Related papers: Flexible and robust patterning by centralized gene…
Biological systems rely on robust internal information processing: Survival depends on highly reproducible dynamics of regulatory processes. Biological information processing elements, however, are intrinsically noisy (genetic switches,…
A mechanism for self-organization of the degree of connectivity in model neural networks is studied. Network connectivity is regulated locally on the basis of an order parameter of the global dynamics which is estimated from an observable…
For many networks, it is useful to think of their nodes as being embedded in a latent space, and such embeddings can affect the probabilities for nodes to be adjacent to each other. In this paper, we extend existing models of synthetic…
We investigate the synchronization features of a network of spiking neurons under a distance-dependent coupling following a power-law model. The interplay between topology and coupling strength leads to the existence of different…
Generative mechanisms which lead to empirically observed structure of networked systems from diverse fields like biology, technology and social sciences form a very important part of study of complex networks. The structure of many…
Genetic regulatory networks are defined by their topology and by a multitude of continuously adjustable parameters. Here we present a class of simple models within which the relative importance of topology vs. interaction strengths becomes…
Genetic regulatory networks with adaptive responses are widely studied in biology. Usually, models consisting only of a few nodes have been considered. They present one input receptor for activation and one output node where the adaptive…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…
We study the versatile performance of networks of coupled circuits. Each of these circuits is composed of a positive and a negative feedback loop in a motif that is frequently found in genetic and neural networks. When two of these circuits…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
Power-law networks such as the Internet, terrorist cells, species relationships, and cellular metabolic interactions are susceptible to node failures, yet maintaining network connectivity is essential for network functionality.…
We explore the interplay of network structure, topology, and dynamic interactions between nodes using the paradigm of distributed synchronization in a network of coupled oscillators. As the network evolves to a global steady state,…
We propose a network model with a fixed number of nodes and links with a dynamics which favors links between nodes differing in connectivity. Parameter regimes where the degree distributions follow power-laws, P(k) ~ k^-gamma, high…
Boolean networks (BNs) are discrete-time systems where nodes are inter-connected (here we call such connection rule among nodes as network structure), and the dynamics of each gene node is determined by logical functions. In this paper, we…
Several approaches to cognition and intelligence research rely on statistics-based models testing, namely factor analysis. In the present work we exploit the emerging dynamical systems perspective putting the focus on the role of the…
Recent studies uncovered important core/periphery network structures characterizing complex sets of cooperative and competitive interactions between network nodes, be they proteins, cells, species or humans. Better characterization of the…
We consider here the morphogenesis (pattern formation) problem for some genetic network models. First, we show that any given spatio-temporal pattern can be generated by a genetic network involving a sufficiently large number of genes.…
The Unfolded Protein Response is the cell mechanism for maintaining the balance of properly folded proteins in the endoplasmic reticulum , the specialized cellular compartment. Although it is largely studied from a biological point of view,…
Gene regulatory networks must relay information from extracellular signals to downstream genes in an efficient, timely and coherent manner. Many complex functional tasks such as the immune response require system-wide broadcasting of…
We introduce a simple model of static networks, where nodes are located on a ring structure, and two accompanying dynamic rules of repeated averaging on periodic node states. We assume nodes can interact with neighbors, and will add…