Communications of the
Korean Mathematical Society CKMS

We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots emphasize a biomolecule's entanglement while ignoring their intrachain interactions. We remedy this by using stuck knots and links, which provide a way to emphasize both their entanglement and intrachain interactions. We first give a generating set of the oriented stuck Reidemeister moves for oriented stuck links. We then introduce an algebraic structure to axiomatize the oriented stuck Reidemeister moves. Using this algebraic structure, we define a coloring counting invariant of stuck links and provide explicit computations of the invariant. Lastly, we compute the counting invariant for arc diagrams of RNA foldings through the use of stuck link diagrams.

Keywords: Stuck knots, quandles, stuquandles, arc diagrams, RNA foldings

MSC numbers: Primary 57K10, 57M25, 57Z05

Supported by: The second author was partially supported by Simons Foundation collaboration grant 712462.