Related papers: Transcription fluctuation effects on biochemical o…
We consider a stochastic model of transcription factor (TF)-regulated gene expression. The model describes two genes: Gene A and Gene B which synthesize the TFs and the target gene proteins respectively. We show through analytic…
The irreversibility of trajectories in stochastic dynamical systems is linked to the structure of their causal representation in terms of Bayesian networks. We consider stochastic maps resulting from a time discretization with interval \tau…
We consider a nonlinear differential equation under the combined influence of small state-dependent Brownian perturbations of size $\varepsilon$, and fast periodic sampling with period $\delta$; $0<\varepsilon, \delta \ll 1$. Thus, state…
Expression of many genes varies as a cell transitions through different cell-cycle stages. How coupling between stochastic expression and cell cycle impacts cell-to-cell variability (noise) in the level of protein is not well understood. We…
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…
Experiments in recent years have vividly demonstrated that gene expression can be highly stochastic. How protein concentration fluctuations affect the growth rate of a population of cells, is, however, a wide open question. We present a…
We consider a model for substrate-depletion oscillations in genetic systems, based on a stochastic differential equation with a slowly evolving external signal. We show the existence of critical transitions in the system. We apply two…
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…
We study the spectral effect of the fluctuations of the vibration frequency. Such fluctuations play a major role in nanomechanical and other mesoscopic vibrational systems. We find that, for periodically driven systems, the interplay of the…
Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale…
To study the dynamics of chemical processes, we often adopt rate equations to observe the change in chemical concentrations. However, when the number of the molecules is small, the fluctuations cannot be neglected. We often study the…
We investigate the influence of a stochastically fluctuating step-barrier potential on bimolecular reaction rates by exact analytical theory and stochastic simulations. We demonstrate that the system exhibits a new resonant reaction…
Level fluctuations in quantum system have been used to characterize quantum chaos using random matrix models. Recently time series methods were used to relate level fluctuations to the classical dynamics in the regular and chaotic limit. In…
Time delays, modelling the process of intracellular gene expression, have been shown to have important impacts on the dynamics of pattern formation in reaction-diffusion systems. In particular, past work has shown that such time delays can…
Brownian circuits perform computations using stochastic transitions driven by thermal fluctuations. While the energetic costs of such fluctuation-driven computation have been extensively studied within stochastic thermodynamics, much less…
This paper analyzes how power injections affect frequency quality in power systems. We first derive a general expression linking active and reactive power injections at buses to the system's frequency. This formulation explicitly considers…
Dynamical systems with $\epsilon$ small random perturbations appear in both continuous mechanical motions and discrete stochastic chemical kinetics. The present work provides a detailed analysis of the central limit theorem (CLT), with a…
We study by simulation the effect of the diffusive motion of repressor molecules on the noise in mRNA and protein levels in the case of a repressed gene. We find that spatial fluctuations due to diffusion can drastically enhance the noise…
Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian…
Parametric fluctuations or stochastic signals are introduced into the control pulse sequence to investigate the feasibility of random control over quantum open systems. In a large parameter error region, the out-of-order control pulses work…