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Fatgraph models of RNA structure

Fenix Huang, Christian Reidys, Reza Rezazadegan (2017)

Molecular Based Mathematical Biology

In this review paper we discuss fatgraphs as a conceptual framework for RNA structures. We discuss various notions of coarse-grained RNA structures and relate them to fatgraphs.We motivate and discuss the main intuition behind the fatgraph model and showcase its applicability to canonical as well as noncanonical base pairs. Recent discoveries regarding novel recursions of pseudoknotted (pk) configurations as well as their translation into context-free grammars for pk-structures are discussed. This...

Fibred closed braids with disc-band fibre surfaces

Marta Rampichini (2004)

Bollettino dell'Unione Matematica Italiana

A classical result by Stallings provides a necessary and sufficient condition to decide whether a given embedded surface S is a fibre in S 3 - S . In this paper it is described how to find a candidate fibre surface for a a link presented as a closed braid. Also it is described an implemented algorithm to find the main ingredients of the necessary and sufficient condition of Stallings, namely presentations of the fundamental groups of the surface and of its complement in S 3 , and an explicit expression of...

Flat hierarchy

Vassily O. Manturov (2005)

Fundamenta Mathematicae

We consider the hierarchy flats, a combinatorial generalization of flat virtual links proposed by Louis Kauffman. An approach to constructing invariants for hierarchy flats is presented; several examples are given.

Frobenius algebras and skein modules of surfaces in 3-manifolds

Uwe Kaiser (2009)

Banach Center Publications

For each (commutative) Frobenius algebra there is defined a skein module of surfaces embedded in a given 3-manifold and bounding a prescribed curve system in the boundary. The skein relations are local and generate the kernel of a certain natural extension of the corresponding topological quantum field theory. In particular the skein module of the 3-ball is isomorphic to the ground ring of the Frobenius algebra. We prove a presentation theorem for the skein module with generators incompressible...

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