Related papers: Interplay between degree and Boolean rules in the …
Regulatory dynamics in biology is often described by continuous rate equations for continuously varying chemical concentrations. Binary discretization of state space and time leads to Boolean dynamics. In the latter, the dynamics has been…
Different Boolean networks may reveal similar dynamics although their definition differs, then preventing their distinction from the observations. This raises the question about the sufficiency of a particular Boolean network for properly…
Due to the scarcity of quantitative details about biological phenomena, quantitative modeling in systems biology can be compromised, especially at the subcellular scale. One way to get around this is qualitative modeling because it requires…
We propose that negative degree correlation among nodes in a network of nonlinear oscillators, often detected in real world networks, is motivated by its positive effects on synchronizability. In so doing, we use a novel methodology to…
Two node variables determine the evolution of cascades in random networks: a node's degree and threshold. Correlations between both fundamentally change the robustness of a network, yet, they are disregarded in standard analytic methods as…
We study experimentally the synchronization patterns in time-delayed directed Boolean networks of excitable systems. We observe a transition in the network dynamics when the refractory time of the individual systems is adjusted. When the…
In automata networks, it is well known that the way entities update their states over time has a major impact on their dynamics. In particular, depending on the chosen update schedule, the underlying dynamical systems may exhibit more or…
We examined the effects of inhomogeneity on the dynamics and structural properties using Boolean networks. Two different power-law rank outdegree distributions were embedded to determine the role of hubs. The degree of randomness and…
Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…
The concept of control is crucial for effectively understanding and applying biological network models. Key structural features relate to control functions through gene regulation, signaling, or metabolic mechanisms, and computational…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a…
The performance of attractor neural networks has been shown to depend crucially on the heterogeneity of the underlying topology. We take this analysis a step further by examining the effect of degree-degree correlations -- or assortativity…
Boolean Networks and their dynamics are of great interest as abstract modeling schemes in various disciplines, ranging from biology to computer science. Whereas parallel update schemes have been studied extensively in past years, the level…
Boolean networks are used to model biological networks such as gene regulatory networks. Often Boolean networks show very chaotic behaviour which is sensitive to any small perturbations. In order to reduce the chaotic behaviour and to…
We introduce a model to study the effect of degree-frequency correlations on synchronization in networks of coupled oscillators. Analyzing this model, we find several remarkable characteristics. We find a stationary synchronized state that…
Feedback loops in a dynamic network play an important role in determining the dynamics of that network. Through a computational study, in this paper we show that networks with fewer independent negative feedback loops tend to exhibit more…
The dynamics of noise-resilient Boolean networks with majority functions and diverse topologies is investigated. A wide class of possible topological configurations is parametrized as a stochastic blockmodel. For this class of networks, the…
The problem of controllability of the dynamical state of a network is central in network theory and has wide applications ranging from network medicine to financial markets. The driver nodes of the network are the nodes that can bring the…
Many biological systems, such as metabolic pathways, exhibit bistability behavior: these biological systems exhibit two distinct stable states with switching between the two stable states controlled by certain conditions. Since…