Morphisms and order ideals of toric posets

Toric posets are cyclic analogues of finite posets. They can be viewed combinatorially as equivalence classes of acyclic orientations generated by converting sources into sinks, or geometrically as chambers of toric graphic hyperplane arrangements. In this paper we study toric intervals, morphisms, and order ideals, and we provide a connection to cyclic reducibility and conjugacy in Coxeter groups.

Toric partial orders

We define toric partial orders, corresponding to regions of graphic toric hyperplane arrangements, just as ordinary partial orders correspond to regions of graphic hyperplane arrangements. Combinatorially, toric posets correspond to finite posets under the equivalence relation generated by converting minimal elements into maximal elements, or sources into sinks. We derive toric analogues for several features of ordinary partial orders, such as chains, antichains, transitivity, Hasse diagrams, linear extensions, and total orders.

On the Cyclically Fully Commutative Elements of Coxeter Groups

Let W be an arbitrary Coxeter group. If two elements have expressions that are cyclic shifts of each other (as words), then they are conjugate (as group elements) in W. We say that w is cyclically fully commutative (CFC) if every cyclic shift of any reduced expression for w is fully commutative (i.e., avoids long braid relations). These generalize Coxeter elements in that their reduced expressions can be described combinatorially by acyclic directed graphs, and cyclically shifting corresponds to source-to-sink

Nested canalyzing depth and network stability

We introduce the nested canalyzing depth of a function, which measures the extent to which it retains a nested canalyzing structure. We characterize the structure of functions with a given depth and compute the expected activities and sensitivities of the variables. This analysis quantifies how canalyzation leads to higher stability in Boolean networks. It generalizes the notion of nested canalyzing functions (NCFs), which are precisely the functions with maximum depth. NCFs have been proposed as gene regulatory network models, but their structure is frequently too restrictive and they are extremely sparse. We find that functions become decreasingly sensitive to input perturbations as the canalyzing depth increases, but exhibit rapidly diminishing returns in stability. Additionally, we show that as depth increases, the dynamics of networks using these functions quickly approach the critical regime, suggesting that real networks exhibit some degree of canalyzing depth, and that NCFs are not significantly better than functions of sufficient depth for many applications of the modeling and reverse engineering of biological networks.

Dynamics Groups of Asynchronous Cellular Automata

We say that a finite asynchronous cellular automaton (or more generally, any sequential dynamical system) is pi-independent if its set of periodic points are independent of the order that the local functions are applied. In this case, the local functions permute the periodic points, and these permutations generate the dynamics group. We have previously shown that exactly 104 of the possible 256 cellular automaton rules are pi-independent. In this article, we classify the periodic states of these systems and describe their dynamics groups, which are quotients of Coxeter groups. The dynamics groups provide information about permissible dynamics as a function of update sequence and, as such, connect discrete dynamical systems, group theory, and algebraic combinatorics in a new and interesting way. We conclude with a discussion of numerous open problems and directions for future research.