Volume 19, issue 5 (2019)

Download this article
Download this article For screen
For printing
Recent Issues

Volume 25
Issue 2, 645–1264
Issue 1, 1–644

Volume 24, 9 issues

Volume 23, 9 issues

Volume 22, 8 issues

Volume 21, 7 issues

Volume 20, 7 issues

Volume 19, 7 issues

Volume 18, 7 issues

Volume 17, 6 issues

Volume 16, 6 issues

Volume 15, 6 issues

Volume 14, 6 issues

Volume 13, 6 issues

Volume 12, 4 issues

Volume 11, 5 issues

Volume 10, 4 issues

Volume 9, 4 issues

Volume 8, 4 issues

Volume 7, 4 issues

Volume 6, 5 issues

Volume 5, 4 issues

Volume 4, 2 issues

Volume 3, 2 issues

Volume 2, 2 issues

Volume 1, 2 issues

The Journal
About the Journal
Editorial Board
Subscriptions
 
Submission Guidelines
Submission Page
Policies for Authors
Ethics Statement
 
ISSN 1472-2739 (online)
ISSN 1472-2747 (print)
Author Index
To Appear
 
Other MSP Journals
Distance one lens space fillings and band surgery on the trefoil knot

Tye Lidman, Allison H Moore and Mariel Vazquez

Algebraic & Geometric Topology 19 (2019) 2439–2484
Bibliography
1 T Abe, T Kanenobu, Unoriented band surgery on knots and links, Kobe J. Math. 31 (2014) 21 MR3307286
2 D E Adams, E M Shekhtman, E L Zechiedrich, M B Schmid, N R Cozzarelli, The role of topoisomerase IV in partitioning bacterial replicons and the structure of catenated intermediates in DNA replication, Cell 71 (1992) 277
3 J Arsuaga, M Vazquez, S Trigueros, D Sumners, J Roca, Knotting probability of DNA molecules confined in restricted volumes : DNA knotting in phage capsids, Proc. Natl. Acad. Sci. USA 99 (2002) 5373
4 K L Baker, Surgery descriptions and volumes of Berge knots, I : Large volume Berge knots, J. Knot Theory Ramifications 17 (2008) 1077 MR2457837
5 K L Baker, Surgery descriptions and volumes of Berge knots, II : Descriptions on the minimally twisted five chain link, J. Knot Theory Ramifications 17 (2008) 1099 MR2457838
6 K L Baker, Once-punctured tori and knots in lens spaces, Comm. Anal. Geom. 19 (2011) 347 MR2835883
7 K L Baker, The Poincaré homology sphere, lens space surgeries, and some knots with tunnel number two, preprint (2015) arXiv:1504.06682
8 H W Benjamin, N R Cozzarelli, Geometric arrangements of Tn3 resolvase sites, J. Biol. Chem. 265 (1990) 6441
9 J Berge, Some knots with surgeries yielding lens spaces, unpublished manuscript (1990) arXiv:1802.09722
10 S A Bleiler, C D Hodgson, Spherical space forms and Dehn filling, Topology 35 (1996) 809 MR1396779
11 S A Bleiler, R A Litherland, Lens spaces and Dehn surgery, Proc. Amer. Math. Soc. 107 (1989) 1127 MR984783
12 M Boileau, S Boyer, R Cebanu, G S Walsh, Knot commensurability and the Berge conjecture, Geom. Topol. 16 (2012) 625 MR2928979
13 M Bregu, D J Sherratt, S D Colloms, Accessory factors determine the order of strand exchange in Xer recombination at psi, EMBO J. 21 (2002) 3888
14 D Buck, K Ishihara, Coherent band pathways between knots and links, J. Knot Theory Ramifications 24 (2015) MR3334659
15 D Buck, K Ishihara, M Rathbun, K Shimokawa, Band surgeries and crossing changes between fibered links, J. Lond. Math. Soc. 94 (2016) 557 MR3556454
16 D Buck, M Mauricio, Connect sum of lens spaces surgeries : application to Hin recombination, Math. Proc. Cambridge Philos. Soc. 150 (2011) 505 MR2784772
17 T D Cochran, P D Horn, Structure in the bipolar filtration of topologically slice knots, Algebr. Geom. Topol. 15 (2015) 415 MR3325742
18 A Conway, S Friedl, G Herrmann, Linking forms revisited, Pure Appl. Math. Q. 12 (2016) 493 MR3842851
19 N J Crisona, R L Weinberg, B J Peter, D W Sumners, N R Cozzarelli, The topological mechanism of phage λ integrase, J. Mol. Biol. 289 (1999) 747
