Related papers: The colon-pile
Bacterial communities such as biofilms are widely recognised as being important for survival and persistence of bacteria in harsh environments. Mechanistic models of biofilm growth indicate that the way in which the surface is seeded can…
Microbial populations in the natural environment are likely to experience growth conditions very different from those of a typical laboratory xperiment. In particular, removal rates of biomass and substrate are unlikely to be balanced under…
Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have…
We study diffusion of particles in large-scale simulations of one-dimensional stochastic sandpiles, in both the restricted and unrestricted versions. The results indicate that the diffusion constant scales in the same manner as the activity…
We introduce a sandpile model where, at each unstable site, all grains are transferred randomly to downstream neighbors. The model is local and conservative, but not Abelian. This does not appear to change the universality class for the…
Mechanical stresses stemming from environmental factors are a key determinant of cellular behavior and physiology. Yet, the role of self-induced biomechanical stresses in growing bacterial colonies has remained largely unexplored. Here, we…
We study a generic model for quorum-sensing bacteria in circular confinement. Every bacterium produces signaling molecules, the local concentration of which triggers a response when a certain threshold is reached. If this response lowers…
Biofilms inhabit a range of environments, such as dental plaques or soil micropores, often characterized by intricate, non-even surfaces. However, the impact of surface irregularities on the population dynamics of biofilms remains elusive…
We consider a spatial version of the classical Moran model with seed-banks where the constituent populations have finite sizes. Individuals live in colonies labelled by $\mathbb{Z}^d$, $d\geq 1$, playing the role of a geographic space,…
Microcolonies are aggregates of a few dozen to a few thousand cells exhibited by many bacteria. The formation of microcolonies is a crucial step towards the formation of more mature bacterial communities known as biofilms, but also marks a…
We studied the swimming of \textit{Escherichia coli} bacteria in the vicinity of the critical point in a solution of the non-ionic surfactant \chem{C_{12}E_{5}} in buffer solution. In phase contrast microscopy, each swimming cell produces a…
Sand pile formation is often used to describe stratified chaos in dynamic systems due to self-emergent and scale invariant behaviour. Cellular automata (Bak-Tang-Wiesenfeld model) are often used to describe chaotic behaviour, as simulating…
When sand flows out of a funnel onto a surface, a three dimensional pile that is stabilized by friction grows taller as it spreads. Here we investigate an idealized two dimensional analogue: spreading of a pile of monodisperse oil droplets…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
Diseases emerge, persist and vanish in an ongoing battle for available hosts. Hosts, on the other hand, defend themselves by developing immunity that limits the ability of pathogens to reinfect them. We here explore a multi-disease system…
Anaerobic processes (e.g., methanogenesis and fermentation) largely contribute to element cycling and natural contaminant attenuation/mobilization, even in well-oxygenated porous environments, such as shallow aquifers. This paradox is…
The run-and-tumble dynamics of bacteria, as exhibited by \textit{E. coli}, offers a simple experimental realization of non-Brownian, yet diffusive, particles. Here we present some analytic and numerical results for models of the ideal…
The intestinal microbiota plays important roles in digestion and resistance against entero-pathogens. As with other ecosystems, its species composition is resilient against small disturbances but strong perturbations such as antibiotics can…
A new experimental colonial pattern and pattern transition observed in E. coli MG1655 swarming cells grown on semi-solid agar are described. We present a reaction-diffusion model that, taking into account the slime generated by these cells…
We study colonies of non-motile, rod-shaped bacteria growing on solid substrates. In our model, bacteria interact purely mechanically, by pushing each other away as they grow, and consume a diffusing nutrient. We show that mechanical…