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The Kramers escape problem is a paradigmatic model for the kinetics of rare events, which are usually characterized by Arrhenius law. So far, analytical approaches have failed to capture the kinetics of rare events in the important case of non-Markovian processes with long-term memory, as occurs in the context of reactions involving proteins, long polymers, or strongly viscoelastic fluids. Here, based on a minimal model of non-Markovian Gaussian process with long-term memory, we determine quantitatively the mean FPT to a rare configuration and provide its asymptotics in the limit of a large energy barrier $E$. Our analysis unveils a correction to Arrhenius law, induced by long-term memory, which we determine analytically. This correction, which we show can be quantitatively significant, takes the form of a second effective energy barrier $E'

We consider the motion of a harmonically trapped overdamped particle, which is submitted to a self-phoretic force, that is proportional to the gradient of a diffusive field for which the particle itself is the source. In agreement with existing results for free particles or particles in a bounded domain, we find that the system exhibits a transition between an immobile phase, where the particle stays at the center of the trap, and an oscillatory state. We perform an exact analysis giving access to the bifurcation threshold, as well as the frequency of oscillations and their amplitude near the threshold. Our analysis also characterizes the shape of two-dimensional oscillations, that take place along a circle or a straight line. Our results are confirmed by numerical simulations., Comment: 10 pages 8 figures

Splitting probabilities quantify the likelihood of a given outcome out of competitive events for general random processes. This key observable of random walk theory, historically introduced as the Gambler's ruin problem for a player in a casino, has a broad range of applications beyond mathematical finance in evolution genetics, physics and chemistry, such as allele fixation, polymer translocation, protein folding and more generally competitive reactions. The statistics of competitive events is well understood for memoryless (Markovian) processes. However, in complex systems such as polymer fluids, the motion of a particle should typically be described as a process with memory. Appart from scaling theories and perturbative approaches in one-dimension, the outcome of competitive events is much less characterized analytically for processes with memory. Here, we introduce an analytical approach that provides the splitting probabilities for general $d$-dimensional non-Markovian Gaussian processes. This analysis shows that splitting probabilities are critically controlled by the out of equilibrium statistics of reactive trajectories, observed after the first passage. This hallmark of non-Markovian dynamics and its quantitative impact on splitting probabilities are directly evidenced in a prototypical experimental reaction scheme in viscoelastic fluids. Altogether, these results reveal both experimentally and theoretically the importance of memory effects on competitive reactions.

Domain decay is at the heart of the so-called evaporation-condensation Ostwald-ripening regime of phase ordering kinetics, where the growth of large domains occurs at the expense of smaller ones, which are expected to `evaporate'. We experimentally investigate such decay dynamics at the level of a single spherical domain picked from one phase in coexistence and brought into the other phase by an opto-mechanical approach, in a near-critical phase-separated binary liquid mixture. We observe that the decay dynamics is generally not compatible with the theoretically expected surface-tension decay laws for conserved order parameters. Using a mean-field description, we quantitatively explain this apparent disagreement by the gradient of solute concentrations induced by gravity close to a critical point. Finally, we determine the conditions for which buoyancy becomes negligible compared to capillarity and perform dedicated experiments that retrieve the predicted surface-tension induced decay exponent. The surface-tension driven decay dynamics of conserved order parameter systems in the presence and the absence of gravity, is thus established at the level of a single domain., Comment: 4 pages (main text) + 8 pages (SM); Accepted in PRL

In this chapter, we consider the problem of a non-Markovian random walker (displaying memory effects) searching for a target. We review an approach that links the first passage statistics to the properties of trajectories followed by the random walker in the future of the first passage time. This approach holds in one and higher spatial dimensions, when the dynamics in the vicinity of the target is Gaussian, and it is applied to three paradigmatic target search problems: the search for a target in confinement, the search for a rarely reached configuration (rare event kinetics), or the search for a target in infinite space, for processes featuring stationary increments or transient aging. The theory gives access to the mean first passage time (when it exists) or to the behavior of the survival probability at long times, and agrees with the available exact results obtained perturbatively for examples of weakly non-Markovian processes. This general approach reveals that the characterization of the non-equilibrium state of the system at the instant of first passage is key to derive first-passage kinetics, and provides a new methodology, via the analysis of trajectories after the first-passage, to make it quantitative., Comment: 22 pages, invited chapter for the book "The Target Problem" (Eds. D. S. Grebenkov, R. Metzler, G. Oshanin)

