Anomalous transport of a tracer on percolating clusters

Percolation through voids around toroidal inclusions

In the case of media comprised of impermeable particles, fluid flows through voids around impenetrable grains. For sufficiently low concentrations of the latter, spaces around grains join to allow transport on macroscopic scales, whereas greater impenetrable inclusion densities disrupt void networks and block macroscopic fluid flow. A critical grain concentration ρ_{c} marks the percolation transition or phase boundary separating these two regimes. With a dynamical infiltration technique in which virtual tracer particles explore void spaces, we calculate critical grain concentrations for randomly placed interpenetrating impermeable toroidal inclusions; the latter consist of surfaces of revolution with circular and square cross sections. In this manner, we study continuum percolation transitions involving nonconvex grains. As the radius of revolution increases relative to the length scale of the torus cross section, the tori develop a central hole, a topological transition accompanied by a cusp in the critical porosity fraction for percolation. With a further increase in the radius of revolution, as constituent grains become more ringlike in appearance, we find that the critical porosity fraction converges to that of high-aspect-ratio cylindrical counterparts only for randomly oriented grains.

Subdiffusive Dynamics Lead to Depleted Particle Densities near Cellular Borders

It has long been known that the complex cellular environment leads to anomalous motion of intracellular particles. At a gross level, this is characterized by mean-squared displacements that deviate from the standard linear profile. Statistical analysis of particle trajectories has helped further elucidate how different characteristics of the cellular environment can introduce different types of anomalousness. A significant majority of this literature has, however, focused on characterizing the properties of trajectories that do not interact with cell borders (e.g., cell membrane or nucleus). Numerous biological processes ranging from protein activation to exocytosis, however, require particles to be near a membrane. This study investigates the consequences of a canonical type of subdiffusive motion, fractional Brownian motion, and its physical analog, generalized Langevin equation dynamics, on the spatial localization of particles near reflecting boundaries. Results show that this type of subdiffusive motion leads to the formation of significant zones of depleted particle density near boundaries and that this effect is independent of the specific model details encoding those dynamics. Rather, these depletion layers are a natural and robust consequence of the anticorrelated nature of motion increments that is at the core of fractional Brownian motion (or alternatively generalized Langevin equation) dynamics. If such depletion zones are present, it would be of profound importance given the wide array of signaling and transport processes that occur near membranes. If not, that would suggest our understanding of this type of anomalous motion may be flawed. Either way, this result points to the need to further investigate the consequences of anomalous particle motions near cell borders from both theoretical and experimental perspectives.

Structure Dominates Localization of Tracers within Aging Nanoparticle Glasses

We investigate the transport and localization of tracer probes in a glassy matrix as a function of relative size using dynamic X-ray scattering experiments and molecular dynamics simulations. The quiescent relaxations of tracer particles evolve with increasing waiting time, t_w. The corresponding relaxation times increase exponentially at small t_w and then transition to a power-law behavior at longer t_w. As tracer size decreases, the aging behavior weakens and the particles become less localized within the matrix until they delocalize at a critical size ratio δ₀ ≈ 0.38. Localization does not vary with sample age even as the relaxations slow by approximately an order of magnitude, suggesting that matrix structure controls tracer localization.

Non-universality of the dynamic exponent in two-dimensional random media

The diffusion of solutes in two-dimensional random media is important in diverse physical situations including the dynamics of proteins in crowded cell membranes and the adsorption on nano-structured substrates. It has generally been thought that the diffusion constant, D, should display universal behavior near the percolation threshold, i.e., D ~ (ϕ − ϕ_c)^μ, where ϕ is the area fraction of the matrix, ϕ_c is the value of ϕ at the percolation threshold, and μ is the dynamic exponent. The universality of μ is important because it implies that very different processes, such as protein diffusion in membranes and the electrical conductivity in two-dimensional networks, obey similar underlying physical principles. In this work we demonstrate, using computer simulations on a model system, that the exponent μ is not universal, but depends on the microscopic nature of the dynamics. We consider a hard disc that moves via random walk in a matrix of fixed hard discs and show that μ depends on the maximum possible displacement Δ of the mobile hard disc, ranging from 1.31 at Δ ≤ 0.1 to 2.06 for relatively large values of Δ. We also show that this behavior arises from a power-law singularity in the distribution of transition rates due to a failure of the local equilibrium approximation. The non-universal value of μ obeys the prediction of the renormalization group theory. Our simulations do not, however, exclude the possibility that the non-universal values of μ might be a crossover between two different limiting values at very large and small values of Δ. The results allow one to rationalize experiments on diffusion in two-dimensional systems.

