Diffusion-limited reactions (DLR) are usually described within the Smoluchowski theory, which neglects interactions between the diffusing components. We propose a first extension of such frame- work that incorporates excluded-volume effects, considering hard diffusing agents in the presence of an absorbing sink. For large values of the absorber-to-diffuser size ratio Rs, the encounter rate obtained from the simulations is in very good agreement with a simple generalization of the Smolu- chowski equation at high densities. Reducing Rs, the rate gets substantially depressed at interme- diate packing and become even non-monotonic for Rs << 1. Concurrently with the saturation of the rate, stationary density waves set in close to the absorbing center. A mean-field, effective-potential analysis of the Smoluchowski equation under crowding sheds light on the subtle link between such ordering and the slowing down of the encounter dynamics. Finally, we show how an infinitesimal amount of non-reacting impurities can equally slow down dramatically the reaction.
We study the transport of self-propelled particles in dynamic complex environments. To obtain exact results, we introduce a model of run-and-tumble particles (RTPs) moving in discrete time on a $d$-dimensional cubic lattice in the presence of diffusing hard core obstacles. We derive an explicit expression for the diffusivity of the RTP, which is exact in the limit of low density of fixed obstacles. To do so, we introduce a generalization of Kac's theorem on the mean return times of Markov processes, which we expect to be relevant for a large class of lattice gas problems. Our results show the …
We study memory based random walk models to understand diffusive motion in crowded heterogeneous environment. The models considered are non-Markovian as the current move of the random walk models is determined by randomly selecting a move from history. At each step, particle can take right, left or stay moves which is correlated with the randomly selected past step. There is a perfect stay-stay correlation which ensures that the particle does not move if the randomly selected past step is a stay move. The probability of traversing the same direction as the chosen history or reversing it depend…
We calculate the diffusion coefficient of an active tracer in a schematic crowded environment, represented as a lattice gas of passive particles with hardcore interactions. Starting from the master equation of the problem, we put forward a closure approximation that goes beyond trivial mean-field and provides the diffusion coefficient for an arbitrary density of crowders in the system. We show that our approximation is accurate for a very wide range of parameters, and that it correctly captures numerous nonequilibrium effects, which are the signature of the activity in the system. In addition …
We analyze a pair of diffusion equations which are derived in the infinite system--size limit from a microscopic, individual--based, stochastic model. Deviations from the conventional Fickian picture are found which ultimately relate to the depletion of resources on which the particles rely. The macroscopic equations are studied both analytically and numerically, and are shown to yield anomalous diffusion which does not follow a power law with time, as is frequently assumed when fitting data for such phenomena. These anomalies are here understood within a consistent dynamical picture which app…
We develop a model to compute the first-passage time of a random walker in a crowded environment. Hard-core particles with the same size and diffusion coefficient than the tracer diffuse, and the model allows to compute the first passage time of the tracer on euclidian lattices. The result is compared to classical Nakazato-Kitahara model, and extends previous results obtained for persistent random walker. The crowding in a confined media acts as a memory effect, and thus lead to a persistent-like behavior.
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…
The influence of crowding on the diffusion of tagged particles in a dense medium is investigated in the framework of a mean-field model, derived in the continuum limit from a microscopic stochastic process with exclusion. The probability distribution function of the tagged particles obeys to a nonlinear Fokker-Planck equation, where the drift and diffusion terms are determined self-consistently by the concentration of crowders in the medium. Transient sub-diffusive or super-diffusive behaviours are observed, depending on the selected initial conditions, that bridge normal diffusion regimes cha…
Diffusion of a two component fluid is studied in the framework of differential equations, but where these equations are systematically derived from a well-defined microscopic model. The model has a finite carrying capacity imposed upon it at the mesoscopic level and this is shown to lead to non-linear cross diffusion terms that modify the conventional Fickean picture. After reviewing the derivation of the model, the experiments carried out to test the model are described. It is found that it can adequately explain the dynamics of two dense ink drops simultaneously evolving in a container fille…
A topic of intense current investigation pursues the question how the highly crowded environment of biological cells affects the dynamic properties of passively diffusing particles. Motivated by recent experiments we report results of extensive simulations of the motion of a finite sized tracer particle in a heterogeneously crowded environment. For given spatial distributions of monodisperse crowders we demonstrate how anomalous diffusion with strongly non-Gaussian features arises in this model system. We investigate both biologically relevant situations of particles released either at the sur…
We study a two-dimensional diffusive motion of a tracer particle in restricted, crowded anisotropic geometries. The underlying medium is the same as in our previous work [J. Chem. Phys. 140, 044706 (2014)] in which standard, gaussian diffusion was studied. Here, a tracer is allowed to perform Cauchy random walk with uncorrelated steps. Our analysis shows that presence of obstacles significantly influences motion, which in an obstacle-free space would be of a superdiffusive type. At the same time, the selfdiffusive process reveals different anomalous properties, both at the level of a single tr…
