Related papers: Optimal search in E.coli chemotaxis
Sedimentation in active fluids has come into focus due to the ubiquity of swimming micro-organisms in natural and industrial processes. Here, we investigate sedimentation dynamics of passive particles in a fluid as a function of bacteria E.…
Bacterial chemotaxis in Escherichia coli is a canonical system for the study of signal transduction. A remarkable feature of this system is the coexistence of precise adaptation in population with large fluctuating cellular behavior in…
Gene-knockout experiments on single-cell organisms have established that expression of a substantial fraction of genes is not needed for optimal growth. This problem acquired a new dimension with the recent discovery that environmental and…
We study linear chance-constrained problems where the coefficients follow a Gaussian mixture distribution. We provide mixed-binary quadratic programs that give inner and outer approximations of the chance constraint based on piecewise…
Adaptation of the chemotaxis sensory pathway of the bacterium Escherichia coli is integral for detecting chemicals over a wide range of background concentrations, ultimately allowing cells to swim towards sources of attractant and away from…
The first passage search of a diffusing target (prey) by multiple searchers (predators) in confinement is an important problem in the stochastic process literature. While the analogous problem in open space has been studied in some details,…
Experiments have recently shown the feasibility of utilising bacteria as micro-scale robotic devices, with special attention paid to the development of bacteria-driven micro-swimmers taking advantage of built-in actuation and sensing…
We investigate multitarget search on complex networks and derive an exact expression for the mean random cover time that quantifies the expected time a walker needs to visit multiple targets. Based on this, we recover and extend some…
Biological cells estimate concentration gradients of signaling molecules with a precision that is limited not only by sensing noise, but additionally by the cell's own stochastic motion. We ask for the theoretical limits of gradient…
We study the effect of a resetting point randomly distributed around the origin on the mean first passage time of a Brownian searcher moving in one dimension. We compare the search efficiency with that corresponding to reset to the origin…
Experiments have shown that bacteria can be sensitive to small variations in chemoattractant (CA) concentrations. Motivated by these findings, our focus here is on a regime rarely studied in experiments: bacteria tracking point CA sources…
Many eukaryotic cells are able to sense chemical gradients by directly measuring spatial concentration differences. The precision of such gradient sensing is limited by fluctuations in the binding of diffusing particles to specific…
Membranes regulate transport in a wide variety of industrial and biological applications. The microscale geometry of the membrane can significantly affect overall transport through the membrane, but the precise nature of this multiscale…
A Monte Carlo simulation of chemotactic bacteria is developed on the basis of the kinetic model and is applied to a one-dimensional traveling population wave in a microchannel. In this simulation, the Monte Carlo method, which calculates…
{\it E. coli} bacteria swim in straight runs interrupted by sudden reorientation events called tumbles. The resulting random walks give rise to density fluctuations that can be derived analytically in the limit of non interacting particles…
Bacteria in bulk fluids swim collectively and display fascinating emergent dynamics. Although bacterial collective swimming in three-dimensional (3D) geometries has been well studied, its counterpart in confined two-dimensional (2D)…
A rapidly increasing number of systems is identified in which the stochastic motion of tracer particles follows the Brownian law $\langle\mathbf{r}^2(t) \rangle\simeq Dt$ yet the distribution of particle displacements is strongly…
Classic experiments on the distribution of ducks around separated food sources found consistency with the `ideal free' distribution in which the local population is proportional to the local supply rate. Motivated by this experiment and…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
Using very precise (up to 0.05%) measurements of the growth parameters for bacteria E. coli grown on minimal media, we aimed to determine the lowest deuterium concentration at which the adverse effects that are prominent at higher…