Finding cycles in synchronous Boolean networks with applications to biochemical systems

This paper is an analytical study of Boolean networks. The motivation is our desire to understand the large, complicated and interconnected pathways which comprise intracellular biochemical signal transduction networks. The simplest possible conceptual model that mimics signal transduction with sigmoidal kinetics is the n-node Boolean network each of whose elements or nodes has the value 0 (off) or 1 (on) at any given time T = 0, 1, 2,....A Boolean network has 2(n) states all of which are either on periodic cycles (including fixed points) or transients leading to cycles. Thus one understands a Boolean network by determining the number and length of its cycles. The problem one must circumvent is the large number of states (2n) since the networks we are interested in have 100 or more elements. Thus we concentrate on developing size n methods rather than the impossible task of enumerating all 2n states. This is done as follows: the dynamics of the network can be described by n polynomial equations which describe the logical function which determines the interaction at each node. Iterating the equations one step at a time finds all fixed points, period two cycles, period three cycles, etc. This is a general method that can be used to determine the fixed points and moderately large periodic cycles of any size network, but it is not useful in finding the largest cycles in a large network. However, we also show that the network equations can often be reduced to scalar form, which makes the cycle structure much more transparent. The scalar equations method is a true "size n" method and several examples (including nontrivial biochemical systems) are examined.