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

Dark matter density profiles: A comparison of nonextensive theory with N-body simulations

Density profiles of simulated galaxy cluster-sized dark matter haloes are analysed in the context of a recently introduced nonextensive theory of dark matter and gas density distributions. Nonextensive statistics accounts for long-range interactions in gravitationally coupled systems and is derived from the fundamental concept of entropy generalisation. The simulated profiles are determined down to radii of ~1% of R_200. The general trend of the relaxed, spherically averaged profiles is accurately reproduced by the theory. For the main free parameter kappa, measuring the degree of coupling within the system, and linked to physical quantities as the heat capacity and the polytropic index of the self-gravitating ensembles, we find a value of -15. The significant advantage over empirical fitting functions is provided by the physical content of the nonextensive approach.Comment: 6 pages, 3 figures, accepted for publication in A&

Transient rectification of Brownian diffusion with asymmetric initial distribution

In an ensemble of non-interacting Brownian particles, a finite systematic average velocity may temporarily develop, even if it is zero initially. The effect originates from a small nonlinear correction to the dissipative force, causing the equation for the first moment of velocity to couple to moments of higher order. The effect may be relevant when a complex system dissociates in a viscous medium with conservation of momentum

Analytical results for a Fokker-Planck equation in the small noise limit

We present analytical results for the lowest cumulants of a stochastic process described by a Fokker-Planck equation with nonlinear drift. We show that, in the limit of small fluctuations, the mean, the variance and the covariance of the process can be expressed in compact form with the help of the Lambert W function. As an application, we discuss the interplay of noise and nonlinearity far from equilibrium.Comment: 5 pages, 4 figure

A variational approach to moment-closure approximations for the kinetics of biomolecular reaction networks

Approximate solutions of the chemical master equation and the chemical Fokker-Planck equation are an important tool in the analysis of biomolecular reaction networks. Previous studies have highlighted a number of problems with the moment-closure approach used to obtain such approximations, calling it an ad-hoc method. In this article, we give a new variational derivation of moment-closure equations which provides us with an intuitive understanding of their properties and failure modes and allows us to correct some of these problems. We use mixtures of product-Poisson distributions to obtain a flexible parametric family which solves the commonly observed problem of divergences at low system sizes. We also extend the recently introduced entropic matching approach to arbitrary ansatz distributions and Markov processes, demonstrating that it is a special case of variational moment closure. This provides us with a particularly principled approximation method. Finally, we extend the above approaches to cover the approximation of multi-time joint distributions, resulting in a viable alternative to process-level approximations which are often intractable.Comment: Minor changes and clarifications; corrected some typo

Classical no-cloning theorem under Liouville dynamics by non-Csisz\'ar f-divergence

The Csisz\'ar f-divergence, which is a class of information distances, is known to offer a useful tool for analysing the classical counterpart of the cloning operations that are quantum mechanically impossible for the factorized and marginality classical probability distributions under Liouville dynamics. We show that a class of information distances that does not belong to this divergence class also allows for the formulation of a classical analogue of the quantum no-cloning theorem. We address a family of nonlinear Liouville-like equations, and generic distances, to obtain constraints on the corresponding functional forms, associated with the formulation of classical analogue of the no-cloning principle.Comment: 6 pages, revised, published versio

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

A new view of the spin echo diffusive diffraction on porous structures

Analysis with the characteristic functional of stochastic motion is used for the gradient spin echo measurement of restricted motion to clarify details of the diffraction-like effect in a porous structure. It gives the diffusive diffraction as an interference of spin phase shifts due to the back-flow of spins bouncing at the boundaries, when mean displacement of scattered spins is equal to the spin phase grating prepared by applied magnetic field gradients. The diffraction patterns convey information about morphology of the surrounding media at times long enough that opposite boundaries are restricting displacements. The method explains the dependence of diffraction on the time and width of gradient pulses, as observed at the experiments and the simulations. It also enlightens the analysis of transport properties by the spin echo, particularly in systems, where the motion is restricted by structure or configuration

Stochastic dynamics beyond the weak coupling limit: thermalization

We discuss the structure and asymptotic long-time properties of coupled equations for the moments of a Brownian particle's momentum derived microscopically beyond the lowest approximation in the weak coupling parameter. Generalized fluctuation-dissipation relations are derived and shown to ensure convergence to thermal equilibrium at any order of perturbation theory.Comment: 6+ page

Local Quasiconvexity of Groups acting on Small Cancellation Complexes

Given a group acting cellularly and cocompactly on a simply-connected 2-complex, we provide a criterion establishing that all finitely generated subgroups have quasiconvex orbits. This work generalizes the "perimeter method". As an application, we show that high-powered one-relator products A \ast B / \nclose{r^n} are coherent if $A$ and $B$ are coherent.Comment: version 1. 14 pages, 4 figure