-319-48314-6_16

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Realization of Periodic Functions by Self-stabilizing Population Protocols with Synchronous Handshakes2016

    • Author(s)
      Anissa Lamani, and Masafumi Yamashita
    • Journal Title

      Proceedings of the 5th International Conference on the Theory and Practice of Natural Computing

      Volume: - Pages: 21-33

    • DOI

      DOI: 10.1007/978-3-319-49001-4_2

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Analysis and design of a single-molecule DNA nanodevice for thermal band-pass filters2016

    • Author(s)
      J. A. Rose, K. Komiya
    • Journal Title

      Proceedings of the 11th IEEE Annual International Conference on Nano/Micro Engineered and Molecular Systems

      Volume: - Pages: - (6 pages)

    • DOI

      10.1109/NEMS.2016.7758205

    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Engineering multistate DNA molecules: a tunable thermal band-pass filter2016

    • Author(s)
      J. A. Rose, K. Komiya, S. Kobayashi
    • Journal Title

      Micro & Nano Letters

      Volume: 11 Pages: 595-601

    • DOI

      10.1049/mnl.2016.0345

    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] DNAナノマシン2016

    • Author(s)
      小宮 健
    • Journal Title

      現代化学

      Volume: 548 Pages: 32-35

  • [Presentation] 分子ロボットの知能創出にむけて2017

    • Author(s)
      鈴木泰博
    • Organizer
      NI-SIGNAC-CCS合同研究会
    • Place of Presentation
      東京工業大学(東京都・目黒区)
    • Year and Date
      2017-03-10 – 2017-03-10
  • [Presentation] 生体・分子”感”相互作用の諸相2017

    • Author(s)
      鈴木泰博
    • Organizer
      国際高等研究所プロジェクト「綜合コミュニケーション学」第6回研究会
    • Place of Presentation
      国際高等研究所(京都府・京都市)
    • Year and Date
      2017-02-18 – 2017-02-18
    • Invited
  • [Presentation] Harness nature for computing2016

    • Author(s)
      Yasuhiro Suzuki
    • Organizer
      Proto-computation and Proto-life Workshop
    • Place of Presentation
      マサチューセッツ州ケンブリッジ(米国)
    • Year and Date
      2016-12-10 – 2016-12-10
  • [Presentation] Development of photochemical DNA and RNA manipulation toward for nucleic acid-based drug2016

    • Author(s)
      Kenzo Fujimoto
    • Organizer
      The 39th Annual Meeting of Molecular Biology Society of Japan
    • Place of Presentation
      パシフィコ横浜(神奈川県・横浜市)
    • Year and Date
      2016-11-30 – 2016-12-03
  • [Presentation] 好熱性細菌を対象としたリボソームの立体構造比較2016

    • Author(s)
      若林優太,小宮健,山村雅幸
    • Organizer
      極限環境生物学会2016年度(第17回)年会
    • Place of Presentation
      東京工業大学(神奈川県・横浜市)
    • Year and Date
      2016-11-25 – 2016-11-26
  • [Presentation] 翻訳機構の進化過程解明に向けたリボソームの立体構造比較2016

    • Author(s)
      小宮健,若林優太,山村雅幸
    • Organizer
      「細胞を創る」研究会9.0
    • Place of Presentation
      早稲田大学(東京都・新宿区)
    • Year and Date
      2016-11-21 – 2016-11-22
  • [Presentation] アンチジーン法に向けた光誘起型Double duplex 構造の形成2016

    • Author(s)
      中村重孝、藤本健造
    • Organizer
      日本核酸医薬学会第2回年会
    • Place of Presentation
      東京理科大(東京都・葛飾区)
    • Year and Date
      2016-11-15 – 2016-11-17
  • [Presentation] Chemical Evolution in Computational Proto-Cells2016

    • Author(s)
      Yasuhiro Suzuki
    • Organizer
      ELSI Seminar
    • Place of Presentation
      東京工業大学(東京都・目黒区)
    • Year and Date
      2016-10-13 – 2016-10-13
    • Invited
  • [Presentation] C→U transition in DNA duplex using 3-vinylcarbazole analog mediated reversible photo-cross-linking2016

    • Author(s)
      Yasuharu Takashima, Shigetaka Nakamura, Kenzo Fujimoto
    • Organizer
      The 43rd International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      熊本大学(熊本県・熊本市)
    • Year and Date
      2016-09-27 – 2016-09-29
    • Int'l Joint Research
  • [Presentation] RNA FISH using 3-cyanovinylcarbazole-modified ODNs as photo-cross-linking probe2016

    • Author(s)
      Kano Chinami, Kei Toyosato, Takashi Sakamoto, Kenzo Fujimoto
    • Organizer
      The 43rd International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      熊本大学(熊本県・熊本市)
    • Year and Date
      2016-09-27 – 2016-09-29
    • Int'l Joint Research
  • [Presentation] Effects of hydrogen bonding on the cytosine deamination in photo-cross-linked DNA duplex2016

