Literature DB >> 26339466

On the applicability of entropy potentials in transport problems.

Alexander M Berezhkovskii1, Sergey M Bezrukov2.   

Abstract

Transport in confined structures of varying geometry has become the subject of growing attention in recent years since such structures are ubiquitous in biology and technology. In analyzing transport in systems of this type, the notion of entropy potentials is widely used. Entropy potentials naturally arise in one-dimensional description of equilibrium distributions in multidimensional confined structures. However, their application to transport problems requires some caution. In this article we discuss such applications and summarize the results of recent studies exploring the limits of applicability. We also consider an example of a transport problem in a system of varying geometry, where the conventional approach is inapplicable since the geometry changes abruptly. In addition, we demonstrate how the entropy potential can be used to analyze optimal transport through a tree-dimensional cosine-shaped channel.

Entities:  

Year:  2014        PMID: 26339466      PMCID: PMC4556286          DOI: 10.1140/epjst/e2014-02319-3

Source DB:  PubMed          Journal:  Eur Phys J Spec Top        ISSN: 1951-6355            Impact factor:   2.707


  28 in total

1.  Kinetic equations for diffusion in the presence of entropic barriers.

Authors:  D Reguera; J M Rubí
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2001-11-21

Review 2.  Molecular basis of bacterial outer membrane permeability revisited.

Authors:  Hiroshi Nikaido
Journal:  Microbiol Mol Biol Rev       Date:  2003-12       Impact factor: 11.056

3.  Homogenization of boundary conditions for surfaces with regular arrays of traps.

Authors:  Alexander M Berezhkovskii; Michael I Monine; Cyrill B Muratov; Stanislav Y Shvartsman
Journal:  J Chem Phys       Date:  2006-01-21       Impact factor: 3.488

4.  Diffusion in a tube of varying cross section: numerical study of reduction to effective one-dimensional description.

Authors:  A M Berezhkovskii; M A Pustovoit; S M Bezrukov
Journal:  J Chem Phys       Date:  2007-04-07       Impact factor: 3.488

5.  Diffusion model of solute dynamics in a membrane channel: mapping onto the two-site model and optimizing the flux.

Authors:  Sergey M Bezrukov; Alexander M Berezhkovskii; Attila Szabo
Journal:  J Chem Phys       Date:  2007-09-21       Impact factor: 3.488

6.  One-dimensional description of diffusion in a tube of abruptly changing diameter: Boundary homogenization based approach.

Authors:  Alexander M Berezhkovskii; Alexander V Barzykin; Vladimir Yu Zitserman
Journal:  J Chem Phys       Date:  2009-12-14       Impact factor: 3.488

7.  Mapping of diffusion in a channel with abrupt change of diameter.

Authors:  Pavol Kalinay; Jerome K Percus
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2010-09-30

8.  Entropic particle transport: higher-order corrections to the Fick-Jacobs diffusion equation.

Authors:  S Martens; G Schmid; L Schimansky-Geier; P Hänggi
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2011-05-31

9.  Time scale separation leads to position-dependent diffusion along a slow coordinate.

Authors:  Alexander Berezhkovskii; Attila Szabo
Journal:  J Chem Phys       Date:  2011-08-21       Impact factor: 3.488

Review 10.  VDAC inhibition by tubulin and its physiological implications.

Authors:  Tatiana K Rostovtseva; Sergey M Bezrukov
Journal:  Biochim Biophys Acta       Date:  2011-11-09
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  11 in total

1.  Range of applicability of modified Fick-Jacobs equation in two dimensions.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2015-10-28       Impact factor: 3.488

Review 2.  Inhibiting bacterial toxins by channel blockage.

Authors:  Sergey M Bezrukov; Ekaterina M Nestorovich
Journal:  Pathog Dis       Date:  2015-12-09       Impact factor: 3.166

3.  Mapping Intrachannel Diffusive Dynamics of Interacting Molecules onto a Two-Site Model: Crossover in Flux Concentration Dependence.

Authors:  Alexander M Berezhkovskii; Sergey M Bezrukov
Journal:  J Phys Chem B       Date:  2018-06-29       Impact factor: 2.991

4.  Unbiased diffusion in two-dimensional channels with corrugated walls.

Authors:  Roberto Verdel; Leonardo Dagdug; Alexander M Berezhkovskii; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2016-02-28       Impact factor: 3.488

5.  Brownian motion in confined geometries.

Authors:  S M Bezrukov; L Schimansky-Geier; G Schmid
Journal:  Eur Phys J Spec Top       Date:  2014-12-15       Impact factor: 2.707

6.  Scaling Behavior of Ionic Transport in Membrane Nanochannels.

Authors:  María Queralt-Martín; M Lidón López; Marcel Aguilella-Arzo; Vicente M Aguilella; Antonio Alcaraz
Journal:  Nano Lett       Date:  2018-09-10       Impact factor: 11.189

7.  Intrinsic diffusion resistance of a membrane channel, mean first-passage times between its ends, and equilibrium unidirectional fluxes.

Authors:  Alexander M Berezhkovskii; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2022-02-21       Impact factor: 3.488

Review 8.  Current state of theoretical and experimental studies of the voltage-dependent anion channel (VDAC).

Authors:  Sergei Yu Noskov; Tatiana K Rostovtseva; Adam C Chamberlin; Oscar Teijido; Wei Jiang; Sergey M Bezrukov
Journal:  Biochim Biophys Acta       Date:  2016-03-03

9.  Peculiarities of the Mean Transition Path Time Dependence on the Barrier Height in Entropy Potentials.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Phys Chem B       Date:  2020-03-16       Impact factor: 2.991

10.  Trapping of particles diffusing in two dimensions by a hidden binding site.

Authors:  Leonardo Dagdug; Alexander M Berezhkovskii; Vladimir Yu Zitserman; Sergey M Bezrukov
Journal:  Phys Rev E       Date:  2021-01       Impact factor: 2.529

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