Related papers: Amplified biochemical oscillations in cellular sys…
The effects of intrinsic noise on stochastic delay systems is studied within an expansion in the inverse system size. We show that the stochastic nature of the underlying dynamics may induce oscillatory behaviour in parameter ranges where…
We investigate the propagation of random fluctuations through biochemical networks in which the concentrations of species are large enough so that the unperturbed problem is well-described by ordinary differential equation. We characterize…
It has been generally recognized that stochasticity can play an important role in the information processing accomplished by reaction networks in biological cells. Most treatments of that stochasticity employ Gaussian noise even though it…
Cortical neurons are bistable; as a consequence their local field potentials can fluctuate between quiescent and active states, generating slow 0.5-2 Hz oscillations which are widely known as transitions between Up and Down States. Despite…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
A biochemical oscillator model, describing developmental stage of myxobacteria, is analyzed mathematically. Observations from numerical simulations show that in a certain range of parameters, the corresponding system of ordinary…
The properties of the fluctuations large enough to induce bifurcations at open chemical systems at steady constraints are studied. The fluctuations that come from the diffusion-induced noise are considered. It is a generic for the surface…
Cellular transformations which involve a significant phenotypical change of the cell's state use bistable biochemical switches as underlying decision systems. In this work, we aim at linking cellular decisions taking place on a time scale…
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…
Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have…
The impact of random fluctuations on the dynamical behavior a complex biological systems is a longstanding issue, whose understanding would shed light on the evolutionary pressure that nature imposes on the intrinsic noise levels and would…
Living organisms are non-equilibrium, fluctuating, dynamic systems containing multi-step biological signaling cascades (BSC) with the ability to transduce changes in the concentration of extracellular molecules such as cytokines into…
Embedding sequential computations in biochemical environments is challenging because the computations are carried out by chemical reactions, which are inherently disordered. In this paper we apply modular design to specific calculations…
Statistical properties of environments experienced by biological signaling systems in the real world change, which necessitate adaptive responses to achieve high fidelity information transmission. One form of such adaptive response is gain…
Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how…
A wide range of organisms use circadian clocks to keep internal sense of daily time and regulate their behavior accordingly. Most of these clocks use intracellular genetic networks based on positive and negative regulatory elements. The…
We develop a framework for the general interpretation of the stochastic dynamical system near a limit cycle. Such quasi-periodic dynamics are commonly found in a variety of nonequilibrium systems, including the spontaneous oscillations of…
The dynamics of excitonic energy transfer in molecular complexes triggered by interaction with laser pulses offers a unique window into the underlying physical processes. The absorbed energy moves through the network of interlinked pigments…
Gene Regulatory Networks(GRNs) with feedback are essential components of many cellular processes and may exhibit oscillatory behavior. Analyzing such systems becomes increasingly complex as the number of components increases. Since gene…
Stochastic quasi-cycles for a two species model of the excitatory-inhibitory type, arranged on a triangular loop, are studied. By increasing the strength of the inter-nodes coupling, one moves the system towards the Hopf bifurcation and the…