Quantifying CDS Sortability of Permutations by Strategic Pile Size

Abstract

The special purpose sorting operation, context directed swap (CDS), is an example of the block interchange sorting operation studied in prior work on permutation sorting. CDS has been postulated to model certain molecular sorting events that occur in the genome maintenance program of some species of ciliates. We investigate the mathematical structure of permutations not sortable by the CDS sorting operation. In particular, we present substantial progress towards quantifying permutations with a given strategic pile size, which can be understood as a measure of CDS non-sortability. Our main results include formulas for the number of permutations in $\textsf{S}_n$ with maximum size strategic pile. More generally, we derive a formula for the number of permutations in $\textsf{S}_n$ with strategic pile size $k$, in addition to an algorithm for computing certain coefficients of this formula, which we call merge numbers.