We study diffusion of (fluorescently) tagged hard-core interacting particles of finite size in a finite one-dimensional system. We find an exact analytical expression for the tagged particle probability density using a coordinate Bethe-ansatz, from which the mean square displacement is calculated. The analysis show the existence of three regimes of drastically different behavior for short, intermediate and large times. The results show excellent agreement with stochastic simulations (Gillespie algorithm). The findings of the Letter holds promise for the development of novel bio-nano sensors.
We introduce a stochastic equation for the microscopic motion of a tagged particle in the single file model. This equation provides a compact representation of several of the system's properties such as Fluctuation-Dissipation and Linear Response relations, achieved by means of a diffusion noise approach. Most important, the proposed Langevin Equation reproduces quantitatively the \emph{three} temporal regimes and the corresponding time scales: ballistic, diffusive and subdiffusive.
We study two-component single-file diffusion inside a narrow channel that at its ends is open and connected with particle reservoirs. Using a two-species version of the symmetric simple exclusion process as a model, we propose a hydrodynamic description of the coarse-grained dynamics with a self-diffusion coefficient that is inversely proportional to the length of the channel. The theory predicts an unexpected nonequilibrium phase transition for the bulk particle density as the external total density gradient between the reservoirs is varied. The individual particle currents do not in general …
The path-integral representation of Smoluchowski equation is exploited to explore the stochastic dynamics of a tagged Brownian particle within an interacting system where hydrodynamic effects are neglected. In particular, this formalism is applied to a particle system confined to a one-dimensional infinite line aiming to investigate the single-file diffusion phenomenon in this scenario. In particular, the path-integral method is contrasted against the standard many-particle Langevin equation for a system of interacting Brownian particles in a harmonic chain model, exhibiting excellent agreemen…
In this work we present a general derivation of the non-Fickian behavior for the self-diffusion of identically interacting particle systems with excluded mutual passage. We show that the conditional probability distribution of finding a particle at position $x_{t}$ after time $t$, when the particle was located at $x_{0}$ at $t=0$, follows a Gaussian distribution in the long-time limit, with variance $2W(t)\sim t^{1/2}$ for overdamped systems and with variance $2W(t)\sim t$ for classical systems. The asymptotic behavior of the mean-squared displacement, $W(t)$, is shown to be independent of the…
We investigate the single-file dynamics of a tagged particle in a system consisting of N hardcore interacting particles (the particles cannot pass each other) which are diffusing in a one-dimensional system where the particles have different diffusion constants. For the two particle case an exact result for the conditional probability density function (PDF) is obtained for arbitrary initial particle positions and all times. The two-particle PDF is used to obtain the tagged particle PDF. For the general N-particle case (N large) we perform stochastic simulations using our new computationally ef…
Diffusive properties of a monodisperse system of interacting particles confined to a \textit{quasi}-one-dimensional (Q1D) channel are studied using molecular dynamics (MD) simulations. We calculate numerically the mean-squared displacement (MSD) and investigate the influence of the width of the channel (or the strength of the confinement potential) on diffusion in finite-size channels of different shapes (i.e., straight and circular). The transition from single-file diffusion (SFD) to the two-dimensional diffusion regime is investigated. This transition (regarding the calculation of the scalin…
The term single file (SF) dynamics refers to the motion of an assembly of particles through a channel with cross-section comparable to the particles' diameter. Single file diffusion (SFD) is then the diffusion of a tagged particle in a \emph{single file}, i.e., under the condition that particle passing is not allowed. SFD accounts for a large variety of processes in nature, including diffusion of colloids in synthetic and natural-shaped channels, biological motors along molecular chains, electrons in proteins and liquid helium, ions through membrane, just to mention a few examples. Albeit intr…
We apply the macroscopic fluctuation theory to analyze the long-time statistics of the position of a tracer in the dense and the dilute limits of diffusive single-file systems. Our explicit results are about the corresponding large deviation functions for an initial step density profile with the fluctuating (annealed) and the fixed (quenched) initial conditions. These hydrodynamic results are applicable for a general single-file system and they confirm recent exact results obtained by microscopic solutions for specific model systems.
