Related papers: Sequential pattern formation governed by signaling…
In many adult tissues, stem cells and differentiated cells are not homogeneously distributed : stem cells are arranged in periodic "niches", and differentiated cells are constantly produced and migrate out of these niches. In this article,…
Spatiotemporal patterns are common in biological systems. For electrically-coupled cells previous studies of pattern formation have mainly used external forcing as the main bifurcation parameter. The purpose of this paper is to show that…
We propose a new class of waveform foundation models that departs from conventional sequence based representations by modeling physiological time series as realizations of latent event processes. Rather than treating signals as collections…
Cells are constantly exposed to diverse stimuli-chemical, mechanical, or electrical-that guide their movement. In physiological conditions, these signals often overlap, as seen during infections, where neutrophils and dendritic cells…
Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…
Spatio-temporal pattern formation over the square and rectangular domain has received significant attention from researchers. A wide range of stationary and non-stationary patterns produced by two interacting populations is abundant in the…
Biological patterns generated during development and regeneration often scale with organism size. Some organisms, e.g., flatworms, can regenerate a rescaled body plan from tissue fragments of varying sizes. Inspired by these examples, we…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
Systemic properties of living cells are the result of molecular dynamics governed by so-called genetic regulatory networks (GRN). These networks capture all possible features of cells and are responsible for the immense levels of adaptation…
A key feature of many developmental systems is their ability to self-organize spatial patterns of functionally distinct cell fates. To ensure proper biological function, such patterns must be established reproducibly, by controlling and…
Emergence of regular spatial patterns is a hallmark in living matter ranging from subcellular organelles to developing embryos and to ecosystems. Mechanisms for the formation of ordered spatial patterns in biology often require chemical…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Proteins are macromolecules that mediate a significant fraction of the cellular processes that underlie life. An important task in bioengineering is designing proteins with specific 3D structures and chemical properties which enable…
The spontaneous generation of electrical activity underpins a number of essential physiological processes, and is observed even in tissues where specialized pacemaker cells have not been identified. The emergence of periodic oscillations in…
A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the…
In this paper we use a continuous model to describe the development of a single cell lineage following the committal of stem cells. Three separate controls are implemented in the model, namely the proliferative control of stem cells, the…
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…
Oscillatory phase pattern formation and amplitude control for a linearized stochastic neuron field model was investigated by simulating coupled stochastic processes defined by stochastic differential equations. It was found, for several…
From tumour invasion to cell sorting and animal territoriality, many biological systems rely on nonlocal interactions that drive complex spatial organisation. Partial differential equations (PDEs) with nonlocal advection are increasingly…