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

Fidelity of holonomic quantum computations in the case of random errors in the values of control parameters

We investigate the influence of random errors in external control parameters on the stability of holonomic quantum computation in the case of arbitrary loops and adiabatic connections. A simple expression is obtained for the case of small random uncorrelated errors. Due to universality of mathematical description our results are valid for any physical system which can be described in terms of holonomies. Theoretical results are confirmed by numerical simulations.Comment: 7 pages, 3 figure

Generalized Fokker-Planck equation, Brownian motion, and ergodicity

Microscopic theory of Brownian motion of a particle of mass $M$ in a bath of molecules of mass $m\ll M$ is considered beyond lowest order in the mass ratio $m/M$. The corresponding Langevin equation contains nonlinear corrections to the dissipative force, and the generalized Fokker-Planck equation involves derivatives of order higher than two. These equations are derived from first principles with coefficients expressed in terms of correlation functions of microscopic force on the particle. The coefficients are evaluated explicitly for a generalized Rayleigh model with a finite time of molecule-particle collisions. In the limit of a low-density bath, we recover the results obtained previously for a model with instantaneous binary collisions. In general case, the equations contain additional corrections, quadratic in bath density, originating from a finite collision time. These corrections survive to order $(m/M)^2$ and are found to make the stationary distribution non-Maxwellian. Some relevant numerical simulations are also presented

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

Coarse grained dynamics of the freely cooling granular gas in one dimension

We study the dynamics and structure of clusters in the inhomogeneous clustered regime of a freely cooling granular gas of point particles in one dimension. The coefficient of restitution is modeled as $r_0<1$ or 1 depending on whether the relative speed is greater or smaller than a velocity scale $\delta$. The effective fragmentation rate of a cluster is shown to rise sharply beyond a $\delta$ dependent time scale. This crossover is coincident with the velocity fluctuations within a cluster becoming order $\delta$. Beyond this crossover time, the cluster size distribution develops a nontrivial power law distribution, whose scaling properties are related to those of the velocity fluctuations. We argue that these underlying features are responsible behind the recently observed nontrivial coarsening behaviour in the one dimensional freely cooling granular gas.Comment: 7 Pages, 9 Figure

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

Positive Feedback Regulation Results in Spatial Clustering and Fast Spreading of Active Signaling Molecules on a Cell Membrane

Positive feedback regulation is ubiquitous in cell signaling networks, often leading to binary outcomes in response to graded stimuli. However, the role of such feedbacks in clustering, and in spatial spreading of activated molecules, has come to be appreciated only recently. We focus on the latter, using a simple model developed in the context of Ras activation with competing negative and positive feedback mechanisms. We find that positive feedback, in the presence of slow diffusion, results in clustering of activated molecules on the plasma membrane, and rapid spatial spreading as the front of the cluster propagates with a constant velocity (dependent on the feedback strength). The advancing fronts of the clusters of the activated species are rough, with scaling consistent with the Kardar-Parisi-Zhang (KPZ) equation in one dimension. Our minimal model is general enough to describe signal transduction in a wide variety of biological networks where activity in the membrane-proximal region is subject to feedback regulation.Comment: 37 pages, 8 figures. Journal of Chemical Physics (in press

The Accuracy of Perturbative Master Equations

We consider open quantum systems with dynamics described by master equations that have perturbative expansions in the system-environment interaction. We show that, contrary to intuition, full-time solutions of order-2n accuracy require an order-(2n+2) master equation. We give two examples of such inaccuracies in the solutions to an order-2n master equation: order-2n inaccuracies in the steady state of the system and order-2n positivity violations, and we show how these arise in a specific example for which exact solutions are available. This result has a wide-ranging impact on the validity of coupling (or friction) sensitive results derived from second-order convolutionless, Nakajima-Zwanzig, Redfield, and Born-Markov master equations.Comment: 6 pages, 0 figures; v2 updated references; v3 updated references, extension to full-time and nonlocal regime

Intermittent quakes and record dynamics in the thermoremanent magnetization of a spin-glass

A novel method for analyzing the intermittent behavior of linear response data in aging systems is presented and applied to spin-glass thermoremanent magnetization (TRM) (Rodriguez et al. Phys. Rev. Lett. 91, 037203, 2003). The probability density function (PDF) of magnetic fluctuations is shown to have an asymmetric exponential tail, demonstrating that the demagnetization process is carried by intermittent, significant, spin rearrangements or \emph{quakes}. These quakes are most pronounced shortly after the field removal, $t/t_w \approx 1$ and in the non-equilibrium aging regime $t/t_w >>1$. For a broad temperature range, we study the dependence of the TRM decay rate on $t$, the time since the initial quench and on $t_w$, the time at which the magnetic field is cut. The $t$ and $t_w$ dependence of the rate is extracted numerically from the data and described analytically using the assumption that the linear response is subordinated to the intermittent process which spasmodically release the initial imbalances created by the quench.Comment: 8 pages, 9 figures. The paper has been expanded and restructured, the figures have been enlarged and improved. Final version, to appear in Phy. Rev.

Demographic growth and the distribution of language sizes

It is argued that the present log-normal distribution of language sizes is, to a large extent, a consequence of demographic dynamics within the population of speakers of each language. A two-parameter stochastic multiplicative process is proposed as a model for the population dynamics of individual languages, and applied over a period spanning the last ten centuries. The model disregards language birth and death. A straightforward fitting of the two parameters, which statistically characterize the population growth rate, predicts a distribution of language sizes in excellent agreement with empirical data. Numerical simulations, and the study of the size distribution within language families, validate the assumptions at the basis of the model.Comment: To appear in Int. J. Mod. Phys. C (2008