Related papers: Dynamic landscapes and statistical limits on growt…

Network science provides an indispensable theoretical framework for studying the structure and function of real complex systems. Different network models are often used for finding the rules that govern their evolution, whereby the correct…

Spatial and temporal resource constraints are critical for both biological and artificial intelligent systems. Here we define differentiable cost terms for breadth, depth, and time within a recurrent convolutional neural network conceived…

Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…

Here we introduce a model in which individuals differ in the rate at which they seek new interactions with others, making rational decisions modeled as general symmetric two-player games. Once a link between two individuals has formed, the…

Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…

Cells can often choose among several stably heritable phenotypes. Examples are the expression of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states, that may be associated…

The migratory dynamics of cells can be influenced by the complex micro-environment through which they move. It remains unclear how the motility machinery of confined cells responds and adapts to their micro-environment. Here, we propose a…

In any ecosystem, the conditions of the environment and the characteristics of the species that inhabit it are entangled, co-evolving in space and time. We introduce a model that couples active agents with a dynamic environment, interpreted…

Networks of gene regulation govern morphogenesis, determine cell identity and regulate cell function. But we have little understanding, at the local level, of which logics are biologically preferred or even permitted. To solve this puzzle,…

For the first time the phenomenon of cellular structure coarsening are consistently analysed from the positions of kinetic, hydrodynamic and stochastodynamic theories of nonequilibrium statistical systems. Thereby micro-, meso- and…

Motivation: Networks underlie the generation and interpretation of many biological datasets: gene networks shed light on the regulatory structure of the genome, and cell networks can capture structure of the tumor micro-environment.…

Time-discrete dynamical systems on a finite state space have been used with great success to model natural and engineered systems such as biological networks, social networks, and engineered control systems. They have the advantage of being…

Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically…

A theoretical model for stratified epithelium is presented. The viscoelastic properties of the tissue is assumed to be dependent on the spatial distribution of proliferative and differentiated cells. Based on this assumption, a hydrodynamic…

Life systems are complex and hierarchical, with diverse components at different scales, yet they sustain themselves, grow, and evolve over time. How can a theory of such complex biological states be developed? Here we note that for a…

We systematically study the boundaries of one-dimensional, 2-color cellular automata depending on 4 cells, begun from simple initial conditions. We determine the exact growth rates of the boundaries that appear to be reducible. Morphic…

The dynamical processes taking place on a network depend on its topology. Influencing the growth process of a network therefore has important implications on such dynamical processes. We formulate the problem of influencing the growth of a…

We propose a kind of reaction-diffusion equations for cell differentiation, which exhibits the Turing instability. If the diffusivity of some variables is set to be infinity, we get coupled competitive reaction-diffusion equations with a…

This article is a presentation of specific recent results describing scaling limits of individual-based models. Thanks to them, we wish to relate the time-scales typical of demographic dynamics and natural selection to the parameters of the…

During developmental processes such as embryogenesis, how a group of cells fold into specific structures, is a central question in biology that defines how living organisms form. Establishing tissue-level morphology critically relies on how…