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Construction of Theory and Design Principle of Molecular Computing Systems Realizing Functional Multiplicity by Control Signal Sequences

Research Project

Project/Area Number 19H04204
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 62010:Life, health and medical informatics-related
Research InstitutionThe University of Electro-Communications

Principal Investigator

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

Co-Investigator(Kenkyū-buntansha) 小宮 健  国立研究開発法人海洋研究開発機構, 超先鋭研究開発部門(超先鋭研究プログラム), 研究員 (20396790)
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) 2019-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥17,810,000 (Direct Cost: ¥13,700,000、Indirect Cost: ¥4,110,000)
Fiscal Year 2021: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Fiscal Year 2020: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
Fiscal Year 2019: ¥11,310,000 (Direct Cost: ¥8,700,000、Indirect Cost: ¥2,610,000)
Keywords分子コンピュータ / 分子ロボティクス / 計算モデル / 分子計算 / DNAコンピュータ / DNA計算
Outline of Research at the Start

本研究は,従来のDNAコンピュータがベースとしている DNA 配列に情報処理機能をプログラミングするというアプローチから転換して,光照射や温度変化のような環境因子の変化系列(制御信号系列と呼ぶことにする)に個々の情報処理機能をプログラミングことにより,外部からの信号で多機能性を実現する汎用的な DNA コンピュータを設計する枠組みを提案することを目的とする.この目的の達成のため,外部信号によって制御される分子コンピュータの計算理論と,そこで得られる指針に基づいた設計基盤を構築する.これにより,DNAコンピュータの設計に新たな潮流を生み出す.

Outline of Final Research Achievements

In order to develop the foundation for designing molecular computers which can execute various computational functions according to sequences of external control signals, we devised novel computational models with unknown behaviors which can be controlled by external signals, novel DNA devices responsive to external signals, a new sequence design system for finding DNA sequences for temperature dependent DNA devices, and finally collected data and knowledge which are important when using two different DNA devices in a system. The theoretical and experimental research discussions enabled to find an important knowledge that, when we construct a system, we need to partition reactions into reversible and irreversible ones based on their computational functions. Furthermore, the development of the new photo-responsive device makes us distinguish a single base difference of input DNA sequences, which suggests an important improvement in the developed computational models.

Academic Significance and Societal Importance of the Research Achievements

従来の DNA コンピュータは,各計算機能ごとに DNA 配列を設計して実装する必要があったが,本研究は,外部からの信号(光照射や温度変化)系列による制御により,さまざまな計算機能を実現できる新しい分子コンピュータを提案し,そのような分子コンピュータによって何ができるのかを明らかにするために必要となる計算理論を構築した.これまでは,DNA 配列に計算機能をプログラミングしていたが,本研究により,外部信号系列にプログラミングするという新しい分子コンピュータの可能性を開拓した.

Report

(4 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • Research Products

    (46 results)

All 2022 2021 2020 2019

All Journal Article (12 results) (of which Peer Reviewed: 12 results,  Open Access: 1 results) Presentation (32 results) (of which Int'l Joint Research: 11 results,  Invited: 5 results) Book (1 results) Funded Workshop (1 results)

  • [Journal Article] Monotone Control of R Systems2022

    • Author(s)
      Ryutaro Yako, Daihei Ise, Ken Komiya, Kenzo Fujimoto, Satoshi Kobayashi
    • Journal Title

      New Generation Computing

      Volume: -

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Molecular programming2022

    • Author(s)
      Ken Komiya
    • Journal Title

      Encyclopedia of Robotics

      Volume: -

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Photocrosslinking of DNA using 4-methylpyranocarbazole nucleoside with thymine base selectivity2021

    • Author(s)
      Mihara Jun-ichi、Fujimoto Kenzo
    • Journal Title

      Organic and Biomolecular Chemistry

      Volume: 19 Issue: 45 Pages: 9860-9866

    • DOI

      10.1039/d1ob01621k

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reducing control alphabet size for the control of right linear grammars with unknown behaviors2021

