Publications

  • 34. Ladder [2]catenane: A chiral molecular graph
    Toshio Nishino, Yasuyuki Yamada, Koya Shimokawa, Shigehisa Akine, Kunihisa Sugimoto, and Kentaro Tanaka,
    submitted.
  • 33. Enumeration of irreducible lattice knots and links confined to a tube in the simple cubic lattice
    preprint.
  • 32. Pathways of DNA unlinking: a story of stepwise simplification
    Robert Stolz, Masaaki Yoshida, Reuben Brasher, Kai Ishihara, David J. Sherratt, Koya Shimokawa, and Mariel Vazquez,
    Scientific Reports 7, Article number: 12420 (2017).
  • 31. Bounds for the minimum step number of knots confined to tubes in the simple cubic lattice
    Kai Ishihara, Maxime Pouokam, Atsumi Suzuki, Robert Scharein, Mariel Vazquez, Javier Arsuaga, and Koya Shimokawa,
    J. Phys. A: Math. Theor. 50 (2017) 215601. (Selected as cover image)
  • 30. Dehn surgery and Seifert surface system
    Makoto Ozawa and Koya Shimokawa,
    Ann. Sc. Norm. Super. Pisa Cl. Sci. (5) XVII (2017) 267-276.
    (arXive 1406.6264)
  • 29. Band surgeries and crossing changes between fibered links
    Dorothy Buck, Kai Ishihara, Matt Rathbun, and Koya Shimokawa,
    J. London Math. Soc. 94(2016) 557-582. (doi: 10.1112/jlms/jdw049) (open access)
    (arXive 1304.6781)
  • 28. Tangle sums and factorization of A-polynomials
    Masaharu Ishikawa, Thomas W. Mattman, and Koya Shimokawa,
    New York Journal of Mathematics 21 (2015) 823-835.
    (arXive 1107.2640)
  • 27. Site-specific recombination modeled as a band surgery: Applications to Xer recombination
    Kai Ishihara, Koya Shimokawa, and Mariel Vazquez
    "Discrete and Topological Models in Molecular Biology" (2014) pp 387-401,
    Jonoska, Natasa; Saito, Masahico (Eds.), Natural Computing Series, Springer.
  • 26. FtsK-dependent XerCD-dif recombination unlinks replication catenanes in a stepwise manner
    Koya Shimokawa, Kai Ishihara, Ian Grainge, David J. Sherratt, and Mariel Vazquez.
    Proc. Natl. Acad. Sci. U S A 110 (52) 20906-20911 (2013)
    See also Commentary by Makkuni Jayaram,
    "Mathematical validation of a biological model for unlinking replication catenanes by recombination", Proc. Natl. Acad. Sci. U S A 110 (52) 20854-20855 (2013)
  • 25. Tangle sums, norm curves and cyclic surgeries
    Masaharu Ishikawa, Thomas W. Mattman, and Koya Shimokawa,
    RIMS Kôkyûroku 1836 18-33 (2013)
  • 24. Rational tangle surgery and Xer recombination on catenanes
    Isabel K. Darcy, Kai Ishihara, Ram Medikonduri and Koya Shimokawa,
    Algebr. Geom. Topol. 12 1183-1210 (2012)
    (arXive 1108.0724)
  • 23. Bounds for the minimum step number of knots confined to slabs in the simple cubic lattice
    K. Ishihara, R. Scharein, Y. Diao, J. Arsuaga, M. Vazquez and K. Shimokawa
    J. Phys. A: Math. Theor. 45 065003 (2012)
    Featured article of the issue
  • 22. Signed unknotting number and knot chirality discrimination via strand passage
    Chris Soteros, Kai Ishihara, Koya Shimokawa, Michael Szafron, and Mariel Vazquez
    Progress of Theoretical Physics Supplement 191 78-95 (2011)
  • 21. Band surgeries between knots and links with small crossing numbers
    Kai Ishihara and Koya Shimokawa
    Progress of Theoretical Physics Supplement 191 245-255 (2011)
  • 20. DNA and knot theory
    Koya Shimokawa and Mariel Vazquez
    Sugaku 63 237-242 (2011)
  • 19. Bounds for the minimum step number of knots in the simple cubic lattice
