Related papers: A Spatial Filtering Approach to Biological Pattern…
We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary and intuitive placement of cells over a two-dimensional manifold. Using a bitmap image as input, where the color indicates the…
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…
Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic…
Developmental processes in multicellular organisms occur far from equilibrium, yet produce complex patterns with astonishing reproducibility. We measure the precision and reproducibility of bilaterally symmetric fly wings across the natural…
The shape of a cell influences and it is influenced by interactions with its neighbouring partners. Here, we introduce a coarse-grained model of non-reciprocal interactions between single-cell organisms to study emergent morphologies during…
Biological rhythms are generated by pacemaker organs, such as the heart pacemaker organ (the sinoatrial node) and the master clock of the circadian rhythms (the suprachiasmatic nucleus), which are composed of a network of autonomously…
This paper deals with the numerical modeling of wave propagation in porous media described by Biot's theory. The viscous efforts between the fluid and the elastic skeleton are assumed to be a linear function of the relative velocity, which…
The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in…
We study an abstracted model of neuronal activity via numerical simulation, and report spatiotemporal pattern formation and critical like dynamics. A population of pulse coupled, discretised, relaxation oscillators is simulated over…
Understanding the evolution of cellular microenvironments in spatiotemporal data is essential for deciphering tissue development and disease progression. While experimental techniques like spatial transcriptomics now enable high-resolution…
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…
In complex systems, groups of interacting objects may form prevalent and persistent spatiotemporal patterns, which we refer to as motifs. These motifs can exhibit features that reveal how individual objects interact with one another.…
From flocking birds to schooling fish, organisms interact to form collective dynamics across the natural world. Self-organization is present at smaller scales as well: cells interact and move during development to produce patterns in fish…
Spatially annotated single-cell datasets provide unprecedented opportunities to dissect cell-cell communication in development and disease. Heterotypic signaling includes interactions between different cell types and is well established in…
Systems of dynamical interactions between competing species can be used to model many complex systems, and can be mathematically described by {\em random} networks. Understanding how patterns of activity arise in such systems is important…
In many developmental systems, cells differentiate into a tissue by reading out morphogen concentration fields, a process fundamentally limited by noise. How much can the precision of this process be improved by nonlocal information, e.g.,…
Spatial organisation is a hallmark of all living cells, and recreating it in model systems is a necessary step in the creation of synthetic cells. It is therefore of both fundamental and practical interest to better understand the basic…
How can dense biological tissue maintain sharp boundaries between coexisting cell populations? We explore this question within a simple vertex model for cells, focusing on the role of topology and tissue surface tension. We show that the…
Dynamical systems theory provides powerful methods to extract effective macroscopic dynamics from complex systems with slow modes and fast modes. Here we derive and theoretically support a macroscopic, spatially discrete, model for a class…
Spiral waves are spatial-temporal patterns that can emerge in different systems as heart tissues, chemical oscillators, ecological networks and the brain. These waves have been identified in the neocortex of turtles, rats, and humans,…