Effective diffusivity of a Brownian particle in a two-dimensional periodic channel of abruptly alternating width

Adsorption of Diffusing Tracers, Apparent Tortuosity, and Application to Mesoporous Silica

The apparent tortuosity due to adsorption of diffusing tracers in a porous material is determined by a scaling approach and is used to analyze recent data on LiCl and alkane diffusion in mesoporous silica. The slope of the adsorption isotherm at small loadings is written as β = qA/qG, where qA is the adsorption-desorption ratio and qG = ϵ/(as) - 1 is a geometrical factor depending on the range a of the tracer-wall interaction, the porosity ϵ, and the specific surface area s. The adsorption leads to a decrease of effective diffusion coefficient, which is quantified by multiplying the geometrical tortuosity factor τgeom by an apparent tortuosity factor τapp. In wide pores or when the adsorption barrier is high, τapp = β + 1, as obtained in previous works, but in narrow pores there is an additional contribution from frequent adsorption-desorption transitions. These results are obtained in media with parallel pores of constant cross sections, where the ratio between the effective pore width ϵ/s and the actual width is ≈0.25. Applications to mesoporous silica samples are justified by the small deviations from this ideal ratio. In the analysis of alkane self-diffusion data, the fractions of adsorbed molecules predicted in a recent theoretical work are used to estimate τgeom of the silica samples, which is ≫1 only in the sample with the narrowest pores (nominal 3 nm). The application of the model to Li+ ion diffusion leads to similar values of τgeom and to a difference of energy barriers of desorption and adsorption for those ions of ∼0.06 eV. Comparatively, alkane self-diffusion provides the correct order of magnitude of τgeom, with adsorption playing a less important role, whereas adsorption effects on Li+ diffusion are much more important.

Brownian particles in periodic potentials: Coarse-graining versus fine structure

We study the motion of an overdamped particle connected to a thermal heat bath in the presence of an external periodic potential in one dimension. When we coarse-grain, i.e., bin the particle positions using bin sizes that are larger than the periodicity of the potential, the packet of spreading particles, all starting from a common origin, converges to a normal distribution centered at the origin with a mean-squared displacement that grows as 2D^{*}t, with an effective diffusion constant that is smaller than that of a freely diffusing particle. We examine the interplay between this coarse-grained description and the fine structure of the density, which is given by the Boltzmann-Gibbs (BG) factor e^{-V(x)/k_{B}T}, the latter being nonnormalizable. We explain this result and construct a theory of observables using the Fokker-Planck equation. These observables are classified as those that are related to the BG fine structure, like the energy or occupation times, while others, like the positional moments, for long times, converge to those of the large-scale description. Entropy falls into a special category as it has a coarse-grained and a fine structure description. The basic thermodynamic formula F=TS-E is extended to this far-from-equilibrium system. The ergodic properties are also studied using tools from infinite ergodic theory.

Parallel computing for mobilities in periodic geometries

We examine methods for calculating the effective mobilities of molecules driven through periodic geometries in the context of particle-based simulation. The standard formulation of the mobility, based on the long-time limit of the mean drift velocity, is compared to a formulation based on the mean first-passage time of molecules crossing a single period of the system geometry. The equivalence of the two definitions is derived under weaker assumptions than similar conclusions obtained previously, requiring only that the state of the system at subsequent period crossings satisfy the Markov property. Approximate theoretical analyses of the computational costs of estimating these two mobility formulations via particle simulations suggest that the definition based on first-passage times may be substantially better suited to exploiting parallel computation hardware. This claim is investigated numerically on an example system modeling the passage of nanoparticles through the slit-well device. In this case, the traditional mobility formulation is found to perform best when the Péclet number is small, whereas the mean first-passage time formulation is found to converge much more quickly when the Péclet number is moderate or large. The results suggest that, given relatively modest access to modern GPU hardware, this alternative mobility formulation may be an order of magnitude faster than the standard technique for computing effective mobilities of biomolecules through periodic geometries.