Aging Scaled Brownian Motion

Scaled Brownian motion (SBM) is widely used to model anomalous diffusion of passive tracers in complex and biological systems. It is a highly non-stationary process governed by the Langevin equation for Brownian motion, however, with a power-law time dependence of the noise strength. Here we study the aging properties of SBM for both unconfined and confined motion. Specifically, we derive the ensemble and time averaged mean squared displacements and analyze their behavior in the regimes of weak, intermediate, and strong aging. A very rich behavior is revealed for confined aging SBM depending on different aging times and whether the process is sub- or superdiffusive. We demonstrate that the information on the aging factorizes with respect to the lag time and exhibits a functional form, that is identical to the aging behavior of scale free continuous time random walk processes. While SBM exhibits a disparity between ensemble and time averaged observables and is thus weakly non-ergodic, strong aging is shown to effect a convergence of the ensemble and time averaged mean squared displacement. Finally, we derive the density of first passage times in the semi-infinite domain that features a crossover defined by the aging time.Comment: 10 pages, 8 figures, REVTe

Occurrence of normal and anomalous diffusion in polygonal billiard channels

From extensive numerical simulations, we find that periodic polygonal billiard channels with angles which are irrational multiples of pi generically exhibit normal diffusion (linear growth of the mean squared displacement) when they have a finite horizon, i.e. when no particle can travel arbitrarily far without colliding. For the infinite horizon case we present numerical tests showing that the mean squared displacement instead grows asymptotically as t log t. When the unit cell contains accessible parallel scatterers, however, we always find anomalous super-diffusion, i.e. power-law growth with an exponent larger than 1. This behavior cannot be accounted for quantitatively by a simple continuous-time random walk model. Instead, we argue that anomalous diffusion correlates with the existence of families of propagating periodic orbits. Finally we show that when a configuration with parallel scatterers is approached there is a crossover from normal to anomalous diffusion, with the diffusion coefficient exhibiting a power-law divergence.Comment: 9 pages, 15 figures. Revised after referee reports: redrawn figures, additional comments. Some higher quality figures available at http://www.fis.unam.mx/~dsander

Subordinated Langevin Equations for Anomalous Diffusion in External Potentials - Biasing and Decoupled Forces

The role of external forces in systems exhibiting anomalous diffusion is discussed on the basis of the describing Langevin equations. Since there exist different possibilities to include the effect of an external field the concept of {\it biasing} and {\it decoupled} external fields is introduced. Complementary to the recently established Langevin equations for anomalous diffusion in a time-dependent external force-field [{\it Magdziarz et al., Phys. Rev. Lett. {\bf 101}, 210601 (2008)}] the Langevin formulation of anomalous diffusion in a decoupled time-dependent force-field is derived

Blinking statistics of a molecular beacon triggered by end-denaturation of DNA

We use a master equation approach based on the Poland-Scheraga free energy for DNA denaturation to investigate the (un)zipping dynamics of a denaturation wedge in a stretch of DNA, that is clamped at one end. In particular, we quantify the blinking dynamics of a fluorophore-quencher pair mounted within the denaturation wedge. We also study the behavioural changes in the presence of proteins, that selectively bind to single-stranded DNA. We show that such a setup could be well-suited as an easy-to-implement nanodevice for sensing environmental conditions in small volumes.Comment: 14 pages, 5 figures, LaTeX, IOP style. Accepted to J Phys Cond Mat special issue on diffusio

Fractional Klein-Kramers equation for superdiffusive transport: normal versus anomalous time evolution in a differential L{\'e}vy walk model

We introduce a fractional Klein-Kramers equation which describes sub-ballistic superdiffusion in phase space in the presence of a space-dependent external force field. This equation defines the differential L{\'e}vy walk model whose solution is shown to be non-negative. In the velocity coordinate, the probability density relaxes in Mittag-Leffler fashion towards the Maxwell distribution whereas in the space coordinate, no stationary solution exists and the temporal evolution of moments exhibits a competition between Brownian and anomalous contributions.Comment: 4 pages, REVTe

Universal Multifractality in Quantum Hall Systems with Long-Range Disorder Potential

We investigate numerically the localization-delocalization transition in quantum Hall systems with long-range disorder potential with respect to multifractal properties. Wavefunctions at the transition energy are obtained within the framework of the generalized Chalker--Coddington network model. We determine the critical exponent $\alpha_0$ characterizing the scaling behavior of the local order parameter for systems with potential correlation length $d$ up to $12$ magnetic lengths $l$. Our results show that $\alpha_0$ does not depend on the ratio $d/l$. With increasing $d/l$, effects due to classical percolation only cause an increase of the microscopic length scale, whereas the critical behavior on larger scales remains unchanged. This proves that systems with long-range disorder belong to the same universality class as those with short-range disorder.Comment: 4 pages, 2 figures, postsript, uuencoded, gz-compresse

Bubble coalescence in breathing DNA: Two vicious walkers in opposite potentials

We investigate the coalescence of two DNA-bubbles initially located at weak segments and separated by a more stable barrier region in a designed construct of double-stranded DNA. The characteristic time for bubble coalescence and the corresponding distribution are derived, as well as the distribution of coalescence positions along the barrier. Below the melting temperature, we find a Kramers-type barrier crossing behaviour, while at high temperatures, the bubble corners perform drift-diffusion towards coalescence. The results are obtained by mapping the bubble dynamics on the problem of two vicious walkers in opposite potentials.Comment: 7 pages, 4 figure

Bubble dynamics in DNA

The formation of local denaturation zones (bubbles) in double-stranded DNA is an important example for conformational changes of biological macromolecules. We study the dynamics of bubble formation in terms of a Fokker-Planck equation for the probability density to find a bubble of size n base pairs at time t, on the basis of the free energy in the Poland-Scheraga model. Characteristic bubble closing and opening times can be determined from the corresponding first passage time problem, and are sensitive to the specific parameters entering the model. A multistate unzipping model with constant rates recently applied to DNA breathing dynamics [G. Altan-Bonnet et al, Phys. Rev. Lett. 90, 138101 (2003)] emerges as a limiting case.Comment: 9 pages, 2 figure