Related papers: Stochastic analysis of a miRNA-protein toggle swit…
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…
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…
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…
Engineering biology requires precise control of biomolecular circuits, and Cybergenetics is the field dedicated to achieving this goal. A significant challenge in developing controllers for cellular functions is designing systems that can…
Fluctuating environments pose tremendous challenges to bacterial populations. It is observed in numerous bacterial species that individual cells can stochastically switch among multiple phenotypes for the population to survive in rapidly…
Epigenetic cell memory, the inheritance of gene expression patterns across subsequent cell divisions, is a critical property of multi-cellular organisms. In recent work [10], a subset of the authors observed in a simulation study how the…
In the last years, tens of thousands gene expression profiles for cells of several organisms have been monitored. Gene expression is a complex transcriptional process where mRNA molecules are translated into proteins, which control most of…
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…
We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their…
We study the stochastic dynamics of a system of interacting species in a stochastic environment by means of a continuous-time Markov chain with transition rates depending on the state of the environment. Models of gene regulation in systems…
In small systems, quantitative discrepancies between stochastic and deterministic descriptions of chemical kinetics can be significant, with their magnitude depending on the specific reaction network. Here, we study the Finke-Watzky…
Synthetic biology is an interdisciplinary field aiming to design biochemical systems with desired behaviors. To this end, molecular controllers have been developed which, when embedded into a pre-existing ambient biochemical network,…
Since gene regulatory systems contain sometimes only a small number of molecules, these systems are not described well by macroscopic rate equations; a master equation approach is needed for such cases. We develop an approximation scheme…
In biology phenotypic switching is a common bet-hedging strategy in the face of uncertain environmental conditions. Existing mathematical models often focus on periodically changing environments to determine the optimal phenotypic response.…
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,…
Phage lambda is one of the most studied biological models in modern molecular biology. Over the past 50 years quantitative experimental knowledge on this biological model has been accumulated at all levels: physics, chemistry, genomics,…
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,…
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…
Causal ordering of key events in the cell cycle is essential for proper functioning of an organism. Yet, it remains a mystery how a specific temporal program of events is maintained despite ineluctable stochasticity in the biochemical…
The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current…