Paper detail

A semi-bijective algorithm for saturated extended 2-regular simple stacks

Combinatorics of biopolymer structures, especially enumeration of various RNA secondary structures and protein contact maps, is of significant interest for communities of both combinatorics and computational biology. However, most of the previous combinatorial enumeration results for these structures are presented in terms of generating functions, and few are explicit formulas. This paper is mainly concerned with finding explicit enumeration formulas for a particular class of biologically relevant structures, say, saturated 2-regular simple stacks, whose configuration is related to protein folds in the 2D honeycomb lattice. We establish a semi-bijective algorithm that converts saturated 2-regular simple stacks into forests of small trees, which produces a uniform formula for saturated extended 2-regular simple stacks with any of the six primary component types. Summarizing the six different primary component types, we obtain a bivariate explicit formula for saturated extended 2-regular simple stacks with $n$ vertices and $k$ arcs. As consequences, the uniform formula can be reduced to Clote's results on $k$-saturated 2-regular simple stacks and the optimal 2-regular simple stacks, and Guo et al.'s result on the optimal extended 2-regular simple stacks.