We consider the kinetics of the imperfect narrow escape problem, i.e. the time it takes for a particle diffusing in a confined medium of generic shape to reach and to be adsorbed by a small, imperfectly reactive patch embedded in the boundary of the domain, in two or three dimensions. Imperfect reactivity is modeled by an intrinsic surface reactivity $\kappa$ of the patch, giving rise to Robin boundary conditions. We present a formalism to calculate the exact asymptotics of the mean reaction time in the limit of large volume of the confining domain. We obtain exact explicit results in the two limits of large and small reactivities of the reactive patch, and a semi-analytical expression in the general case. Our approach reveals an anomalous scaling of the mean reaction time as the inverse square root of the reactivity in the large reactivity limit, valid for an initial position near the extremity of the reactive patch. We compare our exact results with those obtained within the ``constant flux approximation''; we show that this approximation turns out to give exactly the next-to-leading order term of the small reactivity limit, and provides a good approximation of the reaction time far from the reactive patch for all reactivities, but not in the vicinity of the boundary of the reactive patch due to the above mentioned anomalous scaling. These results thus provide a general framework to quantify the mean reaction times for the imperfect narrow escape problem.

We study the diffusion of particles confined close to a single wall and in double-wall planar channel geometries where the local diffusivities depend on the distance to the boundaries. Displacement parallel to the walls is Brownian as characterized by its variance, but it is non-Gaussian having a non-zero fourth cumulant. Establishing a link with Taylor dispersion, we calculate the fourth cumulant and the tails of the displacement distribution for general diffusivity tensors along with potentials generated by either the walls or externally, for instance gravity. Experimental and numerical studies of the motion of a colloid in the direction parallel to the wall give measured fourth cumulants which are correctly predicted by our theory. Interestingly, contrary to models of Brownian-yet-non-Gaussian diffusion, the tails of the displacement distribution are shown to be Gaussian rather than exponential. All together, our results provide additional tests and constraints for the inference of force maps and local transport properties near surfaces.

Persistence, defined as the probability that a fluctuating signal has not reached a threshold up to a given observation time, plays a crucial role in the theory of random processes. It quantifies the kinetics of processes as varied as phase ordering, reaction diffusion or interface relaxation dynamics. The fact that persistence can decay algebraically with time with non trivial exponents has triggered a number of experimental and theoretical studies. However, general analytical methods to calculate persistence exponents cannot be applied to the ubiquitous case of non-Markovian systems relaxing transiently after an imposed initial perturbation. Here, we introduce a theoretical framework that enables the non perturbative determination of persistence exponents of $d$-dimensional Gaussian non-Markovian processes with general non stationary dynamics relaxing to a steady state after an initial perturbation. Two prototypical classes of situations are analyzed: either the system is subjected to a temperature quench at initial time, or its past trajectory is assumed to have been observed and thus known. Altogether, our results reveal and quantify, on the basis of Gaussian processes, the deep impact of initial perturbations on first-passage statistics of non-Markovian processes. Our theory covers the case of spatial dimension higher than one, opening the way to characterize non-trivial reaction kinetics for complex systems with non-equilibrium initial conditions.

The paradigmatic model for heterogeneous media used in diffusion studies is built from reflecting obstacles and surfaces. It is well known that the crowding effect produced by these reflecting surfaces slows the dispersion of Brownian tracers. Here, using a general adsorption desorption model with surface diffusion, we show analytically that making surfaces or obstacles attractive can accelerate dispersion. In particular, we show that this enhancement of diffusion can exist even when the surface diffusion constant is smaller than that in the bulk. Even more remarkably, this enhancement effect occurs when the effective diffusion constant, when restricted to surfaces only, is lower than the effective diffusivity with purely reflecting boundaries. We give analytical formulas for this intriguing effect in periodic arrays of spheres as well as undulating micro-channels. Our results are confirmed by numerical calculations and Monte Carlo simulations.