    • Author(s)
      Siddhant Sethi, Minako Ooe, Takashi Sakamoto, Kenzo Fujimoto
    • Organizer
      The 43rd International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      熊本大学(熊本県・熊本市)
    • Year and Date
      2016-09-27 – 2016-09-29
    • Int'l Joint Research
  • [Presentation] Detection of DNA B-Z transition by 19F NMR based on 19F chemical shift change2016

    • Author(s)
      Hui Yang, Chihiro Hirata, Shigetaka Nakamura, Kenzo Fujimoto
    • Organizer
      43rd International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      熊本大学(熊本県・熊本市)
    • Year and Date
      2016-09-27 – 2016-09-29
    • Int'l Joint Research
  • [Presentation] The effect of 5-substitution of pyrimidine base in DNA photo-cross-linking using 3-cyanovinylcarbazole2016

    • Author(s)
      Shigetaka Nakamura, Hayato Kawabata, Hodaka Muramatsu, Kenzo Fujimoto
    • Organizer
      The 43rd International Symposium on Nucleic Acids Chemistry
    • Place of Presentation
      熊本大学(熊本県・熊本市)
    • Year and Date
      2016-09-27 – 2016-09-29
    • Int'l Joint Research
  • [Presentation] Construction of an isothermal DNA amplification reaction system for simplified nucleic acid test2016

    • Author(s)
      K. Komiya, C. Noda, M. Komori, K. Dong, T. Takenaka, T. Enomoto, T. Yoshimura, M. Yamamura
    • Organizer
      第10回バイオ関連化学シンポジウム
    • Place of Presentation
      石川県立音楽堂(石川県・金沢市)
    • Year and Date
      2016-09-07 – 2016-09-09
  • [Presentation] Autonomous and Programmable Strand Generator Implemented as DNA Chemical Reaction Network2016

    • Author(s)
      I. Kawamata, S. Kawakami, Y.-C. Chen, S. Hiratsuka, S. Aradachi, D. Tamatsuki, H. Yuuki, T. Takahashi, E. Ishihara, S. Imai, H. Otaka, Y. Otaki, K. Suzuki, T. Watanabe, K. Komiya, F. Takabatake, S. Nomura, S. Murata
    • Organizer
      22nd International Meeting on DNA Computing and Molecular Programming
    • Place of Presentation
      Munich(Germany)
    • Year and Date
      2016-09-04 – 2016-09-08
    • Int'l Joint Research
  • [Presentation] Towards a Theory of Formal Distributed Systems2016

    • Author(s)
      Masafumi Yamashita
    • Organizer
      The 23rd International Colloquium on Structural Information and Communication Complexity
    • Place of Presentation
      Helsinki (Finland)
    • Year and Date
      2016-07-19 – 2016-07-21
    • Int'l Joint Research / Invited
  • [Presentation] A Neural Network by Using Self-Reinforcement Reactions2016

    • Author(s)
      Yasuhiro Suzuki
    • Organizer
      10th International Workshop on Natural Computing
    • Place of Presentation
      国際教養大学(秋田県・秋田市)
    • Year and Date
      2016-05-14 – 2016-05-14
  • [Presentation] 核酸医薬を指向した光化学的RNA編集法の開発2016

    • Author(s)
      藤本健造
    • Organizer
      第55回日本生体医工学会大会
    • Place of Presentation
      富山国際会議場(富山県・富山市)
    • Year and Date
      2016-04-26 – 2016-04-28
    • Invited
  • [Presentation] Analysis and Design of a Single-Molecule DNA Nanodevice for Thermal Band-Pass Filters2016

    • Author(s)
      J. A. Rose, K. Komiya
    • Organizer
      The 11th Annual IEEE International Conference on Nano/Micro Engineered and Molecular Systems
    • Place of Presentation
      ホテル松島大観荘(宮城県・宮城郡)
    • Year and Date
      2016-04-17 – 2016-04-20
    • Int'l Joint Research / Invited
  • [Book] Chapter7 "Photo-Cross-Linking reaction in Nucleic Acids: Chemistry and Applications" of "Modified Nucleic Acids"2016

    • Author(s)
      Takashi Sakamoto, Kenzo Fujimoto
    • Total Pages
      14 pages in total 268 pages
    • Publisher
      Springer
  • [Book] DNA分子デザインのすべて~BIOMOD虎の巻~2016

    • Author(s)
      村田智, 浜田省吾, 小宮健, ほか全21名
    • Total Pages
      224
    • Publisher
      情報計算化学生物学会(CBI学会)出版
  • [Patent(Industrial Property Rights)] アンチジーン法用光応答性人工核酸プローブ2016

    • Inventor(s)
      藤本健造、中村重孝
    • Industrial Property Rights Holder
      北陸先端科学技術大学院大学
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      特願2016-105622
    • Filing Date
      2016-05-28

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Published: 2018-01-16  

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