Related papers: Selective sweeps in growing microbial colonies

High-throughput experimental techniques and bioinformatics tools make it possible to obtain reconstructions of the metabolism of microbial species. Combined with mathematical frameworks such as flux balance analysis, which assumes that…

A contemporary procedure to grow artificial tissue is to seed cells onto a porous biomaterial scaffold and culture it within a perfusion bioreactor to facilitate the transport of nutrients to growing cells. Typical models of cell growth for…

The solution space of genome-scale models of cellular metabolism provides a map between physically viable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the corresponding growth rates. By…

The field of active matter explores the behaviors of self propelled agents out of equilibrium, with active suspensions, such as swimming bacteria in solutions, serving as impactful models. These systems exhibit spatio-temporal patterns akin…

The idea that there are any large-scale trends in the evolution of biological organisms is highly controversial. It is commonly believed, for example, that there is a large-scale trend in evolution towards increasing complexity, but…

We study the evolution of recombination using a microscopic model developed within the frame of the theory of quantitative traits. Two components of fitness are considered: a static one that describes adaptation to environmental factors not…

We consider a mutation-selection model of a population structured by the spatial variables and a trait variable which is the diffusion rate. Competition for resource is local in spatial variables, but nonlocal in the trait variable. We…

Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…

We study the interplay of population growth and evolutionary dynamics using a stochastic model based on birth and death events. In contrast to the common assumption of an independent population size, evolution can be strongly affected by…

We introduce a non-diffusive spatial coupling term into the replicator equation of evolutionary game theory. The spatial flux is based on motion due to local gradients in the relative fitness of each strategy, providing a game-dependent…

We introduce and study a stochastic model for the dynamics of colonial species, which reproduce through fission or fragmentation. The fission rate depends on the relative sizes of colonies in the population, and the growth rate of colonies…

I present three models of plant--pathogen interactions. The models are stochastic and spatially explicit at the scale of individual plants. For each model, I use a version of pair approximation or moment closure along with a separation of…

We report experimental and theoretical results on spatiotemporal pattern formation in cell populations, where the parameters vary in space and time due to mechanisms intrinsic to the system, namely Dictyostelium discoideum (D.d.) in the…

In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense,…

Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…

Selective adsorption in a two-dimensional model of a binary hard-disk mixture on patterned adhesive surfaces is studied using grand canonical Monte Carlo simulations. The two species have equal diameters and equal bulk chemical potentials,…

In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the…

Baker's yeast (Saccharomyces cerevisiae) is a model organism for studying the morphology that emerges at the scale of multi-cell colonies. To look at how morphology develops, we collect a dataset of time-lapse photographs of the growth of…

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…

Microbial populations generally evolve in volatile environments, under conditions fluctuating between harsh and mild, e.g. as the result of sudden changes in toxin concentration or nutrient abundance. Environmental variability thus shapes…