We revisit the classic problem of the effective diffusion constant of a Brownian particle in a square lattice of reflecting impenetrable hard disks. This diffusion constant is also related to the effective conductivity of non-conducting and infinitely conductive disks in the same geometry. We show how a recently derived Green's function for the periodic lattice can be exploited to derive a series expansion of the diffusion constant in terms of the disk's volume fraction $\varphi$. Secondly we propose a variant of the Fick-Jacobs approximation to study the large volume fraction limit. This combination of analytical results is shown to describe the behavior of the diffusion constant for all volume fractions.

Chemical reactions generically require that particles come into contact. In practice, reaction is often imperfect and can necessitate multiple random encounters between reactants. In confined geometries, despite notable recent advances, there is to date no general analytical treatment of such imperfect transport-limited reaction kinetics. Here, we determine the kinetics of imperfect reactions in confining domains for any diffusive or anomalously diffusive Markovian transport process, and for different models of imperfect reactivity. We show that the full distribution of reaction times is obtained in the large confining volume limit from the knowledge of the mean reaction time only, which we determine explicitly. This distribution for imperfect reactions is found to be identical to that of perfect reactions upon an appropriate rescaling of parameters, which highlights the robustness of our results. Strikingly, this holds true even in the regime of low reactivity where the mean reaction time is independent of the transport process, and can lead to large fluctuations of the reaction time even in simple reaction schemes. We illustrate our results for normal diffusion in domains of generic shape, and for anomalous diffusion in complex environments, where our predictions are confirmed by numerical simulations., Comment: to appear in Communications Chemistry

Optically trapped particles are often subject to a non-conservative scattering force arising from radiation pressure. In this paper we present an exact solution for the steady state statistics of an overdamped Brownian particle subjected to a commonly used force field model for an optical trap. The model is the simplest of its kind that takes into account non-conservative forces. In particular, we present exact results for certain marginals of the full three dimensional steady state probability distribution as well as results for the toroidal probability currents which are present in the steady state, as well as for the circulation of theses currents. Our analytical results are confirmed by numerical solution of the steady state Fokker-Planck equation., Comment: 14 pages, 3 figures

We consider Taylor dispersion for tracer particles in micro-fluidic planar channels with strong confinement. In this context, the channel walls modify the local diffusivity tensor and also interactions between the tracer particles and the walls become important. We provide a simple and general formula for the effective diffusion constant along the channel as well as the first non-trivial finite time correction for arbitrary flows along the channel, arbitrary interaction potentials with the walls and arbitrary expressions for the diffusion tensor. The formula are in particular amenable to a straightforward numerical implementation, rendering them extremely useful for comparison with experiments. We present a number of applications, notably for systems which have parabolically varying diffusivity profiles, to systems with attractive interactions with the walls as well as electroosmotic flows between plates with differing surface charges within the Debye-H\"uckel approximation., Comment: 33 pages, 7 figures

How much time does it take for a fluctuating system, such as a polymer chain, to reach a target configuration that is rarely visited -- typically because of a high energy cost ? This question generally amounts to the determination of the first-passage time statistics to a target zone in phase space with lower occupation probability. Here, we present an analytical method to determine the mean first-passage time of a generic non-Markovian random walker to a rarely visited threshold, which goes beyond existing weak-noise theories. We apply our method to polymer systems, to determine (i) the first time for a flexible polymer to reach a large extension, and (ii) the first closure time of a stiff inextensible wormlike chain. Our results are in excellent agreement with numerical simulations and provide explicit asymptotic laws for the mean first-passage times to rarely visited configurations., Comment: Accepted in Physical Review Research (Rapid Communication) Main text + SI

