Probing microscopic origins of confined subdiffusion by first-passage observables

Subdiffusive motion of tracer particles in complex crowded environments, such as biological cells, has been shown to be widepsread. This deviation from brownian motion is usually characterized by a sublinear time dependence of the mean square displacement (MSD). However, subdiffusive behavior can stem from different microscopic scenarios, which can not be identified solely by the MSD data. In this paper we present a theoretical framework which permits to calculate analytically first-passage observables (mean first-passage times, splitting probabilities and occupation times distributions) in disordered media in any dimensions. This analysis is applied to two representative microscopic models of subdiffusion: continuous-time random walks with heavy tailed waiting times, and diffusion on fractals. Our results show that first-passage observables provide tools to unambiguously discriminate between the two possible microscopic scenarios of subdiffusion. Moreover we suggest experiments based on first-passage observables which could help in determining the origin of subdiffusion in complex media such as living cells, and discuss the implications of anomalous transport to reaction kinetics in cells.Comment: 21 pages, 3 figures. Submitted versio

Exact expressions of mean first-passage times and splitting probabilities for random walks in bounded rectangular domains

We give exact and explicit expressions of mean first-passage times for random walks in a rectangular domain, in both cases of reflecting boundary conditions and periodic boundary conditions. The situations with one or two absorbing targets are considered.Comment: To appear as a note in J. Chem. Phy

Geometry-controlled kinetics

It has long been appreciated that transport properties can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target -- the first-passage time (FPT). Although essential to quantify the kinetics of reactions on all time scales, determining the FPT distribution was deemed so far intractable. Here, we calculate analytically this FPT distribution and show that transport processes as various as regular diffusion, anomalous diffusion, diffusion in disordered media and in fractals fall into the same universality classes. Beyond this theoretical aspect, this result changes the views on standard reaction kinetics. More precisely, we argue that geometry can become a key parameter so far ignored in this context, and introduce the concept of "geometry-controlled kinetics". These findings could help understand the crucial role of spatial organization of genes in transcription kinetics, and more generally the impact of geometry on diffusion-limited reactions.Comment: Submitted versio

Diffusion-limited reactions and mortal random walkers in confined geometries

Motivated by the diffusion-reaction kinetics on interstellar dust grains, we study a first-passage problem of mortal random walkers in a confined two-dimensional geometry. We provide an exact expression for the encounter probability of two walkers, which is evaluated in limiting cases and checked against extensive kinetic Monte Carlo simulations. We analyze the continuum limit which is approached very slowly, with corrections that vanish logarithmically with the lattice size. We then examine the influence of the shape of the lattice on the first-passage probability, where we focus on the aspect ratio dependence: Distorting the lattice always reduces the encounter probability of two walkers and can exhibit a crossover to the behavior of a genuinely one-dimensional random walk. The nature of this transition is also explained qualitatively.Comment: 18 pages, 16 figure

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

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

Occupation times of random walks in confined geometries: From random trap model to diffusion limited reactions

We consider a random walk in confined geometry, starting from a site and eventually reaching a target site. We calculate analytically the distribution of the occupation time on a third site, before reaching the target site. The obtained distribution is exact, and completely explicit in the case or parallepipedic confining domains. We discuss implications of these results in two different fields: The mean first passage time for the random trap model is computed in dimensions greater than 1, and is shown to display a non-trivial dependence with the source and target positions ; The probability of reaction with a given imperfect center before being trapped by another one is also explicitly calculated, revealing a complex dependence both in geometrical and chemical parameters

Scaling of mean first-passage time as efficiency measure of nodes sending information on scale-free Koch networks

A lot of previous work showed that the sectional mean first-passage time (SMFPT), i.e., the average of mean first-passage time (MFPT) for random walks to a given hub node (node with maximum degree) averaged over all starting points in scale-free small-world networks exhibits a sublinear or linear dependence on network order $N$ (number of nodes), which indicates that hub nodes are very efficient in receiving information if one looks upon the random walker as an information messenger. Thus far, the efficiency of a hub node sending information on scale-free small-world networks has not been addressed yet. In this paper, we study random walks on the class of Koch networks with scale-free behavior and small-world effect. We derive some basic properties for random walks on the Koch network family, based on which we calculate analytically the partial mean first-passage time (PMFPT) defined as the average of MFPTs from a hub node to all other nodes, excluding the hub itself. The obtained closed-form expression displays that in large networks the PMFPT grows with network order as $N \ln N$, which is larger than the linear scaling of SMFPT to the hub from other nodes. On the other hand, we also address the case with the information sender distributed uniformly among the Koch networks, and derive analytically the entire mean first-passage time (EMFPT), namely, the average of MFPTs between all couples of nodes, the leading scaling of which is identical to that of PMFPT. From the obtained results, we present that although hub nodes are more efficient for receiving information than other nodes, they display a qualitatively similar speed for sending information as non-hub nodes. Moreover, we show that the location of information sender has little effect on the transmission efficiency. The present findings are helpful for better understanding random walks performed on scale-free small-world networks.Comment: Definitive version published in European Physical Journal

Non-Markovian polymer reaction kinetics

Describing the kinetics of polymer reactions, such as the formation of loops and hairpins in nucleic acids or polypeptides, is complicated by the structural dynamics of their chains. Although both intramolecular reactions, such as cyclization, and intermolecular reactions have been studied extensively, both experimentally and theoretically, there is to date no exact explicit analytical treatment of transport-limited polymer reaction kinetics, even in the case of the simplest (Rouse) model of monomers connected by linear springs. We introduce a new analytical approach to calculate the mean reaction time of polymer reactions that encompasses the non-Markovian dynamics of monomer motion. This requires that the conformational statistics of the polymer at the very instant of reaction be determined, which provides, as a by-product, new information on the reaction path. We show that the typical reactive conformation of the polymer is more extended than the equilibrium conformation, which leads to reaction times significantly shorter than predicted by the existing classical Markovian theory.Comment: Main text (7 pages, 5 figures) + Supplemantary Information (13 pages, 2 figures

Geometrical organization of solutions to random linear Boolean equations

The random XORSAT problem deals with large random linear systems of Boolean variables. The difficulty of such problems is controlled by the ratio of number of equations to number of variables. It is known that in some range of values of this parameter, the space of solutions breaks into many disconnected clusters. Here we study precisely the corresponding geometrical organization. In particular, the distribution of distances between these clusters is computed by the cavity method. This allows to study the `x-satisfiability' threshold, the critical density of equations where there exist two solutions at a given distance.Comment: 20 page