Stability Structures of Conjunctive Boolean Networks
  A Boolean network is a finite dynamical system, whose variables take values from a binary set. The value update rule for each variable is a Boolean function, depending on a selected subset of variables. Boolean networks have been widely used in modeling gene regulatory networks. We focus in this paper on a special class of Boolean networks, termed as conjunctive Boolean networks. A Boolean network is conjunctive if the associated value update rule is comprised of only AND operations. It is known that any trajectory of a finite dynamical system will enter a periodic orbit. We characterize in this paper all periodic orbits of a conjunctive Boolean network whose underlying graph is strongly connected. In particular, we establish a bijection between the set of periodic orbits and the set of binary necklaces of a certain length. We further investigate the stability of a periodic orbit. Specifically, we perturb a state in the periodic orbit by changing the value of a single entry of the state. The trajectory, with the perturbed state being the initial condition, will enter another (possibly the same) periodic orbit in finite time steps. We then provide a complete characterization of all such transitions from one periodic orbit to another. In particular, we construct a digraph, with the vertices being the periodic orbits, and the (directed) edges representing the transitions among the orbits. We call such a digraph the stability structure of the conjunctive Boolean network. 
Zuguang Gao, Xudong Chen, Tamer Ba\c{s}ar
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