Related papers: A connection between bacterial chemotactic network…
An important objective of the classical processing of stationary random sequences under nonparametric uncertainty is the problem of filtering in case when the distribution of the underlying signal is unknown. In this paper it is assumed…
We study a simplified, solvable model of a fully-connected metabolic network with constrained quenched disorder to mimic the conservation laws imposed by stoichiometry on chemical reactions. Within a spin-glass type of approach, we show…
Bacterial chemotaxis for E.coli is controlled by methylation of chemoreceptors, which in a biochemical pathway regulates the concentration of the CheY-P protein that finally controls the tumbling rate. As a consequence, the tumbling rate…
Understanding relationship between noisy dynamics and biological network architecture is a fundamentally important question, particularly in order to elucidate how cells encode and process information. We analytically and numerically…
A useful approach to the mathematical analysis of large-scale biological networks is based upon their decompositions into monotone dynamical systems. This paper deals with two computational problems associated to finding decompositions…
Modeling and optimization of metabolic networks has been one of the hottest topics in computational systems biology within recent years. However, the complexity and uncertainty of these networks in addition to the lack of necessary data has…
Networks of biochemical reactions, like cellular metabolic networks, are kept in non-equilibrium steady states by the exchange fluxes connecting them to the environment. In most cases, feasible flux configurations can be derived from…
Many eukaryotic cells are able to sense chemical gradients by directly measuring spatial concentration differences. The precision of such gradient sensing is limited by fluctuations in the binding of diffusing particles to specific…
Spatially or chemically isolated functional modules composed of several cellular components and carrying discrete functions are considered fundamental building blocks of cellular organization, but their presence in highly integrated…
Many motile biological cells navigate along concentration gradients of signaling molecules: This chemotaxis guides for instance sperm cells from marine invertebrates, which have to find egg cells in the ocean. While chemotaxis has been…
Escherichia coli is a motile bacterium that moves up a chemoattractant gradient by performing a biased random walk composed of alternating runs and tumbles. Previous models of run and tumble chemotaxis neglect one or more features of the…
A generically observed mechanism that drives the self-organization of living systems is interaction via chemical signals among the individual elements -- which may represent cells, bacteria, or even enzymes. Here we propose a novel…
In order to grow in any given environment, bacteria need to collect information about the medium composition and implement suitable growth strategies by adjusting their regulatory and metabolic degrees of freedom. In the standard sense,…
We consider an initial-boundary value problem describing the formation of colony patterns of bacteria Escherichia coli. This model consists of reaction-diffusion equations coupled with the Keller-Segel system from the chemotaxis theory in a…
Mathematical and computational modelling of biochemical networks is often done in terms of either the concentrations of molecular species or the fluxes of biochemical reactions. When is mathematical modelling from either perspective…
Living systems continuously sense, integrate, and act on chemical information using multiscale biochemical networks whose dynamics are inherently nonlinear, adaptive, and energy-efficient. Yet, most attempts to harness such "wetware" for…
An information theoretic approach inspired by quantum statistical mechanics was recently proposed as a means to optimize network models and to assess their likelihood against synthetic and real-world networks. Importantly, this method does…
Collective cell migration in response to a chemical cue occurs in many biological processes such as morphogenesis and cancer metastasis. Clusters of migratory cells in these systems are capable of responding to gradients of less than 1%…
Cells use biochemical networks to translate environmental information into intracellular responses. These responses can be highly dynamic, but how the information is encoded in these dynamics remains poorly understood. Here we investigate…
This work clarifies the relation between network circuit (topology) and behavior (information transmission and synchronization) in active networks, e.g. neural networks. As an application, we show how to determine a network topology that is…