Related papers: Chemotaxing E. coli do not count single molecules
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
The mean size of exponentially dividing E. coli cells cultured in different nutrient conditions is known to depend on the mean growth rate only. However, the joint fluctuations relating cell size, doubling time and individual growth rate…
Swimming bacteria detect chemical gradients by performing temporal comparisons of recent measurements of chemical concentration. These comparisons are described quantitatively by the chemotactic response function, which we expect to…
Single-molecule tracking is a powerful way to look at the dynamic organization of plasma membranes. However, there are some limitations to its use. For example, it was recently observed, using numerical simulation, that time-averaging…
We show how one can measure the signal from slow jumps of a single molecule between metastable positions using a setup where the molecule is fixed to one lead, and one of the coupling strengths is controlled externally. Such a measurement…
Bacterial chemotaxis is controlled by the conformational changes of the receptors, in response to the change of the ambient chemical concentration. In a statistical mechanical approach, the signalling due to the conformational changes is a…
In molecular communications, the direct detection of signaling molecules may be challenging due to a lack of suitable sensors and interference in the environment. Motivated by research in molecular biology, we investigate an indirect…
Active particles with their characteristic feature of self-propulsion are regarded as the simplest models for motility in living systems. The accumulation of active particles in low activity regions has led to the general belief that…
Switching of the direction of flagella rotations is the key control mechanism governing the chemotactic activity of E. coli and many other bacteria. Power-law distributions of switching times are most peculiar because their emergence cannot…
Cells can be considered as systems that utilize changes in thermodynamic entropy as information. Therefore, they serve as useful models for investigating the relationships between entropy production and information transmission, i.e.,…
Advances in DNA sequencing have revolutionized our ability to read genomes. However, even in the most well-studied of organisms, the bacterium ${\it Escherichia coli}$, for $\approx$ 65$\%$ of the promoters we remain completely ignorant of…
Across diverse biological systems -- ranging from neural networks to intracellular signaling and genetic regulatory networks -- the information about changes in the environment is frequently encoded in the full temporal dynamics of the…
Gradient sensing requires at least two measurements at different points in space. These measurements must then be communicated to a common location to be compared, which is unavoidably noisy. While much is known about the limits of…
Cells perform directed motion in response to external stimuli that they detect by sensing the environment with their membrane protrusions. In particular, several biochemical and biophysical cues give rise to tactic migration in the…
We study a chemotaxis system that includes two competitive prey and one predator species in a two-dimensional domain, where the movement of prey (resp. predators) is driven by chemicals secreted by predators (resp. prey), called mutually…
The Escherichia coli chemoreceptors form an extensive array that achieves cooperative and adaptive sensing of extracellular signals. The receptors control the activity of histidine kinase CheA, which drives a nonequilibrium…
Chemotaxis is the process by which cells behave in a way that follows the chemical gradient. Applications to bacteria growth, tissue inflammation, and vascular tumors provide a focus on optimization strategies. Experiments can characterize…
We describe a mechanism for pronounced biochemical oscillations, relevant to microscopic systems, such as the intracellular environment. This mechanism operates for reaction schemes which, when modeled using deterministic rate equations,…
Chemotaxis is a directed cell movement in response to external chemical stimuli. In this paper, we propose a simple model for the origin of chemotaxis - namely how a directed movement in response to an external chemical signal may occur…