Related papers: Boolean networks with veto functions
The effects of the finite size of the network on the evolutionary dynamics of a Boolean network are analyzed. In the model considered, Boolean networks evolve via a competition between nodes that punishes those in the majority. It is found…
This paper investigates the stabilization of probabilistic Boolean networks (PBNs) via a novel pinning control strategy based on network structure. In a PBN, the evolution equation of each gene switches among a collection of candidate…
The control of complex networks is of paramount importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that perturbations to one node can affect other nodes,…
We construct and investigate Boolean networks that follow a given reliable trajectory in state space, which is insensitive to fluctuations in the updating schedule, and which is also robust against noise. Robustness is quantified as the…
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…
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 molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
Living systems are often described utilizing informational analogies. An important open question is whether information is merely a useful conceptual metaphor, or intrinsic to the operation of biological systems. To address this question,…
The study of control mechanisms of biological systems allows for interesting applications in bioengineering and medicine, for instance in cell reprogramming or drug target identification. A control strategy often consists of a set of…
Interactions between genes and gene products give rise to complex circuits that enable cells to process information and respond to external signals. Theoretical studies often describe these interactions using continuous, stochastic, or…
Boolean networks, widely used to model gene regulation, exhibit a phase transition between regimes in which small perturbations either die out or grow exponentially. We show and numerically verify that this phase transition in the dynamics…
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into…
Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's…
Flow networks are essential for both living organisms and enginneered systems. These networks often present complex dynamics controlled, at least in part, by their topology. Previous works have shown that topologically complex networks…
Four terminal switching network is an alternative structure to realize the logic functions in electronic circuit modeling. This network can be used to implement a Boolean function with less number of switches than the two terminal based…
Understanding the inductive bias of neural networks is critical to explaining their ability to generalise. Here, for one of the simplest neural networks -- a single-layer perceptron with n input neurons, one output neuron, and no threshold…
We investigate the dynamical behavior of simple modules composed of two genes with two or three regulating connections. Continuous dynamics for mRNA and protein concentrations is compared to a Boolean model for gene activity. Using a…
Many underlying structural and functional factors that determine the fault behavior of a combinational network, are not yet fully understood. In this paper, we show that there exists a large class of Boolean functions, called root…
We study the target control problem of asynchronous Boolean networks, to identify a set of nodes, the perturbation of which can drive the dynamics of the network from any initial state to the desired steady state (or attractor). We are…
The dynamics of Boolean networks (the N-K model) with scale-free topology are studied here. The existence of a phase transition governed by the value of the scale-free exponent of the network is shown analytically by analyzing the overlap…