Related papers: A connection between bacterial chemotactic network…
Noise in transduction of chemotactic stimuli to the flagellar motor of E. coli will affect the random run-and-tumble motion of the cell and the ability to perform chemotaxis. Here we use numerical simulations to show that an intermediate…
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,…
Bacteria such as Escherichia coli (E. coli) exhibit biased motion if kept in a spatially non-uniform chemical environment. Here, we bring out unique time-dependent characteristics of bacterial chemotaxis, in response to a diffusing spatial…
Metabolic models condense biochemical knowledge about organisms in a structured and standardised way. As large-scale network reconstructions are readily available for many organisms, genome-scale models are being widely used among modellers…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
Inputs to signaling pathways can have complex statistics that depend on the environment and on the behavioral response to previous stimuli. Such behavioral feedback is particularly important in navigation. Successful navigation relies on…
A biological system achieve homeostasis when there is a regulated quantity that is maintained within a narrow range of values. Here we consider homeostasis as a phenomenon of network dynamics. In this context, we improve a general theory…
Flagellated bacteria, such as Escherichia coli, perform directed motion in gradients of concentration of attractants and repellents in a process called chemotaxis. The E. coli chemotaxis signaling pathway is a model for signal transduction,…
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…
The major biochemical networks of the living cell, the network of interacting genes and the network of biochemical reactions, are highly interdependent, however, they have been studied mostly as separate systems so far. In the last years an…
Models of the dynamics of cellular interaction networks have become increasingly larger in recent years. Formal verification based on model checking provides a powerful technology to keep up with this increase in scale and complexity. The…
We study single cell E.coli chemotaxis in a spatio-temporally varying attractant environment. Modeling the attractant concentration in the form of a traveling sine wave, we measure in our simulations, the chemotactic drift velocity of the…
We study chemotaxis of a single {\sl E.coli} bacterium in a medium where the nutrient chemical is also undergoing diffusion and its concentration has the form of a Gaussian whose width increases with time. We measure the average first…
Reliability on complex biological networks reconstructions remains a concern. Although observations are getting more and more precise, the data collection process is yet error prone and the proofs display uneven certitude. In the case of…
Hybrid models of chemotaxis combine agent-based models of cells with partial differential equation models of extracellular chemical signals. In this paper, travelling wave properties of hybrid models of bacterial chemotaxis are…
E. coli chemotactic motion in the presence of a chemoattractant field has been extensively studied using wet laboratory experiments, stochastic computational models as well as partial differential equation-based models (PDEs). The most…
Many chemotactic bacteria inhabit environments in which chemicals appear as localized pulses and evolve by processes such as diffusion and mixing. We show that, in such environments, physical limits on the accuracy of temporal gradient…
In chemotaxis, cells are modulating their migration patterns in response to concentration gradients of a guiding substance. Immune cells are believed to use such chemotactic sensing for remotely detecting and homing in on pathogens.…
The rapidly developing theory of complex networks indicates that real networks are not random, but have a highly robust large-scale architecture, governed by strict organizational principles. Here, we focus on the properties of biological…
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…