Related papers: Non-monotony and Boolean automata networks
Gene regulatory networks exhibit remarkable stability, maintaining functional phenotypes despite genetic and environmental perturbations. Discrete dynamical models, such as Boolean networks, provide systems biologists with a tractable…
The persistence of biodiversity of species is a challenging proposition in ecological communities in the face of Darwinian selection. The present article investigates beyond the pairwise competitive interactions and provides a novel…
In many natural synchronization phenomena, communication between individual elements occurs not directly, but rather through the environment. One of these instances is bacterial quorum sensing, where bacteria release signaling molecules in…
Boolean networks (BNs) are important models for gene regulatory networks and many other biological systems. In this paper, we study the minimal controllability problem of threshold and XOR BNs with degree constraints. Firstly, we derive…
Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
We study two measures of the complexity of heterogeneous extended systems, taking random Boolean networks as prototypical cases. A measure defined by Shalizi et al. for cellular automata, based on a criterion for optimal statistical…
Many multi-agent systems in nature are comprised of agents that interact with, and respond to, the dynamics of their environment. In this paper, we approach the study of such agent-environment interactions through the study of passively…
We consider networks of dynamical units that evolve in time according to different laws, and are coupled to each other in highly irregular ways. Studying how to steer the dynamics of such systems towards a desired evolution is of great…
Flow networks can describe many natural and artificial systems. We present a model for a flow system that allows for volume accumulation, includes conduits with a non-linear relation between current and pressure difference, and can be…
Boolean networks (BNs) are widely used to model the qualitative dynamics of biological systems. Besides the logical rules determining the evolution of each component with respect to the state of its regulators, the scheduling of component…
Biological networks such as gene regulatory networks possess desirable properties. They are more robust and controllable than random networks. This motivates the search for structural and dynamical features that evolution has incorporated…
It is known that there are no more Lyndon words of length n than there are periodic necklaces of same length. This paper considers a similar problem where, additionally, the necklaces must be without some forbidden factors. This problem…
I briefly survey several fascinating topics in networks and nonlinearity. I highlight a few methods and ideas, including several of personal interest, that I anticipate to be especially important during the next several years. These topics…
Random Boolean networks, originally invented as models of genetic regulatory networks, are simple models for a broad class of complex systems that show rich dynamical structures. From a biological perspective, the most interesting networks…
We analyse a model of fixed in-degree Random Boolean Networks in which the fraction of input-receiving nodes is controlled by a parameter gamma. We investigate analytically and numerically the dynamics of graphs under a parallel XOR…
The co-evolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of gene regulatory network. We find that a critical state emerges spontaneously resulting from interplay between…
The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…
The paper examines the discrete-time dynamics of neuron models (of excitatory and inhibitory types) with piecewise linear activation functions, which are connected in a network. The properties of a pair of neurons (one excitatory and the…
An increasing number of complex systems are now modeled as networks of coupled dynamical entities. Nonlinearity and high-dimensionality are hallmarks of the dynamics of such networks but have generally been regarded as obstacles to control.…