    • Author(s)
      Kimoto Nobuya、Nakamura Shigetaka、Komiya Ken、Fujimoto Kenzo、Kobayashi Satoshi
    • Journal Title

      Theoretical Computer Science

      Volume: 862 Pages: 193-213

    • DOI

      10.1016/j.tcs.2020.11.051

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The effect of 5-substituent in cytosine to the photochemical C to U transition in DNA strand2021

    • Author(s)
      Kenzo Fujimoto, Wan Licheng, Shigetaka Nakamura
    • Journal Title

      Bioorganic & Medicinal Chemistry Letters

      Volume: 35 Pages: 127812-127812

    • DOI

      10.1016/j.bmcl.2021.127812

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Complete Photochemical Regulation of 8-17 DNAzyme Activity using Reversible DNA Photo-cross-linking2020

    • Author(s)
      Yasuha Watanabe, Kenzo Fujimoto
    • Journal Title

      ChemBioChem

      Volume: 21 Issue: 22 Pages: 3244-3248

    • DOI

      10.1002/cbic.202000227

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Photochemical RNA editing of C to U using ultrafast reversible RNA photo-cross-linking in DNA/RNA duplexes2020

    • Author(s)
      Shigetaka Nakamura, Kanako Ishino, Kenzo Fujimoto
    • Journal Title

      ChemBioChem

      Volume: 21 Issue: 21 Pages: 3067-3070

    • DOI

      10.1002/cbic.202000269

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Computational Models for Design of Molecular Computers2019

    • Author(s)
      小林 聡
    • Journal Title

      Journal of The Society of Instrument and Control Engineers

      Volume: 58 Issue: 4 Pages: 241-246

    • DOI

      10.11499/sicejl.58.241

    • NAID

      130007633045

    • ISSN
      0453-4662, 1883-8170
    • Year and Date
      2019-04-10
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Monotonically controlling right linear grammars with unknown behaviors to output a target string2019

    • Author(s)
      Nobuya Kimoto, Ken Komiya, Kenzo Fujimoto, Satoshi Kobayashi
    • Journal Title

      Theoretical Computer Science

      Volume: 777 Pages: 387-408

    • DOI

      10.1016/j.tcs.2019.01.009

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Leak-free million-fold DNA amplification with locked nucleic acid and targeted hybridization in one pot2019

    • Author(s)
      Komiya K.、Komori M.、Noda C.、Kobayashi S.、Yoshimura T.、Yamamura M.
    • Journal Title

      Organic & Biomolecular Chemistry

      Volume: 17 Issue: 23 Pages: 5708-5713

    • DOI

      10.1039/c9ob00521h

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Measurement of microRNA with isothermal DNA amplification on fully automated immunoassay analyzers2019

    • Author(s)
      Komori M.、Komiya K.、Shirakawa T.、Morikawa T.J.、Yoshimura T.
    • Journal Title

      Analytical and Bioanalytical Chemistry

      Volume: 411 Issue: 17 Pages: 3789-3800

    • DOI

      10.1007/s00216-019-01878-z

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Isothermal amplification of specific DNA molecules inside giant unilamellar vesicles2019

    • Author(s)
      Yusuke Sato, Ken Komiya, Ibuki Kawamata, Satoshi Murata, Shin-ichiro M. Nomura
    • Journal Title

      Chemical Communications

      Volume: 印刷中 Issue: 62 Pages: 9084-9087

    • DOI

      10.1039/c9cc03277k

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] 分子サイバネティクスのための上流からのRRI実践のこころみ2022

    • Author(s)
      小宮健
    • Organizer
      発動分子科学 × 分子サイバネティクス共催ワークショップ
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] 分子ロボット技術の将来像を共創する対話と研究者の自治2022

    • Author(s)
      小宮健
    • Organizer
      分子ロボット倫理キックオフ研究会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] On Monotone Control of Right Linear Grammars with Unknown Behaviors2021

