Related papers: Bacterial chemotaxis: information processing, ther…
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…
We propose a model of chemostat where the bacterial population is individually-based, each bacterium is explicitly represented and has a mass evolving continuously over time. The substrate concentration is represented as a conventional…
Molecular communication is an expanding body of research. Recent advances in biology have encouraged using genetically engineered bacteria as the main component in the molecular communication. This has stimulated a new line of research that…
The multifarious internal workings of organisms are difficult to reconcile with a single feature defining a state of being alive. Indeed, definitions of life rely on emergent properties (growth, capacity to evolve, agency) only symptomatic…
We experimentally study the emergence of collective bacterial swimming, a phenomenon often referred to as bacterial turbulence. A phase diagram of the flow of 3D E. coli suspensions spanned by bacterial concentration, the swimming speed of…
Peritrichously-flagellated bacteria, such as Escherichia coli, self-propel in fluids by using specialised motors to rotate multiple helical filaments. The rotation of each motor is transmitted to a short flexible segment called the hook…
Biological tissues have been observed to display emergent fluid-like properties, owing to physical interactions between cells. However, it remains unclear in general how these fluid-like properties affect tissue structure and function.…
Escherichia coli has long been a trusty companion, maintaining health in our guts and advancing biological knowledge in the laboratory. In light of recent findings, we discuss multicellular self-organization in E. coli and develop general…
A large number of biological systems - from bacteria to sheep - can be described as ensembles of self-propelled agents (active particles) with a complex internal dynamic that controls the agent's behavior: resting, moving slow, moving fast,…
The recently emerged molecular communication (MC) paradigm intends to leverage communication engineering tools for the design of synthetic chemical communication systems. These systems are envisioned to operate at nanoscale and in…
Multicellular chemotaxis can occur via individually chemotaxing cells that are mechanically coupled. Alternatively, it can emerge collectively, from cells chemotaxing differently in a group than they would individually. Here we consider…
Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses…
In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than…
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…
Chemotaxis receptors in E. coli form clusters at the cell poles and also laterally along the cell body, and this clustering plays an important role in signal transduction. Recently, experiments using flourrescence imaging have shown that,…
The heterogeneity of reaction fluxes present in a metabolic network within a single flux state can be exploited to construct the so-called backbone as a reduced version of metabolism. The backbone maintains all significant fluxes producing…
The purpose of this work is the study of \textit{chemotaxis} and how to model it through the equations of Keller-Segel. \textit{Chemotaxis} is a natural process which induces the organisms to direct their movement according to certain…
Escherichia coli is a motile bacterium that moves up a chemoattractant gradient by performing a biased random walk composed of alternating runs and tumbles. Previous models of run and tumble chemotaxis neglect one or more features of the…
A wide array of biological systems can navigate in shallow gradients of chemoattractant with remarkable precision. Whilst previous approaches model such systems using coarse-grained chemical density profiles, we construct a dynamical model…
Microorganisms employ sophisticated mechanisms for intercellular communication and environmental sensing, with quorum sensing serving as a fundamental regulatory process. Dysregulation of quorum sensing has been implicated in various…