Discrete Mathematics & Theoretical Computer Science |

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.

Section:
Permutation Patterns

We study a randomized algorithm for graph domination, by which, according to a uniformly chosen permutation, vertices are revealed and added to the dominating set if not already dominated. We determine the expected size of the dominating set produced by the algorithm for the path graph $P_n$ and use this to derive the expected size for some related families of graphs. We then provide a much-refined analysis of the worst and best cases of this algorithm on $P_n$ and enumerate the permutations for which the algorithm has the worst-possible performance and best-possible performance. The case of dominating the path graph has connections to previous work of Bouwer and Star, and of Gessel on greedily coloring the path.

Section:
Permutation Patterns

We consolidate what is currently known about packing densities of 4-point permutations and in the process improve the lower bounds for the packing densities of 1324 and 1342. We also provide rigorous upper bounds for the packing densities of 1324, 1342, and 2413. All our bounds are within $10^{-4}$ of the true packing densities. Together with the known bounds, this gives us a fairly complete picture of all 4-point packing densities. We also provide new upper bounds for several small permutations of length at least five. Our main tool for the upper bounds is the framework of flag algebras introduced by Razborov in 2007.

Section:
Permutation Patterns

A permutation class $C$ is splittable if it is contained in a merge of two of its proper subclasses, and it is 1-amalgamable if given two permutations $\sigma$ and $\tau$ in $C$, each with a marked element, we can find a permutation $\pi$ in $C$ containing both $\sigma$ and $\tau$ such that the two marked elements coincide. It was previously shown that unsplittability implies 1-amalgamability. We prove that unsplittability and 1-amalgamability are not equivalent properties of permutation classes by showing that the class $Av(1423, 1342)$ is both splittable and 1-amalgamable. Our construction is based on the concept of LR-inflations, which we introduce here and which may be of independent interest.

Section:
Permutation Patterns

For a variety of pattern-avoiding classes, we describe the limiting distribution for the number of fixed points for involutions chosen uniformly at random from that class. In particular we consider monotone patterns of arbitrary length as well as all patterns of length 3. For monotone patterns we utilize the connection with standard Young tableaux with at most $k$ rows and involutions avoiding a monotone pattern of length $k$. For every pattern of length 3 we give the bivariate generating function with respect to fixed points for the involutions that avoid that pattern, and where applicable apply tools from analytic combinatorics to extract information about the limiting distribution from the generating function. Many well-known distributions appear.

Section:
Permutation Patterns

Two mesh patterns are coincident if they are avoided by the same set of permutations, and are Wilf-equivalent if they have the same number of avoiders of each length. We provide sufficient conditions for coincidence of mesh patterns, when only permutations also avoiding a longer classical pattern are considered. Using these conditions we completely classify coincidences between families containing a mesh pattern of length 2 and a classical pattern of length 3. Furthermore, we completely Wilf-classify mesh patterns of length 2 inside the class of 231-avoiding permutations.

Section:
Permutation Patterns

We establish asymptotic bounds for the number of partitions of $[n]$ avoiding a given partition in Klazar's sense, obtaining the correct answer to within an exponential for the block case. This technique also enables us to establish a general lower bound. Additionally, we consider a graph theoretic restatement of partition avoidance problems, and propose several conjectures.

Section:
Permutation Patterns

We review and extend what is known about the generating functions for consecutive pattern-avoiding permutations of length 4, 5 and beyond, and their asymptotic behaviour. There are respectively, seven length-4 and twenty-five length-5 consecutive-Wilf classes. D-finite differential equations are known for the reciprocal of the exponential generating functions for four of the length-4 and eight of the length-5 classes. We give the solutions of some of these ODEs. An unsolved functional equation is known for one more class of length-4, length-5 and beyond. We give the solution of this functional equation, and use it to show that the solution is not D-finite. For three further length-5 c-Wilf classes we give recurrences for two and a differential-functional equation for a third. For a fourth class we find a new algebraic solution. We give a polynomial-time algorithm to generate the coefficients of the generating functions which is faster than existing algorithms, and use this to (a) calculate the asymptotics for all classes of length 4 and length 5 to significantly greater precision than previously, and (b) use these extended series to search, unsuccessfully, for D-finite solutions for the unsolved classes, leading us to conjecture that the solutions are not D-finite. We have also searched, unsuccessfully, for differentially algebraic solutions.

