Related papers: Emergent Criticality from Co-evolution in Random B…
We consider a general model in which there is a coupled dynamics of node states and links states in a network. This coupled dynamics coevolves with dynamical changes of the topology of the network caused by a link rewiring mechanism. Such…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
Genetic regulatory networks are usually modeled by systems of coupled differential equations and by finite state models, better known as logical networks, are also used. In this paper we consider a class of models of regulatory networks…
The study of network structural controllability focuses on the minimum number of driver nodes needed to control a whole network. Despite intensive studies on this topic, most of them consider static networks only. It is well-known, however,…
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 nets and are proposed as on extended approach to genetic…
We define a dynamic model of random networks, where new vertices are connected to old ones with a probability proportional to a sublinear function of their degree. We first give a strong limit law for the empirical degree distribution, and…
An important feature of many complex systems, both natural and artificial, is the structure and organization of their interaction networks with interesting properties. Here we present a theory of self-organization by evolutionary adaptation…
Complex evolving systems such as the biosphere, ecosystems and societies exhibit sudden collapses, for reasons that are only partially understood. Here we study this phenomenon using a mathematical model of a system that evolves under…
The study of the interplay between the structure and dynamics of complex multilevel systems is a pressing challenge nowadays. In this paper, we use a semi-annealed approximation to study the stability properties of Random Boolean Networks…
The problem of reliability of the dynamics in biological regulatory networks is studied in the framework of a generalized Boolean network model with continuous timing and noise. Using well-known artificial genetic networks such as the…
We analyze a model of interacting agents (e.g. prebiotic chemical species) which are represended by nodes of a network, whereas their interactions are mapped onto directed links between these nodes. On a fast time scale, each agent follows…
For years, we have been building models of gene regulatory networks, where recent advances in molecular biology shed some light on new structural and dynamical properties of such highly complex systems. In this work, we propose a novel…
We study the evolution of the network properties of a populated network embedded in a genotype space characterised by either a low or a high number of potential links, with particular emphasis on the connectivity and clustering. Evolution…
The dynamical organization in the presence of noise of a Boolean neural network with random connections is analyzed. For low levels of noise, the system reaches a stationary state in which the majority of its elements acquire the same…
The emergence of complex networks from evolutionary games is studied occurring when agents are allowed to switch interaction partners. For this purpose a coevolutionary iterated Prisoner's Dilemma game is defined on a random network with…
We investigate the dynamics of two models of biological networks with purely suppressive interactions between the units; species interacting via niche competition and neurons via inhibitory synaptic coupling. In both of these cases,…
Empirical evidence has revealed that biological regulatory systems are controlled by high-level coordination between topology and Boolean rules. In this study, we study the joint effects of degree and Boolean functions on the stability of…
Discrete dynamical models underpin systems biology, but we still lack substrate-agnostic diagnostics for identifying finite-horizon dynamical signatures that may be relevant to open-ended evolution (OEE), such as the recurrent production of…
We investigate the propagation of perturbations in Boolean networks by evaluating the Derrida plot and modifications of it. We show that even small Random Boolean Networks agree well with the predictions of the annealed approximation, but…
We model the robustness against random failure or intentional attack of networks with arbitrary large-scale structure. We construct a block-based model which incorporates --- in a general fashion --- both connectivity and interdependence…