Related papers: Maximum entropy and population heterogeneity in co…
Stochastic models that incorporate birth, death and immigration (also called birth-death and innovation models) are ubiquitous and applicable to many research topics such as quantifying species sizes in ecological populations, describing…
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time…
We suggest a natural approach that leads to a modification of classical quasispecies models and incorporates the possibility of population extinction in addition to growth. The resulting modified models are called open. Their essential…
A novel theory for cell differentiation is proposed, based on simulations with interacting artificial cells which have metabolic networks within, and divide into two when the final product is accumulated. Results of simulations with coupled…
A classic problem in metabolism is that fast-proliferating cells use seemingly wasteful fermentation for energy biogenesis in the presence of sufficient oxygen. This counterintuitive phenomenon, known as overflow metabolism or the Warburg…
Cell-to-cell heterogeneity drives a range of (patho)physiologically important phenomena, such as cell fate and chemotherapeutic resistance. The role of metabolism, and particularly mitochondria, is increasingly being recognised as an…
Most population models assume that individuals within a given population are identical, that is, the fundamental role of variation is ignored. Inhomogeneous models of populations and communities allow for birth and death rates to vary among…
We consider the chemostat model with the substrate concentration as the single measurement. We propose a control strategy that drives the system at a steady state maximizing the gas production without the knowledge of the specific growth…
Understanding the behaviors of ecological systems is challenging given their multi-faceted complexity. To proceed, theoretical models such as Lotka-Volterra dynamics with random interactions have been investigated by the dynamical…
Mixture models provide a flexible representation of heterogeneity in a finite number of latent classes. From the Bayesian point of view, Markov Chain Monte Carlo methods provide a way to draw inferences from these models. In particular,…
Chemotaxis-driven invasions have been proposed across a broad spectrum of biological processes, from cancer to ecology. The influential system of equations introduced by Keller and Segel has proven a popular choice in the modelling of such…
Biological systems are modular, and this modularity evolves over time and in different environments. A number of observations have been made of increased modularity in biological systems under increased environmental pressure. We here…
Cells sense environmental signals and transmit information intracellularly through changes in the abundance of molecular components. Such molecular abundances can be measured in single cells and exhibit significant heterogeneity in clonal…
The dynamics of molecular collisions in a macroscopic body are encoded by the parameter Thermodynamic entropy - a statistical measure of the number of molecular configurations that correspond to a given macrostate. Directionality in the…
This paper studies a two microbial species model in competition for a single resource in the chemostat including general interspecific density-dependent growth rates with distinct removal rates for each species. We give the necessary and…
We introduce a new coordination problem in distributed computing that we call the population stability problem. A system of agents each with limited memory and communication, as well as the ability to replicate and self-destruct, is…
Cell growth, division and death are defining features of biological tissues that contribute to morphogenesis. In hydrodynamic descriptions of cohesive tissues, their occurrence implies a non-zero rate of variation of cell density. We show…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
The processes of interplant competition within a field are still poorly understood. However, they explain a large part of the heterogeneity in a field and may have longer-term consequences, especially in mixed stands. Modeling can help to…
Many biological populations exhibit diversity in their strategy for survival and reproduction in a given environment, and microbes are an example. We explore the fate of different strategies under sustained environmental change by…