Section:
Permutation Patterns

We study the number of occurrences of any fixed vincular permutation pattern. We show that this statistics on uniform random permutations is asymptotically normal and describe the speed of convergence. To prove this central limit theorem, we use the method of dependency graphs. The main difficulty is then to estimate the variance of our statistics. We need a lower bound on the variance, for which we introduce a recursive technique based on the law of total variance.

Section:
Permutation Patterns

When considering binary strings, it's natural to wonder how many distinct subsequences might exist in a given string. Given that there is an existing algorithm which provides a straightforward way to compute the number of distinct subsequences in a fixed string, we might next be interested in the expected number of distinct subsequences in random strings. This expected value is already known for random binary strings where each letter in the string is, independently, equally likely to be a 1 or a 0. We generalize this result to random strings where the letter 1 appears independently with probability $\alpha \in [0,1]$. Also, we make some progress in the case of random strings from an arbitrary alphabet as well as when the string is generated by a two-state Markov chain.

Section:
Permutation Patterns

We explore a bijection between permutations and colored Motzkin paths that has been used in different forms by Foata and Zeilberger, Biane, and Corteel. By giving a visual representation of this bijection in terms of so-called cycle diagrams, we find simple translations of some statistics on permutations (and subsets of permutations) into statistics on colored Motzkin paths, which are amenable to the use of continued fractions. We obtain new enumeration formulas for subsets of permutations with respect to fixed points, excedances, double excedances, cycles, and inversions. In particular, we prove that cyclic permutations whose excedances are increasing are counted by the Bell numbers.

Section:
Permutation Patterns

Given a permutation $\sigma = \sigma_1 \ldots \sigma_n$ in the symmetric group $\mathcal{S}_{n}$, we say that $\sigma_i$ matches the quadrant marked mesh pattern $\mathrm{MMP}(a,b,c,d)$ in $\sigma$ if there are at least $a$ points to the right of $\sigma_i$ in $\sigma$ which are greater than $\sigma_i$, at least $b$ points to the left of $\sigma_i$ in $\sigma$ which are greater than $\sigma_i$, at least $c$ points to the left of $\sigma_i$ in $\sigma$ which are smaller than $\sigma_i$, and at least $d$ points to the right of $\sigma_i$ in $\sigma$ which are smaller than $\sigma_i$. Kitaev, Remmel, and Tiefenbruck systematically studied the distribution of the number of matches of $\mathrm{MMP}(a,b,c,d)$ in 132-avoiding permutations. The operation of reverse and complement on permutations allow one to translate their results to find the distribution of the number of $\mathrm{MMP}(a,b,c,d)$ matches in 231-avoiding, 213-avoiding, and 312-avoiding permutations. In this paper, we study the distribution of the number of matches of $\mathrm{MMP}(a,b,c,d)$ in 123-avoiding permutations. We provide explicit recurrence relations to enumerate our objects which can be used to give closed forms for the generating functions associated with such distributions. In many cases, we provide combinatorial explanations of the coefficients that appear in our generating functions.

Section:
Permutation Patterns

Using techniques from Poisson approximation, we prove explicit error bounds on the number of permutations that avoid any pattern. Most generally, we bound the total variation distance between the joint distribution of pattern occurrences and a corresponding joint distribution of independent Bernoulli random variables, which as a corollary yields a Poisson approximation for the distribution of the number of occurrences of any pattern. We also investigate occurrences of consecutive patterns in random Mallows permutations, of which uniform random permutations are a special case. These bounds allow us to estimate the probability that a pattern occurs any number of times and, in particular, the probability that a random permutation avoids a given pattern.

Section:
Permutation Patterns

In this paper, we consider pattern avoidance in a subset of words on $\{1,1,2,2,\dots,n,n\}$ called reverse double lists. In particular a reverse double list is a word formed by concatenating a permutation with its reversal. We enumerate reverse double lists avoiding any permutation pattern of length at most 4 and completely determine the corresponding Wilf classes. For permutation patterns $\rho$ of length 5 or more, we characterize when the number of $\rho$-avoiding reverse double lists on $n$ letters has polynomial growth. We also determine the number of $1\cdots k$-avoiders of maximum length for any positive integer $k$.

Section:
Permutation Patterns