We investigate memory effects in barrier-crossing in the overdamped setting. We focus on the scenario where the hidden degrees of freedom relax on exactly the same time scale as the observable. As a prototypical model, we analyze tagged-particle diffusion in a single file confined to a bi-stable potential. We identify the signatures of memory and explain their origin. The emerging memory is a result of the projection of collective many-body eigenmodes onto the motion of a tagged-particle. We are interested in the "confining" (all background particles in front of the tagged-particle) and "pushi…
We numerically study structure and dynamics of single files composed of active particles, as well as, active-passive binary mixtures. Our simulation results show that when the persistent length of self-propelled particles is much larger than the average inter-particle separation and the self-propulsion velocity is larger than the thermal velocity, particles in the file exist as clusters of various sizes. Average cluster size and structures of the file are very sensitive to self-propulsion properties, thermal fluctuations and composition of the mixture. In addition to the variation of file comp…
The crossover from single-file diffusion, where the mean-square displacement scales as <x^2> ~t^(1/2), to normal Fickian diffusion, where <x^2>~t$, is studied as a function of channel width for colloidal particles. By comparing Brownian dynamics to a hybrid molecular dynamics and mesoscopic simulation technique, we can study the effect of hydrodynamic interactions on the single file mobility and on the crossover to Fickian diffusion for wider channel widths. For disc-like particles with a steep interparticle repulsion, the single file mobilities for different particle densities are well descri…
Diffusive properties of interacting magnetic dipoles confined in a parabolic narrow channel and in the presence of a periodic modulated (corrugated) potential along the unconfined direction are studied using Brownian dynamics simulations. We compare our simulation results with the analytical result for the effective diffusion coefficient of a single-particle by Festa and d'Agliano [Physica A \textbf{90}, 229 (1978)] and show the importance of inter-particle interaction on the diffusion process. We present results for the diffusion of magnetic dipoles as a function of linear density, strength o…
Dynamical density functional theory (DDFT) is a powerful variational framework to study the nonequilibrium properties of colloids by only considering a time-dependent one-body number density. Despite the large number of recent successes, properly modeling the long-time dynamics in interacting systems within DDFT remains a notoriously difficult problem, since structural information, accounting for temporary or permanent particle cages, gets lost. Here we address such a caging scenario by reducing it to a clean one-dimensional problem, where the particles are naturally ordered (arranged on a lin…
We report an experimental study of diffusion in a quasi-one-dimensional (q1D) colloid suspension which behaves like a Tonks gas. The mean squared displacement as a function of time is described well with an ansatz encompassing a time regime that is both shorter and longer than the mean time between collisions. This ansatz asserts that the inverse mean squared displacement is the sum of the inverse mean squared displacement for short time normal diffusion (random walk) and the inverse mean squared displacement for asymptotic single-file diffusion (SFD). The dependence of the single-file 1D mobi…
We report computer simulation studies of the kinetics of ordering of a two dimensional system of particles on a template with a one dimensional periodic pattern. In equilibrium one obtains a re-entrant liquid-solid-liquid phase transition as the strength of the substrate potential is varied. We show that domains of crystalline order grow as $\sim t^{1/z}$, with $z \sim 4$ with a possible cross-over to $z \sim 2$ at late times. We argue that the $t^{1/4}$ law originates from {\em single-file} motion and annihilation of defect pairs of opposite topological charge along channels created by the te…
In colloidal systems, Brownian motion emerges from the massive separation of time and length scales associated to characteristic dynamics of the solute and solvent constituents. This separation of scales produces several temporal regimes in the colloidal dynamics when combined with the effects of the interaction between the particles, confinement conditions, and state variables, such as density and temperature. Some examples are the short- and long-time regimes in two- and three-dimensional open systems and the diffusive and sub-diffusive regimes observed in the single-file dynamics along a st…
Strong positional correlations between particles render the diffusion of a tracer particle in a single file anomalous and non-Markovian. While ensemble average observables of tracer particles are nowadays well understood, little is known about the statistics of the corresponding functionals, i.e. the time-average observables. It even remains unclear how the non-Markovian nature emerges from correlations between particle trajectories at different times. Here, we first present rigorous results for fluctuations and two-tag correlations of general bounded functionals of ergodic Markov processes wi…
Diffusion in colloidal suspensions can be very slow due to the cage effect, which confines each particle within a short radius on one hand, and involves large-scale cooperative motions on the other. In search of insight into this cooperativity, here the authors develop a formalism to calculate the displacement correlation in colloidal systems, mainly in the two-dimensional case. To clarify the idea for it, studies are reviewed on cooperativity among the particles in the one-dimensional case, i.e. the single-file diffusion (SFD). As an improvement over the celebrated formula by Alexander and Pi…
