Literature DB >> 33601544

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

Leonardo Dagdug1, Alexander M Berezhkovskii2, Vladimir Yu Zitserman3, Sergey M Bezrukov4.   

Abstract

We study trapping of particles diffusing in a two-dimensional rectangular chamber by a binding site located at the end of a rectangular sleeve. To reach the site a particle first has to enter the sleeve. After that it has two options: to come back to the chamber or to diffuse to the site where it is trapped. The main result of the present work is a simple expression for the mean particle lifetime as a function of its starting position and geometric parameters of the system. This expression is obtained by an approximate reduction of the initial two-dimensional problem to the effective one-dimensional one which can be solved with relative ease. Our analytical predictions are tested against the results obtained from Brownian dynamics simulations. The test shows excellent agreement between the two for a wide range of the geometric parameters of the system.

Entities:  

Year:  2021        PMID: 33601544      PMCID: PMC9006174          DOI: 10.1103/PhysRevE.103.012135

Source DB:  PubMed          Journal:  Phys Rev E        ISSN: 2470-0045            Impact factor:   2.529


  18 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

2.  Diffusion in a two-dimensional channel with curved midline and varying width: reduction to an effective one-dimensional description.

Authors:  R Mark Bradley
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-12-31

3.  On the applicability of entropy potentials in transport problems.

Authors:  Alexander M Berezhkovskii; Sergey M Bezrukov
Journal:  Eur Phys J Spec Top       Date:  2014-12       Impact factor: 2.707

4.  Corrections to the Fick-Jacobs equation.

Authors:  P Kalinay; J K Percus
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2006-10-05

5.  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

6.  Escape from cavity through narrow tunnel.

Authors:  Alexander M Berezhkovskii; Alexander V Barzykin; Vladimir Yu Zitserman
Journal:  J Chem Phys       Date:  2009-06-28       Impact factor: 3.488

7.  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

8.  Non-steady-state diffusion in two-dimensional periodic channels.

Authors:  Matan Sivan; Oded Farago
Journal:  Phys Rev E       Date:  2019-02       Impact factor: 2.529

9.  Universal Formula for the Mean First Passage Time in Planar Domains.

Authors:  Denis S Grebenkov
Journal:  Phys Rev Lett       Date:  2016-12-23       Impact factor: 9.161

10.  Synthetic biology. Programmable on-chip DNA compartments as artificial cells.

Authors:  Eyal Karzbrun; Alexandra M Tayar; Vincent Noireaux; Roy H Bar-Ziv
Journal:  Science       Date:  2014-08-15       Impact factor: 47.728

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  1 in total

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

Authors:  Leonardo Dagdug; Alexander M Berezhkovskii; Vladimir Yu Zitserman; Sergey M Bezrukov
Journal:  Phys Rev E       Date:  2021-06       Impact factor: 2.529

  1 in total

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