For many stochastic processes, the probability $S(t)$ of not-having reached a target in unbounded space up to time $t$ follows a slow algebraic decay at long times, $S(t)\sim S_0/t^\theta$. This is typically the case of symmetric compact (i.e. recurrent) random walks. While the persistence exponent $\theta$ has been studied at length, the prefactor $S_0$, which is quantitatively essential, remains poorly characterized, especially for non-Markovian processes. Here we derive explicit expressions for $S_0$ for a compact random walk in unbounded space by establishing an analytic relation with the mean first-passage time of the same random walk in a large confining volume. Our analytical results for $S_0$ are in good agreement with numerical simulations, even for strongly correlated processes such as Fractional Brownian Motion, and thus provide a refined understanding of the statistics of longest first-passage events in unbounded space.

We consider a model of a particle trapped in a harmonic optical trap but with the addition of a non-conservative radiation induced force. This model is known to correctly describe experimentally observed trapped particle statistics for a wide range of physical parameters such as temperature and pressure. We theoretically analyse the effect of non-conservative force on the underlying steady state distribution as well as the power spectrum for the particle position. We compute perturbatively the probability distribution of the resulting non-equilibrium steady states for all dynamical regimes, underdamped through to overdamped and give expressions for the associated currents in phase space (position and velocity). We also give the spectral density of the trapped particle's position in all dynamical regimes and for any value of the non-conservative force. Signatures of the presence non-conservative forces are shown to be particularly strong for in the underdamped regime at low frequencies., Comment: 25 pages, 5 figures

As a first approximation, the forces acting on optically trapped particles are commonly assumed to be conservative. The influence of the nonconservative force has been shown to be negligible in overdamped liquid environments. However, its impact in the underdamped regime remains unexplored. Here, we experimentally study the combined effects of gradient and scattering forces on the nonlinear dynamics of trapped particles at various air pressures, leading to significant low-frequency noise excess along the optical axis and the emergence of toroidal Brownian vortices. Our results supported, by numerical simulations and a theoretical model, provide fundamental insights into the functioning of optical tweezers and a means for investigating nonequilibrium steady states in the presence of nonconservative forces.

The effective diffusivity of Brownian tracer particles confined in periodic micro-channels is smaller than the microscopic diffusivity due to entropic trapping. Here, we study diffusion in two-dimensional periodic channels whose cross-section presents singular points, such as abrupt changes of radius or the presence of thin walls, with openings, delimiting periodic compartments composing the channel. Dispersion in such systems is analyzed using the Fick-Jacobs' approximation. This approximation assumes a much faster equilibration in the lateral than in the axial direction, along which the dispersion is measured. If the characteristic width $a$ of the channel is much smaller than the period $L$ of the channel, i.e. $\varepsilon = a/L$ is small, this assumption is clearly valid for Brownian particles. For discontinuous channels, the Fick-Jacobs' approximation is only valid at the lowest order in $\varepsilon$ and provides a rough, though on occasions rather accurate, estimate of the effective diffusivity. Here we provide formulas for the effective diffusivity in discontinuous channels that are asymptotically exact at the next-to-leading order in $\varepsilon$. Each discontinuity leads to a reduction of the effective diffusivity. We show that our theory is consistent with the picture of effective {\em trapping rates} associated with each discontinuity, for which our theory provides explicit and asymptotically exact formulas. Our analytical predictions are confirmed by numerical analysis. Our results provide a precise quantification of the kinetic entropic barriers associated with profile singularities., Comment: 13 pages, 7 figures

We examine the dispersion of Brownian particles in a symmetric two dimensional channel, this classical problem has been widely studied in the literature using the so called Fick-Jacobs' approximation and its various improvements. Most studies rely on the reduction to an effective one dimensional diffusion equation, here we drive an explicit formula for the diffusion constant which avoids this reduction. Using this formula the effective diffusion constant can be evaluated numerically without resorting to Brownian simulations. In addition a perturbation theory can be developed in $\varepsilon = h_0/L$ where $h_0$ is the characteristic channel height and $L$ the period. This perturbation theory confirms the results of Kalinay and Percus (Phys. Rev. E 74, 041203 (2006)), based on the reduction, to one dimensional diffusion are exact at least to ${\cal O}(\varepsilon^6)$. Furthermore, we show how the Kalinay and Percus pseudo-linear approximation can be straightforwardly recovered. The approach proposed here can also be exploited to yield exact results an appropriate limit $\varepsilon \to \infty$, we show that here the diffusion constant remains finite and show how the result can be obtained with a simple physical argument. Moreover we show that the correction to the effective diffusion constant is of order $1/\varepsilon$ and remarkably has a some universal characteristics. Numerically we compare the analytical results obtained with exact numerical calculations for a number of interesting channel geometries., Comment: 21 pages, 5 figures

