Related papers: Representing perturbed dynamics in biological netw…
We study the effect of intrinsic noise on the thermodynamic balance of complex chemical networks subtending cellular metabolism and gene regulation. A topological network property called deficiency, known to determine the possibility of…
The regulatory mechanisms driving progression of the yeast cell cycle appears to be comprised of an interacting network of transcription factors (TFs), cyclin-dependent kinases (CDK) and ubiquitin ligases. From a systems perspective the…
We study how the dynamics of a class of discrete dynamical system models for neuronal networks depends on the connectivity of the network. Specifically, we assume that the network is an Erd\H{o}s-R\'{enyi} random graph and analytically…
The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
Large-scale white matter pathways crisscrossing the cortex create a complex pattern of connectivity that underlies human cognitive function. Generative mechanisms for this architecture have been difficult to identify in part because little…
We propose a simple adaptive-network model describing recent swarming experiments. Exploiting an analogy with human decision making, we capture the dynamics of the model by a low-dimensional system of equations permitting analytical…
The importance of structured, complex connectivity patterns found in several real-world systems is to a great extent related to their respective effects in constraining and even defining the respective dynamics. Yet, while complex networks…
In this work we investigate time varying networks with complex dynamics at the nodes. We consider two scenarios of network change in an interval of time: first, we have the case where each link can change with probability pt, i.e. the…
A computer model is described which is used to assess the dynamical complexity of a class of networks of spiking neurons with small-world properties. Networks are constructed by forming an initially segregated set of highly intra-connected…
Inferring topological characteristics of complex networks from observed data is critical to understand the dynamical behavior of networked systems, ranging from the Internet and the World Wide Web to biological networks and social networks.…
Interactions between neighboring cells are essential for generating or refining patterns in a number of biological systems. We propose a discrete filtering approach to predict how networks of cells modulate spatially varying input signals…
We investigate the propagation of random fluctuations through biochemical networks in which the concentrations of species are large enough so that the unperturbed problem is well-described by ordinary differential equation. We characterize…
The network paradigm is increasingly used to describe the dynamics of complex systems. Here we review the current results and propose future development areas in the assessment of perturbation waves, i.e. propagating structural changes in…
Networks are fundamental for our understanding of complex systems. Interactions between individual nodes in networks generate network motifs - small recurrent patterns that can be considered the network's building-block components,…
The interest in dynamic processes on networks is steadily rising in recent years. In this paper, we consider the $(\alpha,\beta)$-Thresholded Network Dynamics ($(\alpha,\beta)$-Dynamics), where $\alpha\leq \beta$, in which only structural…
The deterministic dynamics of randomly connected neural networks are studied, where a state of binary neurons evolves according to a discreet-time synchronous update rule. We give a theoretical support that the overlap of systems' states…
Turing instability in activator-inhibitor systems provides a paradigm of nonequilibrium pattern formation; it has been extensively investigated for biological and chemical processes. Turing pattern formation should furthermore be possible…
We investigate urban street networks as a whole within the frameworks of information physics and statistical physics. Urban street networks are envisaged as evolving social systems subject to a Boltzmann-mesoscopic entropy conservation. For…
Attractors of dynamical systems may be networks in phase space that can be heteroclinic (where there are dynamical connections between simple invariant sets) or excitable (where a perturbation threshold needs to be crossed to a dynamical…