Residual mean first-passage time for jump processes: theory and applications to L\'evy flights and fractional Brownian motion

We derive a functional equation for the mean first-passage time (MFPT) of a generic self-similar Markovian continuous process to a target in a one-dimensional domain and obtain its exact solution. We show that the obtained expression of the MFPT for continuous processes is actually different from the large system size limit of the MFPT for discrete jump processes allowing leapovers. In the case considered here, the asymptotic MFPT admits non-vanishing corrections, which we call residual MFPT. The case of L/'evy flights with diverging variance of jump lengths is investigated in detail, in particular, with respect to the associated leapover behaviour. We also show numerically that our results apply with good accuracy to fractional Brownian motion, despite its non-Markovian nature.Comment: 13 pages, 8 figure

Measurement techniques for cryogenic Ka-band microstrip antennas

The measurement of cryogenic antennas poses unique logistical problems since the antenna under test must be embedded in a cooling chamber. A method of measuring the performance of cryogenic microstrip antennas using a closed cycle gas cooled refrigerator in a far field range is described. Antenna patterns showing the performance of gold and superconducting Ka-band microstrip antennas at various temperatures are presented

Topologically Driven Swelling of a Polymer Loop

Numerical studies of the average size of trivially knotted polymer loops with no excluded volume are undertaken. Topology is identified by Alexander and Vassiliev degree 2 invariants. Probability of a trivial knot, average gyration radius, and probability density distributions as functions of gyration radius are generated for loops of up to N=3000 segments. Gyration radii of trivially knotted loops are found to follow a power law similar to that of self avoiding walks consistent with earlier theoretical predictions.Comment: 6 pages, 4 figures, submitted to PNAS (USA) in Feb 200

Subdiffusion-limited reactions

We consider the coagulation dynamics A+A -> A and A+A A and the annihilation dynamics A+A -> 0 for particles moving subdiffusively in one dimension. This scenario combines the "anomalous kinetics" and "anomalous diffusion" problems, each of which leads to interesting dynamics separately and to even more interesting dynamics in combination. Our analysis is based on the fractional diffusion equation

Diffusion mechanisms of localised knots along a polymer

We consider the diffusive motion of a localized knot along a linear polymer chain. In particular, we derive the mean diffusion time of the knot before it escapes from the chain once it gets close to one of the chain ends. Self-reptation of the entire chain between either end and the knot position, during which the knot is provided with free volume, leads to an L^3 scaling of diffusion time; for sufficiently long chains, subdiffusion will enhance this time even more. Conversely, we propose local ``breathing'', i.e., local conformational rearrangement inside the knot region (KR) and its immediate neighbourhood, as additional mechanism. The contribution of KR-breathing to the diffusion time scales only quadratically, L^2, speeding up the knot escape considerably and guaranteeing finite knot mobility even for very long chains.Comment: 7 pages, 2 figures. Accepted to Europhys. Let

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

Directed motion emerging from two coupled random processes: Translocation of a chain through a membrane nanopore driven by binding proteins

We investigate the translocation of a stiff polymer consisting of M monomers through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind onto the polymer, and partially prevent backsliding of the polymer through the pore. The process is characterized by the rates: k for the polymer to make a diffusive jump through the pore, q for unbinding of a chaperone, and the rate q kappa for binding (with a binding strength kappa); except for the case of no binding kappa=0 the presence of the chaperones give rise to an effective force that drives the translocation process. Based on a (2+1) variate master equation, we study in detail the coupled dynamics of diffusive translocation and (partial) rectification by the binding proteins. In particular, we calculate the mean translocation time as a function of the various physical parameters.Comment: 22 pages, 5 figures, IOP styl

Driven polymer translocation through a nanopore: a manifestation of anomalous diffusion

We study the translocation dynamics of a polymer chain threaded through a nanopore by an external force. By means of diverse methods (scaling arguments, fractional calculus and Monte Carlo simulation) we show that the relevant dynamic variable, the translocated number of segments $s(t)$, displays an {\em anomalous} diffusive behavior even in the {\em presence} of an external force. The anomalous dynamics of the translocation process is governed by the same universal exponent $\alpha = 2/(2\nu +2 - \gamma_1)$, where $\nu$ is the Flory exponent and $\gamma_1$ - the surface exponent, which was established recently for the case of non-driven polymer chain threading through a nanopore. A closed analytic expression for the probability distribution function $W(s, t)$, which follows from the relevant {\em fractional} Fokker - Planck equation, is derived in terms of the polymer chain length $N$ and the applied drag force $f$. It is found that the average translocation time scales as $\tau \propto f^{-1}N^{\frac{2}{\alpha} -1}$. Also the corresponding time dependent statistical moments, $\propto t^{\alpha}$ and $\propto t^{2\alpha}$ reveal unambiguously the anomalous nature of the translocation dynamics and permit direct measurement of $\alpha$ in experiments. These findings are tested and found to be in perfect agreement with extensive Monte Carlo (MC) simulations.Comment: 6 pages, 4 figures, accepted to Europhys. Lett; some references were supplemented; typos were correcte

DNA bubble dynamics as a quantum Coulomb problem

We study the dynamics of denaturation bubbles in double-stranded DNA on the basis of the Poland-Scheraga model. We demonstrate that the associated Fokker-Planck equation is equivalent to a Coulomb problem. Below the melting temperature the bubble lifetime is associated with the continuum of scattering states of the repulsive Coulomb potential, at the melting temperature the Coulomb potential vanishes and the underlying first exit dynamics exhibits a long time power law tail, above the melting temperature, corresponding to an attractive Coulomb potential, the long time dynamics is controlled by the lowest bound state. Correlations and finite size effects are discussed.Comment: 4 pages, 3 figures, revte