On the effective and automatic enumeration of polynomial permutation classes

We describe an algorithm, implemented in Python, which can enumerate any permutation class with polynomial enumeration from a structural description of the class. In particular, this allows us to find formulas for the number of permutations of length n which can be obtained by a finite number of block sorting operations (e.g., reversals, block transpositions, cut-and-paste moves)

The effect of negative feedback loops on the dynamics of Boolean networks

Feedback loops in a dynamic network play an important role in determining the dynamics of that network. Through a computational study, in this paper we show that networks with fewer independent negative feedback loops tend to exhibit more regular behavior than those with more negative loops. To be precise, we study the relationship between the number of independent feedback loops and the number and length of the limit cycles in the phase space of dynamic Boolean networks. We show that, as the number of independent negative feedback loops increases, the number (length) of limit cycles tends to decrease (increase). These conclusions are consistent with the fact, for certain natural biological networks, that they on the one hand exhibit generally regular behavior and on the other hand show less negative feedback loops than randomized networks with the same numbers of nodes and connectivity

Piles of Cubes, Monotone Path Polytopes and Hyperplane Arrangements

Monotone path polytopes arise as a special case of the construction of fiber polytopes, introduced by Billera and Sturmfels. A simple example is provided by the permutahedron, which is a monotone path polytope of the standard unit cube. The permutahedron is the zonotope polar to the braid arrangement. We show how the zonotopes polar to the cones of certain deformations of the braid arrangement can be realized as monotone path polytopes. The construction is an extension of that of the permutahedron and yields interesting connections between enumerative combinatorics of hyperplane arrangements and geometry of monotone path polytopes

Monotone Hurwitz numbers in genus zero

Hurwitz numbers count branched covers of the Riemann sphere with specified ramification data, or equivalently, transitive permutation factorizations in the symmetric group with specified cycle types. Monotone Hurwitz numbers count a restricted subset of the branched covers counted by the Hurwitz numbers, and have arisen in recent work on the the asymptotic expansion of the Harish-Chandra-Itzykson-Zuber integral. In this paper we begin a detailed study of monotone Hurwitz numbers. We prove two results that are reminiscent of those for classical Hurwitz numbers. The first is the monotone join-cut equation, a partial differential equation with initial conditions that characterizes the generating function for monotone Hurwitz numbers in arbitrary genus. The second is our main result, in which we give an explicit formula for monotone Hurwitz numbers in genus zero.Comment: 22 pages, submitted to the Canadian Journal of Mathematic