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Natural selection driven structure building in a tunable DNA-only system

Research Project

Project/Area Number 17K00399
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionOchanomizu University

Principal Investigator

Aubert-Kato Nathanael  お茶の水女子大学, 基幹研究院, 講師 (10749659)

Project Period (FY) 2017-04-01 – 2022-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2019: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2018: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
KeywordsDNA Nanostructures / Molecular Robotics / Quality-Diversity / Robustness to failure / Stochastic Simulations / CRN / Evolvability / Origins of Life / DNA nanostructures / Liquid-handling robot
Outline of Final Research Achievements

In the present research, we proposed that relying on chemical reaction networks (CRNs) is a way to implement large DNA structures with a limited set of DNA strands, producing families of structures rather than a single target structure. Our goal was to implement a framework for the design and evaluation of sets of DNA strands capable of folding into rich families of structures. We used the framework we developed during this project to analyze three libraries of DNA strands with different features and analyzed the typical structures emerging from sets of strands based on those libraries.

Academic Significance and Societal Importance of the Research Achievements

最終的に構造体の設計者を支援する設計規則を示し、構造体の開発コストを削減することを目指す。特に、これらの結果から、ある程度の複雑性を持たせるには、一定数のドメインタイプが必要であると考えられる。また、フレームワークのコードをオープンソースプロジェクトとしてシェアした。

Report

(6 results)
  • 2021 Annual Research Report   Final Research Report ( PDF )
  • 2020 Research-status Report
  • 2019 Research-status Report
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (20 results)

All 2021 2020 2019 2018 Other

All Int'l Joint Research (1 results) Journal Article (7 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 7 results,  Open Access: 2 results) Presentation (12 results) (of which Int'l Joint Research: 8 results)

  • [Int'l Joint Research] CIBIO, University of Trento(イタリア)

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Automated exploration of DNA-based structure self-assembly networks2021

    • Author(s)
      Cazenille L.、Baccouche A.、Aubert-Kato N.
    • Journal Title

      Royal Society Open Science

      Volume: 8 Issue: 10

    • DOI

      10.1098/rsos.210848

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Emergence of structures from parasitic species in a spatially distributed molecular system2021

    • Author(s)
      Aubert-Kato Nathanael、Gines Guillaume、Fujii Teruo、Rondelez Yannick
    • Journal Title

      ALIFE 2021: The 2021 Conference on Artificial Life

      Volume: 2021

    • DOI

      10.1162/isal_a_00454

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Designing Controllers for Molecular Robots with the PEN DNA Toolbox2019

    • Author(s)
      Aubert-Kato Nathanael, Hagiya Masami
    • Journal Title

      Journal of The Society of Instrument and Control Engineers

      Volume: 58 Issue: 4 Pages: 270-275

    • DOI

      10.11499/sicejl.58.270

    • NAID

      130007632981

    • ISSN
      0453-4662, 1883-8170
    • Year and Date
      2019-04-10
    • Related Report
      2018 Research-status Report
    • Peer Reviewed
  • [Journal Article] Surrogate-Assisted Optimization of the Opt-IA Artificial Immune System Algorithm2019

    • Author(s)
      Sakanaka Yuko、Aubert-Kato Nathanael
    • Journal Title

      2019 IEEE Symposium Series on Computational Intelligence (SSCI)

      Volume: 2019 Pages: 1937-1944

    • DOI

      10.1109/ssci44817.2019.9002901

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Exploring Self-Assembling Behaviors in a Swarm of Bio-micro-robots using Surrogate-Assisted MAP-Elites2019

    • Author(s)
      Cazenille Leo、Bredeche Nicolas、Aubert-Kato Nathanael
    • Journal Title

      2019 IEEE Symposium Series on Computational Intelligence (SSCI)

      Volume: 2019 Pages: 238-246

    • DOI

      10.1109/ssci44817.2019.9003047

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Using map-elites to optimize self-assembling behaviors in a swarm of bio-micro-robots2019