The effective diffusivity $D_e$ of tracer particles diffusing in periodically corrugated axisymmetric two and three dimensional channels is studied. The majority of previous studies of this class of problems are based on perturbative analyses about narrow channels, where the problem can be reduced to an effectively one dimensional one. Here we show how to analyze this class of problems using a much more general approach which even includes the limit of infinitely wide channels. Using the narrow and wide channel asymptotics, we provide a Pad{\'e} approximant scheme that is able to describe the dispersion properties of a wide class of channels. Furthermore, we systematically identify all the exact asymptotic scaling regimes of $D_e$ and the accompanying physical mechanisms that control dispersion, clarifying the distinction between smooth channels and compartmentalized ones, and identifying the regimes in which $D_e$ can be linked to first passage problems., Comment: Main text (6 pages) + Supplementary Information (5 pages)

Many out of equilibrium phenomena, such as diffusion-limited reactions or target search processes, are controlled by first-passage events. So far the general determination of the mean first-passage time (FPT) to a target in confinement has left aside aging processes, involved in contexts as varied as glassy dynamics, tracer diffusion in biological membranes or transport of cold atoms in optical lattices. Here we consider general non-Markovian scale-invariant processes in arbitrary dimension, displaying aging, and demonstrate that all the moments of the FPT obey universal scalings with the confining volume with non trivial exponents. Our analysis shows that a nonlinear scaling of the mean FPT with the volume is the hallmark of aging and provides a general tool to quantify its impact on first-passage kinetics in confinement.

This paper presents a theoretical analysis of the closure kinetics of a polymer with hydrodynamic interactions. This analysis, which takes into account the non-Markovian dynamics of the end-to-end vector and relies on the preaveraging of the mobility tensor (Zimm dynamics), is shown to reproduce very accurately the results of numerical simulations of the complete non linear dynamics. It is found that Markovian treatments, based on a Wilemski-Fixman approximation, significantly overestimate cyclization times (up to a factor 2), showing the importance of memory effects in the dynamics. In addition, this analysis provides scaling laws of the mean first cyclization time (MFCT) with the polymer size $N$ and capture radius $b$, which are identical in both Markovian and non-Markovian approaches. In particular, it is found that the scaling of the MFCT for large $N$ is given by $T\sim N^{3/2}\ln (N/b^2)$, which differs from the case of the Rouse dynamics where $T\sim N^{2}$. The extension to the case of the reaction kinetics of a monomer of a Zimm polymer with an external target in a confined volume is also presented.

The first-passage time (FPT), defined as the time a random walker takes to reach a target point in a confining domain, is a key quantity in the theory of stochastic processes. Its importance comes from its crucial role to quantify the efficiency of processes as varied as diffusion-limited reactions, target search processes or spreading of diseases. Most methods to determine the FPT properties in confined domains have been limited to Markovian (memoryless) processes. However, as soon as the random walker interacts with its environment, memory effects can not be neglected. Examples of non Markovian dynamics include single-file diffusion in narrow channels or the motion of a tracer particle either attached to a polymeric chain or diffusing in simple or complex fluids such as nematics \cite{turiv2013effect}, dense soft colloids or viscoelastic solution. Here, we introduce an analytical approach to calculate, in the limit of a large confining volume, the mean FPT of a Gaussian non-Markovian random walker to a target point. The non-Markovian features of the dynamics are encompassed by determining the statistical properties of the trajectory of the random walker in the future of the first-passage event, which are shown to govern the FPT kinetics.This analysis is applicable to a broad range of stochastic processes, possibly correlated at long-times. Our theoretical predictions are confirmed by numerical simulations for several examples of non-Markovian processes including the emblematic case of the Fractional Brownian Motion in one or higher dimensions. These results show, on the basis of Gaussian processes, the importance of memory effects in first-passage statistics of non-Markovian random walkers in confinement., Comment: Submitted version. Supplementary Information can be found on the Nature website : http://www.nature.com/nature/journal/v534/n7607/full/nature18272.html

