Related papers: Substrate geometry affects population dynamics in …
Evolution occurs in populations of reproducing individuals. The structure of a biological population affects which traits evolve. Understanding evolutionary game dynamics in structured populations is difficult. Precise results have been…
Bacteria evolve resistance to antibiotics by a multitude of mechanisms. A central, yet unsolved question is how resistance evolution affects cell growth at different drug levels. Here we develop a fitness model that predicts growth rates of…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
The evolution of antimicrobial resistance generally occurs in an environment where antimicrobial concentration is variable, which has dramatic consequences on the microorganisms' fitness landscape, and thus on the evolution of resistance.…
We introduce a general theoretical framework to study the shape dynamics of actively growing and remodeling surfaces. Using this framework we develop a physical model for growing bacterial cell walls and study the interplay of cell shape…
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…
We analyze evolutionary dynamics in a confluent, branching cellular population, such as in a growing duct, vasculature, or in a branching microbial colony. We focus on the coarse-grained features of the evolution and build a statistical…
A hallmark of bacterial populations cultured in vitro is their homogeneity of growth, where the majority of cells display identical growth rate, cell size and content. Recent insights, however, have revealed that even cells growing in…
Laboratory experiments with bacterial colonies, under well-controlled conditions often lead to evolutionary diversification, where at least two ecotypes emerge from an initially monomorphic population. Empirical evidence suggests that such…
We quantitatively study the transport of E. coli near the walls of confined microfluidic channels, and in more detail along the edges formed by the interception of two perpendicular walls. Our experiments establish the connection between…
The growth and evolution of microbial populations is often subjected to advection by fluid flows in spatially extended environments, with immediate consequences for questions of spatial population genetics in marine ecology, planktonic…
We study the transport of bacteria in a porous media modeled by a square channel containing one cylindrical obstacle via molecular dynamics simulations coupled to a lattice Boltzmann fluid. Our bacteria model is a rod-shaped rigid body…
Biofilms in human tonsillar crypts show long term persistence with episodic dispersal that current biochemical and microbiological descriptions do not fully explain, particularly with respect to spatial localization. We introduce a…
Surface-adhesion and stiffness of underlying substrates mediate geometry, mechanics and self-organization of bacterial colonies. Recent studies have qualitatively indicted that stiffness may impact bacterial attachment, yet the variation of…
Horizontal gene transfer consists in exchanging genetic materials between microorganisms during their lives. This is a major mechanism of bacterial evolution and is believed to be of main importance in antibiotics resistance. We consider a…
Bacterial biofilms, surface-attached communities of cells, are in some respects similar to colloidal solids; both are densely packed with non-zero yield stresses. However, unlike non-living materials, bacteria reproduce and die, breaking…
The bacterium {\em Bacilus subtilis} frequently forms biofilms at the interface between the culture medium and the air. We develop a mathematical model that couples a description of bacteria as individual discrete objects to the standard…
There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can…
Microbial interactions regulate their spread and survival in competitive environments. It is not clear if the physical parameters of the environment regulate the outcome of these interactions. In this work, we show that the opportunistic…
The growth of crystals confined in porous or cellular materials is ubiquitous in Nature and industry. Confinement affects the formation of biominerals in living organisms, of minerals in the Earth's crust and of salt crystals damaging…