3,541 research outputs found
Ion transport through confined ion channels in the presence of immobile charges
We study charge transport in an ionic solution in a confined nanoscale
geometry in the presence of an externally applied electric field and immobile
background charges. For a range of parameters, the ion current shows
non-monotonic behavior as a function of the external ion concentration. For
small applied electric field, the ion transport can be understood from simple
analytic arguments, which are supported by Monte Carlo simulation. The results
qualitatively explain measurements of ion current seen in a recent experiment
on ion transport through a DNA-threaded nanopore (D. J. Bonthuis et. al., Phys.
Rev. Lett, vol. 97, 128104 (2006)).Comment: 5 pages, 3 figure
On the Physics of Size Selectivity
We demonstrate that two mechanisms used by biological ion channels to select
particles by size are driven by entropy. With uncharged particles in an
infinite cylinder, we show that a channel that attracts particles is
small-particle selective and that a channel that repels water from the wall is
large-particle selective. Comparing against extensive density-functional theory
calculations of our model, we find that the main physics can be understood with
surprisingly simple bulk models that neglect the confining geometry of the
channel completely.Comment: 4 pages, 3 figures, Phys. Rev. Lett. (accepted
Effect of Interactions on Molecular Fluxes and Fluctuations in the Transport Across Membrane Channels
Transport of molecules across membrane channels is investigated theoretically
using exactly solvable one-dimensional discrete-state stochastic models. An
interaction between molecules and membrane pores is modeled via a set of
binding sites with different energies. It is shown that the interaction
potential strongly influences the particle currents as well as fluctuations in
the number of translocated molecules. For small concentration gradients the
attractive sites lead to largest currents and fluctuations, while the repulsive
interactions yield the largest fluxes and dispersions for large concentration
gradients. Interaction energies that lead to maximal currents and maximal
fluctuations are the same only for locally symmetric potentials, while they
differ for the locally asymmetric potentials. The conditions for the most
optimal translocation transport with maximal current and minimal dispersion are
discussed. It is argued that in this case the interaction strength is
independent of local symmetry of the potential of mean forces. In addition, the
effect of the global asymmetry of the interaction potential is investigated,
and it is shown that it also strongly affects the particle translocation
dynamics. These phenomena can be explained by analyzing the details of the
particle entering and leaving the binding sites in the channel.Comment: submitted to J. Chem. Phy
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
Voltage sensing in ion channels: Mesoscale simulations of biological devices
Electrical signaling via voltage-gated ion channels depends upon the function
of a voltage sensor (VS), identified with the S1-S4 domain in voltage-gated K+
channels. Here we investigate some energetic aspects of the sliding-helix model
of the VS using simulations based on VS charges, linear dielectrics and
whole-body motion. Model electrostatics in voltage-clamped boundary conditions
are solved using a boundary element method. The statistical mechanical
consequences of the electrostatic configurational energy are computed to gain
insight into the sliding-helix mechanism and to predict experimentally measured
ensemble properties such as gating charge displaced by an applied voltage.
Those consequences and ensemble properties are investigated for two alternate
S4 configurations, \alpha- and 3(10)-helical. Both forms of VS are found to
have an inherent electrostatic stability. Maximal charge displacement is
limited by geometry, specifically the range of movement where S4 charges and
counter-charges overlap in the region of weak dielectric. Charge displacement
responds more steeply to voltage in the \alpha-helical than the 3(10)-helical
sensor. This difference is due to differences on the order of 0.1 eV in the
landscapes of electrostatic energy. As a step toward integrating these VS
models into a full-channel model, we include a hypothetical external load in
the Hamiltonian of the system and analyze the energetic in/output relation of
the VS.Comment: arXiv admin note: substantial text overlap with arXiv:1112.299
Asymmetry in shape causing absolute negative mobility
We propose a simple classical concept of nanodevices working in an absolute
negative mobility (ANM) regime: The minimal spatial asymmetry required for ANM
to occur is embedded in the geometry of the transported particle, rather than
in the channel design. This allows for a tremendous simplification of device
engineering, thus paving the way towards practical implementations of ANM.
Operating conditions and performance of our model device are investigated, both
numerically and analytically.Comment: 6 pages; accepted for publication in PR
A nonlinear equation for ionic diffusion in a strong binary electrolyte
The problem of the one dimensional electro-diffusion of ions in a strong
binary electrolyte is considered. In such a system the solute dissociates
completely into two species of ions with unlike charges. The mathematical
description consists of a diffusion equation for each species augmented by
transport due to a self consistent electrostatic field determined by the
Poisson equation. This mathematical framework also describes other important
problems in physics such as electron and hole diffusion across semi-conductor
junctions and the diffusion of ions in plasmas. If concentrations do not vary
appreciably over distances of the order of the Debye length, the Poisson
equation can be replaced by the condition of local charge neutrality first
introduced by Planck. It can then be shown that both species diffuse at the
same rate with a common diffusivity that is intermediate between that of the
slow and fast species (ambipolar diffusion). Here we derive a more general
theory by exploiting the ratio of Debye length to a characteristic length scale
as a small asymptotic parameter. It is shown that the concentration of either
species may be described by a nonlinear integro-differential equation which
replaces the classical linear equation for ambipolar diffusion but reduces to
it in the appropriate limit. Through numerical integration of the full set of
equations it is shown that this nonlinear equation provides a better
approximation to the exact solution than the linear equation it replaces.Comment: 4 pages, 1 figur
Unidirectional hopping transport of interacting particles on a finite chain
Particle transport through an open, discrete 1-D channel against a mechanical
or chemical bias is analyzed within a master equation approach. The channel,
externally driven by time dependent site energies, allows multiple occupation
due to the coupling to reservoirs. Performance criteria and optimization of
active transport in a two-site channel are discussed as a function of reservoir
chemical potentials, the load potential, interparticle interaction strength,
driving mode and driving period. Our results, derived from exact rate
equations, are used in addition to test a previously developed time-dependent
density functional theory, suggesting a wider applicability of that method in
investigations of many particle systems far from equilibrium.Comment: 33 pages, 8 figure
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
Sensing of Fluctuating Nanoscale Magnetic Fields Using NV Centres in Diamond
New magnetometry techniques based on Nitrogen-Vacancy (NV) defects in diamond
allow for the imaging of static (DC) and oscillatory (AC) nanoscopic magnetic
systems. However, these techniques require accurate knowledge and control of
the sample dynamics, and are thus limited in their ability to image fields
arising from rapidly fluctuating (FC) environments. We show here that FC fields
place restrictions on the DC field sensitivity of an NV qubit magnetometer, and
that by probing the dephasing rate of the qubit in a magnetic FC environment,
we are able to measure fluctuation rates and RMS field strengths that would be
otherwise inaccessible with the use of DC and AC magnetometry techniques. FC
sensitivities are shown to be comparable to those of AC fields, whilst
requiring no additional experimental overheads or control over the sample.Comment: 5 pages, 4 figure
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