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Application of knot theory to molecular biology

Research Project

Project/Area Number 25400080
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Geometry
Research InstitutionSaitama University

Principal Investigator

SHMOKAWA Koya  埼玉大学, 理工学研究科, 教授 (60312633)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Fiscal Year 2015: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2014: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2013: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Keywords結び目 / DNA / 組換え / バンド手術 / 格子結び目 / 組換え酵素 / デーン手術
Outline of Final Research Achievements

We studied band surgeries of knots and links, lattice knots in the simple cubic lattice, Dehn surgery on knots and A-polynomial of knots and applied results to modeling of DNA and proteins and the research of site-specific recombination.
In particular we studied (1)characterization of unlinking of DNA catenane by site-specific recombination of Xer-dif-FtsK system, (2)tangle decomposition of knots and their A-polynomial, (3)lattice knots and links in a tube region in the simple cubic lattice.
We published 4 research papers and give plenary and invited talks in international conferences. We also organized a special session on DNA topology in Australia.

Report

(4 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (24 results)

All 2016 2015 2014 2013 Other

All Int'l Joint Research (2 results) Journal Article (5 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 4 results,  Open Access: 2 results,  Acknowledgement Compliant: 2 results) Presentation (14 results) (of which Int'l Joint Research: 5 results,  Invited: 14 results) Remarks (3 results)

  • [Int'l Joint Research] University of California, Davis/California state university, Chico(米国)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] University of Saskatchewan(カナダ)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Dehn surgery and Seifert surface system2016

    • Author(s)
      Makoto Ozawa and Koya Shimokawa
    • Journal Title

      Ann. Sc. Norm. Super. Pisa Cl. Sci. (5)

      Volume: - Pages: 267-276

    • DOI

      10.2422/2036-2145.201410_008

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Tangle sums and factorization of A-polynomials2015

    • Author(s)
      Masaharu Ishikawa, Thomas W. Mattman, and Koya Shimokawa
    • Journal Title

      New York Journal of Mathematics

      Volume: 21 Pages: 823-835

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Site-specific recombination modeled as a band surgery: Applications to Xer recombination2014

    • Author(s)
      Kai Ishihara, Koya Shimokawa, and Mariel Vazquez
    • Journal Title

      Discrete and Topological Models in Molecular Biology

      Volume: 1 Pages: 387-401

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] FtsK-dependent XerCD-dif recombination unlinks replication catenanes in a stepwise manner2013

    • Author(s)
      Koya Shimokawa, Kai Ishihara, Ian Grainge, David J. Sherratt, and Mariel Vazquez
    • Journal Title

      Proc. Natl. Acad. Sci. U S A

      Volume: 110 Issue: 52 Pages: 20906-20911

    • DOI

      10.1073/pnas.1308450110

    • Related Report
      2013 Research-status Report
    • Peer Reviewed
  • [Journal Article] Tangle sums, norm curves and cyclic surgeries2013

    • Author(s)
      Masaharu Ishikawa, Thomas W. Mattman, and Koya Shimokawa
    • Journal Title

      RIMS Kokyuroku

      Volume: 1836 Pages: 18-33

    • Related Report
      2013 Research-status Report
  • [Presentation] 結び目理論と3 次元トポロジーの化学への応用2016

    • Author(s)
      下川航也
    • Organizer
      日本化学会 第96 春季年会 「幾何学が誘起する新電子系物質科学」
    • Place of Presentation
      同志社大学京田辺キャンパス(京都府京田辺市)
    • Year and Date
      2016-03-27
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Knots and links in the simple cubic lattice2016

    • Author(s)
      Koya Shimokawa
    • Organizer
      mini symposium: ”Mathematical Modeling and Analysis of Protein Cages”
    • Place of Presentation
      沖縄科学技術大学院大学(沖縄県国頭郡恩納村)
    • Year and Date
      2016-01-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Application of graph theory and knot theory to polymer chemistry2015

    • Author(s)
      Koya Shimokawa
    • Organizer
      Cyclic and Topological Polymers, Pacifichem
    • Place of Presentation
      Hawaii Convention center, Honolulu, Hawaii, USA
    • Year and Date
      2015-12-19
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Knots and graphs in polymer chemistry2015