Single-file diffusion refers to the motion in narrow channels of particles which cannot bypass each other. These strong correlations between particles lead to tracer subdiffusion, which has been observed in contexts as varied as transport in porous media, zeolites or confined colloidal suspensions, and theoretically studied in numerous works. Most approaches to this celebrated many-body problem were restricted to the description of the tracer only, whose essential properties, such as large deviation functions or two-time correlation functions, were determined only recently. Here, we go beyond …
Active particles may happen to be confined in channels so narrow that they cannot overtake each other (Single File conditions). This interesting situation reveals nontrivial physical features as a consequence of the strong inter-particle correlations developed in collective rearrangements. We consider a minimal model for active Brownian particles with the aim of studying the modifications introduced by activity with respect to the classical (passive) Single File picture. Depending on whether their motion is dominated by translational or rotational diffusion, we find that active Brownian partic…
The diffusion process of N hard rods in a 1D interval of length L (--> inf) is studied using scaling arguments and an asymptotic analysis of the exact N-particle probability density function (PDF). In the class of such systems, the universal scaling law of the tagged particle's mean absolute displacement reads, <|r|>~ <|r|>_{free}/n^mu, where <|r|>_{free} is the result for a free particle in the studied system and n is the number of particles in the covered length. The exponent mu is given by, mu=1/(1+a), where a is associated with the particles' density law of the system, rho~rho_0*L^(-a), 0<…
Single-file Brownian motion in periodic structures is an important process in nature and technology, which becomes increasingly amenable for experimental investigation under controlled conditions. To explore and understand generic features of this motion, the Brownian asymmetric simple exclusion process (BASEP) was recently introduced. The BASEP refers to diffusion models, where hard spheres are driven by a constant drag force through a periodic potential. Here, we derive general properties of the rich collective dynamics in the BASEP. Average currents in the steady state change dramatically w…
Particles confined to a single file, in a narrow quasi-one dimensional channel, exhibit a dynamic crossover from single file diffusion to Fickian diffusion as the channel radius increases and the particles can begin to pass each other. The long time diffusion coefficient for a system in the crossover regime can be described in terms of a hopping time, which measures the time it takes for a particle to escape the cage formed by its neighbours. In this paper, we develop a transition state theory approach to the calculation of the hopping time, using the small system isobaric--isothermal ensemble…
Single-file diffusion is a ubiquitous physical process exploited by living and synthetic systems to exchange molecules with their environment. It is paramount quantifying the escape time needed for single files of particles to exit from constraining synthetic channels and biological pores. This quantity depends on complex cooperative effects, whose predominance can only be established through a strict comparison between theory and experiments. By using colloidal particles, optical manipulation, microfluidics, digital microscopy and theoretical analysis we uncover the self-similar character of …
Transport of colloid particles through narrow channels is ubiquitous in cell biology as well as becoming increasingly important for microfluidic applications or targeted drug delivery. Membrane channels in cells are useful models for artificial designs because of their high efficiency, selectivity and robustness to external fluctuations. Here we model the passive channels that let cargo simply diffuse through them, affected by a potential profile along the way. Passive transporters achieve high levels of efficiency and specificity from binding interactions with the cargo inside the channel. Th…
We study propagation dynamics of a particle phase in a single-file pore connected to a reservoir of particles (bulk liquid phase). We show that the total mass $M(t)$ of particles entering the pore up to time $t$ grows as $M(t) = 2 m(J,ρ_F) \sqrt{D_0 t}$, where $D_0$ is the "bare" diffusion coefficient and the prefactor $m(J,ρ_F)$ is a non-trivial function of the reservoir density $ρ_F$ and the amplitude $J$ of attractive particle-particle interactions. Behavior of the dynamic density profiles is also discussed.
We summarise different results on the diffusion of a tracer particle in lattice gases of hard-core particles with stochastic dynamics, which are confined to narrow channels -- single-files, comb-like structures and quasi-one-dimensional channels with the width equal to several particle diameters. We show that in such geometries a surprisingly rich, sometimes even counter-intuitive, behaviour emerges, which is absent in unbounded systems. We also present a survey of different results obtained for a tracer particle diffusion in unbounded systems, which will permit a reader to have an exhaustivel…
Normal dynamics in a quasi-one-dimensional channel of length L (\to\infty) of N hard spheres are analyzed. The spheres are heterogeneous: each has a diffusion coefficient D that is drawn from a probability density function (PDF), W D^(-γ), for small D, where 0\leqγ<1. The initial spheres' density ρ is non-uniform and scales with the distance (from the origin) l as, ρ l^(-a), 0\leqa\leq1. An approximation for the N-particle PDF for this problem is derived. From this solution, scaling law analysis and numerical simulations, we show here that the mean square displacement for a particle in such a …
