Towards deterministic equations for Levy walks: the fractional material derivative

Levy walks are random processes with an underlying spatiotemporal coupling. This coupling penalizes long jumps, and therefore Levy walks give a proper stochastic description for a particle's motion with broad jump length distribution. We derive a generalized dynamical formulation for Levy walks in which the fractional equivalent of the material derivative occurs. Our approach will be useful for the dynamical formulation of Levy walks in an external force field or in phase space for which the description in terms of the continuous time random walk or its corresponding generalized master equation are less well suited

Optimal target search on a fast folding polymer chain with volume exchange

We study the search process of a target on a rapidly folding polymer (`DNA') by an ensemble of particles (`proteins'), whose search combines 1D diffusion along the chain, Levy type diffusion mediated by chain looping, and volume exchange. A rich behavior of the search process is obtained with respect to the physical parameters, in particular, for the optimal search.Comment: 4 pages, 3 figures, REVTe

Aging renewal theory and application to random walks

The versatility of renewal theory is owed to its abstract formulation. Renewals can be interpreted as steps of a random walk, switching events in two-state models, domain crossings of a random motion, etc. We here discuss a renewal process in which successive events are separated by scale-free waiting time periods. Among other ubiquitous long time properties, this process exhibits aging: events counted initially in a time interval [0,t] statistically strongly differ from those observed at later times [t_a,t_a+t]. In complex, disordered media, processes with scale-free waiting times play a particularly prominent role. We set up a unified analytical foundation for such anomalous dynamics by discussing in detail the distribution of the aging renewal process. We analyze its half-discrete, half-continuous nature and study its aging time evolution. These results are readily used to discuss a scale-free anomalous diffusion process, the continuous time random walk. By this we not only shed light on the profound origins of its characteristic features, such as weak ergodicity breaking. Along the way, we also add an extended discussion on aging effects. In particular, we find that the aging behavior of time and ensemble averages is conceptually very distinct, but their time scaling is identical at high ages. Finally, we show how more complex motion models are readily constructed on the basis of aging renewal dynamics.Comment: 21 pages, 7 figures, RevTe

Fine structure of distributions and central limit theorem in diffusive billiards

We investigate deterministic diffusion in periodic billiard models, in terms of the convergence of rescaled distributions to the limiting normal distribution required by the central limit theorem; this is stronger than the usual requirement that the mean square displacement grow asymptotically linearly in time. The main model studied is a chaotic Lorentz gas where the central limit theorem has been rigorously proved. We study one-dimensional position and displacement densities describing the time evolution of statistical ensembles in a channel geometry, using a more refined method than histograms. We find a pronounced oscillatory fine structure, and show that this has its origin in the geometry of the billiard domain. This fine structure prevents the rescaled densities from converging pointwise to gaussian densities; however, demodulating them by the fine structure gives new densities which seem to converge uniformly. We give an analytical estimate of the rate of convergence of the original distributions to the limiting normal distribution, based on the analysis of the fine structure, which agrees well with simulation results. We show that using a Maxwellian (gaussian) distribution of velocities in place of unit speed velocities does not affect the growth of the mean square displacement, but changes the limiting shape of the distributions to a non-gaussian one. Using the same methods, we give numerical evidence that a non-chaotic polygonal channel model also obeys the central limit theorem, but with a slower convergence rate.Comment: 16 pages, 19 figures. Accepted for publication in Physical Review E. Some higher quality figures at http://www.maths.warwick.ac.uk/~dsander

Harmonic operation of a free-electron laser

Harmonic operation of a free-electron-laser amplifier is studied. The key issue investigated here is suppression of the fundamental. For a tapered amplifier with the right choice of parameters, it is found that the presence of the harmonic mode greatly reduces the growth rate of the fundamental. A limit on the reflection coefficient of the fundamental mode that will ensure stable operation is derived. The relative merits of tripling the frequency by operating at the third harmonic versus decreasing the wiggler period by a factor of 3 are discussed

Thermodynamics and Fractional Fokker-Planck Equations

The relaxation to equilibrium in many systems which show strange kinetics is described by fractional Fokker-Planck equations (FFPEs). These can be considered as phenomenological equations of linear nonequilibrium theory. We show that the FFPEs describe the system whose noise in equilibrium funfills the Nyquist theorem. Moreover, we show that for subdiffusive dynamics the solutions of the corresponding FFPEs are probability densities for all cases where the solutions of normal Fokker-Planck equation (with the same Fokker-Planck operator and with the same initial and boundary conditions) exist. The solutions of the FFPEs for superdiffusive dynamics are not always probability densities. This fact means only that the corresponding kinetic coefficients are incompatible with each other and with the initial conditions

Helix untwisting and bubble formation in circular DNA

The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path integral techniques, simulates a distribution of topoisomers with various twist numbers and finds the energetically most favorable molecular conformation as a function of temperature. The method can predict helical repeat, openings loci and bubble sizes for specific sequences in a broad temperature range. Some results are presented for a short DNA circle recently identified in mammalian cells.Comment: The Journal of Chemical Physics, vol. 138 (2013), in pres