Percolation through Voids around Randomly Oriented Polyhedra and Axially Symmetric Grains

Porous materials made up of impermeable grains constrain fluid flow to voids around the impenetrable inclusions. A percolation transition marks the boundary between densities of grains permitting bulk transport and concentrations blocking traversal on macroscopic scales. With dynamical infiltration of void spaces using virtual tracer particles, we treat inclusion geometries exactly. We calculate the critical number density per volume ρ_{c} for a variety of axially symmetric shapes and faceted solids with the former including cylinders, ellipsoids, cones, and tablet shaped grains from highly oblate (platelike) to highly prolate (needlelike) extremes. For the latter, results suggest a common asymptotic value identical to the counterpart for aligned cylindrical grains. We find percolation thresholds for each of the five platonic solids (i.e., tetrahedra, cubes, octahedra, dodecahedra, and icosahedra) as well as truncated icosahedra. For each polyhedron type, we consider aligned and randomly oriented grains, finding distinct percolation thresholds for the former versus the latter only for cubes. The anomalous diffusion exponents we find differ from those of the universality class for discrete models on 3D lattices.

Dynamic heterogeneities and non-Gaussian behavior in two-dimensional randomly confined colloidal fluids

A binary mixture of superparamagnetic colloidal particles is confined between glass plates such that the large particles become fixed and provide a two-dimensional disordered matrix for the still mobile small particles, which form a fluid. By varying fluid and matrix area fractions and tuning the interactions between the superparamagnetic particles via an external magnetic field, different regions of the state diagram are explored. The mobile particles exhibit delocalized dynamics at small matrix area fractions and localized motion at high matrix area fractions, and the localization transition is rounded by the soft interactions [T. O. E. Skinner et al., Phys. Rev. Lett. 111, 128301 (2013)PRLTAO0031-900710.1103/PhysRevLett.111.128301]. Expanding on previous work, we find the dynamics of the tracers to be strongly heterogeneous and show that molecular dynamics simulations of an ideal gas confined in a fixed matrix exhibit similar behavior. The simulations show how these soft interactions make the dynamics more heterogeneous compared to the disordered Lorentz gas and lead to strong non-Gaussian fluctuations.

Splitting of the Universality Class of Anomalous Transport in Crowded Media

We investigate the emergence of subdiffusive transport by obstruction in continuum models for molecular crowding. While the underlying percolation transition for the accessible space displays universal behavior, the dynamic properties depend in a subtle nonuniversal way on the transport through narrow channels. At the same time, the different universality classes are robust with respect to introducing correlations in the obstacle matrix as we demonstrate for quenched hard-sphere liquids as underlying structures. Our results confirm that the microscopic dynamics can dominate the relaxational behavior even at long times, in striking contrast to glassy dynamics.

Anomalous Magnetotransport in Disordered Structures: Classical Edge-State Percolation

By event-driven molecular dynamics simulations we investigate magnetotransport in a two-dimensional model with randomly distributed scatterers close to the field-induced localization transition. This transition is generated by percolating skipping orbits along the edges of obstacle clusters. The dynamic exponents differ significantly from those of the conventional transport problem on percolating systems, thus establishing a new dynamic universality class. This difference is tentatively attributed to a weak-link scenario, which emerges naturally due to barely overlapping edge trajectories. We make predictions for the frequency-dependent conductivity and discuss implications for active colloidal circle swimmers in a hetegogeneous environment.

An analytical correlated random walk model and its application to understand subdiffusion in crowded environment

Subdiffusion in crowded environment such as movement of macromolecule in a living cell has often been observed experimentally. The primary reason for subdiffusion is volume exclusion by the crowder molecules. However, other effects such as hydrodynamic interaction may also play an important role. Although there are a large number of computer simulation studies on understanding molecular crowding, there is a lack of theoretical models that can be connected to both experiment and simulation. In the current work, we have formulated a one-dimensional correlated random walk model by connecting this to the motion in a crowded environment. We have found the exact solution of the probability distribution function of the model by solving it analytically. The parameters of our model can be obtained either from simulation or experiment. It has been shown that this analytical model captures some of the general features of diffusion in crowded environment as given in the previous literature and its prediction for transient subdiffusion closely matches the observations of a previous study of computer simulation of Escherichia coli cytoplasm. It is likely that this model will open up more development of theoretical models in this area.