The diffusion type is determined not only by microscopic dynamics but also by the environment properties. For example, the environment's fractal structure is responsible for the emergence of subdiffusive scaling of the mean square displacement in Markovian systems because the presence of non-trivially placed obstacles puts constraints on possible displacements. We investigate how the additional action of drift changes properties of the diffusion in the crowded environment. It is shown that the action of a constant drift increases chances of trapping, which suppresses the persistent ballistic m…
We study the single-species diffusion-annihilation process with a time-dependent reaction rate, lambda(t)=lambda_0 t^-omega. Scaling arguments show that there is a critical value of the decay exponent omega_c(d) separating a reaction-limited regime for omega > omega_c from a diffusion-limited regime for omega < omega_c. The particle density displays a mean-field, omega-dependent, decay when the process is reaction limited whereas it behaves as for a constant reaction rate when the process is diffusion limited. These results are confirmed by Monte Carlo simulations. They allow us to discuss the…
We study the behavior of the stationary velocity of a driven particle in an environment of mobile hard-core obstacles. Based on a lattice gas model, we demonstrate analytically that the drift velocity can exhibit a nonmonotonic dependence on the applied force, and show quantitatively that such negative differential mobility (NDM), observed in various physical contexts, is controlled by both the density and diffusion time scale of obstacles. Our study unifies recent numerical and analytical results obtained in specific regimes, and makes it possible to determine analytically the region of the f…
We study various combinations of active diffusion with branching, as an extension of standard reaction-diffusion processes. We concentrate on the selection of the asymptotic wavefront speed for thermal run-and-tumble and for thermal active Brownian processes in general spatial dimensions. Comparing 1D active branching processes with a passive counterpart (which has the same effective diffusion constant and reproduction rate), we find that the active process has a smaller propagation speed. In higher dimensions, a similar comparison yields the opposite conclusion.
We study a strongly interacting crowded system of self-propelled stiff filaments by event-driven Brownian dynamics simulations and an analytical theory to elucidate the intricate interplay of crowding and self-propulsion. We find a remarkable increase of the effective diffusivity upon increasing the filament number density by more than one order of magnitude. This counter-intuitive 'crowded is faster' behavior can be rationalized by extending the concept of a confining tube pioneered by Doi and Edwards for highly entangled crowded, passive to active systems. We predict a scaling theory for the…
Reaction-diffusion equations deliver a versatile tool for the description of reactions in inhomogeneous systems under the assumption that the characteristic reaction scales and the scales of the inhomogeneities in the reactant concentrations separate. In the present work we discuss the possibilities of a generalization of reaction-diffusion equations to the case of anomalous diffusion described by continuous-time random walks with decoupled step length and waiting time probability densities, the first being Gaussian or Levy, the second one being an exponential or a power-law lacking the first …
In a two species reaction diffusion system,we show that it is possible to generate a set of wavelength doubling bifuractions leading to spatially chaotic state.The wavelength doubling bifurcations are preceded by a symmetry breaking transition which acts as a precursor.
A new asymptotic method is presented for the analysis of the traveling waves in the one-dimensional reaction-diffusion system with the diffusion with a finite velocity and Kolmogorov-Petrovskii-Piskunov kinetics. The analysis makes use of the path-integral approach, scaling procedure and the singular perturbation techniques involving the large deviations theory for the Poisson random walk. The exact formula for the position and speed of reaction front is derived. It is found that the reaction front dynamics is formally associated with the relativistic Hamiltonian/Lagrangian mechanics.
We formulate the generalized master equation for a class of continuous time random walks in the presence of a prescribed deterministic evolution between successive transitions. This formulation is exemplified by means of an advection-diffusion and a jump-diffusion scheme. Based on this master equation, we also derive reaction-diffusion equations for subdiffusive chemical species, using a mean field approximation.
Stochastic particle--based models are useful tools for describing the collective movement of large crowds of pedestrians in crowded confined environments. Using descriptions based on the simple exclusion process, two populations of particles, mimicking pedestrians walking in a built environment, enter a room from two opposite sides. One population is passive -- being unaware of the local environment; particles belonging to this group perform a symmetric random walk. The other population has information on the local geometry in the sense that as soon as particles enter a visibility zone, a drif…
We propose the deterministic rate equation of three-species in the reaction - diffusion system. For this case, our purpose is to carry out the decay process in our three-species reaction-diffusion model of the form $A+B+C\to D$. The particle density and the global reaction rate are also shown analytically and numerically on a two-dimensional square lattice with the periodic boundary conditions. Especially, the crossover of the global reaction rate is discussed in both early-time and long-time regimes.
