Literature DB >> 28688439

Bulk-mediated surface transport in the presence of bias.

Alexander M Berezhkovskii1, Leonardo Dagdug1, Sergey M Bezrukov1.   

Abstract

Surface transport, when the particle is allowed to leave the surface, travel in the bulk for some time, and then return to the surface, is referred to as bulk-mediated surface transport. Recently, we proposed a formalism that significantly simplifies analysis of bulk-mediated surface diffusion [A. M. Berezhkovskii, L. Dagdug, and S. M. Bezrukov, J. Chem. Phys. 143, 084103 (2015)]. Here this formalism is extended to bulk-mediated surface transport in the presence of bias, i.e., when the particle has arbitrary drift velocities on the surface and in the bulk. A key advantage of our approach is that the transport problem reduces to that of a two-state problem of the particle transitions between the surface and the bulk. The latter can be solved with relative ease. The formalism is used to find the Laplace transforms of the first two moments of the particle displacement over the surface in time t at arbitrary values of the particle drift velocities and diffusivities on the surface and in the bulk. This allows us to analyze in detail the time dependence of the effective drift velocity of the particle on the surface, which can be highly nontrivial.

Entities:  

Year:  2017        PMID: 28688439      PMCID: PMC5500123          DOI: 10.1063/1.4991730

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  30 in total

1.  Narrow-escape times for diffusion in microdomains with a particle-surface affinity: mean-field results.

Authors:  G Oshanin; M Tamm; O Vasilyev
Journal:  J Chem Phys       Date:  2010-06-21       Impact factor: 3.488

2.  A new approach to the problem of bulk-mediated surface diffusion.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2015-08-28       Impact factor: 3.488

Review 3.  Facilitated target location in biological systems.

Authors:  P H von Hippel; O G Berg
Journal:  J Biol Chem       Date:  1989-01-15       Impact factor: 5.157

Review 4.  The kinetics of interfacial catalysis by phospholipase A2 and regulation of interfacial activation: hopping versus scooting.

Authors:  M K Jain; O G Berg
Journal:  Biochim Biophys Acta       Date:  1989-04-03

5.  Target search of N sliding proteins on a DNA.

Authors:  Igor M Sokolov; Ralf Metzler; Kiran Pant; Mark C Williams
Journal:  Biophys J       Date:  2005-05-20       Impact factor: 4.033

6.  Single molecule measurements of repressor protein 1D diffusion on DNA.

Authors:  Y M Wang; Robert H Austin; Edward C Cox
Journal:  Phys Rev Lett       Date:  2006-07-27       Impact factor: 9.161

7.  Bulk-mediated surface diffusion along a cylinder: Propagators and crossovers.

Authors:  Aleksei V Chechkin; Irwin M Zaid; Michael A Lomholt; Igor M Sokolov; Ralf Metzler
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2009-04-27

8.  Quantifying hopping and jumping in facilitated diffusion of DNA-binding proteins.

Authors:  C Loverdo; O Bénichou; R Voituriez; A Biebricher; I Bonnet; P Desbiolles
Journal:  Phys Rev Lett       Date:  2009-05-04       Impact factor: 9.161

9.  Biased diffusion in three-dimensional comb-like structures.

Authors:  Alexander M Berezhkovskii; Leonardo Dagdug; Sergey M Bezrukov
Journal:  J Chem Phys       Date:  2015-04-07       Impact factor: 3.488

10.  Rate enhancement by guided diffusion. Chain length dependence of repressor-operator association rates.

Authors:  R Schranner; P H Richter
Journal:  Biophys Chem       Date:  1978-05       Impact factor: 2.352

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