Related papers: Positive and negative cycles in Boolean networks
Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signalling processes. Positive feedback loops,…
Human decisional processes result from the employment of selected quantities of relevant information, generally synthesized from environmental incoming data and stored memories. Their main goal is the production of an appropriate and…
Many biological, technological, and social systems can be effectively described as networks of interacting subsystems. Typically, these networks are not isolated objects, but interact with their environment through both signals and…
We explore a new mechanism to explain polarization phenomena in opinion dynamics in which agents evaluate alternative views on the basis of the social feedback obtained on expressing them. High support of the favored opinion in the social…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
Synchronization of coupled continuous-time linear systems is studied in a general setting. For identical neutrally-stable linear systems that are detectable from their outputs, it is shown that a linear output feedback law exists under…
Biomolecular networks have already found great utility in characterizing complex biological systems arising from pair-wise interactions amongst biomolecules. Here, we review how graph theoretical approaches can be applied not only for a…
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 concept of a controlled flow of a dynamical system, especially when the controlling process feeds information back about the system, is of central importance in control engineering. In this paper we build on the ideas presented by…
Symmetries naturally occur in real-world networks and can significantly influence the observed dynamics. For instance, many synchronization patterns result from the underlying network symmetries, and high symmetries are known to increase…
Multiple interlinked positive feedback loops shape the stimulus responses of various biochemical systems, such as the cell cycle or intracellular calcium release. Recent studies with simplified models have identified two advantages of…
The closed feedback loop in recommender systems is a common setting that can lead to different types of biases. Several studies have dealt with these biases by designing methods to mitigate their effect on the recommendations. However, most…
Finite dynamical systems (e.g. Boolean networks and logical models) have been used in modeling biological systems to focus attention on the qualitative features of the system, such as the wiring diagram. Since the analysis of such systems…
We derive an exact representation of the topological effect on the dynamics of sequence processing neural networks within signal-to-noise analysis. A new network structure parameter, loopiness coefficient, is introduced to quantitatively…
Dynamical networks are important models for the behaviour of complex systems, modelling physical, biological and societal systems, including the brain, food webs, epidemic disease in populations, power grids and many other. Such dynamical…
Networks of coupled phase oscillators are one of the most studied dynamical systems with numerous applications in physics, chemistry, biology, and engineering. Their behaviour is often characterized by the emergence of various partially…
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…
A model of Boolean agents competing in a market is presented where each agent bases his action on information obtained from a small group of other agents. The agents play a competitive game that rewards those in the minority. After a long…
Biological systems operate under persistent noise, which can alter system states and induce transitions between attractors. Here, we study the attractor dynamics of Boolean networks focusing on the transitions between attractors induced by…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…