Related papers: A connection between bacterial chemotactic network…
Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from…
Chemotaxis is the response of a particle to a gradient in the chemical composition of the environment. While it was originally observed for biological organisms, it is of great interest in the context of synthetic active particles such as…
Recent work on synthetic rescues has shown that the targeted deletion of specific metabolic genes can often be used to rescue otherwise non-viable mutants. This raises a fundamental biophysical question: to what extent can the whole-cell…
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…
For navigation, microscopic agents such as biological cells rely on noisy sensory input. In cells performing chemotaxis, such noise arises from the stochastic binding of signaling molecules at low concentrations. Using chemotaxis of sperm…
Living cells can leverage correlations in environmental fluctuations to predict the future environment and mount a response ahead of time. To this end, cells need to encode the past signal into the output of the intracellular network from…
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…
Motivation: One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and…
The chemotaxis pathway of the bacterium Rhodobacter sphaeroides has many similarities to the well-studied pathway in Escherichia coli. It exhibits robust adaptation and has several homologues of the latter's chemotaxis proteins. Recent…
We use the lac operon in Escherichia coli as a prototype system to illustrate the current state, applicability, and limitations of modeling the dynamics of cellular networks. We integrate three different levels of description -molecular,…
The bacterium E. coli maneuvers itself to regions with high chemoattractant concentrations by performing two stereotypical moves: `runs', in which it moves in near straight lines, and `tumbles', in which it does not advance but changes…
Cell-to-cell variations in protein abundance in clonal cell populations are ubiquitous in living systems. Since protein composition determines responses in individual cells, it stands to reason that the variations themselves are subject to…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
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…
Bacteria can chemotactically migrate up attractant gradients by controlling run-and-tumble motility patterns. In addition to this well-known chemotactic behaviour, several soil and marine bacterial species perform chemokinesis: they adjust…
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 develop a thermodynamic framework for closed and open chemical networks applicable to non-elementary reactions that do not need to obey mass action kinetics. It only requires the knowledge of the kinetics and of the standard chemical…
Biological systems are promising substrates for computation because they naturally process environmental information through complex internal dynamics. In this study, we investigate whether bacterial metabolic models can act as physical…
Network models are widely used as structural summaries of biochemical systems. Statistical estimation of networks is usually based on linear or discrete models. However, the dynamics of these systems are generally nonlinear, suggesting that…
We compare the informational architecture of biological and random networks to identify informational features that may distinguish biological networks from random. The study presented here focuses on the Boolean network model for…