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Design and implementation of programmable reaction diffusion system using nucleic acids

Research Project

Project/Area Number 26880002
Research Category

Grant-in-Aid for Research Activity Start-up

Allocation TypeSingle-year Grants
Research Field Life / Health / Medical informatics
Research InstitutionTohoku University

Principal Investigator

Kawamata Ibuki  東北大学, 工学(系)研究科(研究院), 助教 (30733977)

Project Period (FY) 2014-08-29 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
KeywordsDNAコンピュータ / 分子プログラミング / 反応拡散系 / パターン形成 / ゲルオートマトン / DNAコンピューティング / 分子計算 / セルオートマトン / 分子ロボティクス
Outline of Final Research Achievements

I succeeded in researching reaction diffusion system using DNA in both theory and experiment. I wrote a manuscript of 14 pages about one of the topics which we defined as “a maze solving model”. The manuscript is accepted by an international conference called UCNC16. I also carried a collaborative research about the computational universality of gellular automaton with Prof. Isokawa in Hyogo University, Prof. Peper in NICT, and Prof. Hagiya in The University of Tokyo. The result will be summarized and submitted in the future. Experimental result of gel beads communication is in under preparation for journal submission. This experimental demonstration is of interest and got student poster award in an international conference called DNA21 and young researcher award in the conference of Molecular Robotics.

Report

(3 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • Research Products

    (11 results)

All 2016 2015 2014

All Journal Article (2 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 2 results,  Open Access: 2 results,  Acknowledgement Compliant: 2 results) Presentation (8 results) (of which Int'l Joint Research: 2 results,  Invited: 1 results) Book (1 results)

  • [Journal Article] Supramolecular 1-D polymerization of DNA origami through a dynamic process at the 2-dimensionally confined air-water interface2016

    • Author(s)
      Yusuke Yonamine , Keitel Abraham Cervantes , Kosuke Minami , Ibuki Kawamata , Waka Nakanishi , Jonathan P Hill , Satoshi Murata and Katsuhiko Ariga
    • Journal Title

      Phys. Chem. Chem. Phys.

      Volume: NA Issue: 18 Pages: 12576-12581

    • DOI

      10.1039/c6cp01586g

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] In situ 2D-extraction of DNA wheels by 3D through-solution transport2015

    • Author(s)
      Yusuke Yonamine *ab, Keitel Cervantes-Salguero *c, Waka Nakanishi *a, Ibuki Kawamata c, Kosuke Minami a, Hirokazu Komatsu a, Satoshi Murata *c, Jonathan P. Hill ab and Katsuhiko Ariga *ab
    • Journal Title

      Phys. Chem. Chem. Phys.

      Volume: 17 Issue: 48 Pages: 32122-32125

    • DOI

      10.1039/c5cp05765e

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] DNAによるゾルゲル・ゲルゾル相転移の時空間発展2016

    • Author(s)
      川又生吹
    • Organizer
      新学術領域分子ロボティクス領域会議
    • Place of Presentation
      愛知県蒲郡市、ホテルたつき
    • Year and Date
      2016-03-14
    • Related Report
      2015 Annual Research Report
  • [Presentation] DNA反応のカスケードをプログラムして時間的・空間的に発展させる2015

    • Author(s)
      川又生吹
    • Organizer
      分子ロボティクス定例研究会
    • Place of Presentation
      宮城県仙台市、東北大学青葉山キャンパス
    • Year and Date
      2015-12-05
    • Related Report
      2015 Annual Research Report
  • [Presentation] Traveling of gelation and solation of polymer using reaction and diffusion of DNA2015

    • Author(s)
      Ibuki Kawamata
    • Organizer
      Japanese Society for Cell Synthesis Research 8.0
    • Place of Presentation
      大阪府吹田市、大阪大学吹田キャンパス 銀杏会館
    • Year and Date
      2015-11-12
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Molecular information processing in micro gel beads with entrapped DNAs2015

    • Author(s)
      Satoru Yoshizawa
    • Organizer
      The 21th International Meeting on DNA Computing and Molecular Programming
    • Place of Presentation
      Harvard Univeristy, Cambridge, Massachusetts, United States of America
    • Year and Date
      2015-08-17
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Encapsulated DNA and Enzyme Reaction-Diffusion Network for Simple Cellular Automaton2015

    • Author(s)
      Ibuki Kawamata
    • Organizer
      The 21th International Meeting on DNA Computing and Molecular Programming
    • Place of Presentation
      Harvard Univeristy, Cambridge, Massachusetts, United States of America
    • Year and Date
      2015-08-17
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Toward Programmable and Autonomous DNA Computing2015

    • Author(s)
      Ibuki Kawamata
    • Organizer
      分子ロボティクス若手研究会
    • Place of Presentation
      東京都港区、東京工業大学田町キャンパス
    • Year and Date
      2015-08-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] Toward Spatiotemporal Gel-sol and Sol-gel Transitions by Programmed Nano-scale DNA Reactions2014

    • Author(s)
      Ibuki Kawamata
    • Organizer
      The International Conference on Small Science (ICSS 2014)
    • Place of Presentation
      香港
    • Year and Date
      2014-12-08 – 2014-12-11
    • Related Report
      2014 Annual Research Report
  • [Presentation] Spatial Sol-Gel Transition by Diffusing DNA Strand that Triggers Hybridization Chain Reaction2014

    • Author(s)
      Ibuki Kawamata
    • Organizer
      Chem-Bio Informatics Society (CBI) Annual Meeting 2014
    • Place of Presentation
      タワーホール船堀、東京都江戸川区
    • Year and Date
      2014-10-28 – 2014-10-29
    • Related Report
      2014 Annual Research Report
  • [Book] Book chapter “Design Automation of Nucelic Acid Reaction System Simulated by Chemical Kinetics Based on Graph Rewriting Model” in Evolutionary Computation in Gene Regulatory Network Research2016

    • Author(s)
      Ibuki Kawamata, Masami Hagiya
    • Total Pages
      464
    • Publisher
      WILEY
    • Related Report
      2015 Annual Research Report

URL: 

Published: 2014-09-09   Modified: 2017-05-10  

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