Related papers: Operating Regimes of Signaling Cycles: Statics, Dy…

The multisite phosphorylation-dephosphorylation cycle is a motif repeatedly used in cell signaling. This motif itself can generate a variety of dynamic behaviors like bistability and ultrasensitivity without direct positive feedbacks. In…

Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…

We study classes of dynamical systems that can be obtained by constructing recursive networks with monotone Boolean functions. Stack filters in nonlinear signal processing are special cases of such systems. We show an analytical connection…

Posttranslational modification of proteins is key in transmission of signals in cells. Many signaling pathways contain several layers of modification cycles that mediate and change the signal through the pathway. Here, we study a simple…

Signal transduction, the information processing mechanism in biological cells, is carried out by a network of biochemical reactions. The dynamics of driven biochemical reactions can be studied in terms of nonequilibrium statistical physics.…

Chemical reactions in cell are subject to intense stochastic fluctuations. An important question is how the fundamental physiological behavior of cell is kept stable against those noisy perturbations. In this paper a stochastic model 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…

Cellular signaling involves the transmission of environmental information through cascades of stochastic biochemical reactions, inevitably introducing noise that compromises signal fidelity. Each stage of the cascade often takes the form of…

The phase diagrams and transitions of nonequilibrium systems with multiplicative noise are studied theoretically. We show the existence of both strong and weak-coupling critical behavior, of two distinct active phases, and of a nonzero…

Cells are constantly exposed to fluctuating environmental conditions. External signals are sensed, processed and integrated by cellular signal transduction networks, which translate input signals into specific cellular responses by means of…

Many biological systems form colonies at high density. Passive granular systems will be jammed at such densities, yet for the survival of biological systems it is crucial that they are dynamic. We construct a phase diagram for a system of…

Complex dynamical systems may exhibit multiple steady states, including time-periodic limit cycles, where the final trajectory depends on initial conditions. With tuning of parameters, limit cycles can proliferate or merge at an exceptional…

The functions of many networked systems in physics, biology or engineering rely on a coordinated or synchronized dynamics of its constituents. In power grids for example, all generators must synchronize and run at the same frequency and…

In recent years it is increasingly being recognized that biochemical signals are not necessarily constant in time and that the temporal dynamics of a signal can be the information carrier. Moreover, it is now well established that…

Single-cell studies often show significant phenotypic variability due to the stochastic nature of intra-cellular biochemical reactions. When the numbers of molecules, e.g., transcription factors and regulatory enzymes, are in low abundance,…

Cells receive signaling molecules by receptors and relay information via sensory networks so that they can respond properly depending on the type of signal. Recent studies have shown that cells can extract multi-dimensional information from…

Limit cycles are self-sustained, closed trajectories in phase space representing (un)-stable, periodic behavior in nonlinear dynamical systems. They underpin diverse natural phenomena, from neuronal firing patterns to engineering…

Multistationarity in biological systems is a mechanism of cellular decision making. In particular, signaling pathways regulated by protein phosphorylation display features that facilitate a variety of responses to different biological…

The multiple futile cycle is a phosphorylation system in which a molecular substrate might be phosphorylated sequentially n times by means of an enzymatic mechanism. The system has been studied mathematically using reaction network theory…

Many cellular functions are based on the rhythmic organization of biological processes into self-repeating cascades of events. Some of these periodic processes, such as the cell cycles of several species, exhibit conspicuous irregularities…