Related papers: Relationship between cellular response and behavio…
Elucidating the architecture and dynamics of large scale genetic regulatory networks of cells is an important goal in systems biology. We study the system level dynamical properties of the genetic network of Escherichia coli that regulates…
Organisms must acquire and use environmental information to guide their behaviors. However, it is unclear whether and how information quantitatively limits behavioral performance. Here, we relate information to behavioral performance in…
Bacteria track chemical gradients using a biased random walk, a process called chemotaxis. Experiments suggest that bacteria also communicate during this process. Using a mathematical model, we find that sufficiently strong communication…
A stochastic version of the Barkai-Leibler model of chemotaxis receptors in {\it E. coli} is studied here to elucidate the effects of intrinsic network noise in their conformational dynamics. It was originally proposed to explain the robust…
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.…
Bacteria are often exposed to multiple stimuli in complex environments, and their efficient chemotactic decisions are critical to survive and grow in their native environments. Bacterial responses to the environmental stimuli depend on the…
We show how the competition between sensing and adaptation can result in a performance peak in E.coli chemotaxis using extensive numerical simulations in a detailed theoretical model. Receptor clustering amplifies the input signal coming…
{\sl Escherichia coli} ({\sl E. coli}) bacteria govern their trajectories by switching between running and tumbling modes as a function of the nutrient concentration they experienced in the past. At short time one observes a drift of the…
The chemotaxis sensory system allows bacteria such as Escherichia coli to swim towards nutrients and away from repellents. The underlying pathway is remarkably sensitive in detecting chemical gradients over a wide range of ambient…
Motile bacteria can migrate along chemical gradients in a process known as chemotaxis. When exposed to uniform environmental stress, Escherichia coli cells coordinate their chemotactic responses to form millimeter-sized condensates…
The dynamics of cellular aggregates is driven by the interplay of mechanochemical processes and cellular activity. Although deterministic models may capture mechanical features, local chemical fluctuations trigger random cell responses,…
Which properties of metabolic networks can be derived solely from stoichiometric information about the network's constituent reactions? Predictive results have been obtained by Flux Balance Analysis (FBA), by postulating that cells set…
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…
Chemotaxis in bacteria such as \textit{E.\ coli} is controlled by the slow methylation of chemoreceptors. As a consequence, intrinsic time and length scales of tens of seconds and hundreds of micrometers emerge, making the Keller--Segel…
Bacterial chemotaxis has long been viewed as operating near the physical limits of sensing, as originally articulated by Berg and Purcell. Recent information-theoretic analyses challenge this view, suggesting that Escherichia coli uses only…
Chemotaxis, the directional locomotion of cells towards a source of a chemical gradient, is an integral part of many biological processes - for example, bacteria motion, single-cell or multicellular organisms development, immune response,…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…
The cooperative binding of molecular agents onto a substrate is pervasive in living systems. To study whether a system shows cooperativity, one can rely on a fluctuation analysis of quantities such as the number of substrate-bound units and…
Chemotaxis of the bacterium Escherichia coli is well understood in shallow chemical gradients, but its swimming behavior remains difficult to interpret in steep gradients. By focusing on single-cell trajectories from simulations, we…
Colonies of bacteria grown on thin agar plate exhibit fractal patterns as a result of adaptation to their environments. The bacterial colony pattern formation is regulated crucially by chemotaxis, the movement of cells along a chemical…