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We propose a statistical model of a large random network with high connectivity in order to describe the behavior of {\it E.\,coli} cells after exposure to acute stress. The building blocks of this network are feedback cycles typical of the…
Metastable brain dynamics are characterized by abrupt, jump-like modulations so that the neural activity in single trials appears to unfold as a sequence of discrete, quasi-stationary states. Evidence that cortical neural activity unfolds…
We study in this paper the effect of an unique initial stimulation on random recurrent networks of leaky integrate and fire neurons. Indeed given a stochastic connectivity this so-called spontaneous mode exhibits various non trivial…
Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by…
Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of…
Metabolic networks consist of linked functional components, or modules. The mechanism underlying metabolic network modularity is of great interest not only to researchers of basic science but also to those in fields of engineering. Previous…
Background: A classical problem in metabolic design is to maximize the production of desired compound in a given chemical reaction network by appropriately directing the mass flow through the network. Computationally, this problem is…
Metabolic flux balance analyses are a standard tool in analysing metabolic reaction rates compatible with measurements, steady-state and the metabolic reaction network stoichiometry. Flux analysis methods commonly place unrealistic…
We study the effect of confinement on diffusion limited bimolecular reactions within a lattice model where a small number of reactants diffuse amongst a much larger number of inert particles. When the number of inert particles is held…
The survival and proliferation of cells and organisms require a highly coordinated allocation of cellular resources to ensure the efficient synthesis of cellular components. In particular, the total enzymatic capacity for cellular…
Microbes require several complex organic molecules for growth. A species may obtain a required factor by taking up molecules released by other species or by synthesizing the molecule. The patterns of uptake and synthesis set a flow of…
Cellular responses to death-promoting stimuli typically proceed through a differentiated multistage process, involving a lag phase, extensive death, and potential adaptation. Deregulation of this chain of events is at the root of many…
We study the emergence of the collective spatio-temporal macroscopic properties of the immune system, by representing individually the elementary interactions between its microscopic components (antibodies, antigens, cytokines). The results…
We study a stochastic system of interacting neurons and its metastable properties. The system consists of $N$ neurons, each spiking randomly with rate depending on its membrane potential. At its spiking time, the neuron potential is reset…
Motivated by single-molecule experiments on synaptic membrane protein domains, we use a stochastic lattice model to study protein reaction and diffusion processes in crowded membranes. We find that the stochastic reaction-diffusion dynamics…
A number of microorganisms leave persistent trails while moving along surfaces. For single-cell organisms, the trail-mediated self-interaction will influence its dynamics. It has been discussed recently [Kranz \textit{et al.} Phys. Rev.…
We propose a new mechanism to increase the reactions ratesin multistable autocatalytic systems. The mechanism is based upon the possibility for the enhancement of the response of the system due to the cooperative behavior between the noise…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
Synthetic lethal reaction/gene-sets are sets of reactions/genes where only the simultaneous removal of all reactions/genes in the set abolishes growth of an organism. In silico, synthetic lethal sets can be identified by simulating the…
Yeast cells grown in culture can spontaneously synchronize their respiration, metabolism, gene expression and cell division. Such metabolic oscillations in synchronized cultures reflect single-cell oscillations, but the relationship between…