We consider the time dependent dispersion properties of overdamped tracer particles diffusing in a one dimensional periodic potential under the influence of an additional constant tilting force $F$. The system is studied in the region where the force is close to the critical value $F_c$ at which the barriers separating neighboring potential wells disappear. We show that, when $F$ crosses the critical value, the shape of the Mean-Square Displacement (MSD) curves is strongly modified. We identify a diffusive regime at intermediate time scales, with an effective diffusion coefficient which is much larger than the late time diffusion coefficient for $F>F_c$, whereas for $F

We study the dynamics of local bond orientation in regular hyperbranched polymers modeled by Vicsek fractals. The local dynamics is investigated through the temporal autocorrelation functions of single bonds and the corresponding relaxation forms of the complex dielectric susceptibility. We show that the dynamic behavior of single segments depends on their remoteness from the periphery rather than on the size of the whole macromolecule. Remarkably, the dynamics of the core segments (which are most remote from the periphery) shows a scaling behavior that differs from the dynamics obtained after structural average. We analyze the most relevant processes of single segment motion and provide an analytic approximation for the corresponding relaxation times. Furthermore, we describe an iterative method to calculate the orientational dynamics in the case of very large macromolecular sizes., Comment: 11 pages, 9 figures

We consider the kinetics of first contact between two monomers of the same macromolecule. Relying on a fractal description of the macromolecule, we develop an analytical method to compute the Mean First Contact Time (MFCT) for various molecular sizes. In our theoretical description, the non-Markovian feature of monomer motion, arising from the interactions with the other monomers, is captured by accounting for the non-equilibrium conformations of the macromolecule at the very instant of first contact. This analysis reveals a simple scaling relation for the MFCT between two monomers, which involves only their equilibrium distance and the spectral dimension of the macromolecule, independently of its microscopic details. Our theoretical predictions are in excellent agreement with numerical stochastic simulations.

We consider the dispersion properties of tracer particles moving in non-equilibrium heterogeneous periodic media. The tracer motion is described by a Fokker-Planck equation with arbitrary spatially periodic (but constant in time) local diffusion tensors and drift, eventually with the presence of obstacles. We derive a Kubo-like formula for the time dependent effective diffusion tensor valid in any dimension. From this general formula, we derive expressions for the late time effective diffusion tensor and drift in these systems. In addition, we find an explicit formula for the late finite time corrections to these transport coefficients. In one dimension, we give closed analytical formula for the transport coefficients. The formulas derived here are very general and provide a straightforward method to compute the dispersion properties in arbitrary non-equilibrium periodic advection-diffusion systems.

The effect of a constant applied external force, induced for instance by an electric or gravitational field, on the dispersion of Brownian particles in periodic media with spatially varying diffusivity, and thus mobility, is studied. We show that external forces can greatly enhance dispersion in the direction of the applied force and also modify, to a lesser extent and in some cases non-monotonically, dispersion perpendicular to the applied force. Our results thus open up the intriguing possibility of modulating the dispersive properties of heterogeneous media by using externally applied force fields. These results are obtained via a Kubo formula which can be applied to any periodic advection diffusion system in any spatial dimension., Comment: Main text (4 pages, 2 figures) + Supplemental Material (4 pages)

