A bijection between the set of nesting-similarity classes and L & P matchings

Matchings are frequently used to model RNA secondary structures; however, not all matchings can be realized as RNA motifs. One class of matchings, called the L $\&$ P matchings, is the most restrictive model for RNA secondary structures in the Largest Hairpin Family (LHF). The L $\&$ P matchings were enumerated in $2015$ by Jefferson, and they are equinumerous with the set of nesting-similarity classes of matchings, enumerated by Klazar. We provide a bijection between these two sets. This bijection preserves noncrossing matchings, and preserves the sequence obtained reading left to right of whether an edge begins or ends at that vertex.Comment: 9 pages, 7 figure

Pattern Avoidance in Task-Precedence Posets

We have extended classical pattern avoidance to a new structure: multiple task-precedence posets whose Hasse diagrams have three levels, which we will call diamonds. The vertices of each diamond are assigned labels which are compatible with the poset. A corresponding permutation is formed by reading these labels by increasing levels, and then from left to right. We used Sage to form enumerative conjectures for the associated permutations avoiding collections of patterns of length three, which we then proved. We have discovered a bijection between diamonds avoiding 132 and certain generalized Dyck paths. We have also found the generating function for descents, and therefore the number of avoiders, in these permutations for the majority of collections of patterns of length three. An interesting application of this work (and the motivating example) can be found when task-precedence posets represent warehouse package fulfillment by robots, in which case avoidance of both 231 and 321 ensures we never stack two heavier packages on top of a lighter package.Comment: 17 page

Pattern Avoidance in k-ary Heaps

In this paper, we consider pattern avoidance in k-ary heaps, where the permutation associated with the heap is found by recording the nodes as they are encountered in a breadth-first search. We enumerate heaps that avoid patterns of length 3 and collections of patterns of length 3, first with binary heaps and then more generally with k-ary heaps

Pattern avoidance in forests of binary shrubs

We investigate pattern avoidance in permutations satisfying some additional restrictions. These are naturally considered in terms of avoiding patterns in linear extensions of certain forest-like partially ordered sets, which we call binary shrub forests. In this context, we enumerate forests avoiding patterns of length three. In four of the five non-equivalent cases, we present explicit enumerations by exhibiting bijections with certain lattice paths bounded above by the line y = lx, for some l in Q+, one of these being the celebrated Duchon’s club paths with l = 2/3. In the remaining case, we use the machinery of analytic combinatorics to determine the minimal polynomial of its generating function, and deduce its growth rate

Modeling RNA:DNA Hybrids with Formal Grammars

R-loops are nucleic acid structures consisting of a DNA:RNA hybrid and a DNA single strand. They form naturally during transcription when the nascent RNA hybridizes to the template DNA, forcing the coding DNA strand to wrap around the RNA:DNA duplex. Although formation of R-loops can have deleterious effects on genome integrity, there is evidence of their role as potential regulators of gene expression and DNA repair. Here we initiate an abstract model based on formal grammars to describe RNA:DNA interactions and the formation of R-loops. Separately we use a sliding window approach that accounts for properties of the DNA nucleotide sequence, such as C-richness and CG-skew, to identify segments favoring R-loops. We evaluate these properties on two DNA plasmids that are known to form R-loops and compare results with a recent energetics model from the Chédin Lab. Our abstract approach for R-loops is an initial step toward a more sophisticated framework which can take into account the effect of DNA topology on R-loop formation

Generating Functions and Wilf Equivalence for Generalized Interval Embeddings

In 1999 in [J. Difference Equ. Appl. 5, 355–377], Noonan and Zeilberger extended the Goulden-Jackson Cluster Method to find generating functions of word factors. Then in 2009 in [Electron. J. Combin. 16(2), RZZ], Kitaev, Liese, Remmel and Sagan found generating functions for word embeddings and proved several results on Wilf-equivalence in that setting. In this article, the authors focus on generalized interval embeddings, which encapsulate both factors and embeddings, as well as the “space between” these two ideas. The authors present some results in the most general case of interval embeddings. Two special cases of interval embeddings are also discussed, as well as their relationship to results in previous works in the area of pattern avoidance in words

Generalized pattern avoidance condition for the wreath product of cyclic groups with symmetric groups

We continue the study of the generalized pattern avoidance condition for Ck ≀ Sn, the wreath product of the cyclic group Ck with the symmetric group Sn, initiated in the work by Kitaev et al., In press. Among our results, there are a number of (multivariable) generating functions both for consecutive and nonconsecutive patterns, as well as a bijective proof for a new sequence counted by the Catalan numbers