Related papers: Selection and control of pathways by using externa…
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…
We study the effect of noise on the renormalizability of a specific reaction-diffusion system of equations describing a cubic autocatalytic chemical reaction. The noise we are using is gaussian with power-law correlations in space,…
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…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
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…
Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement of strand-displacement DNA computing, a large class of…
We characterize the influence that external noise, with both spatial and temporal correlations, has on the scale dependence of the reaction parameters of a cubic autocatalytic reaction diffusion (CARD) system. Interpreting the CARD model as…
Due to inherent noise in intracellular networks cellular decisions can be random, so genetically identical cells can display different phenotypic behavior even in identical environments. Most previous work in understanding the…
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 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…
According to the chemical reaction network theory, the topology of a certain class of chemical reaction networks, regardless of the kinetic details, sets a limit on the dynamical properties that a particular network can potentially admit;…
We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under1 quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady…
Many approaches to modelling reaction-diffusion systems with anomalous transport rely on deterministic equations and ignore fluctuations arising due to finite particle numbers. Starting from an individual-based model we use a…
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…
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…
The activated rate process for non-equilibrium open systems is studied taking into account both internal and external noise fluctuations in a unified way. The probability of a particle diffusing passing over the saddle point and the rate…
Starting from our recent chemical master equation derivation of the model of an autocatalytic reaction-diffusion chemical system with reactions $U+2V {\stackrel {\lambda_0}{\rightarrow}}~ 3 V;$ and $V {\stackrel {\mu}{\rightarrow}}~P$, $U…
Positive feedback and cooperativity in the regulation of gene expression are generally considered to be necessary for obtaining bistable expression states. Recently, a novel mechanism of bistability termed emergent bistability has been…
In this work we focus on how noise propagates in biochemical reaction networks and affects sensitivities of the system. We discover that the stochastic fluctuations can enhance sensitivities in one region of the value of control parameters…
In this paper, a non-autonomous stochastic logistic system is considered. An interesting result on the effect of stochastically perturbation for the dynamic behavior are obtained. That is, under certain conditions the stochastic system have…