Related papers: Colored extrinsic fluctuations and stochastic gene…

We describe how noise propagates through a network by calculating the variance of the outputs. Using stochastic calculus and dynamical systems theory, we study the network topologies that accentuate or alleviate the effect of random…

The intrinsic stochasticity of gene expression can lead to large variations in protein levels across a population of cells. To explain this variability, different sources of mRNA fluctuations ('Poisson' and 'Telegraph' processes) have been…

Cued and un-cued cell polarization is a fundamental mechanism in cell biology. As an alternative to the classical Turing bifurcation, it has been proposed that the cell polarity might onset by means of the well-known phenomenon of…

The study of biochemical pathways usually focuses on a small section of a protein interactions network. Two distinct sources contribute to the noise in such a system: intrinsic noise, inherent in the studied reactions, and extrinsic noise…

Effect of noise in inducing order on various chaotically evolving systems is reviewed, with special emphasis on systems consisting of coupled chaotic elements. In many situations it is observed that the uncoupled elements when driven by…

Stochasticity (or noise) at cellular and molecular levels has been observed extensively as a universal feature for living systems. However, how living systems deal with noise while performing desirable biological functions remains a major…

Molecular noise in gene regulatory networks has two intrinsic components, one part being due to fluctuations caused by the birth and death of protein or mRNA molecules which are often present in small numbers and the other part arising from…

In a system of non-linear chemical reactions called the Brusselator, we show that {\it intrinsic noise} can be regulated to drive it to exhibit resonance in the presence of a sub-threshold signal. The phenomena of periodic stochastic…

Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…

Many networks must maintain synchrony despite the fact that they operate in noisy environments. Important examples are stochastic inertial oscillators, which are known to exhibit fluctuations with broad tails in many applications, including…

A central challenge in computational modeling of dynamic biological systems is parameter inference from experimental time course measurements. However, one would not only like to infer kinetic parameters but also study their variability…

The dynamics of cellular aggregates is driven by the interplay of mechanochemical processes and cellular activity. Although deterministic models may capture mechanical features, local chemical fluctuations trigger random cell responses,…

We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…

Gene expression is a noisy process that leads to regime shift between alternative steady states among individual living cells, inducing phenotypic variability. The effects of white noise on the regime shift in bistable systems have been…

Biological machines like molecular motors and enzymes operate in dynamic cycles representable as stochastic flows on networks. Current stochastic dynamics describes such flows on fixed networks. Here, we develop a scalable approach to…

The presence of correlated noise, arising from a mixture of independent fluctuations and a common noisy input shared across the neural population, is a ubiquitous feature of neural circuits, yet its impact on collective network dynamics…

Describing reaction rates in stochastic bio-circuits is commonly done by directly introducing the deterministically deduced Hill function into the master equation. However, when fluctuations in enzymatic reaction rates are not neglectable,…

We consider a generic class of gene circuits affected by nonlinear extrinsic noise. To address this nonlinearity we introduce a general perturbative methodology based on assuming timescale separation between noise and genes dynamics, with…

Information transmission in cells occurs quite accurately even when concentration changes are "read" by individual target molecules. In this Letter we study molecule number fluctuations when molecules diffuse and react. We show that, for…

Recurrent networks of dynamic elements frequently exhibit emergent collective oscillations, which can display substantial regularity even when the individual elements are considerably noisy. How noise-induced dynamics at the local level…