Related papers: Failure of antibiotic treatment in microbial popul…
Biological systems perform complex multi-step processes in a reproducible way despite underlying stochasticity. The standard explanation is micromanagement by molecular machinery that recognizes and corrects specific errors. Here we study…
We investigate the propagating profiles of a degenerate chemotaxis model describing the bacteria chemotaxis and consumption of oxygen by aerobic bacteria, in particular, the effect of the initial attractant distribution on bacterial…
The CRISPR (clustered regularly interspaced short palindromic repeats) mechanism allows bacteria to adaptively defend against phages by acquiring short genomic sequences (spacers) that target specific sequences in the viral genome. We…
Ecology and evolution under changing environments are important in many subfields of biology with implications for medicine. Here, we explore an example: the consequences of fluctuating environments on the emergence of antibiotic…
We study the chemotaxis of a population of genetically identical swimming bacteria undergoing run and tumble dynamics driven by stochastic switching between clockwise and counterclockwise rotation of the flagellar rotary system.…
We show that a chemostat community of bacteria and bacteriophage in which bacteria compete for a single nutrient and for which the bipartite infection network is perfectly nested is permanent, a.k.a. uniformly persistent, provided that…
Disease control is of paramount importance in public health with infectious disease extinction as the ultimate goal. Although diseases may go extinct due to random loss of effective contacts where the infection is transmitted to new…
Many organisms form colonies for a transient period of time to withstand environmental pressure. Bacterial biofilms are a prototypical example of such behavior. Despite significant interest across disciplines, physical mechanisms governing…
The sustainable use of multicomponent treatments such as combination therapies, combination vaccines/chemicals, and plants carrying multigenic resistance requires an understanding of how their population-wide deployment affects the speed of…
New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial…
The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform…
We study the growth of a population of bacteria in a dynamical hostile environment corresponding to the immune system of the colonised organism. The immune cells evolve as subcritical open clusters of oriented percolation and are…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
We study distributed agreement in microbial distributed systems under stochastic population dynamics and competitive interactions. Motivated by recent applications in synthetic biology, we examine how the presence and absence of direct…
We consider optimal vaccination protocol where the vaccine is in short supply. In this case, disease extinction results from a large and rare fluctuation. We show that the probability of such fluctuation can be exponentially increased by…
Bacteria are able to respond to environmental signals by changing their rules of movement. When we take into account chemical signals in the environment, this behaviour is often called chemotaxis. At the individual-level, chemotaxis…
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…
We present a model for a biological reactor in which bacteria tend to aggregate in flocs, as encountered in wastewater treatment plants. The influence of this flocculation on the growth dynamics of the bacteria is studied. We argue that a…
Antibiotics are the wonder discoveries to combat microbes. For decades, multiple varieties of antibiotics have been used for therapeutic purposes in hospital settings and communities throughout the world. Unfortunately, bacteria have become…
Phages use bacterial host resources to replicate, intrinsically linking phage and host survival. To understand phage dynamics, it is essential to understand phage-host ecology. A key step in this ecology is infection of bacterial hosts.…