    R. Scharein, K. Ishihara, J. Arsuaga, Y. Diao, K. Shimokawa, and M. Vazquez,
    J. Phys. A: Math. Theor. 42 (2009) 475006 (24pp)
  • 18. Finite surgeries on three-tangle pretzel knots
    David Futer,Masaharu Ishikawa, Yuichi Kabaya, Thomas W. Mattman, and Koya Shimokawa,
    Algebr. Geom. Topol. 9 issue 2, 743-771 (2009)
    (arXive 0809.4278)
  • 17. Tangle analysis of DNA unlinking by the Xer/FtsK system
    Koya Shimokawa, Kai Ishihara, and Mariel Vazquez,
    Bussei Kenkyu 92 no.1 89-92 (2009)
    Proceedings of the International Conference "Knots and soft-matter physics: topology of polymers and related topics in physics, mathematics and biology",
  • 16. Exceptional surgery and boundary slopes
    Masaharu Ishikawa, Thomas W. Mattman, and Koya Shimokawa,
    Osaka J. Math. 43 No.4, 807-821 (2006)
    (math.GT/0211147)
  • 15. Essential laminations and branched surfaces in the exteriors of links
    Mark Brittenham, Chuichiro Hayashi, Mikami Hirasawa, Tsuyoshi Kobayashi, and Koya Shimokawa,
    Japan. J. Math. 31 No.1, 25-96 (2005)
  • 14. Tangle sum and constructible spheres
    Masahiro Hachimori and Koya Shimokawa,
    J. Knot Theory Ramifications 13, 373-383 (2004)
  • 13. On non-simple reflexive links
    Hiroshi Matsuda, Makoto Ozawa, and Koya Shimokawa,
    J. Knot Theory Ramifications 11 787-791 (2002)
  • 12. Heegaard splittings of the pair of the solid torus and the core loop
    Chuichiro Hayashi and Koya Shimokawa,
    Rev. Mat. Complut. 14 No.2, 479-501 (2001)
  • 11. Heegaard splittings of trivial arcs in compression bodies
    Chuichiro Hayashi and Koya Shimokawa,
    J. Knot Theory Ramifications 10, 71-87 (2001)
  • 10. Thin position of a pair (3-manifold, 1-submanifold)
    Chuichiro Hayashi and Koya Shimokawa,
    Pacific J. Math. 197, 301-324 (2001)
  • 9. A condition for a graph in the disc to contain the half hemisphere of the dodecahedron -- Application to Dehn surgery theory --
    Chuichiro Hayashi and Koya Shimokawa
    Interdiscip. Inform. Sci. 7, 5-16 (2001)
    Proceedings of the Workshop "Graph Theory and Related Topics"
  • 8. Dehn surgeries on strongly invertible knots which yield lens spaces
    Mikami Hirasawa and Koya Shimokawa,
    Proc. Amer. Math. Soc. 128 number 11, 3445-3451 (2000)
  • 7. Hyperbolicity and boudary-irreducibility of alternating tangles
    Koya Shimokawa,
    Topology Appl. 96 issue 3, 217-239 (1999)
  • 6. Heegaard splittings of the trivial knot
    Chuichiro Hayashi and Koya Shimokawa,
    J. Knot Theory Ramifications 7, 1073-1085 (1998)
  • 5. On tunnel number one alternating knots and links
    Koya Shimokawa,
    J. Math. Sci. Univ. Tokyo 5, 547-560 (1998)
  • 4. Parallelism of two strings in alternating tangles
    Koya Shimokawa,
    J. Knot Theory Ramifications 7, 489-502 (1998)
  • 3. Symmetric knots satisfy the cabling conjecture
    Chuichiro Hayashi and Koya Shimokawa,
    Math. Proc. Camb. Phil. Soc. 123, 501-529 (1998)
  • 2. Incompressibility of closed surfaces in toroidally alternating link complements
    Koya Shimokawa,
    Osaka J. Math. 35, 191-234 (1998)
  • 1. Tangles with alternating diagrams --Alternating tanlge decompositions of knots and laminar surgery--
    Koya Shimokawa,
    Proceedings of the 5-th Korea-Japan School of Knots and Links,
    267--272 (1997), Center for Applied Mathematics, KAIST, Korea.