20 D Cristofaro-Gardiner, The absolute gradings on embedded contact homology and Seiberg–Witten Floer cohomology, Algebr. Geom. Topol. 13 (2013) 2239 MR3073915
21 M Culler, C M Gordon, J Luecke, P B Shalen, Dehn surgery on knots, Ann. of Math. 125 (1987) 237 MR881270
22 I K Darcy, K Ishihara, R K Medikonduri, K Shimokawa, Rational tangle surgery and Xer recombination on catenanes, Algebr. Geom. Topol. 12 (2012) 1183 MR2928910
23 M Delbrück, Knotting problems in biology, from: "Mathematical problems in the biological sciences" (editor R Bellman), Proceedings of Symposia in Applied Mathematics 14, Amer. Math. Soc. (1962) 55
24 Y Diao, The knotting of equilateral polygons in 3, J. Knot Theory Ramifications 4 (1995) 189 MR1331746
25 Y Diao, N Pippenger, D W Sumners, On random knots, J. Knot Theory Ramifications 3 (1994) 419 MR1291869
26 M Doig, S Wehrli, A combinatorial proof of the homology cobordism classification of lens spaces, preprint (2015) arXiv:1505.06970
27 C Ernst, D W Sumners, A calculus for rational tangles : applications to DNA recombination, Math. Proc. Cambridge Philos. Soc. 108 (1990) 489 MR1068451
28 H L Frisch, E Wasserman, Chemical topology, J. Am. Chem. Soc. 83 (1961) 3789
29 H Geiges, C Lange, Seifert fibrations of lens spaces, Abh. Math. Semin. Univ. Hambg. 88 (2018) 1 MR3785783
30 H Goda, M Teragaito, Dehn surgeries on knots which yield lens spaces and genera of knots, Math. Proc. Cambridge Philos. Soc. 129 (2000) 501 MR1780501
31 R E Gompf, A I Stipsicz, 4–manifolds and Kirby calculus, 20, Amer. Math. Soc. (1999) MR1707327
32 M E Gottesman, R A Weisberg, Prophage insertion and excision, from: "The bacteriophage lambda" (editor A D Hershey), CHS Monographs 2 (1971) 113
33 I Grainge, M Bregu, M Vazquez, V Sivanathan, S C Y Ip, D J Sherratt, Unlinking chromosome catenanes in vivo by site-specific recombination, EMBO J. 26 (2007) 4228
34 J E Greene, The lens space realization problem, Ann. of Math. 177 (2013) 449 MR3010805
35 M Hedden, On Floer homology and the Berge conjecture on knots admitting lens space surgeries, Trans. Amer. Math. Soc. 363 (2011) 949 MR2728591
36 K A Heichman, R C Johnson, The Hin invertasome: protein-mediated joining of distant recombination sites at the enhancer, Science 249 (1990) 511
37 M Hirasawa, K Shimokawa, Dehn surgeries on strongly invertible knots which yield lens spaces, Proc. Amer. Math. Soc. 128 (2000) 3445 MR1676336
38 Y Huang, V G B Ramos, An absolute grading on Heegaard Floer homology by homotopy classes of oriented 2–plane fields, J. Symplectic Geom. 15 (2017) 51 MR3652073
39 K Ishihara, K Shimokawa, Band surgeries between knots and links with small crossing numbers, Prog. Theor. Phys. Suppl. 191 (2011) 245
40 K Ishihara, K Shimokawa, M Vazquez, Site-specific recombination modeled as a band surgery : applications to Xer recombination, from: "Discrete and topological models in molecular biology" (editors N Jonoska, M Saito), Springer (2014) 387 MR3220014
41 T Kanenobu, Band surgery on knots and links, III, J. Knot Theory Ramifications 25 (2016) MR3548474
42 D Kleckner, W Irvine, Creation and dynamics of knotted vortices, Nat. Phys. 9 (2013) 253
43 L Li, J Zheng, H Peter, E Priest, H Cheng, L Guo, F Chen, D Mackay, Magnetic reconnection between a solar filament and nearby coronal loops, Nat. Phys. 12 (2016) 847
44 T Lidman, S Sivek, Quasi-alternating links with small determinant, Math. Proc. Cambridge Philos. Soc. 162 (2017) 319 MR3604917
45 F Lin, Monopoles and Pin(2)–symmetry, PhD thesis, Massachusetts Institute of Technology (2016)
