相关论文: Deciphering noise amplification and reduction in o…
Noise-assisted transport phenomena highlight the nontrivial interplay between environmental effects and quantum coherence in achieving maximal efficiency. Due to the complexity of biochemical systems and their environments, effective open…
Gaussian macroscopic fluctuation theory underpins the understanding of noise in a broad class of nonequilibrium systems. We derive exact fluctuation-response relations linking the power spectral density of stationary fluctuations to the…
Interest in understanding the interplay between noise and the response of a non-linear device cuts across disciplinary boundaries. It is as relevant for unmasking the dynamics of neurons in noisy environments as it is for designing reliable…
The stochastic mutual repressor model is analysed using perturbation methods. This simple model of a gene circuit consists of two genes and three promotor states. Either of the two protein products can dimerize, forming a repressor molecule…
For cellular biochemical reaction systems where the numbers of molecules is small, significant noise is associated with chemical reaction events. This molecular noise can give rise to behavior that is very different from the predictions of…
To study the fluctuations and dynamics in chemical reaction processes, stochastic differential equations based on the rate equation involving chemical concentrations are often adopted. When the number of molecules is very small, however,…
This paper analyses of a stochastic model of a chemical reaction network with three types of chemical species ${\cal R}$, ${\cal M}$ and ${\cal U}$ that interact to transform a flow of external resources, the chemical species ${\cal Q}$, to…
Stochastic phenomena in which the noise amplitude is proportional to the fluctuating variable itself, usually called {\it multiplicative noise}, appear ubiquitously in physics, biology, economy and social sciences. The properties of…
Stochastic transitions between discrete microscopic states play an important role in many physical and biological systems. Often, these transitions lead to fluctuations on a macroscopic scale. A classic example from neuroscience is the…
Quantum walks in dynamically-disordered networks have become an invaluable tool for understanding the physics of open quantum systems. In this work, we introduce a novel approach to describe the dynamics of indistinguishable particles in…
Stochasticity plays important roles in reaction systems. Vector fields of probability flux and velocity characterize time-varying and steady-state properties of these systems, including high probability paths, barriers, checkpoints among…
Motivated by recent experiments with Josephson-junction circuits, we analyze the influence of various noise sources on the dynamics of two-level systems at optimal operation points where the linear coupling to low-frequency fluctuations is…
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…
System-environment interactions are intrinsically nonlinear and dependent on the interplay between many degrees of freedom. The complexity may be even more pronounced when one aims to describe biologically motivated systems. In that case,…
We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under1 quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady…
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…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
Flow and Diffusion Distributed Structures (FDS) are stationary spatially periodic patterns that can be observed in reaction-diffusion-advection systems. These structures arise when the flow rate exceeds a certain bifurcation point provided…
Many cellular behaviors are regulated by gene regulation networks, kinetics of which is one of the main subjects in the study of systems biology. Because of the low number molecules in these reacting systems, stochastic effects are…
In this paper I show that, for a class of reaction networks, the discrete stochastic nature of the reacting species and reactions results in qualitative and quantitative differences between the mean of exact stochastic simulations and the…