Related papers: Statistical dynamics of spatial-order formation by…

Communication in a network generally takes place through a sequence of intermediate nodes connected by communication channels. In the standard theory of communication, it is assumed that the communication network is embedded in a classical…

Generative models, such as GANs and diffusion models, have been used to augment training sets and boost performances in different tasks. We focus on generative models for cell detection instead, i.e., locating and classifying cells in given…

A central question in developmental biology is how size and position are determined. The genetic code carries instructions on how to control these properties in order to regulate the pattern and morphology of structures in the developing…

Rhythmic and sequential segmentation of the embryonic body plan is a vital developmental patterning process in all vertebrate species. However, a theoretical framework capturing the emergence of dynamic patterns of gene expression from the…

Classical particles driven through periodically modulated potential energy landscapes are predicted to follow a Devil's staircase hierarchy of commensurate trajectories depending on the orientation of the driving force. Recent experiments…

Simplicial complexes constitute the underlying topology of interacting complex systems including among the others brain and social interaction networks. They are generalized network structures that allow to go beyond the framework of…

The ability of cells to reorganize in response to external stimuli is important in areas ranging from morphogenesis to tissue engineering. Elongated cells can co-align due to steric effects, forming states with local order. We show that…

We show that when cells communicate by contact-mediated interactions, heterogeneity in cell shapes and sizes leads to qualitatively distinct collective behavior in the tissue. For inter-cellular coupling that implements lateral inhibition,…

Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…

A variety of living and non-living systems exhibit collective motion. From swarm robotics to bacterial swarms, and tissue wound healing to human crowds, examples of collective motion are highly diverse but all of them share the common…

A novel mechanism for cell differentiation is proposed, based on the dynamic clustering in a globally coupled chaotic system. A simple model with metabolic reaction, active transport of chemicals from media, and cell division is found to…

The transport and chemical reactions of solutes are modelled as a cellular automaton in which molecules of different species perform a random walk on a regular lattice and react according to a local probabilistic rule. The model describes…

This paper proposes a control theoretic framework to model and analyze the self-organized pattern formation of molecular concentrations in biomolecular communication networks, emerging applications in synthetic biology. In biomolecular…

Many imaging techniques for biological systems -- like fixation of cells coupled with fluorescence microscopy -- provide sharp spatial resolution in reporting locations of individuals at a single moment in time but also destroy the dynamics…

Networks having the geometry and the connectivity of trees are considered as the spatial support of spatiotemporal dynamical processes. A tree is characterized by two parameters: its ramification and its depth. The local dynamics at the…

Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behaviour of single cells, we use extensive Monte Carlo simulations to predict non-trivial…

Proteins control many vital functions in living cells, such as cell growth and cell division. Reliable coordination of these functions requires the spatial and temporal organizaton of proteins inside cells, which encodes information about…

Self-organization phenomena in ensembles of self-propelled particles open pathways to the synthesis of new dynamic states not accessible by traditional equilibrium processes. The challenge is to develop a set of principles that facilitate…

Exchange of molecules allows cells to exchange information. How robust is the information to changes in cell parameters? We use a mapping between the stochastic dynamics of two cells sharing a stimulatory molecule, and parameters akin to an…

We study the random walk of a particle in a compartmentalized environment, as realized in biological samples or solid state compounds. Each compartment is characterized by its length $L$ and the boundaries transmittance $T$. We identify two…