Related papers: Corrected Hill Function in Stochastic Gene Regulat…
Multisite phosphorylation plays an important role in regulating switchlike protein activity and has been used widely in mathematical models. With the development of new experimental techniques and more molecular data, molecular…
Cell phenotype dynamic homeostasis contrasts with the inherent randomness of intracellular reactions. Although feedback control of master regulatory genes (MRG) is a key strategy for maintaining gene network expression ranges limited,…
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…
Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology. Because of the low number molecules in these reacting systems, stochastic effects are…
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…
Biochemical processes typically involve many chemical species, some in abundance and some in low molecule numbers. Here we first identify the rate constant limits under which the concentrations of a given set of species will tend to…
Conventional studies of biomolecular behaviors rely largely on the construction of kinetic schemes. Since the selection of these networks is not unique, a concern is raised whether and under which conditions hierarchical schemes can reveal…
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…
The dynamics of stochastic reaction networks within cells are inevitably modulated by factors considered extrinsic to the network such as for instance the fluctuations in ribsome copy numbers for a gene regulatory network. While several…
Stochasticity in gene expression can give rise to fluctuations in protein levels and lead to phenotypic variation across a population of genetically identical cells. Recent experiments indicate that bursting and feedback mechanisms play…
Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can…
Investigation of protein self-assembly processes is important for the understanding of the growth processes of functional proteins as well as disease-causing amyloids. Inside cells, intrinsic molecular fluctuations are so high that they…
We analyze three simple genetic circuits which involve transcriptional regulation and feedback: the autorepressor, the switch and the repressilator, that consist of one, two and three genes, respectively. Such systems are commonly simulated…
The neural dynamics generating sensory, motor, and cognitive functions are commonly understood through field theories for neural population activity. Classic neural field theories are derived from highly simplified models of individual…
Regulatory networks describe the interactions between molecular or cellular regulators, like transcription factors and genes in gene regulatory networks, kinases and their receptors in signalling networks, or neurons in neural networks. A…
Hill functions dominate gene regulatory network (GRN) modeling, but their fractional exponents create analytical pathologies when the Hill coefficient $n$ is non-integer -- a ubiquitous occurrence in experimental fits. We replace the Hill…
Hill's equations arise in a wide variety of physical problems, and are specified by a natural frequency, a periodic forcing function, and a forcing strength parameter. This classic problem is generalized here in two ways: [A] to Random…
How do single cell fate decisions induced by activation of key signaling proteins above threshold concentrations within a time interval are affected by stochastic fluctuations in biochemical reactions? We address this question using minimal…
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…
Single cell experiments of simple regulatory networks can markedly differ from cell population experiments. Such differences arise from stochastic events in individual cells that are averaged out in cell populations. For instance, while…