Related papers: Compensatory interactions to stabilize multiple st…

The response of complex networks to perturbations is of utmost importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that the perturbation of one node can…

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…

Boolean networks serve as discrete models of regulation and signaling in biological cells. Identifying the key controllers of such processes is important for understanding the dynamical systems and planning further analysis. Here we…

Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory…

Intracellular networks process cellular-level information and control cell fate. They can be computationally modeled using Boolean networks, which are implicit-time causal models of discrete binary events. These networks can be embedded in…

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…

This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…

We evaluate the probability that a Boolean network returns to an attractor after perturbing h nodes. We find that the return probability as function of h can display a variety of different behaviours, which yields insights into the…

The regulation of the cell state is a complex process involving several components. These complex dynamics can be modeled using Boolean networks, allowing us to explain the existence of different cell states and the transition between them.…

To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…

In a complex system, the interactions between individual agents often lead to emergent collective behavior like spontaneous synchronization, swarming, and pattern formation. The topology of the network of interactions can have a dramatic…

The dynamics of a multiplex heterogeneous network of oscillators is studied. Two types of similar models based on the Hodgkin-Huxley formalism are used as the basic elements of the networks. The first type model demonstrates bursting…

Discrete dynamic models are a powerful tool for the understanding and modeling of large biological networks. Although a lot of progress has been made in developing analysis tools for these models, there is still a need to find approaches…

Complex systems are often modeled as Boolean networks in attempts to capture their logical structure and reveal its dynamical consequences. Approximating the dynamics of continuous variables by discrete values and Boolean logic gates may,…

Boolean networks have been proposed as potentially useful models for genetic control. An important aspect of these networks is the stability of their dynamics in response to small perturbations. Previous approaches to stability have assumed…

Disease awareness in infection dynamics can be modeled with adaptive contact networks whose rewiring rules reflect the attempt by susceptibles to avoid infectious contacts. Simulations of this type of models show an active phase with…

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…

Random Boolean networks have been used widely to explore aspects of gene regulatory networks. A modified form of the model through which to systematically explore the effects of increasing the number of gene states has previously been…

The mammalian brain could contain dense and sparse network connectivity structures, including both excitatory and inhibitory neurons, but is without any clearly defined output layer. The neurons have time constants, which mean that the…

Boolean networks have been successfully used in modelling gene regulatory networks. In this paper we propose a reduction method that reduces the complexity of a Boolean network but keeps dynamical properties and topological features and…