Ultra-Slow Vacancy-Mediated Tracer Diffusion in Two Dimensions: The Einstein Relation Verified

We study the dynamics of a charged tracer particle (TP) on a two-dimensional lattice all sites of which except one (a vacancy) are filled with identical neutral, hard-core particles. The particles move randomly by exchanging their positions with the vacancy, subject to the hard-core exclusion. In case when the charged TP experiences a bias due to external electric field ${\bf E}$, (which favors its jumps in the preferential direction), we determine exactly the limiting probability distribution of the TP position in terms of appropriate scaling variables and the leading large-N ($n$ being the discrete time) behavior of the TP mean displacement $\bar{{\bf X}}_n$; the latter is shown to obey an anomalous, logarithmic law $|\bar{{\bf X}}_n| = \alpha_0(|{\bf E}|) \ln(n)$. On comparing our results with earlier predictions by Brummelhuis and Hilhorst (J. Stat. Phys. {\bf 53}, 249 (1988)) for the TP diffusivity $D_n$ in the unbiased case, we infer that the Einstein relation $\mu_n = \beta D_n$ between the TP diffusivity and the mobility $\mu_n = \lim_{|{\bf E}| \to 0}(|\bar{{\bf X}}_n|/| {\bf E} |n)$ holds in the leading in $n$ order, despite the fact that both $D_n$ and $\mu_n$ are not constant but vanish as $n \to \infty$. We also generalize our approach to the situation with very small but finite vacancy concentration $\rho$, in which case we find a ballistic-type law $|\bar{{\bf X}}_n| = \pi \alpha_0(|{\bf E}|) \rho n$. We demonstrate that here, again, both $D_n$ and $\mu_n$, calculated in the linear in $\rho$ approximation, do obey the Einstein relation.Comment: 25 pages, one figure, TeX, submitted to J. Stat. Phy

Averaged residence times of stochastic motions in bounded domains

Two years ago, Blanco and Fournier (Blanco S. and Fournier R., Europhys. Lett. 2003) calculated the mean first exit time of a domain of a particle undergoing a randomly reoriented ballistic motion which starts from the boundary. They showed that it is simply related to the ratio of the volume's domain over its surface. This work was extended by Mazzolo (Mazzolo A., Europhys. Lett. 2004) who studied the case of trajectories which start inside the volume. In this letter, we propose an alternative formulation of the problem which allows us to calculate not only the mean exit time, but also the mean residence time inside a sub-domain. The cases of any combinations of reflecting and absorbing boundary conditions are considered. Lastly, we generalize our results for a wide class of stochastic motions.Comment: 7 pages, 3 figure

Kinetics of active surface-mediated diffusion in spherically symmetric domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. We generalize the results of [J. Stat. Phys. {\bf 142}, 657 (2011)] and consider a biased diffusion in a general annulus with an arbitrary number of regularly spaced targets on a partially reflecting surface. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.Comment: Published online in J. Stat. Phy

Mean first-passage time of surface-mediated diffusion in spherical domains

We present an exact calculation of the mean first-passage time to a target on the surface of a 2D or 3D spherical domain, for a molecule alternating phases of surface diffusion on the domain boundary and phases of bulk diffusion. The presented approach is based on an integral equation which can be solved analytically. Numerically validated approximation schemes, which provide more tractable expressions of the mean first-passage time are also proposed. In the framework of this minimal model of surface-mediated reactions, we show analytically that the mean reaction time can be minimized as a function of the desorption rate from the surface.Comment: to appear in J. Stat. Phy

Facilitated diffusion of proteins on chromatin

We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which has been recently evidenced experimentally. Facilitated diffusion is shown quantitatively to be favorable for a fast localization of a target locus by a transcription factor, and even to enable the minimization of the search time by tuning the affinity of the transcription factor with DNA. This study shows the robustness of the facilitated diffusion mechanism, invoked so far only for linear conformations of DNA.Comment: 4 pages, 4 figures, accepted versio

Exact calculations of first-passage quantities on recursive networks

We present general methods to exactly calculate mean-first passage quantities on self-similar networks defined recursively. In particular, we calculate the mean first-passage time and the splitting probabilities associated to a source and one or several targets; averaged quantities over a given set of sources (e.g., same-connectivity nodes) are also derived. The exact estimate of such quantities highlights the dependency of first-passage processes with respect to the source-target distance, which has recently revealed to be a key parameter to characterize transport in complex media. We explicitly perform calculations for different classes of recursive networks (finitely ramified fractals, scale-free (trans)fractals, non-fractals, mixtures between fractals and non-fractals, non-decimable hierarchical graphs) of arbitrary size. Our approach unifies and significantly extends the available results in the field.Comment: 16 pages, 10 figure

First exit times and residence times for discrete random walks on finite lattices

In this paper, we derive explicit formulas for the surface averaged first exit time of a discrete random walk on a finite lattice. We consider a wide class of random walks and lattices, including random walks in a non-trivial potential landscape. We also compute quantities of interest for modelling surface reactions and other dynamic processes, such as the residence time in a subvolume, the joint residence time of several particles and the number of hits on a reflecting surface.Comment: 19 pages, 2 figure

Enhanced reaction kinetics in biological cells

The cell cytoskeleton is a striking example of "active" medium driven out-of-equilibrium by ATP hydrolysis. Such activity has been shown recently to have a spectacular impact on the mechanical and rheological properties of the cellular medium, as well as on its transport properties : a generic tracer particle freely diffuses as in a standard equilibrium medium, but also intermittently binds with random interaction times to motor proteins, which perform active ballistic excursions along cytoskeletal filaments. Here, we propose for the first time an analytical model of transport limited reactions in active media, and show quantitatively how active transport can enhance reactivity for large enough tracers like vesicles. We derive analytically the average interaction time with motor proteins which optimizes the reaction rate, and reveal remarkable universal features of the optimal configuration. We discuss why active transport may be beneficial in various biological examples: cell cytoskeleton, membranes and lamellipodia, and tubular structures like axons.Comment: 10 pages, 2 figure

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

Windings of the 2D free Rouse chain

We study long time dynamical properties of a chain of harmonically bound Brownian particles. This chain is allowed to wander everywhere in the plane. We show that the scaling variables for the occupation times T_j, areas A_j and winding angles \theta_j (j=1,...,n labels the particles) take the same general form as in the usual Brownian motion. We also compute the asymptotic joint laws P({T_j}), P({A_j}), P({\theta_j}) and discuss the correlations occuring in those distributions.Comment: Latex, 17 pages, submitted to J. Phys.