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Psybrackets, pseudoknots and singular knots. (English) Zbl 1518.57015

Pseudoknots are generalizations of knots where, in addition to classical over/under crossings, the diagrams of pseudoknots also present crossings of undetermined nature, i.e. which are not known to be over or under crossings. Such a situation can be imagined in a probabilistic manner, where we associate to such an undetermined crossing a probabiliy of it being an over-crossing, or an under-crossing. The study of such structures arises rather naturally in certain biological situations, such as the study of DNA, where experimental uncertainty results in undetermined combinatorial information. The isotopy classes of pseudoknots are described by a set of Reidemeister moves where precrossings appear as well. These moves are the same as those for singular knots, except for a single move.
The article under review utilizes a ternary operation called psybracket, similar to the notion of Niebrzydowski tribracket, with some extra axioms to introduce certain coloring (counting) invariants of pseudoknots. The authors show that the defining axioms correspond to the combinatorial moves that characterize isotopy classes of pseudoknots upon defining a notion of region coloring of a diagram of a pseudoknot. The article presents extensive examples and computations to showcase the theory introduced. Finally, the authors provide a compendium of questions for future perspectives on the subject.

MSC:

57K12 Generalized knots (virtual knots, welded knots, quandles, etc.)

References:

[1] L. Aggarwal, S. Nelson and P. Rivera, Quantum enhancements via tribracket brackets, preprint (2019), arXiv:1907.03011.
[2] K. Bataineh, M. Elhamdadi, M. Hajij and W. Youmans, Generating sets of reidemeister moves of oriented singular links and quandles, preprint (2017), arXiv:1702.01150.
[3] Choi, W., Needell, D. and Nelson, S., Boltzmann enhancements of biquasile counting invariants, J. Knot Theory Ramifications27(14) (2018) 1850068. · Zbl 1411.57023
[4] Clote, P., Dobrev, S., Dotu, I., Kranakis, E., Krizanc, D. and Urrutia, J., On the page number of RNA secondary structures with pseudoknots, J. Math. Biol.65(6-7) (2012) 1337-1357. · Zbl 1252.92021
[5] Evans, P. A., Finding common RNA pseudoknot structures in polynomial time, J. Discrete Algorithms9(4) (2011) 335-343. · Zbl 1228.92024
[6] Graves, P., Nelson, S. and Tamagawa, S., Niebrzydowski algebras and trivalent spatial graphs, Int. J. Math.29(14) (2018) 1850102. · Zbl 1406.57010
[7] Hanaki, R., Pseudo diagrams of knots, links and spatial graphs, Osaka J. Math.47(3) (2010) 863-883. · Zbl 1219.57006
[8] Henrich, A., Hoberg, R., Jablan, S., Johnson, L., Minten, E. and Radović, L., The theory of pseudoknots, J. Knot Theory Ramifications22(7) (2013) 1350032. · Zbl 1271.57037
[9] Henrich, A. and Jablan, S., On the coloring of pseudoknots, J. Knot Theory Ramifications23(12) (2014) 1450061. · Zbl 1419.57025
[10] Kim, J. and Nelson, S., Biquasile colorings of oriented surface-links, Topol. Appl.236 (2018) 64-76. · Zbl 1383.57031
[11] Li, T. J. X. and Reidys, C. M., Statistics of topological RNA structures, J. Math. Biol.74(7) (2017) 1793-1821. · Zbl 1365.05020
[12] Needell, D. and Nelson, S., Biquasiles and dual graph diagrams, J. Knot Theory Ramifications26(8) (2017) 1750048. · Zbl 1372.57030
[13] Needell, D., Nelson, S. and Shi, Y., Tribracket Modules, Int. J. Math.31(4) (2020) 2050028. · Zbl 1440.57008
[14] Nelson, S., Orrison, M. E. and Rivera, V., Quantum enhancements and biquandle brackets, J. Knot Theory Ramifications26(5) (2017) 1750034. · Zbl 1396.57023
[15] Nelson, S., Oshiro, K. and Oyamaguchi, N., Local biquandles and Niebrzydowski’s tribracket theory, Topol. Appl.258 (2019) 474-512. · Zbl 1415.57007
[16] Nelson, S., Oyamaguchi, N. and Sazdanovic, R., Psyquandles, singular knots and pseduoknots, Tokyo J. Math.42(2) (2019) 405-429. · Zbl 1452.57010
[17] Nelson, S. and Pauletich, E., Multi-tribrackets, J. Knot Theory Ramifications28(12) (2019) 1950075. · Zbl 1440.57009
[18] Nelson, S. and Pico, S., Virtual tribrackets, J. Knot Theory Ramifications28(4) (2019) 1950026. · Zbl 1426.57029
[19] Niebrzydowski, M., On some ternary operations in knot theory, Fund. Math.225(1) (2014) 259-276. · Zbl 1294.57008
[20] Niebrzydowski, M., Pilitowska, A. and Zamojska-Dzienio, A., Knot-theoretic ternary groups, Fund. Math.247(3) (2019) 299-320. · Zbl 1457.20055
[21] Oyamaguchi, N., Enumeration of spatial 2-bouquet graphs up to flat vertex isotopy, Topol. Appl.196(B) (2015) 805-814. · Zbl 1330.57003
[22] Qin, J. and Reidys, C. M., On topological RNA interaction structures, J. Comput. Biol.20(7) (2013) 495-513.
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