Literature DB >> 21599212

Ergodicity convergence test suggests telomere motion obeys fractional dynamics.

E Kepten1, I Bronshtein, Y Garini.   

Abstract

Anomalous diffusion, observed in many biological processes, is a generalized description of a wide variety of processes, all obeying the same law of mean-square displacement. Identifying the basic mechanisms of these observations is important for deducing the nature of the biophysical systems measured. We implement a previously suggested method for distinguishing between fractional Langevin dynamics, fractional Brownian motion, and continuous time random walk based on the ergodic nature of the data. We apply the method together with the recently suggested P-variation test and the displacement correlation to the lately measured dynamics of telomeres in the nucleus of mammalian cells and find strong evidence that the telomeres motion obeys fractional dynamics. The ergodic dynamics are observed experimentally to fit fractional Brownian or Langevin dynamics. ©2011 American Physical Society

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Year:  2011        PMID: 21599212     DOI: 10.1103/PhysRevE.83.041919

Source DB:  PubMed          Journal:  Phys Rev E Stat Nonlin Soft Matter Phys        ISSN: 1539-3755


  13 in total

1.  Analytical tools to distinguish the effects of localization error, confinement, and medium elasticity on the velocity autocorrelation function.

Authors:  Stephanie C Weber; Michael A Thompson; W E Moerner; Andrew J Spakowitz; Julie A Theriot
Journal:  Biophys J       Date:  2012-06-05       Impact factor: 4.033

2.  Chromosomal locus tracking with proper accounting of static and dynamic errors.

Authors:  Mikael P Backlund; Ryan Joyner; W E Moerner
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2015-06-29

3.  Universal algorithm for identification of fractional Brownian motion. A case of telomere subdiffusion.

Authors:  Krzysztof Burnecki; Eldad Kepten; Joanna Janczura; Irena Bronshtein; Yuval Garini; Aleksander Weron
Journal:  Biophys J       Date:  2012-11-07       Impact factor: 4.033

4.  Diffusion of DNA-Binding Species in the Nucleus: A Transient Anomalous Subdiffusion Model.

Authors:  Michael J Saxton
Journal:  Biophys J       Date:  2020-04-04       Impact factor: 4.033

Review 5.  Rad4 recognition-at-a-distance: Physical basis of conformation-specific anomalous diffusion of DNA repair proteins.

Authors:  Muwen Kong; Bennett Van Houten
Journal:  Prog Biophys Mol Biol       Date:  2016-12-08       Impact factor: 3.667

6.  Probing local chromatin dynamics by tracking telomeres.

Authors:  Rebecca Benelli; Matthias Weiss
Journal:  Biophys J       Date:  2022-06-22       Impact factor: 3.699

7.  Guidelines for the fitting of anomalous diffusion mean square displacement graphs from single particle tracking experiments.

Authors:  Eldad Kepten; Aleksander Weron; Grzegorz Sikora; Krzysztof Burnecki; Yuval Garini
Journal:  PLoS One       Date:  2015-02-13       Impact factor: 3.240

8.  Loss of lamin A function increases chromatin dynamics in the nuclear interior.

Authors:  I Bronshtein; E Kepten; I Kanter; S Berezin; M Lindner; Abena B Redwood; S Mai; S Gonzalo; R Foisner; Y Shav-Tal; Y Garini
Journal:  Nat Commun       Date:  2015-08-24       Impact factor: 14.919

9.  Analysis of Single Locus Trajectories for Extracting In Vivo Chromatin Tethering Interactions.

Authors:  Assaf Amitai; Mathias Toulouze; Karine Dubrana; David Holcman
Journal:  PLoS Comput Biol       Date:  2015-08-28       Impact factor: 4.475

10.  Multiscale modeling of genome organization with maximum entropy optimization.

Authors:  Xingcheng Lin; Yifeng Qi; Andrew P Latham; Bin Zhang
Journal:  J Chem Phys       Date:  2021-07-07       Impact factor: 3.488

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