Related papers: Optimal search in E.coli chemotaxis
We propose two nonlinear random walk models which are suitable for the analysis of both chemotaxis and anomalous transport. We derive the balance equations for the population density for the case when the transition rate for a random walk…
Diverse processes--e.g. bioremediation, biofertilization, and microbial drug delivery--rely on bacterial migration in disordered, three-dimensional (3D) porous media. However, how pore-scale confinement alters bacterial motility is unknown…
In this chapter, we consider the problem of a non-Markovian random walker (displaying memory effects) searching for a target. We review an approach that links the first passage statistics to the properties of trajectories followed by the…
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…
We study chemotaxis in a porous medium using as a model a biased ("hungry") random walk on a percolating cluster. In close resemblance to the 1980s arcade game Pac-Man, the hungry random walker consumes food, which is initially distributed…
Motility is fundamental to the survival and proliferation of microorganisms. The E. coli bacterium propels itself using a bundle of rotating helical flagella. If one flagellum reverses its rotational direction, it leaves the bundle,…
The viscosity of an active suspension of E-Coli bacteria is determined experimentally in the dilute and semi dilute regime using a Y shaped micro-fluidic channel. From the position of the interface between the pure suspending fluid and the…
The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture, in which all cells have equal access to nutrients. In the real world, bacteria are more likely to live in…
There are various cases of animal movement where behaviour broadly switches between two modes of operation, corresponding to a long distance movement state and a resting or local movement state. Here a mathematical description of this…
Efficient search acts as a strong selective force in biological systems ranging from cellular populations to predator-prey systems. The search processes commonly involve finding a stationary or mobile target within a heterogeneously…
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…
We have developed and implemented a numerical evolution scheme for a class of stochastic problems in which the temporal evolution occurs on widely-separated time scales, and for which the slow evolution can be described in terms of a small…
Motivated by observations of the dynamics of {\it Myxococcus xanthus}, we present a self-interacting random walk model that describes the competition between chemokinesis and chemotaxis. Cells are constrained to move in one dimension, but…
An increasing number of experimental studies employ single particle tracking to probe the physical environment in complex systems. We here propose and discuss new methods to analyze the time series of the particle traces, in particular, for…
Growing living cultures of Escherichia coli bacteria were investigated using real-time in situ rheology and rheo-imaging measurements. In the early stages of growth (lag phase), and when subjected to a constant stationary shear, the…
We study non-equilibrium bacterial colony growth using a geometry-first, time-resolved analysis of morphology. From time-lapse microscopy data, we track the coupled evolution of area, perimeter, and boundary-sensitive shape descriptors…
Cells frequently employ extracellular vesicles, or exosomes, to signal across long distances and coordinate collective actions. Exosomes diffuse slowly, can be actively degraded, and contain stochastic amounts of molecular cargo. These…
A quantum walk on a lattice is a paradigm of a quantum search in a database. The database qubit strings are the lattice sites, qubit rotations are tunneling events, and the target site is tagged by an energy shift. For quantum walks on a…
Enzymes have been recently proposed to have mechanical activity associated with their chemical activity. In a number of recent studies, it has been reported that enzymes undergo enhanced diffusion in the presence of their corresponding…
We obtain optimal Gaussian concentration bounds (GCBs) for stochastic chains of unbounded memory (SCUMs) on countable alphabets. These stochastic processes are also known as "chains with complete connections" or "$g$-measures". We consider…