Related papers: A connection between bacterial chemotactic network…
Living systems operate in a critical dynamical regime -- between order and chaos -- where they are both resilient to perturbation, and flexible enough to evolve. To characterize such critical dynamics, the established 'structural theory' of…
The analysis of non-equilibrium steady states of biochemical reaction networks relies on finding the configurations of fluxes and chemical potentials satisfying stoichiometric (mass balance) and thermodynamic (energy balance) constraints.…
We study the effect of chemotactic signaling among mesenchymal cells. We show that the particular physiology of the mesenchymal cells allows one-dimensional collapse in contrast to the case of bacteria, and that the mesenchymal…
Aerotaxis is the particular form of chemotaxis in which oxygen plays the role of both the attractant and the repellent. Aerotaxis occurs without methylation adaptation, and it leads to fast and complete aggregation toward the most favorable…
Models for chemotaxis are based on gradient sensing of individual organisms. The key contribution of Keller and Segel is showing that erratic movements of individuals may result in an accurate chemotaxis phenomenon as a group. In this paper…
Bacterial chemotaxis is controlled by the signalling of a cluster of receptors. A cooperative model is presented, in which coupling between neighbouring receptor dimers enhances the sensitivity with which stimuli can be detected, without…
The representation of a biochemical network as a graph is the coarsest level of description in cellular biochemistry. By studying the network structure one can draw conclusions on the large scale organisation of the biochemical processes.…
Determining the functional structure of biological networks is a central goal of systems biology. One approach is to analyze gene expression data to infer a network of gene interactions on the basis of their correlated responses to…
Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…
A system responding to a stochastic driving signal can be interpreted as computing, by means of its dynamics, an implicit model of the environmental variables. The system's state retains information about past environmental fluctuations,…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
We propose a general parametrizable model to capture the dynamic interaction among bacteria in the formation of micro-colonies. micro-colonies represent the first social step towards the formation of structured multicellular communities…
The proper functioning of the nervous system depends critically on the intricate network of synaptic connections that are generated during the system development. During the network formation, the growth cones migrate through the embryonic…
A detailed algorithmic explanation is required for how a network of chemical reactions can generate the sophisticated behavior displayed by living cells. Though several previous works have shown that reaction networks are computationally…
It has been generally recognized that stochasticity can play an important role in the information processing accomplished by reaction networks in biological cells. Most treatments of that stochasticity employ Gaussian noise even though it…
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
Motivated by recent discoveries of microbial communities that transfer electrons across centimeter-length scales, this paper studies the information capacity of bacterial cables via electron transfer, which coexists with molecular…
Simulation of biomolecular networks is now indispensable for studying biological systems, from small reaction networks to large ensembles of cells. Here we present a novel approach for stochastic simulation of networks embedded in the…
Mutual information is a theoretically grounded metric for quantifying cellular signaling pathways. However, its measurement demands characterization of both input and output distributions, limiting practical applications. Here, we present…
A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between…