The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with increase in macromolecular crowding. Moreover, many cellular processes are dependent on molecular diffusion in the cell cytosol. The enzymatic reaction rate has been shown to be affected by the presence of such macromolecules. A simple numerical model is proposed here based on percolation and diffusion in disordered systems to study the effect of macromolecul…
Theory of diffusion-mediated reactions is already established for the target problem in the dilute limit, where the immobile target is surrounded by many quenchers. For lattice random walks in the crowded situation, each quencher is surrounded by other quenchers differently. As a result, each quencher migrates differently in the presence of site blocking effects. However, in the conventional theory, such difference is ignored and quenchers are assumed to move independently of each other. In this paper, theory of diffusion-mediated reactions of target problem is developed by taking into account…
The reversible A <-> B reaction-diffusion process, when species A and B are initially mixed and diffuse with different diffusion coefficients, is investigated using the boundary layer function method. It is assumed that the ratio of the characteristic time of the reaction to the characteristic time of diffusion is taken as a small parameter of the task. It was shown that diffusion-reaction process can be considered as a quasi-equilibrium process. Despite this fact the contribution of the reaction in changes of the species concentration is comparable with the diffusion contributions. Moreover t…
The problem of velocity selection of reaction-diffusion fronts has been widely investigated. While the mean field limit results are well known theoretically, there is a lack of analytic progress in those cases in which fluctuations are to be taken into account. Here, we construct an analytic theory connecting the first principles of the reaction-diffusion process to an effective equation of motion via field-theoretic arguments, and we arrive at the results already confirmed by numerical simulations.
A fractional reaction-diffusion equation is derived from a continuous time random walk model when the transport is dispersive. The exit from the encounter distance, which is described by the algebraic waiting time distribution of jump motion, interferes with the reaction at the encounter distance. Therefore, the reaction term has a memory effect. The derived equation is applied to the geminate recombination problem. The recombination is shown to depend on the intrinsic reaction rate, in contrast with the results of Sung et al. [J. Chem. Phys. {\bf 116}, 2338 (2002)], which were obtained from t…
We consider solvability of the generalized reaction-diffusion equation with both space- and time-dependent diffusion and reaction terms by means of the similarity method. By introducing the similarity variable, the reaction-diffusion equation is reduced to an ordinary differential equation. Matching the resulting ordinary differential equation with known exactly solvable equations, one can obtain corresponding exactly solvable reaction-diffusion systems. Several representative examples of exactly solvable reaction-diffusion equations are presented.
We consider similarity solutions of the generalized convection-diffusion-reaction equation with both space- and time-dependent convection, diffusion and reaction terms. By introducing the similarity variable, the reaction-diffusion equation is reduced to an ordinary differential equation. Matching the resulting ordinary differential equation with known exactly solvable equations, one can obtain corresponding exactly solvable convection-diffusion-reaction systems. Some representative examples of exactly solvable systems are presented. We also describe how an equivalent convection-diffusion-reac…
Diffusion in the crowded environments of the biological membranes or materials interfaces often involves intermittent binding to surface proteins or defects. To account for this situation we study a 2-dimensional lattice gas in a field of immobilized traps. Using kinetic Monte Carlo simulations, we calculate the effective diffusion coefficient in the long-time limit as a function of the traps and particle densities. We find a remarkable result - an increase of the diffusion coefficient with particle density, an effect that we coin as crowding-enhanced diffusion. We rationalize this result usin…
Daily, are reported systems in nature that present anomalous diffusion phenomena due to irregularities of medium, traps or reactions process. In this scenario, the diffusion with traps or localised--reactions emerge through various investigations that include numerical, analytical and experimental techniques. In this work, we construct a model which involves a coupling of two diffusion equations to approach the random walkers in a medium with localised reaction point (or controlled diffusion). We present the exact analytical solutions to the model. In the following, we obtain the survival prob…
We investigate reversible diffusion-influenced reactions of an isolated pair in two dimensions. To this end, we employ convolution relations that permit deriving the survival probability of the reversible reaction directly in terms of the survival probability of the irreversible reaction. Furthermore, we make use of the mean reaction time approximation to write the irreversible survival probability in restricted spaces as a single exponential. In this way, we obtain exact and approximative expressions in the time domain for the reversible survival probability for three different two dimensiona…
In this work we are concerned with generating solutions of a class of Convection-Diffusion-Reaction equation from the solutions of another CDR equation through the Darboux transformations. The method is elucidated by cases with certain types of the reaction coefficients. We have also discussed briefly supersymmetric pairs of Convection-Diffusion-Reaction equations connected through similarity solutions.
We study diffusion of particles on the surface of a sphere toward a partially reactive circular target with partly reversible binding kinetics. We solve the coupled diffusion-reaction equations and obtain the exact expressions for the time-dependent concentration of particles and the total diffusive flux. Explicit asymptotic formulas are derived in the small target limit. This study reveals the strong effects of reversible binding kinetics onto diffusion-mediated reactions that may be relevant for many biochemical reactions on cell membranes.
The mean-field reaction-diffusion equations of the diffusive pair-annihilation and triplett-annihilation processes are considered. A direct lower bound on the time-dependent mean particle-density is derived. The results are applied to the mean-field theory of the diffusive pair-contact process.
