Related papers: Dynamical Instability in Boolean Networks as a Per…
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.…
Boolean networks are discrete dynamical systems in which the state (zero or one) of each node is updated at each time t to a state determined by the states at time t-1 of those nodes that have links to it. When these systems are used to…
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…
Random Boolean networks, the Kauffman model, are revisited by means of a novel decimation algorithm, which reduces the networks to their dynamical cores. The average size of the removed part, the stable core, grows approximately linearly…
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…
Continuous-time systems with switch-like behaviour occur in chemical kinetics, gene regulatory networks and neural networks. Networks with hard switching, as a limiting case of smooth sigmoidal switching, retain the richest possible range…
We study a coupled dynamics of a network and a particle system. Particles of density $\rho$ diffuse freely along edges, each of which is rewired at a rate given by a decreasing function of particle flux. We find that the coupled dynamics…
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…
The function of a real network depends not only on the reliability of its own components, but is affected also by the simultaneous operation of other real networks coupled with it. Robustness of systems composed of interdependent network…
Recently, new results on percolation of interdependent networks have shown that the percolation transition can be first order. In this paper we show that, when considering antagonistic interactions between interacting networks, the…
We continue our consideration of a class of models describing the reversible dynamics of $N$ Boolean variables, each with $K$ inputs. We investigate in detail the behavior of the Hamming distance as well as of the distribution of orbit…
Boolean networks are an important class of computational models for molecular interaction networks. Boolean canalization, a type of hierarchical clustering of the inputs of a Boolean function, has been extensively studied in the context of…
Recently, the percolation transition has been characterized on interacting networks both in presence of interdependent and antagonistic interactions. Here we characterize the phase diagram of the percolation transition in two Poisson…
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…
Oscillatory dynamics are ubiquitous in biological networks. Possible sources of oscillations are well understood in low-dimensional systems, but have not been fully explored in high-dimensional networks. Here we study large networks…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
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…
The distribution of entanglement between the nodes of a quantum network plays a fundamental role in quantum information applications. In this work, we investigate the dynamics of a network of qubits where each edge corresponds to an…
Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by…
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex…