Related papers: Colored extrinsic fluctuations and stochastic gene…
Chemical reactions in cell are subject to intense stochastic fluctuations. An important question is how the fundamental physiological behavior of cell is kept stable against those noisy perturbations. In this paper a stochastic model of…
We present a study investigating the role of mitochondrial variability in generating noise in eukaryotic cells. Noise in cellular physiology plays an important role in many fundamental cellular processes, including transcription,…
We consider the general problem of describing the dynamics of subnetworks of larger biochemical reaction networks, e.g. protein interaction networks involving complex formation and dissociation reactions. We propose the use of model…
Neurons in the nervous system are submitted to distinct sources of noise, such as ionic-channel and synaptic noise, which introduces variability in their responses to repeated presentations of identical stimuli. This motivates the use of…
Many cellular components are present in such low numbers that individual stochastic production and degradation events lead to significant fluctuations in molecular abundances. Although feedback control can, in principle, suppress such…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
A common model of stochastic auto-regulatory gene expression describes promoter switching via cooperative protein binding, effective protein production in the active state and dilution of proteins. Here we consider an extension of this…
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…
Intrinsic or demographic noise has been shown to play an important role in the dynamics of a variety of systems including predator-prey populations, intracellular biochemical reactions, and oscillatory chemical reaction systems, and is…
In this paper we present a framework for investigating coloured noise in reaction-diffusion systems. We start by considering a deterministic reaction-diffusion equation and show how external forcing can cause temporally correlated or…
We show that noise-induced oscillations in a gene circuit model display stochastic coherence, that is, a maximum in the regularity of the oscillations as a function of noise amplitude. The effect is manifest as a system-size effect in a…
The Notch-Delta signaling pathway mediates cell differentiation implicated in many regulatory processes including spatiotemporal patterning in tissues by promoting alternate cell fates between neighboring cells. At the multicellular level,…
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…
Gene regulatory dynamics is governed by molecular processes and therefore exhibits an inherent stochasticity. However, for the survival of an organism it is a strict necessity that this intrinsic noise does not prevent robust functioning of…
The intrinsic stochasticity of gene expression can lead to large variability of protein levels across a population of cells. Variability (or noise) in protein distributions can be modulated by cellular mechanisms of gene regulation; in…
The dynamics of cellular chemical reactions are variable due to stochastic noise from intrinsic and extrinsic sources. The intrinsic noise is the intracellular fluctuations of molecular copy numbers caused by the probabilistic encounter of…
In spatially distributed cellular systems, it is often convenient to represent complicated auxiliary pathways and spatial transport by time-delayed reaction rates. Furthermore, many of the reactants appear in low numbers necessitating a…
While noise is generally associated with uncertainties and often has a negative connotation in engineering, living organisms have evolved to adapt to (and even exploit) such uncertainty to ensure the survival of a species or implement…
We study the effect of extrinsic noise in metabolic networks. We introduce external random fluctuations at the kinetic level, and show how these lead to a stochastic generalization of standard Metabolic Control Analysis. While Summation and…
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic…