Fast-ion transport in peptide nanochannels

Baumgaertner, A.

doi:10.1016/j.mseb.2009.04.021

Cited by 4 publications

(2 citation statements)

References 37 publications

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“…In fact, the present model shares some similarities with models used to describe the mechanism of fast ion conduction which is of importance in science and technology [12,13] as e.g. in nanofluidic devices such as nanodiodes [14], diffusion of colloids in narrow channels [16], and biological ion channels [15,34,35].…”

Section: Discussionmentioning

confidence: 76%

Phase transitions in the driven lattice gas (TASEP) with repulsive energies

Baumgaertner

Narasimhan

2023

J. Phys. A: Math. Theor.

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We report on non-equilibrium phase transitions in the driven lattice gas model TASEP (totally asymmetric exclusion processes) caused by nearest-neighbor repulsions between particles, ε > 0, employing extensive Monte Carlo simulations and mean-ﬁeld calculations. The phase diagram has ﬁve different regimes which are separated by distinct boundaries. We discuss the density of particles and the current which depend differently in the various regimes on the system’s entry and exit rates of particles, α and β, respectively. The steady state can be described by quasi-particles called ’soft dimerons’, where each dimeron consists of a particle dragging an empty nearest-neighbor site on its left. The asymptotic state of dimerons at ε →∞ is equivalent to the state of hard dimers at ε = 0. Since the model is a uni-directional ﬂuid, it has an internal hydrodynamic pressure which increases with increasing inter-particle repulsion ε . This leads to a collective effect which causes phase transitions between high and low densities of particles at certain critical points εc.

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Section: Discussionmentioning

confidence: 76%

Phase transitions in the driven lattice gas (TASEP) with repulsive energies

Baumgaertner

Narasimhan

2023

J. Phys. A: Math. Theor.

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“…Single-file diffusion of a system of hardcore particles is a well-studied process that provides a basic description of transport, for example, in fast ion transport through channels [1,2], in zeolites [3] and in superionic or organic conductors [4]. While their collective diffusion is like that of a set of independent particles, the diffusion of a tagged particle is known to be different -namely, its mean squared displacement (MSD) is proportional to √ t and its positions are Gaussian-distributed [5][6][7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

Dynamics of a stochastically driven Brownian particle in one dimension

Narasimhan¹,

Baumgaertner²

2012

Physica A: Statistical Mechanics and its Applications

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We present a study on the dynamics of a system consisting of a pair of hardcore particles diffusing with different rates. We solved the drift-diffusion equation for this model in the case when one particle, labeled F, drifts and diffuses slowly towards the second particle, labeled M. The displacements of particle M exhibits a crossover from diffusion to drift at a characteristic time which depends on the rate constants. We show that the positional fluctuation of M exhibits an intermediate crossover regime of subdiffusion separating initial and asymptotic diffusive behavior; this is in agreement with the complete set of Master Equations that describe the stochastic evolution of the model. The intermediate crossover regime can be considerably large depending on the hopping probabilities of the two particles. This is in contrast to the known crossover from diffusive to subdiffusive behavior of a tagged particle that is in the interior of a large single-file system on an unbound real line. We discuss our model with respect to the biological phenomena of membrane protrusions where polymerizing actin filaments (F) push the cell membrane (M).

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Molecular dynamics study of Na+ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube

et al. 2013

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The dynamics of Na(+) transportation in a transmembrane cyclic peptide nanotube of 8 × (WL)4/POPE has been simulated. The curve of PMF (potential of mean force) for Na(+) moving through the tube, based on ABF (adaptive biasing force) method, indicates that Na(+) possesses lower free energy in an α-plane region than in a mid-plane one. It was found that Na(+) would desorb one or two water molecules in the first solvation shell when entering the tube and later maintain in a solvation state. The average numbers of water molecules around Na(+) are 4.50, 4.09 in the first solvation shell, and 3.10, 4.08 in the second one for Na(+) locating in an α-plane zone and a mid-plane region, respectively. However, water molecules far away from Na(+) location still nearly arrange in a form of 1-2-1-2 file. The dipole orientations of water molecules in the regions of gaps 1 and 7 display "D-defects", resulted from the simultaneous electrostatic potentials generated by Na(+) and the bare carbonyls at the tube mouths. Such "D-defects" accommodate the energetically favorable water orientations thereby.

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Fast-ion transport in peptide nanochannels

Cited by 4 publications

References 37 publications

Phase transitions in the driven lattice gas (TASEP) with repulsive energies

Phase transitions in the driven lattice gas (TASEP) with repulsive energies

Dynamics of a stochastically driven Brownian particle in one dimension

Molecular dynamics study of Na+ transportation in a cyclic peptide nanotube and its influences on water behaviors in the tube

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