PMID: 15244613Jul 13, 2004Paper

Diffusion in correlated random potentials, with applications to DNA

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Michael SlutskyLeonid A Mirny

Abstract

Many biological processes involve one-dimensional diffusion over a correlated inhomogeneous energy landscape with a correlation length xi(c). Typical examples are specific protein target location on DNA, nucleosome repositioning, or DNA translocation through a nanopore, in all cases with xi(c) approximately 10 nm. We investigate such transport processes by the mean first passage time (MFPT) formalism, and find diffusion times which exhibit strong sample to sample fluctuations. For a displacement N, the average MFPT is diffusive, while its standard deviation over the ensemble of energy profiles scales as N(3/2) with a large prefactor. Fluctuations are thus dominant for displacements smaller than a characteristic N(c) > xi(c) : typical values are much less than the mean, and governed by an anomalous diffusion rule. Potential biological consequences of such random walks, composed of rapid scans in the vicinity of favorable energy valleys and occasional jumps to further valleys, is discussed.

References

Nov 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·J D Bryngelson, P G Wolynes
Sep 9, 1996·FEBS Letters·A Gabrielian, S Pongor
May 9, 1997·Science·R D Astumian
Jul 1, 1998·Annual Review of Biophysics and Biomolecular Structure·J Widom
Oct 27, 1998·Trends in Biochemical Sciences·M G MunteanuS Pongor
Apr 1, 1986·Physical Review A: General Physics·I Goldhirsch, Y Gefen
Aug 15, 1989·Physical Review A: General Physics·K P Murthy, K W Kehr
Jan 15, 1990·Physical Review. a·K P Murthy, K W Kehr
Aug 1, 1988·Physical Review Letters·S H Noskowicz, I Goldhirsch
Oct 8, 1999·Biophysical Journal·D K Lubensky, D R Nelson
May 1, 2001·Physical Review Letters·A MellerD Branton
May 1, 2001·Physical Review Letters·H SchiesselW M Gelbart
Jun 8, 2001·Proceedings of the National Academy of Sciences of the United States of America·H SalmanM Elbaum
Jun 20, 2001·Accounts of Chemical Research·C BustamanteG Oster
Feb 13, 2002·Quarterly Reviews of Biophysics·J Widom
Jul 12, 2002·Journal of Mathematical Biology·Jonathan P WhiteleyClive E W Hahn
Jul 19, 2002·FEBS Letters·Ryoiti Kiyama, Edward N Trifonov
Sep 10, 2002·Bulletin of Mathematical Biology·Max Shpak, Kevin Atteson
Sep 10, 2002·Proceedings of the National Academy of Sciences of the United States of America·Ulrich GerlandTerence Hwa
Mar 4, 2003·EMBO Reports·Andrew A Travers
Apr 4, 2003·Proceedings of the National Academy of Sciences of the United States of America·Terence HwaLei-han Tang
Jun 26, 2003·Nucleic Acids Research·Kristian VlahovicekSándor Pongor

❮ Previous
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Citations

Jun 9, 2005·Mutation Research·Dmitry O Zharkov, Arthur P Grollman
May 10, 2008·The Journal of Chemical Physics·Michel G Gauthier, Gary W Slater
Aug 18, 2012·The Journal of Chemical Physics·Stephen MirigianMurugappan Muthukumar
Jul 11, 2006·The Journal of Chemical Physics·Semen A Trygubenko, David J Wales
Dec 18, 2015·Nucleic Acids Research·Kevin HauserCarlos Simmerling
Dec 17, 2015·The Journal of Chemical Physics·Itay BarelFrank L H Brown
Sep 25, 2015·Nucleic Acids Research·Anupam Mondal, Arnab Bhattacherjee
Mar 19, 2014·DNA Repair·Jong-Bong LeeRichard Fishel
Feb 16, 2008·Structure·Nir London, Ora Schueler-Furman
Feb 18, 2010·Structure·Nir LondonOra Schueler-Furman
May 24, 2005·Biophysical Journal·Igor M SokolovMark C Williams
Jul 5, 2011·Biophysical Journal·Itamar Sela, David B Lukatsky
May 6, 2008·Biophysical Journal·Longhua HuRobijn Bruinsma
Oct 7, 2004·Biophysical Journal·Michael Slutsky, Leonid A Mirny
Oct 15, 2014·Proceedings of the National Academy of Sciences of the United States of America·Ariel AfekDavid B Lukatsky
Jan 21, 2017·The Journal of Physical Chemistry. B·Lin LiuRalf Metzler
Jan 16, 2018·Physical Chemistry Chemical Physics : PCCP·Prathitha KarRalf Metzler
May 12, 2011·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Anahita TafviziAntoine M van Oijen
Sep 13, 2018·Physical Chemistry Chemical Physics : PCCP·Igor Goychuk
May 8, 2010·Physical Chemistry Chemical Physics : PCCP·Rahul K Das, Anatoly B Kolomeisky
Aug 11, 2005·Physical Review Letters·C VaillantA Arnéodo
Feb 16, 2006·The European Physical Journal. E, Soft Matter·C VaillantA Arnéodo
Jun 13, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Rajamanickam Murugan
Aug 8, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Rajamanickam Murugan
Aug 8, 2014·Biochemistry. Biokhimii︠a︡·G V Mechetin, D O Zharkov
May 17, 2012·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Denis BoyerGleb Oshanin
Nov 22, 2008·Biochemical Society Transactions·Nir London, Ora Schueler-Furman
Feb 3, 2011·Theory in Biosciences = Theorie in Den Biowissenschaften·Dominique Chu
Jun 20, 2019·Physical Review. E·Takuma Akimoto, Keiji Saito
Jul 18, 2018·Physical Review. E·Meng Hu, Jing-Dong Bao
Nov 30, 2010·Physical Chemistry Chemical Physics : PCCP·Anatoly B Kolomeisky
Jul 23, 2015·Physical Biology·Jérôme Cartailler, Jürgen Reingruber
Jan 8, 2015·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Guénola DrillonAlain Arneodo
Aug 16, 2012·Molecular BioSystems·Nicolae Radu Zabet, Boris Adryan
Feb 4, 2014·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·R Salgado-García, Cesar Maldonado
Jul 1, 2019·The Journal of Chemical Physics·Itay BarelFrank L H Brown

❮ Previous
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