    • Author(s)
      Daihei Ise, Shigetaka, Nakamura, Ken Komiya, Kenzo Fujimoto, Satoshi Kobayashi
    • Organizer
      International Conference on DNA Computing and Molecular Programming
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] DNA Sequence Search for Temperature Dependent DNA Devices2021

    • Author(s)
      Takayuki Suzuki, Ken Komiya, Satoshi Kobayashi
    • Organizer
      International Conference on DNA Computing and Molecular Programming
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] DNA 光架橋反応を用いたDNA 鎖置換反応の光制御2021

    • Author(s)
      平井佑宜, 橋本浩寿, 中村重孝, 小林聡, 藤本健造
    • Organizer
      2021年度北陸地区講演会と研究発表会
    • Related Report
      2021 Annual Research Report
  • [Presentation] Investigation of the optimal arrangement of state sequences for efficient operation of a DNA state machine2021

    • Author(s)
      Ken Komiya, Satoshi Kobayashi, Masayuki Yamamura, John A. Rose
    • Organizer
      CBI学会2021年大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] DNAが切り拓くものつくりについて2021

    • Author(s)
      小宮健
    • Organizer
      近畿青年技術士懇談会 2021年7月度例会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] Reduction of the length of state sequences for efficient operation of a DNA state machine under low temperature conditions2021

    • Author(s)
      Ken Komiya
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Annual Research Report
  • [Presentation] 「細胞を創る」を社会に接続する素朴な対話2021

    • Author(s)
      小宮健
    • Organizer
      「細胞を創る」研究会14.0
    • Related Report
      2021 Annual Research Report
  • [Presentation] 分子ロボット技術の継続的なRRI実践モデルの構築2021

    • Author(s)
      小宮健
    • Organizer
      第5回分子ロボティクス年次大会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] On the control of R systems2021

    • Author(s)
      Ryutaro Yako, Satoshi Kobayashi
    • Organizer
      26th International Conference on DNA Computing and Molecular Programming
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 未知の振る舞いを持つ制御付き右正則文法の生成能力について2021

    • Author(s)
      伊勢大平,小林聡
    • Organizer
      電子情報通信学会,コンピュ―テーション研究会
    • Related Report
      2020 Annual Research Report
  • [Presentation] DNAコンピューティングによる“機器不要”診断薬の創製に向けて2021

    • Author(s)
      小宮健
    • Organizer
      バイオインダストリー奨励賞受賞者セミナー
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Optimization of the multi-step DNA computing reaction that implements a state machine2020

    • Author(s)
      Shuntaro Sato, Masayuki Yamamura, Ken Komiya
    • Organizer
      第58回日本生物物理学会年会
    • Related Report
      2020 Annual Research Report
  • [Presentation] Optimization of the multi-step DNA computing reaction using oxDNA MD simulation2020

    • Author(s)
      Shuntaro Sato, Masayuki Yamamura, Ken Komiya
    • Organizer
      CBI学会2020年大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 分子ロボット将来像の共創に向けて2020

    • Author(s)
      小宮健
    • Organizer
      第4回分子ロボティクス年次大会
    • Related Report
      2020 Annual Research Report
  • [Presentation] 反応システムの制御における信号数の削減2019

    • Author(s)
      矢光隆太郎,小林聡
    • Organizer
      電子情報通信学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 未知の振る舞いを持つ正則文法に対する制御システムの信号数の削減2019

    • Author(s)
      木元達哉,小林聡
    • Organizer
      電子情報通信学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Hill型の融解曲線をもつDNA塩基配列の設計2019

    • Author(s)
      池田 亮太, 小林 聡, 小宮 健
    • Organizer
      情報処理学会バイオ情報学研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Development of photochemical DNA and GCN4 peptide conjugation mediated by 3-cyanovinylcarbazole amino acid2019

    • Author(s)
      Qiu Zhiyong, Shigetaka Nakamura, Kenzo Fujimoto
    • Organizer
      ISNAC2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Photochemical mC to T transition in dsDNA using reversible DNA photo-cross-linking2019

