Literature DB >> 20489716

Geometry-controlled kinetics.

O Bénichou1, C Chevalier, J Klafter, B Meyer, R Voituriez.   

Abstract

It has long been appreciated that the transport properties of molecules can control reaction kinetics. This effect can be characterized by the time it takes a diffusing molecule to reach a target-the first-passage time (FPT). Determining the FPT distribution in realistic confined geometries has until now, however, seemed intractable. Here, we calculate this FPT distribution analytically and show that transport processes as varied as regular diffusion, anomalous diffusion, and diffusion in disordered media and fractals, fall into the same universality classes. Beyond the theoretical aspect, this result changes our views on standard reaction kinetics and we introduce the concept of 'geometry-controlled kinetics'. More precisely, we argue that geometry-and in particular the initial distance between reactants in 'compact' systems-can become a key parameter. These findings could help explain the crucial role that the spatial organization of genes has in transcription kinetics, and more generally the impact of geometry on diffusion-limited reactions.

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Year:  2010        PMID: 20489716     DOI: 10.1038/nchem.622

Source DB:  PubMed          Journal:  Nat Chem        ISSN: 1755-4330            Impact factor:   24.427


  32 in total

1.  Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy.

Authors:  M Wachsmuth; W Waldeck; J Langowski
Journal:  J Mol Biol       Date:  2000-05-12       Impact factor: 5.469

2.  Observation of laser speckle effects and nonclassical kinetics in an elementary chemical reaction.

Authors:  E Monson; R Kopelman
Journal:  Phys Rev Lett       Date:  2000-07-17       Impact factor: 9.161

3.  First-passage time distributions for subdiffusion in confined geometry.

Authors:  S Condamin; O Bénichou; J Klafter
Journal:  Phys Rev Lett       Date:  2007-06-22       Impact factor: 9.161

4.  Probing transcription factor dynamics at the single-molecule level in a living cell.

Authors:  Johan Elf; Gene-Wei Li; X Sunney Xie
Journal:  Science       Date:  2007-05-25       Impact factor: 47.728

5.  First-passage times for random walks in bounded domains.

Authors:  S Condamin; O Bénichou; M Moreau
Journal:  Phys Rev Lett       Date:  2005-12-19       Impact factor: 9.161

6.  Optimizing intermittent reaction paths.

Authors:  O Bénichou; C Loverdo; M Moreau; R Voituriez
Journal:  Phys Chem Chem Phys       Date:  2008-10-21       Impact factor: 3.676

7.  Global first-passage times of fractal lattices.

Authors:  C P Haynes; A P Roberts
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2008-10-10

8.  Narrow-escape time problem: time needed for a particle to exit a confining domain through a small window.

Authors:  O Bénichou; R Voituriez
Journal:  Phys Rev Lett       Date:  2008-04-23       Impact factor: 9.161

9.  Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin.

Authors:  Aurélien Bancaud; Sébastien Huet; Nathalie Daigle; Julien Mozziconacci; Joël Beaudouin; Jan Ellenberg
Journal:  EMBO J       Date:  2009-12-16       Impact factor: 11.598

Review 10.  Nuclear organization of the genome and the potential for gene regulation.

Authors:  Peter Fraser; Wendy Bickmore
Journal:  Nature       Date:  2007-05-24       Impact factor: 49.962

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  43 in total

1.  Non-Markovian polymer reaction kinetics.

Authors:  T Guérin; O Bénichou; R Voituriez
Journal:  Nat Chem       Date:  2012-06-10       Impact factor: 24.427

2.  Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure.

Authors:  Shlomi Reuveni; Rony Granek; Joseph Klafter
Journal:  Proc Natl Acad Sci U S A       Date:  2010-07-16       Impact factor: 11.205

3.  Reaction kinetics: Catalysis without a catalyst.

Authors:  Raoul Kopelman
Journal:  Nat Chem       Date:  2010-06       Impact factor: 24.427

4.  Light-scattering technologies for field carcinogenesis detection: a modality for endoscopic prescreening.

Authors:  Vadim Backman; Hemant K Roy
Journal:  Gastroenterology       Date:  2010-11-12       Impact factor: 22.682

5.  When Brownian diffusion is not Gaussian.

Authors:  Bo Wang; James Kuo; Sung Chul Bae; Steve Granick
Journal:  Nat Mater       Date:  2012-05-22       Impact factor: 43.841

6.  Solute diffusion is hindered in the mitochondrial matrix.

Authors:  Cindy E J Dieteren; Stan C A M Gielen; Leo G J Nijtmans; Jan A M Smeitink; Herman G Swarts; Roland Brock; Peter H G M Willems; Werner J H Koopman
Journal:  Proc Natl Acad Sci U S A       Date:  2011-05-09       Impact factor: 11.205

7.  Theoretical and computational modeling of target-site search kinetics in vitro and in vivo.

Authors:  Elena F Koslover; Mario A Díaz de la Rosa; Andrew J Spakowitz
Journal:  Biophys J       Date:  2011-08-17       Impact factor: 4.033

Review 8.  Protein sorting and membrane-mediated interactions.

Authors:  Mária Hanulová; Matthias Weiss
Journal:  Biophys Rev       Date:  2012-02-15

9.  Geometry-induced bursting dynamics in gene expression.

Authors:  B Meyer; O Bénichou; Y Kafri; R Voituriez
Journal:  Biophys J       Date:  2012-05-02       Impact factor: 4.033

Review 10.  Mitochondrial Morphofunction in Mammalian Cells.

Authors:  Elianne P Bulthuis; Merel J W Adjobo-Hermans; Peter H G M Willems; Werner J H Koopman
Journal:  Antioxid Redox Signal       Date:  2018-11-29       Impact factor: 8.401

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