    • Author(s)
      Cazenille Leo、Bredeche Nicolas、Aubert-Kato Nathanael
    • Journal Title

      SWARM 2019

      Volume: 2019 Pages: 845594-845594

    • Related Report
      2019 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A reservoir computing approach for molecular computing2018

    • Author(s)
      Yahiro Wataru, Aubert-Kato Nathanael, Hagiya Masami
    • Journal Title

      Proceedings of ALIFE 2018: The 2018 Conference on Artificial Life

      Volume: 30 Pages: 31-38

    • DOI

      10.1162/isal_a_00013

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Emergence of structures from parasitic species in a spatially distributed molecular system2021

    • Author(s)
      Aubert-Kato Nathanael、Gines Guillaume、Fujii Teruo、Rondelez Yannick
    • Organizer
      ALIFE 2021: The 2021 Conference on Artificial Life
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Automated exploration of DNA-structures-building CRNs2020

    • Author(s)
      Leo Cazenille, Alexandre Baccouche, Nathanael Aubert-Kato
    • Organizer
      26th international conference on DNA computing and molecular programming
    • Related Report
      2020 Research-status Report
    • Int'l Joint Research
  • [Presentation] Automated exploration of CRN generating DNA structures2020

    • Author(s)
      Nathanael Aubert-Kato
    • Organizer
      CBI学会2020
    • Related Report
      2020 Research-status Report
  • [Presentation] Surrogate-Assisted Optimization of the Opt-IA Artificial Immune System Algorithm2019

    • Author(s)
      Sakanaka Yuko、Aubert-Kato Nathanael
    • Organizer
      2019 IEEE Symposium Series on Computational Intelligence (SSCI)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Exploring Self-Assembling Behaviors in a Swarm of Bio-micro-robots using Surrogate-Assisted MAP-Elites2019

    • Author(s)
      Cazenille Leo、Bredeche Nicolas、Aubert-Kato Nathanael
    • Organizer
      2019 IEEE Symposium Series on Computational Intelligence (SSCI)
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Using map-elites to optimize self-assembling behaviors in a swarm of bio-micro-robots2019

    • Author(s)
      Cazenille Leo、Bredeche Nicolas、Aubert-Kato Nathanael
    • Organizer
      SWARM 2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] サロゲートモデルによる人工免疫アルゴリズムOpt-IAの改善2019

    • Author(s)
      Sakanaka Yuko、Aubert-Kato Nathanael
    • Organizer
      SIGNAC 第33回研究会 人工知能学会合同研究会
    • Related Report
      2019 Research-status Report
  • [Presentation] Optimizing Molecular-based Reservoir Computers with NSGA-II2019

    • Author(s)
      Emi Morikawa and Nathanael Aubert-kato
    • Organizer
      Unconventional Computation and Natural Computation 2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Designing adaptable molecular robot controllers with reservoir computing2019

    • Author(s)
      Aubert-Kato Nathanael
    • Organizer
      第2回分子ロボティクス年次大会
    • Related Report
      2018 Research-status Report
  • [Presentation] 多目的最適化アルゴリズムを用いたReservoir Computingの最適化2019

    • Author(s)
      Morikawa Emi, Aubert-Kato Nathanael
    • Organizer
      第2回分子ロボティクス年次大会
    • Related Report
      2018 Research-status Report
  • [Presentation] A reservoir computing approach for molecular computing2018

    • Author(s)
      Aubert-Kato Nathanael, Yahiro Wataru, Hagiya Masami
    • Organizer
      ALIFE 2018: The 2018 Conference on Artifici
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Decomposing multivariate information2018

    • Author(s)
      Nathaniel Virgo
    • Organizer
      The Ninth International Conference on Guided Self-Organisation (GSO-2018)
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research

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Published: 2017-04-28   Modified: 2023-01-30  

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