46 F Lin, The surgery exact triangle in Pin(2)–monopole Floer homology, Algebr. Geom. Topol. 17 (2017) 2915 MR3704248
47 L F Liu, J L Davis, R Calendar, Novel topologically knotted DNA from bacteriophage P4 capsids : studies with DNA topoisomerases, Nucleic. Acids. Res. 9 (1981) 3979
48 B Martelli, C Petronio, Dehn filling of the “magic” 3–manifold, Comm. Anal. Geom. 14 (2006) 969 MR2287152
49 J M Montesinos, Three-manifolds as 3–fold branched covers of S3, Quart. J. Math. Oxford Ser. 27 (1976) 85 MR0394630
50 L Moser, Elementary surgery along a torus knot, Pacific J. Math. 38 (1971) 737 MR0383406
51 K Murasugi, On a certain numerical invariant of link types, Trans. Amer. Math. Soc. 117 (1965) 387 MR0171275
52 Y Ni, F Vafaee, Null surgery on knots in L–spaces, preprint (2016) arXiv:1608.07050
53 Y Ni, Z Wu, Cosmetic surgeries on knots in S3, J. Reine Angew. Math. 706 (2015) 1 MR3393360
54 P Ozsváth, Z Szabó, Absolutely graded Floer homologies and intersection forms for four-manifolds with boundary, Adv. Math. 173 (2003) 179 MR1957829
55 P Ozsváth, Z Szabó, On knot Floer homology and lens space surgeries, Topology 44 (2005) 1281 MR2168576
56 P Ozsváth, Z Szabó, Holomorphic triangles and invariants for smooth four-manifolds, Adv. Math. 202 (2006) 326 MR2222356
57 P S Ozsváth, Z Szabó, Knot Floer homology and integer surgeries, Algebr. Geom. Topol. 8 (2008) 101 MR2377279
58 P S Ozsváth, Z Szabó, Knot Floer homology and rational surgeries, Algebr. Geom. Topol. 11 (2011) 1 MR2764036
59 V G B Ramos, Absolute gradings on ECH and Heegaard Floer homology, Quantum Topol. 9 (2018) 207 MR3812797
60 J A Rasmussen, Floer homology and knot complements, PhD thesis, Harvard University (2003) arXiv:math/0306378v1 MR2704683
61 J Rasmussen, Lens space surgeries and a conjecture of Goda and Teragaito, Geom. Topol. 8 (2004) 1013 MR2087076
62 V V Rybenkov, N R Cozzarelli, A V Vologodskii, Probability of DNA knotting and the effective diameter of the DNA double helix, Proc. Natl. Acad. Sci. USA 90 (1993) 5307
63 M Scharlemann, A Thompson, Link genus and the Conway moves, Comment. Math. Helv. 64 (1989) 527 MR1022995
64 S Y Shaw, J C Wang, Knotting of a DNA chain during ring closure, Science 260 (1993) 533
65 K Shimokawa, K Ishihara, I Grainge, D J Sherratt, M Vazquez, FtsK-dependent XerCD-dif recombination unlinks replication catenanes in a stepwise manner, Proc. Natl. Acad. Sci. USA 110 (2013) 20906
66 S J Spengler, A Stasiak, N R Cozzarelli, The stereostructure of knots and catenanes produced by phage λ integrative recombination : implications for mechanism and DNA structure, Cell 42 (1985) 325
67 C Stirling, G Stewart, D Sherratt, Multicopy plasmid stability in Escherichia coli requires host-encoded functions that lead to plasmid site-specific recombination, Mol. Gen. Genet. 214 (1988) 80
68 R Stolz, M Yoshida, R Brasher, M Flanner, K Ishihara, D Sherratt, K Shimokawa, M Vazquez, Pathways of DNA unlinking : a story of stepwise simplification, Sci. Rep. 7 (2017)
69 D W Sumners, C Ernst, S J Spengler, N R Cozzarelli, Analysis of the mechanism of DNA recombination using tangles, Q. Rev. Biophys. 28 (1995) 253
70 D W Sumners, S G Whittington, Knots in self-avoiding walks, J. Phys. A 21 (1988) 1689 MR951053
71 M Vazquez, S D Colloms, D Sumners, Tangle analysis of Xer recombination reveals only three solutions, all consistent with a single three-dimensional topological pathway, J. Mol. Biol. 346 (2005) 493
72 M Vazquez, D W Sumners, Tangle analysis of Gin site-specific recombination, Math. Proc. Cambridge Philos. Soc. 136 (2004) 565 MR2055047