    • Author(s)
      Koya Shimokawa
    • Organizer
      International Workshop on Topology/Geometry-driven Electron Systems toward New Horizon of Functional Materials
    • Place of Presentation
      名古屋大学 野依記念学術交流館(愛知県名古屋市)
    • Year and Date
      2015-12-12
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Knots and links in the simple cubic lattice2015

    • Author(s)
      Koya Shimokawa
    • Organizer
      Simons Center's Workshop: Symplectic and Algebraic Geometry in the Statistical Physics of Polymers
    • Place of Presentation
      Simons Center of Geometry and Physics, Stony Brook University, NY, USA
    • Year and Date
      2015-10-13
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Unknotting operation and growth constant of knots in a tube region2015

    • Author(s)
      Koya Shimokawa
    • Organizer
      Combinatorics, topology and statistical mechanics of polymer models II, CanaDAM 2015
    • Place of Presentation
      University of Saskatchewan in Saskatoon, SK, Canada
    • Year and Date
      2015-06-02
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Site-specific recombination modeled as a band surgery2014

    • Author(s)
      Koya Shimokawa
    • Organizer
      8th Australia and New Zealand Mathematics Convention, Special session on topology, geometry and combinatorics of biopolymers
    • Place of Presentation
      University of Melbourne, Melbourne, Australia
    • Year and Date
      2014-12-11
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] DNA組み換え酵素のタングル解析2014

    • Author(s)
      下川航也
    • Organizer
      生命ダイナミクスの数理とその応用:異分野とのさらなる融合
    • Place of Presentation
      東京大学
    • Year and Date
      2014-12-03
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Site-specific recombination modeled as a band surgery2014

    • Author(s)
      Koya Shimokawa
    • Organizer
      Special Session on "Applications of Knot Theory to the Entanglement of Biopolymers", AMS 2014 Fall Western Sectional Meeting
    • Place of Presentation
      San Francisco State University, San Francisco, USA
    • Year and Date
      2014-10-26
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Site-specific recombination modeled as a band surgery2014

    • Author(s)
      Koya Shimokawa
    • Organizer
      mini-symposium "Biopolymer Entanglements", Canadian Applied and Inductrial Mathematics Society 2014 Annual Meeting
    • Place of Presentation
      Delta Bessborough Hotel, Saskatoon, SK, Canada
    • Year and Date
      2014-06-23
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Minimum step number of knots in the simple cubic lattice2014

    • Author(s)
      Koya Shimokawa
    • Organizer
      Combinatorial Applications to Biology, Chemistry and Physics
    • Place of Presentation
      University of Saskatchewan, Saskatoon, SK, Canada
    • Year and Date
      2014-06-22
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] Site-specific recombination modeled as a band surgery

    • Author(s)
      下川 航也
    • Organizer
      研究集会「力学系と応用トポロジー」
    • Place of Presentation
      京都大学
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] 結び目理論の分子生物学への応用

    • Author(s)
      下川 航也
    • Organizer
      SMART研究会 「応用現代幾何学」
    • Place of Presentation
      東北大学
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Lattice knots and links in tubes

    • Author(s)
      下川 航也
    • Organizer
      Entanglement in biology; how nature controls the topology of proteins and DNA
    • Place of Presentation
      Banff International Research Station for Mathematical Innovation and Discovery, Canada
    • Related Report
      2013 Research-status Report
    • Invited
  • [Remarks] 下川航也 ホームページ

    • URL

      http://www.rimath.saitama-u.ac.jp/lab.jp/KoyaShimokawa.html

    • Related Report
      2015 Annual Research Report 2014 Research-status Report
  • [Remarks] Mathematical analysis of DNA unlinking

    • URL

      http://en.saitama-u.ac.jp/research/researchers/dr-koya-shimokawa/

    • Related Report
      2014 Research-status Report
  • [Remarks] 下川航也ホームページ

    • URL

      http://www.rimath.saitama-u.ac.jp/lab.jp/KoyaShimokawa.html

    • Related Report
      2013 Research-status Report

URL: 

Published: 2014-07-25   Modified: 2022-01-27  

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