Related papers: Early signatures of regime shifts in gene expressi…
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,…
A single gene, regulating its own expression via a positive feedback loop, constitutes a common motif in gene regulatory networks and signalling cascades. Recent experiments on the development of competence in the bacterial population…
The realization that complex systems such as ecological communities can collapse or shift regimes suddenly and without rapid external forcing poses a serious challenge to our understanding and management of the natural world. The potential…
Diverse complex dynamical systems are known to exhibit abrupt regime shifts at bifurcation points of the saddle-node type. The dynamics of most of these systems, however, have a stochastic component resulting in noise driven regime shifts…
Bistable biological regulatory systems need to cope with stochastic noise to fine-tune their function close to bifurcation points. Here, we study stability properties of this regime in generic systems to demonstrate that cooperative…
Considerable evidence suggests that anticipating sudden shifts from one state to another in bistable dynamical systems is a challenging task, examples include ecosystems, financial markets, complex diseases, etc. In this paper, we…
A variety of real world and experimental systems can display a drastic regime shift, as the evolution in one its paramaters crosses a threshold value. Assimilation of such a transition with a bifurcation has allowed to identify so called…
Cell fate determination, the process through which cells commit to differentiated states is commonly mediated by gene regulatory motifs with mutually exclusive expression states. The classical deterministic picture for cell fate…
Cells often exhibit different and stable phenotypes from the same DNA sequence. Robustness and plasticity of such cellular states are controlled by diverse transcriptional and epigenetic mechanisms, among them the modification of…
Gene expression is a noisy process that leads to regime shift between alternative steady states among individual living cells, inducing phenotypic variability. The effects of white noise on the regime shift in bistable systems have been…
Recently, several theoretical and experimental studies have been undertaken to probe the effect of stochasticity on gene expression (GE). In experiments, the GE response to an inducing signal in a cell, measured by the amount of…
The use of critical slowing down as an early warning indicator for regime switching in observations from stochastic environments and noisy dynamical models has been widely studied and implemented in recent years. Some systems, however, have…
In many situations, the gene expression signature is a unique marker of the biological state. We study the modification of the gene expression distribution function when the biological state of a system experiences a change. This change may…
What are the signatures of the onset of catastrophe? Here we present the rich system physics characterizing the transition from homeostasis to stochasticity driven breakdown in an experimentally motivated minimal model. Recent…
Systems biology approaches combining theoretical modeling with experiments have been singularly successful in uncovering novel features of cellular phenomena. One such feature is that of binary gene expression in which the expression level…
Statistical physics can describe the behavior of microbial populations consisting of many heterogeneous individuals. A direct consequence is the existence of phase transitions, where the behavior of a population changes discontinuously upon…
Social ecological systems are often difficult to investigate and manage because of their inherent complexity1. Small variations in external drivers can lead to abrupt changes associated with instabilities and bifurcations in the underlying…
Genetic switch systems with mutual repression of two transcription factors are studied using deterministic and stochastic methods. Numerous studies have concluded that cooperative binding is a necessary condition for the emergence of…
The dynamics of gene transcription is tightly regulated in eukaryotes. Recent experiments have revealed various kinds of transcriptional dynamics, such as RNA polymerase II pausing, that involves regulation at the transcription initiation…
In this paper, dynamical systems theory and bifurcation theory are applied to investi- gate the rich dynamical behaviours observed in three simple disease models. The 2- and 3-dimensional models we investigate have arisen in previous…