The Role of Criticality of Gene Regulatory Networks in Morphogenesis

The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations for their dynamics, is not always suitable. The graph theoretical models may serve as a rough but powerful tool in such cases. In this thesis, I first consider the network modeling for the representation of the biological systems. Both the...

In this work we study the Boolean Networks of different geometric shape and lattice organization. It was revealed that no only a spatial shape but also type of lattice are very important for definition of the structure-dynamics relation. The regular structures do not give a critical regime in the investigated cases. Hierarchy together with the irregular structure reveals characteristic features of criticality.

We investigate analytically and numerically the critical line in undirected random Boolean networks with arbitrary degree distributions, including scale-free topology of connections $P(k)\sim k^{-\gamma}$. We show that in infinite scale-free networks the transition between frozen and chaotic phase occurs for $3<\gamma < 3.5$. The observation is interesting for two reasons. First, since most of critical phenomena in scale-free networks reveal their non-trivial character for $\...

Most models of complex systems have been homogeneous, i.e., all elements have the same properties (spatial, temporal, structural, functional). However, most natural systems are heterogeneous: few elements are more relevant, larger, stronger, or faster than others. In homogeneous systems, criticality -- a balance between change and stability, order and chaos -- is usually found for a very narrow region in the parameter space, close to a phase transition. Using random Boolean n...

Using Boolean networks as prototypical examples, the role of symmetry in the dynamics of heterogeneous complex systems is explored. We show that symmetry of the dynamics, especially in critical states, is a controlling feature that can be used both to greatly simplify analysis and to characterize different types of dynamics. Symmetry in Boolean networks is found by determining the frequency at which the various Boolean output functions occur. There are classes of functions th...

A model of cellular metabolism due to S. Kauffman is analyzed. It consists of a network of Boolean gates randomly assembled according to a probability distribution. It is shown that the behavior of the network depends very critically on certain simple algebraic parameters of the distribution. In some cases, the analytic results support conclusions based on simulations of random Boolean networks, but in other cases, they do not.

This paper reviews a class of generic dissipative dynamical systems called N-K models. In these models, the dynamics of N elements, defined as Boolean variables, develop step by step, clocked by a discrete time variable. Each of the N Boolean elements at a given time is given a value which depends upon K elements in the previous time step. We review the work of many authors on the behavior of the models, looking particularly at the structure and lengths of their cycles, the...

Random Boolean networks were introduced in 1969 by Kauffman as a model for gene regulation. By combining analytical arguments and efficient numerical simulations, we evaluate the properties of relevant components of critical random Boolean networks independently of update scheme. As known from previous work, the number of relevant components grows logarithmically with network size. We find that in most networks all relevant nodes with more than one relevant input sit in the s...

This article discusses how the individual morphological properties of basic objects (e.g. neurons, molecules and aggregates), jointly with their particular spatial distribution, can determine the connectivity and dynamics of systems composed by those objects. This problem is characterized as a particular case of the more general shape and function paradigm, which emphasizes the interplay between shape and function in nature and evolution. Five key issues are addressed: (a) ho...

We propose new activity-dependent adaptive Boolean networks inspired by the cis-regulatory mechanism in gene regulatory networks. We analytically show that our model can be solved for stationary in-degree distribution for a wide class of update rules by employing the annealed approximation of Boolean network dynamics and that evolved Boolean networks have a preassigned average sensitivity that can be set independently of update rules if certain conditions are satisfied. In pa...