Activities of genes are controlled in a combinatorial fashion by the concentrations of chemical called transcription factors. We model this type of network by piecewise linear differential equations formed by embedding a logical switching network in a differential equation. We generate...

Resilience of an organism's physiological and developmental processes against mutations can have two principal causes, the first being overlapping gene functions. In this case, loss-of-function mutations in one gene will have little phenotypic effects if one or more other genes with similar...

The activity of the cell is often coordinated by the organisation of proteins into regulatory circuits that share a common function. Genome-wide expression profiles might contain important information on these circuits. Current approaches for the analysis of gene expression data include...

One of the main challenges facing biology today is the understanding of the joint action of genes, proteins and RNA molecules, interwoven in intricate interdependencies commonly known as genetic networks. To this end, several mathematical approaches have been introduced to date. In addition to...

We investigate the adaptation of random boolean networks that are a model for regulatory gene networks. The model considers a general genetic algorithm and a fitness function that takes into account the full network dynamical behavior. We propose a mathematical function to quantify the...

Evolution of cooperation has attracted considerable attention but so far no definitive answer exists. Probably each kind of problem has specific answers. This paper deals with evolution of cooperation in public goods games. We use random Boolean networks to formalize the non-local influence of K...

A key notion in the study of network dynamics is that state-space is connected into basins of attraction. Convergence in attractor basins correlates with order-complexity-chaos measures on space-time patterns. A network's "memory," its ability to categorize, is provided by the configuration of...

The critical boundaries separating ordered from chaotic behavior in randomly wired S-state networks are calculated. These networks are a natural generalization of random Boolean net and are proposed as an extended approach to genetic regulatory systems, sets of cells in different states or...

In multiagent systems, agents often face binary decisions where one seeks to take either the minority or the majority side. Examples are minority and congestion games in general, i.e., situations that require coordination among the agents in order to depict efficient decisions. In minority games...

Random Boolean networks have been proposed as discrete models of genetic networks. Depending on the values of their control parameters, these networks fall by themselves in order or disorder phases. These networks are autonomous systems: no external inputs are considered. Nevertheless, in the...