Related papers: The interplay between discrete noise and nonlinear…
Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…
Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process…
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from…
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…
We develop a systematic approach to the linear-noise approximation for stochastic reaction systems with distributed delays. Unlike most existing work our formalism does not rely on a master equation, instead it is based upon a dynamical…
Fluorescent and luminescent gene reporters allow us to dynamically quantify changes in molecular species concentration over time on the single cell level. The mathematical modeling of their interaction through multivariate dynamical models…
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…
Stochastic models of biochemical reaction networks are widely used to capture intrinsic noise in cellular systems. The typical formulation of these models are based on Markov processes for which there is extensive research on efficient…
Biochemical signal transduction, a form of molecular communication, can be modeled using graphical Markov channels with input-modulated transition rates. Such channel models are strongly non-Gaussian. In this paper we use a linear noise…
Signaling in enzymatic networks is typically triggered by environmental fluctuations, resulting in a series of stochastic chemical reactions, leading to corruption of the signal by noise. For example, information flow is initiated by…
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,…
Biochemical signalling cascades transduce extracellular stimuli into cellular responses through sequences of discrete, node-to-node activations. While signal fidelity depends critically on local interaction kinetics, the mechanisms…
Signal propagation in biochemical networks is characterized by the inherent randomness in gene expression and fluctuations of the environmental components, commonly known as intrinsic and extrinsic noise, respectively. We present a…
Extrinsic noise-induced transitions to bimodal dynamics have been largely investigated in a variety of chemical, physical, and biological systems. In the standard approach in physical and chemical systems, the key properties that make these…
Stochastic fluctuations of molecule numbers are ubiquitous in biological systems. Important examples include gene expression and enzymatic processes in living cells. Such systems are typically modelled as chemical reaction networks whose…
Gene expression is significantly stochastic making modeling of genetic networks challenging. We present an approximation that allows the calculation of not only the mean and variance but also the distribution of protein numbers. We assume…
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…
After being considered as a nuisance to be filtered out, it became recently clear that biochemical noise plays a complex role, often fully functional, for a genetic network. The influence of intrinsic and extrinsic noises on genetic…
Cells must continuously sense and respond to time-varying environmental stimuli. These signals are transmitted and processed by biochemical signalling networks. However, the biochemical reactions making up these networks are intrinsically…
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…