Long delay times in reaction rates increase intrinsic fluctuations

In spatially distributed cellular systems, it is often convenient to represent complicated auxiliary pathways and spatial transport by time-delayed reaction rates. Furthermore, many of the reactants appear in low numbers necessitating a probabilistic description. The coupling of delayed rates with stochastic dynamics leads to a probability conservation equation characterizing a non-Markovian process. A systematic approximation is derived that incorporates the effect of delayed rates on the characterization of molecular noise, valid in the limit of long delay time. By way of a simple example, we show that delayed reaction dynamics can only increase intrinsic fluctuations about the steady-state. The method is general enough to accommodate nonlinear transition rates, allowing characterization of fluctuations around a delay-induced limit cycle.Comment: 8 pages, 3 figures, to be published in Physical Review

A generalization of the cumulant expansion. Application to a scale-invariant probabilistic model

As well known, cumulant expansion is an alternative way to moment expansion to fully characterize probability distributions provided all the moments exist. If this is not the case, the so called escort mean values (or q-moments) have been proposed to characterize probability densities with divergent moments [C. Tsallis et al, J. Math. Phys 50, 043303 (2009)]. We introduce here a new mathematical object, namely the q-cumulants, which, in analogy to the cumulants, provide an alternative characterization to that of the q-moments for the probability densities. We illustrate this new scheme on a recently proposed family of scale-invariant discrete probabilistic models [A. Rodriguez et al, J. Stat. Mech. (2008) P09006; R. Hanel et al, Eur. Phys. J. B 72, 263268 (2009)] having q-Gaussians as limiting probability distributions

Sub-Poissonian atom number fluctuations by three-body loss in mesoscopic ensembles

We show that three-body loss of trapped atoms leads to sub-Poissonian atom number fluctuations. We prepare hundreds of dense ultracold ensembles in an array of magnetic microtraps which undergo rapid three-body decay. The shot-to-shot fluctuations of the number of atoms per trap are sub-Poissonian, for ensembles comprising 50--300 atoms. The measured relative variance or Fano factor $F=0.53\pm 0.22$ agrees very well with the prediction by an analytic theory ($F=3/5$) and numerical calculations. These results will facilitate studies of quantum information science with mesoscopic ensembles.Comment: 4 pages, 3 figure

Non-Gaussian fluctuations in stochastic models with absorbing barriers

The dynamics of a one-dimensional stochastic model is studied in presence of an absorbing boundary. The distribution of fluctuations is analytically characterized within the generalized van Kampen expansion, accounting for higher order corrections beyond the conventional Gaussian approximation. The theory is shown to successfully capture the non Gaussian traits of the sought distribution returning an excellent agreement with the simulations, for {\it all times} and arbitrarily {\it close} to the absorbing barrier. At large times, a compact analytical solution for the distribution of fluctuations is also obtained, bridging the gap with previous investigations, within the van Kampen picture and without resorting to alternative strategies, as elsewhere hypothesized.Comment: 2 figures, submitted to Phys. Rev. Let

How accurate are the non-linear chemical Fokker-Planck and chemical Langevin equations?

The chemical Fokker-Planck equation and the corresponding chemical Langevin equation are commonly used approximations of the chemical master equation. These equations are derived from an uncontrolled, second-order truncation of the Kramers-Moyal expansion of the chemical master equation and hence their accuracy remains to be clarified. We use the system-size expansion to show that chemical Fokker-Planck estimates of the mean concentrations and of the variance of the concentration fluctuations about the mean are accurate to order $\Omega^{-3/2}$ for reaction systems which do not obey detailed balance and at least accurate to order $\Omega^{-2}$ for systems obeying detailed balance, where $\Omega$ is the characteristic size of the system. Hence the chemical Fokker-Planck equation turns out to be more accurate than the linear-noise approximation of the chemical master equation (the linear Fokker-Planck equation) which leads to mean concentration estimates accurate to order $\Omega^{-1/2}$ and variance estimates accurate to order $\Omega^{-3/2}$. This higher accuracy is particularly conspicuous for chemical systems realized in small volumes such as biochemical reactions inside cells. A formula is also obtained for the approximate size of the relative errors in the concentration and variance predictions of the chemical Fokker-Planck equation, where the relative error is defined as the difference between the predictions of the chemical Fokker-Planck equation and the master equation divided by the prediction of the master equation. For dimerization and enzyme-catalyzed reactions, the errors are typically less than few percent even when the steady-state is characterized by merely few tens of molecules.Comment: 39 pages, 3 figures, accepted for publication in J. Chem. Phy

Framework for state and unknown input estimation of linear time-varying systems

The design of unknown-input decoupled observers and filters requires the assumption of an existence condition in the literature. This paper addresses an unknown input filtering problem where the existence condition is not satisfied. Instead of designing a traditional unknown input decoupled filter, a Double-Model Adaptive Estimation approach is extended to solve the unknown input filtering problem. It is proved that the state and the unknown inputs can be estimated and decoupled using the extended Double-Model Adaptive Estimation approach without satisfying the existence condition. Numerical examples are presented in which the performance of the proposed approach is compared to methods from literature.Comment: This paper has been accepted by Automatica. It considers unknown input estimation or fault and disturbances estimation. Existing approaches considers the case where the effects of fault and disturbance can be decoupled. In our paper, we consider the case where the effects of fault and disturbance are coupled. This approach can be easily extended to nonlinear system

Predicting rare events in chemical reactions: application to skin cell proliferation

In a well-stirred system undergoing chemical reactions, fluctuations in the reaction propensities are approximately captured by the corresponding chemical Langevin equation. Within this context, we discuss in this work how the Kramers escape theory can be used to predict rare events in chemical reactions. As an example, we apply our approach to a recently proposed model on cell proliferation with relevance to skin cancer [P.B. Warren, Phys. Rev. E {\bf 80}, 030903 (2009)]. In particular, we provide an analytical explanation for the form of the exponential exponent observed in the onset rate of uncontrolled cell proliferation.Comment: New materials and references added. To appear in Physical Review

Waiting time distribution for electron transport in a molecular junction with electron-vibration interaction

On the elementary level, electronic current consists of individual electron tunnelling events that are separated by random time intervals. The waiting time distribution is a probability to observe the electron transfer in the detector electrode at time $t+\tau$ given that an electron was detected in the same electrode at earlier time $t$. We study waiting time distribution for quantum transport in a vibrating molecular junction. By treating the electron-vibration interaction exactly and molecule-electrode coupling perturbatively, we obtain master equation and compute the distribution of waiting times for electron transport. The details of waiting time distributions are used to elucidate microscopic mechanism of electron transport and the role of electron-vibration interactions. We find that as nonequilibrium develops in molecular junction, the skewness and dispersion of the waiting time distribution experience stepwise drops with the increase of the electric current. These steps are associated with the excitations of vibrational states by tunnelling electrons. In the strong electron-vibration coupling regime, the dispersion decrease dominates over all other changes in the waiting time distribution as the molecular junction departs far away from the equilibrium

Fluctuating noise drives Brownian transport

The transport properties of Brownian ratchet was studied in the presence of stochastic intensity noise (SIN) in both overdamped and underdamped regimes. In the overdamped case, analytical solution using the matrix continued fraction method revealed the existence of a maximum current when the noise intensity fluctuates on intermediate time scale regions. Similar effects were observed for the underdamped case by Monte Carlo simulations. The optimal time-correlation for the Brownian transport coincided with the experimentally observed time-correlation of the extrinsic noise in Esherichia coli gene expression and implied the importance of environmental noise for molecular mechanisms.Comment: 22 pages, 8 figure