We propose an exactly solvable multisite interaction spin-1/2 Ising-Heisenberg model on a triangulated Husimi lattice for the rigorous studies of chaotic entanglement. By making use of the generalized star-triangle transformation, we map the initial model onto an effective Ising one on a Husimi lattice, which we solve then exactly by applying the recursive method. Expressing the entanglement of the Heisenberg spins, that we quantify by means of the concurrence, in terms of the magnetic quantities of the system, we demonstrate its bifurcation and chaotic behavior. Furthermore, we show that the underlying chaos may slightly enhance the amount of the entanglement, and present on the phase diagram the transition lines from the uniform to periodic and from the periodic to chaotic regimes., Comment: 12 pages, 7 figures. Updated version for publication

We analyze the mean squared displacement of a Brownian particle in a medium with a spatially varying local diffusivity which is assumed to be periodic. When the system is asymptotically diffusive the mean squared displacement, characterizing the dispersion in the system, is, at late times, a linear function of time. A Kubo type formula is given for the mean squared displacement which allows the recovery of some known results for the effective diffusion constant $D_e$ in a direct way, but also allows an understanding of the asymptotic approach to the diffusive limit. In particular, as well as as computing the slope of a linear fit to the late time mean squared displacement, we find a formula for the constant where the fit intersects the y axis., Comment: 8 pages, 2 figures, revtex

We investigate theoretically the physics of diffusion-limited intramolecular polymer reactions. The present work completes and goes beyond a previous study [Nat. Chem. 4, 268 (2012)] that showed that the distribution of the polymer conformations at the very instant of reaction plays a key role in the cyclization kinetics, and takes explicitly into account the non-Markovian nature of the reactant motion. Here, we present in detail this non-Markovian theory, and compare it explicitly with existing Markovian theories and with numerical stochastic simulations. A large focus is made on the description of the non-equilibrium reactive conformations, with both numerical and analytical tools. We show that the reactive conformations are elongated and are characterized by a spectrum with a slowly decreasing tail, implying that the monomers that neighbor the reactive monomers are significantly shifted at the instant of reaction. We complete the study by deriving explicit formulas for the reaction rates in the Markovian Wilemski-Fixman theory when the reactants are located in arbitrary positions in the chain. We also give a simple scaling argument to understand the existence of two regimes in the reaction time, that come from two possible behaviors of monomer motion which can be either diffusive or subdiffusive., Comment: 20 pages, 9 figures

We investigate theoretically a diffusion-limited reaction between a reactant attached to a Rouse polymer and an external fixed reactive site in confinement. The present work completes and goes beyond a previous study [T. Gu\'erin, O. B\'enichou and R. Voituriez, Nat. Chem., 4, 268 (2012)] that showed that the distribution of the polymer conformations at the very instant of reaction plays a key role in the reaction kinetics, and that its determination enables the inclusion of non-Markovian effects in the theory. Here, we describe in detail this non-Markovian theory and we compare it with numerical stochastic simulations and with a Markovian approach, in which the reactive conformations are approximated by equilibrium ones. We establish the following new results. Our analysis reveals a strongly non-Markovian regime in 1D, where the Markovian and non-Markovian dependance of the relation time on the initial distance are different. In this regime, the reactive conformations are so different from equilibrium conformations that the Markovian expressions of the reaction time can be overestimated by several orders of magnitudes for long chains. We also show how to derive qualitative scaling laws for the reaction time in a systematic way that takes into account the different behaviors of monomer motion at all time and length scales. Finally, we also give an analytical description of the average elongated shape of the polymer at the instant of the reaction and we show that its spectrum behaves a a slow power-law for large wave numbers.

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)

Properties of random and fluctuating systems are often studied through the use of Gaussian distributions. However, in a number of situations, rare events have drastic consequences, which can not be explained by Gaussian statistics. Considerable efforts have thus been devoted to the study of non Gaussian fluctuations such as L\'evy statistics, generalizing the standard description of random walks. Unfortunately only macroscopic signatures, obtained by averaging over many random steps, are usually observed in physical systems. We present experimental results investigating the elementary process of anomalous diffusion of photons in hot atomic vapours. We measure the step size distribution of the random walk and show that it follows a power law characteristic of L\'evy flights., Comment: This final version is identical to the one published in Nature Physics