Aging scaled Brownian motion

Scaled Brownian motion (SBM) is widely used to model anomalous diffusion of passive tracers in complex and biological systems. It is a highly nonstationary process governed by the Langevin equation for Brownian motion, however, with a power-law time dependence of the noise strength. Here we study the aging properties of SBM for both unconfined and confined motion. Specifically, we derive the ensemble and time averaged mean squared displacements and analyze their behavior in the regimes of weak, intermediate, and strong aging. A very rich behavior is revealed for confined aging SBM depending on different aging times and whether the process is sub- or superdiffusive. We demonstrate that the information on the aging factorizes with respect to the lag time and exhibits a functional form that is identical to the aging behavior of scale-free continuous time random walk processes. While SBM exhibits a disparity between ensemble and time averaged observables and is thus weakly nonergodic, strong aging is shown to effect a convergence of the ensemble and time averaged mean squared displacement. Finally, we derive the density of first passage times in the semi-infinite domain that features a crossover defined by the aging time.

Fractional diffusion on a fractal grid comb

A grid comb model is a generalization of the well known comb model, and it consists of N backbones. For N=1 the system reduces to the comb model where subdiffusion takes place with the transport exponent 1/2. We present an exact analytical evaluation of the transport exponent of anomalous diffusion for finite and infinite number of backbones. We show that for an arbitrarily large but finite number of backbones the transport exponent does not change. Contrary to that, for an infinite number of backbones, the transport exponent depends on the fractal dimension of the backbone structure.

Anomalous versus slowed-down Brownian diffusion in the ligand-binding equilibrium

Measurements of protein motion in living cells and membranes consistently report transient anomalous diffusion (subdiffusion) that converges back to a Brownian motion with reduced diffusion coefficient at long times after the anomalous diffusion regime. Therefore, slowed-down Brownian motion could be considered the macroscopic limit of transient anomalous diffusion. On the other hand, membranes are also heterogeneous media in which Brownian motion may be locally slowed down due to variations in lipid composition. Here, we investigate whether both situations lead to a similar behavior for the reversible ligand-binding reaction in two dimensions. We compare the (long-time) equilibrium properties obtained with transient anomalous diffusion due to obstacle hindrance or power-law-distributed residence times (continuous-time random walks) to those obtained with space-dependent slowed-down Brownian motion. Using theoretical arguments and Monte Carlo simulations, we show that these three scenarios have distinctive effects on the apparent affinity of the reaction. Whereas continuous-time random walks decrease the apparent affinity of the reaction, locally slowed-down Brownian motion and local hindrance by obstacles both improve it. However, only in the case of slowed-down Brownian motion is the affinity maximal when the slowdown is restricted to a subregion of the available space. Hence, even at long times (equilibrium), these processes are different and exhibit irreconcilable behaviors when the area fraction of reduced mobility changes.

Percolation through voids around overlapping spheres: a dynamically based finite-size scaling analysis

The percolation threshold for flow or conduction through voids surrounding randomly placed spheres is calculated. With large-scale Monte Carlo simulations, we give a rigorous continuum treatment to the geometry of the impenetrable spheres and the spaces between them. To properly exploit finite-size scaling, we examine multiple systems of differing sizes, with suitable averaging over disorder, and extrapolate to the thermodynamic limit. An order parameter based on the statistical sampling of stochastically driven dynamical excursions and amenable to finite-size scaling analysis is defined, calculated for various system sizes, and used to determine the critical volume fraction ϕc=0.0317±0.0004 and the correlation length exponent ν=0.92±0.05.

Anomalous transport in the crowded world of biological cells

A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important role in testing the theoretical models and corroborating the experimental findings. The review is completed by a synthesis of the theoretical and experimental progress identifying open questions for future investigation.

Dynamic arrest of colloids in porous environments: disentangling crowding and confinement

Using numerical simulations we study the slow dynamics of a colloidal hard-sphere fluid adsorbed in a matrix of disordered hard-sphere obstacles. We calculate separately the contributions to the single-particle dynamic correlation functions due to free and trapped particles. The separation is based on a Delaunay tessellation to partition the space accessible to the centres of fluid particles into percolating and disconnected voids. We find that the trapping of particles into disconnected voids of the matrix is responsible for the appearance of a nonzero long-time plateau in the single-particle intermediate scattering functions of the full fluid. The subdiffusive exponent z, obtained from the logarithmic derivative of the mean squared displacement, is essentially unaffected by the motion of trapped particles: close to the percolation transition, we determined z approximately = 0.5 for both the full fluid and the particles moving in the percolating void. Notably, the same value of z is found in single-file diffusion and is also predicted by mode-coupling theory along the diffusion-localization line. We also reveal subtle effects of dynamic heterogeneity in both the free and the trapped component of the fluid particles, and discuss microscopic mechanisms that contribute to this phenomenon.