Related papers: The stochastic behavior of a molecular switching c…
The parameter region of multistationarity of a reaction network contains all the parameters for which the associated dynamical system exhibits multiple steady states. Describing this region is challenging and remains an active area of…
The theory of monotone dynamical systems has been found very useful in the modeling of some gene, protein, and signaling networks. In monotone systems, every net feedback loop is positive. On the other hand, negative feedback loops are…
It has long been hypothesized that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, we develop a quantitative theory for this idea based on…
We analyze a class of network motifs in which a short, two-node positive feed- back motif is inserted in a three-node negative feedback loop. We demonstrate that such networks can undergo a bifurcation to a state where a stable fixed point…
Parametrized polynomial ordinary differential equation systems are broadly used for modeling, specially in the study of biochemical reaction networks under the assumption of mass-action kinetics. Understanding the qualitative behavior of…
This work addresses whether a reaction network, taken with mass-action kinetics, is multistationary, that is, admits more than one positive steady state in some stoichiometric compatibility class. We build on previous work on the effect…
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…
We use a multifractal formalism to study the effect of stochastic resonance in a noisy bistable system driven by various input signals. To characterize the response of a stochastic bistable system we introduce a new measure based on the…
Bistability is considered wide-spread among bacteria and eukaryotic cells, useful e.g. for enzyme induction, bet hedging, and epigenetic switching. However, this phenomenon has mostly been described with deterministic dynamic or well-mixed…
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;…
Bistability is ubiquitous in biological systems. For example, bistability is found in many reaction networks that involve the control and execution of important biological functions, such as signalling processes. Positive feedback loops,…
Feedback uses past detection outcomes to dynamically modify a quantum system and is central to quantum control. These outcomes can be stored in a memory, defined as a stochastic function of past measurements. In this work, we investigate…
Feedback loops are essential for regulating cell proliferation and maintaining the delicate balance between cell division and cell death. Thanks to the exact solution of a few simple models of cell growth it is by now clear that stochastic…
Phosphorelays are a class of signaling mechanisms used by cells to respond to changes in their environment. Phosphorelays (of which two-component systems constitute a special case) are particularly abundant in prokaryotes and have been…
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 reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network.…
Cellular decision-making (CDM) is a dynamic phenomenon often controlled by regulatory networks defining interactions between genes and transcription factor proteins. Traditional studies have focussed on molecular switches such as positive…
We study an information engine operating in an active bath, where a Brownian particle confined in a harmonic trap undergoes feedback-driven displacement cycles. Unlike thermal environments, active baths exhibit temporally correlated…
We study an excitable active rotator with slowly adapting nonlinear feedback and noise. Depending on the adaptation and the noise level, this system may display noise-induced spiking, noise-perturbed oscillations, or stochastic busting. We…
Bistability of MAP kinase (MAPK) activity has been suggested to contribute to several cellular processes, including differentiation and long-term synaptic potentiation. A recent model (48) predicts bistability due to interactions of the…