Related papers: Theory for stability and regulation of epigenetic …
Non-linear maps can possess various dynamical behaviors varying from stable steady states and cycles to chaotic oscillations. Most models assume that individuals within a given population are identical ignoring the fundamental role of…
Linear dynamical systems are canonical models for learning-based control of plants with uncertain dynamics. The setting consists of a stochastic differential equation that captures the state evolution of the plant understudy, while the true…
Understanding the spatial organisation of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical -- or epigenetic -- marks that are deposited along the genome are thought to play an…
We analyst in detail a new approach to the monitoring and forecasting of the onset of transitions in high dimensional complex systems (see Phys. Rev. Lett . vol. 113, 264102 (2014)) by application to the Tangled Nature Model of evolutionary…
We study diffusion-driven pattern-formation in networks of networks, a class of multilayer systems, where different layers have the same topology, but different internal dynamics. Agents are assumed to disperse within a layer by undergoing…
Epigenetic landscapes, represented by patterns of chemical modifications on histone tails, are essential for maintaining cell identity and tissue homeostasis. These landscapes are shaped by multiple factors, including local biochemical…
Dynamics maintaining diversity of cell types in a multi-cellular system are studied in relationship with the plasticity of cellular states. By adopting a simple theoretical framework for intra-cellular chemical reaction dynamics with…
In considering evolution of transcribed regions, regulatory modules, and other genomic loci of interest, we are often faced with a situation in which the number of allelic states greatly exceeds the population size. In this limit, the…
We study long-range interacting systems driven by external stochastic forces that act collectively on all the particles constituting the system. Such a scenario is frequently encountered in the context of plasmas, self-gravitating systems,…
We develop a landscape-flux framework to investigate observed frequency distributions of vegetation and the stability of these ecological systems under fluctuations. The frequency distributions can characterize the population-potential…
How diversity is maintained in natural ecosystems is a long-standing question in Theoretical Ecology. By studying a system that combines ecological dynamics, heterogeneous interactions and spatial structure, we uncover a new mechanism for…
Delay is an inherent feature of genetic regulatory networks. It represents the time required for the assembly of functional regulator proteins. The protein production process is complex, as it includes transcription, translocation,…
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…
When can complex ecological interactions drive an entire ecosystem into a persistent non-equilibrium state, where species abundances keep fluctuating without going to extinction? We show that high-diversity spatially-extended systems, in…
The stability of ecological systems is a fundamental concept in ecology, which offers profound insights into species coexistence, biodiversity, and community persistence. In this article, we provide a systematic and comprehensive review on…
We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are…
Linear systems governed by continuous-time difference equations cover a wide class of linear systems. From the Lyapunov-Krasovskii approach, we investigate stability for such a class of systems. Sufficient conditions, and in some particular…
In this paper we investigate equilibria of continuous differential equation models of network dynamics. The motivation comes from gene regulatory networks where each directed edge represents either down- or up-regulation, and is modeled by…
We investigate the hydrodynamic stability and the formation of patterns in a continuum model of epithelial layers, able to account for the interplay between mechanical activity, lateral adhesion and the $6-$fold orientational order…
We analyze pattern formation on a network of cells where each cell inhibits its neighbors through cell-to-cell contact signaling. The network is modeled as an interconnection of identical dynamical subsystems each of which represents the…