Related papers: Morphogenesis by coupled regulatory networks

Temporal dynamics, characterised by time-varying degree heterogeneity and homophily effects, are often exhibited in many real-world networks. As observed in an MIT Social Evolution study, the in-degree and out-degree of the nodes show…

Living systems implement and execute an extraordinary plethora of computational tasks. The inherent degree of large scale coordination emerges as a global property, from the intricate sea of microscopic interactions. The brain, with its…

Controllable layout generation aims at synthesizing plausible arrangement of element bounding boxes with optional constraints, such as type or position of a specific element. In this work, we try to solve a broad range of layout generation…

We study numerically the coarsening dynamics of the Ising model on a regular lattice with random bonds and on deterministic fractal substrates. We propose a unifying interpretation of the phase-ordering processes based on two classes of…

Intracellular protein patterns regulate many vital cellular functions, such as the processing of spatiotemporal information or the control of shape deformations. To do so, pattern-forming systems can be sensitive to the cell geometry by…

Phase transitions constitute fundamental mechanisms underlying abrupt or qualitative changes in the collective dynamics of interacting units across a wide range of natural and engineered systems. In dynamical networks, such transitions lead…

This paper uses a recently presented abstract, tuneable Boolean regulatory network model extended to consider aspects of mobile DNA, such as transposons. The significant role of mobile DNA in the evolution of natural systems is becoming…

Modeling dynamical systems and unraveling their underlying causal relationships is central to many domains in the natural sciences. Various physical systems, such as those arising in cell biology, are inherently high-dimensional and…

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 dynamics of gene regulatory networks is governed by the interaction between deterministic biochemical reactions and molecular noise. To understand how gene regulatory networks process information during cell state transitions, we study…

During development of biological organisms, multiple complex structures are formed. In many instances, these structures need to exhibit a high degree of order to be functional, although many of their constituents are intrinsically…

We introduce a model of adaptive temporal networks whose evolution is regulated by an interplay between node activity and dynamic exchange of information through links. We study the model by using a master equation approach. Starting from a…

Most biological systems are formed by component parts that to some degree are inter-related. Groups of parts that are more associated among themselves and are relatively autonomous from others are called modules. One of the consequences of…

Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…

We analyze an inhomogeneous system of coupled reaction-diffusion equations representing the dynamics of gene expression during differentiation of nerve cells. The outcome of this developmental phase is the formation of distinct functional…

In densely-packed two-dimensional systems of growing cells, such as rod-shaped bacteria, a number of experimental and numerical studies report distinct patterns of nematic orientational order in the presence of confinement. So far, these…

MicroRNAs are extensively known for post-transcriptional gene regulation and pattern formation in the embryonic developmental stage. We explore the origin of these spatio-temporal patterns mathematically, considering three different motifs…

We present schema redescription as a methodology to characterize canalization in automata networks used to model biochemical regulation and signalling. In our formulation, canalization becomes synonymous with redundancy present in the logic…

Gene expression-based heterogeneity analysis has been extensively conducted. In recent studies, it has been shown that network-based analysis, which takes a system perspective and accommodates the interconnections among genes, can be more…

In this paper, we propose an evolving network model growing fast in units of module, based on the analysis of the evolution characteristics in real complex networks. Each module is a small-world network containing several interconnected…