Related papers: Genetic Toggle Switch Without Cooperative Binding
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic methods (rate equations) and stochastic methods (the master equation and Monte Carlo simulations). These systems exhibit bistability,…
We present an analytical treatment of a genetic switch model consisting of two mutually inhibiting genes operating without cooperative binding of the corresponding transcription factors. Previous studies have numerically shown that these…
We study a stochastic two-species chemical reaction system with two mechanisms. One mechanism consists of chemical interactions which govern the overall drift of species amounts in the system; the other mechanism consists of resampling,…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…
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…
The nonequilibrium stationary state of an exclusive genetic switch is considered. The model comprises two competing species and a single binding site which, when bound to by a protein of one species, causes the other species to be…
Controlling spatial patterns in synthetic biological systems remains challenging due to poor parameter robustness and limited experimental tunability. We introduce two complementary mechanisms-the pattern switch and the pattern dial-to…
Many biochemical processes can successfully be described by dynamical systems allowing some form of switching when, depending on their initial conditions, solutions of the dynamical system end up in different regions of state space…
The origin of stochastic fluctuations in gene expression has received considerable attention recently. Fluctuations in gene expression are particularly pronounced in cellular systems because of the small copy number of species undergoing…
Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks (GRNs). In this view, different phenotypes are associated with alternative states…
Stochastic resonance is a well established phenomenon, which proves relevant for a wide range of applications, of broad trans-disciplinary breath. Consider a one dimensional bistable stochastic system, characterized by a deterministic…
A general class of stochastic gene expression models with self regulation is considered. One or more genes randomly switch between regulatory states, each having a different mRNA transcription rate. The gene or genes are self regulating…
Recently, a large number of studies have been carried out on the early signatures of sudden regime shifts in systems as diverse as ecosystems, financial markets, population biology and complex diseases. Signatures of regime shifts in gene…
The theory of stochastic transcription termination based on free-energy competition requires two or more reaction rates to be delicately balanced over a wide range of physical conditions. A large body of work on glasses and large molecules…
We study by mean-field analysis and stochastic simulations chemical models for genetic toggle switches formed from pairs of genes that mutually repress each other. In order to determine the stability of the genetic switches, we make a…
Living cells need a constant availability of certain resources to have a sustained gene expression process. Limited availability of cellular resources for gene expression, like ribosomes, along with a variation of resource affinity,…
Within systems biology there is an increasing interest in the stochastic behavior of genetic and biochemical reaction networks. An appropriate stochastic description is provided by the chemical master equation, which represents a continuous…
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity between them are essential building blocks…
Biochemical reaction networks are subjected to large fluctuations attributable to small molecule numbers, yet underlie reliable biological functions. Most theoretical approaches describe them as purely deterministic or stochastic dynamical…