    • Author(s)
      Wan Licheng、Shigetaka Nakamura、Kenzo Fujimoto
    • Organizer
      ISNAC2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RNA FISH of 16S rRNA in E. coli using photo-cross-linkable beacon probe containing pyranocarbazole2019

    • Author(s)
      Nanami Watanabe, Misaki Hashimoto, Shigetaka Nakamura, Kenzo Fujimoto
    • Organizer
      ISNAC2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] DNA Photo-cross-linking of GCN4 Peptide Containing L-3-cyanovinylcarbazole Amino Acid to Duplex DNA2019

    • Author(s)
      Qiu Zhiyong, Shigetaka Nakamura, Kenzo Fujimoto
    • Organizer
      The Commemorative International Symposium of the Japan Society of Nucleic Acids Chemistry
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Photochemical Inhibition of GFP Protein Expression by Ultrafast RNA Photo-cross-linking in GFP-HeLa Cell2019

    • Author(s)
      Yasuha Watanabe, Hung Yang, Shigetaka Nakamura, Kenzo Fujimoto
    • Organizer
      The Commemorative International Symposium of the Japan Society of Nucleic Acids Chemistry
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RNA fluorescence In situ hybridization using photo-cross-linkable beacon probes targeted to 16S rRNA in E. coli2019

    • Author(s)
      Shigetaka Nakamura, Misaki Hashimoto, Kenzo Fujimoto
    • Organizer
      The Commemorative International Symposium of the Japan Society of Nucleic Acids Chemistry
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Effect of Surrounding Environment of Target Cytosine in Pinpoint RNA Editing Using RNA Photo-cross-linking2019

    • Author(s)
      Kenzo Fujimoto, Sethi siddhant, Nozomi Honda, Shigetaka Nakamura
    • Organizer
      The Commemorative International Symposium of the Japan Society of Nucleic Acids Chemistry
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Construction of DNA Amplification Circuit for Directing DNA Nanodevices and Quantifying Nucleic Acids2019

    • Author(s)
      Ken Komiya, Teruya Enomoto and Masayuki Yamamura
    • Organizer
      Twentyfifth International Meeting on DNA Computing and Molecular Programming (DNA25)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Characterization of DNA Generation Circuits for Controlling DNA Nanodevices2019

    • Author(s)
      Ken Komiya, Teruya Enomoto and Masayuki Yamamura
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Amplification of specific DNA molecules inside giant unilamellar vesicles at isothermal and physiological temperature2019

    • Author(s)
      Yuske Sato, Ken Komiya, Ibuki Kawamata, Satoshi Murata and Shin-Ichiro M. Nomura
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Experimental Investigation of DNA Generation Circuits toward Molecular Robot Control2019

    • Author(s)
      Ken Komiya, Chizuru Noda, Teruya Enomoto and Masayuki Yamamura
    • Organizer
      CBI学会2019年大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 分子から IoT まで、ものつくりのシンギュラリティ2019

    • Author(s)
      小宮健
    • Organizer
      Tokyo Tech Research Festival 2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] 核酸素子で生命のソフトウェア工学を探究する2019

    • Author(s)
      小宮健
    • Organizer
      核酸化学懇話会2020
    • Related Report
      2019 Annual Research Report
  • [Book] 分子ロボットをめぐる対話要点集2022

    • Author(s)
      小長谷 明彦,小宮 健,河原 直人,河村 賢,標葉 隆馬,瀧ノ上 正浩 ,武田 浩平,森下 翔,山村 雅幸,吉田 省子
    • Total Pages
      108
    • Publisher
      CBI 学会出版
    • ISBN
      9784910628011
    • Related Report
      2021 Annual Research Report
  • [Funded Workshop] International Conference on Unconventional Computation and Natural Computation 20192019

    • Related Report
      2019 Annual Research Report

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Published: 2019-04-18   Modified: 2023-01-30  

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