Entropic transport - A test bed for the Fick-Jacobs approximation

Biased diffusive transport of Brownian particles through irregularly shaped, narrow confining quasi-one-dimensional structures is investigated. The complexity of the higher dimensional diffusive dynamics is reduced by means of the so-called Fick-Jacobs approximation, yielding an effective one-dimensional stochastic dynamics. Accordingly, the elimination of transverse, equilibrated degrees of freedom stemming from geometrical confinements and/or bottlenecks cause entropic potential barriers which the particles have to overcome when moving forward noisily. The applicability and the validity of the reduced kinetic description is tested by comparing the approximation with Brownian dynamics simulations in full configuration space. This non-equilibrium transport in such quasi-one-dimensional irregular structures implies for moderate-to-strong bias a characteristic violation of the Sutherland-Einstein fluctuation-dissipation relation.Comment: 15 pages, 6 figures ; Phil. Trans. R. Soc. A (2009), in pres

Diffusion of multiple species with excluded-volume effects

Stochastic models of diffusion with excluded-volume effects are used to model many biological and physical systems at a discrete level. The average properties of the population may be described by a continuum model based on partial differential equations. In this paper we consider multiple interacting subpopulations/species and study how the inter-species competition emerges at the population level. Each individual is described as a finite-size hard core interacting particle undergoing Brownian motion. The link between the discrete stochastic equations of motion and the continuum model is considered systematically using the method of matched asymptotic expansions. The system for two species leads to a nonlinear cross-diffusion system for each subpopulation, which captures the enhancement of the effective diffusion rate due to excluded-volume interactions between particles of the same species, and the diminishment due to particles of the other species. This model can explain two alternative notions of the diffusion coefficient that are often confounded, namely collective diffusion and self-diffusion. Simulations of the discrete system show good agreement with the analytic results

Kinetics and mechanism of proton transport across membrane nanopores

We use computer simulations to study the kinetics and mechanism of proton passage through a narrow-pore carbon-nanotube membrane separating reservoirs of liquid water. Free energy and rate constant calculations show that protons move across the membrane diffusively in single-file chains of hydrogen-bonded water molecules. Proton passage through the membrane is opposed by a high barrier along the effective potential, reflecting the large electrostatic penalty for desolvation and reminiscent of charge exclusion in biological water channels. At neutral pH, we estimate a translocation rate of about 1 proton per hour and tube.Comment: 4 pages, 4 figure

Entropic Stochastic Resonance

We present a novel scheme for the appearance of Stochastic Resonance when the dynamics of a Brownian particle takes place in a confined medium. The presence of uneven boundaries, giving rise to an entropic contribution to the potential, may upon application of a periodic driving force result in an increase of the spectral amplification at an optimum value of the ambient noise level. This Entropic Stochastic Resonance (ESR), characteristic of small-scale systems, may constitute a useful mechanism for the manipulation and control of single-molecules and nano-devices.Comment: 4 pages, 3 figure

Non-Markovian Stochastic Resonance

The phenomenological linear response theory of non-Markovian Stochastic Resonance (SR) is put forward for stationary two-state renewal processes. In terms of a derivation of a non-Markov regression theorem we evaluate the characteristic SR-quantifiers; i.e. the spectral power amplification (SPA) and the signal-to-noise ratio (SNR), respectively. In clear contrast to Markovian SR, a characteristic benchmark of genuine non-Markovian SR is its distinctive dependence of the SPA and SNR on small (adiabatic) driving frequencies; particularly, the adiabatic SNR becomes strongly suppressed over its Markovian counterpart. This non-Markovian SR theory is elucidated for a fractal gating dynamics of a potassium ion channel possessing an infinite variance of closed sojourn times.Comment: 4 pages, 1 figur

Non-Markovian Stochastic Resonance: three state model of ion channel gating

Stochastic Resonance in single voltage-dependent ion channels is investigated within a three state non-Markovian modeling of the ion channel conformational dynamics. In contrast to a two-state description one assumes the presence of an additional closed state for the ion channel which mimics the manifold of voltage-independent closed subconformations (inactivated ``state''). The conformational transition into the open state occurs through a domain of voltage-dependent closed subconformations (closed ``state''). At distinct variance with a standard two-state or also three-state Markovian approach, the inactivated state is characterized by a broad, non-exponential probability distribution of corresponding residence times. The linear response to a periodic voltage signal is determined for arbitrary distributions of the channel's recovery times. Analytical results are obtained for the spectral amplification of the applied signal and the corresponding signal-to-noise ratio. Alternatively, these results are also derived by use of a corresponding two-state non-Markovian theory which is based on driven integral renewal equations [I. Goychuk and P. Hanggi, Phys. Rev. E 69, 021104 (2004)]. The non-Markovian features of stochastic resonance are studied for a power law distribution of the residence time-intervals in the inactivated state which exhibits a large variance. A comparison with the case of bi-exponentially distributed residence times possessing the same mean value, i.e. a simplest non-Markovian two-state description, is also presented

Psi-series solutions of the cubic H\'{e}non-Heiles system and their convergence

The cubic H\'enon-Heiles system contains parameters, for most values of which, the system is not integrable. In such parameter regimes, the general solution is expressible in formal expansions about arbitrary movable branch points, the so-called psi-series expansions. In this paper, the convergence of known, as well as new, psi-series solutions on real time intervals is proved, thereby establishing that the formal solutions are actual solutions

Biased Brownian motion in extreme corrugated tubes

Biased Brownian motion of point-size particles in a three-dimensional tube with smoothly varying cross-section is investigated. In the fashion of our recent work [Martens et al., PRE 83,051135] we employ an asymptotic analysis to the stationary probability density in a geometric parameter of the tube geometry. We demonstrate that the leading order term is equivalent to the Fick-Jacobs approximation. Expression for the higher order corrections to the probability density are derived. Using this expansion orders we obtain that in the diffusion dominated regime the average particle current equals the zeroth-order Fick-Jacobs result corrected by a factor including the corrugation of the tube geometry. In particular we demonstrate that this estimate is more accurate for extreme corrugated geometries compared to the common applied method using the spatially dependent diffusion coefficient D(x,f). The analytic findings are corroborated with the finite element calculation of a sinusoidal-shaped tube.Comment: 10 pages, 4 figure

Collective shuttling of attracting particles in asymmetric narrow channels

The rectification of a single file of attracting particles subjected to a low frequency ac drive is proposed as a working mechanism for particle shuttling in an asymmetric narrow channel. Increasing the particle attraction results in the file condensing, as signalled by the dramatic enhancement of the net particle current. Magnitude and direction of the current become extremely sensitive to the actual size of the condensate, which can then be made to shuttle between two docking stations, transporting particles in one direction, with an efficiency much larger than conventional diffusive models predict