Related papers: Signaling gradients in surface dynamics as basis f…
During development, cell fates are determined through a combination of intracellular transcriptional regulations and extracellular signaling. As a result, spatial patterns of different cell types arise. We investigate the decision between…
We propose a unified mechanism that reproduces the sequence of dynamical transitions observed during somitogenesis, the process of body segmentation during embryonic development, that is invariant across all vertebrate species. This is…
Chemo-mechanical waves on active deformable surfaces are a key component for many vital cellular functions. In particular, these waves play a major role in force generation and long-range signal transmission in cells that dynamically change…
The evolutionary origins of structural features in reconstructed gene-regulatory networks (GRNs) remain poorly understood, especially given the random aspects of gene expression. Here, we extend a classical model of GRN evolution to allow a…
A cell is polarised when it has developed a main axis of organisation through the reorganisation of its cytosqueleton and its intracellular organelles. Polarisation can occur spontaneously or be triggered by external signals, like gradients…
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…
Reparameterization aims to improve the generalization of deep neural networks by transforming convolutional layers into equivalent multi-branched structures during training. However, there exists a gap in understanding how…
Data-driven dynamic models of cell biology can be used to predict cell response to unseen perturbations. Recent work (CellBox) had demonstrated the derivation of interpretable models with explicit interaction terms, in which the parameters…
The observation and description of collective excitations in solids is a fundamental issue when seeking to understand the physics of a many-body system. Analysis of these excitations is usually carried out by measuring the dynamical…
We study the surface fluctuations of a tissue with a dynamics dictated by cell-rearrangement, cell-division, and cell-death processes. Surface fluctuations are calculated in the homeostatic state, where cell division and cell death…
A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss…
During cell migration, cells become polarized, change their shape, and move in response to various internal and external cues. Cell polarization is defined through the spatio-temporal organization of molecules such as PI3K or small GTPases,…
We introduce a model for describing the dynamics of large numbers of interacting cells. The fundamental dynamical variables in the model are sub-cellular elements, which interact with each other through phenomenological intra- and…
A biophysical model of epimorphic regeneration based on a continuum percolation process of fully penetrable disks in two dimensions is proposed. All cells within a randomly chosen disk of the regenerating organism are assumed to receive a…
Long-time series of neuronal recordings are resulting from the activity of connected neuronal networks. Yet how neuronal properties can be extracted remains empirical. We review here the data analysis based on network models to recover…
The positioning of new cellular walls during cell division plays a key role in shaping plant tissue organization. The influence of cell geometry on the positioning of division planes has been previously captured into various geometrical…
The onset of life is often framed around membrane bound compartments and encoded metabolism, leaving unresolved how spatial organization arose before stable boundaries. In this context, environmental gradients are usually treated as…
Data-driven neural networks are increasingly used as surrogate forward models in geophysics, but it remains unclear whether they recover only the data mapping or also the underlying physical sensitivity structure. Here we test this question…
In the fields of computation and neuroscience, much is still unknown about the underlying computations that enable key cognitive functions including learning, memory, abstraction and behavior. This paper proposes a mathematical and…
Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…