Related papers: Modular Gene Dynamics and Network Theory at Mesosc…

This work concerns a many-body deterministic model that displays life-like properties as emergence, complexity, self-organization, spontaneous compartmentalization, and self-regulation. The model portraits the dynamics of an ensemble of…

In this paper we categorize dynamical regimes demonstrated by star-like networks with chaotic nodes. This analysis is done in view of further studying of chaotic scale-free networks, since a star-like structure is the main motif of them. We…

This paper (parts I and II) provides an expository introduction to monotone and near-monotone dynamical systems associated to biochemical networks, those whose graphs are consistent or near-consistent. Many conclusions can be drawn from…

The interplay between topology and dynamics in complex networks is a fundamental but widely unexplored problem. Here, we study this phenomenon on a prototype model in which the network is shaped by a dynamical variable. We couple the…

Previous efforts in complex networks research focused mainly on the topological features of such networks, but now also encompass the dynamics. In this Letter we discuss the relationship between structure and dynamics, with an emphasis on…

Modeling gene regulatory networks (GRNs) is an important topic in systems biology. Although there has been much work focusing on various specific systems, the generic behavior of GRNs with continuous variables is still elusive. In…

In network science complex systems are represented as a mathematical graphs consisting of a set of nodes representing the components and a set of edges representing their interactions. The framework of networks has led to significant…

During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local,…

Inferring network topology from dynamical observations is a fundamental problem pervading research on complex systems. Here, we present a simple, direct method to infer the structural connection topology of a network, given an observation…

We search for conditions under which a characteristic time scale for ordering dynamics towards either of two absorbing states in a finite complex network of interactions does not exist. With this aim, we study random networks and networks…

A key issue in complex systems regards the relationship between topology and dynamics. In this work, we use a recently introduced network property known as steering coefficient as a means to approach this issue with respect to different…

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

Over the past two decades, complex network theory provided the ideal framework for investigating the intimate relationships between the topological properties characterizing the wiring of connections among a system's unitary components and…

Biological neural networks are notoriously hard to model due to their stochastic behavior and high dimensionality. We tackle this problem by constructing a dynamical model of both the expectations and covariances of the fractions of active…

We study the relationship between topological scales and dynamic time scales in complex networks. The analysis is based on the full dynamics towards synchronization of a system of coupled oscillators. In the synchronization process, modular…

A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between…

Mechanisms of pattern formation---of which the Turing instability is an archetype---constitute an important class of dynamical processes occurring in biological, ecological and chemical systems. Recently, it has been shown that the Turing…

We explore the coupled dynamics of the internal states of a set of interacting elements and the network of interactions among them. Interactions are modeled by a spatial game and the network of interaction links evolves adapting to the…

This paper considers the problem of detecting topology variations in dynamical networks. We consider a network whose behavior can be represented via a linear dynamical system. The problem of interest is then that of finding conditions under…

The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small world property of real…