Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking.
- R. Metzler, Jae-Hyung Jeon, Andrey G. Cherstvy, E. Barkai
- PhysicsPhysical Chemistry, Chemical Physics - PCCP
- 21 October 2014
This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion, and pays special attention to the ergodicity breaking parameters for the different anomalous stochastic processes.
Anomalous diffusion models and their properties
- R. Metzler, Jae-Hyung Jeon, Andrey G. Cherstvy, E. Barkai
- Physics
- 22 September 2014
Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate…
Possibilities and limitations of label-free detection of DNA hybridization with field-effect-based devices
- A. Poghossian, Andrey G. Cherstvy, S. Ingebrandt, A. Offenhäusser, M. Schöning
- Chemistry
- 11 November 2005
Anomalous diffusion and ergodicity breaking in heterogeneous diffusion processes
- Andrey G. Cherstvy, A. Chechkin, R. Metzler
- Mathematics
- 22 March 2013
The non-ergodicity of a simple Markovian stochastic process with space-dependent diffusion coefficient D(x) is demonstrated, which yields anomalous diffusion of the form hx 2 (t)i ' t 2/(2 ) .
Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions
- D. Beshnova, Andrey G. Cherstvy, Y. Vainshtein, V. B. Teif
- BiologyPLoS Comput. Biol.
- 1 July 2014
An integrative biophysical and bioinformatics analysis in species ranging from yeast to frog to mouse where NRL was studied as a function of various parameters shows that in simple eukaryotes, a lower limit for the NRL value exists, determined by internucleosome interactions and remodeler action, and demonstrates that different regimes of the NRL dependence on histone concentrations exist depending on whether DNA sequence-specific effects dominate over boundary effects.
Electrostatic interactions in biological DNA-related systems.
- Andrey G. Cherstvy
- Biology, ChemistryPhysical Chemistry, Chemical Physics - PCCP
- 18 May 2011
For biological DNA-related systems, a theoretical framework is developed to describe the physical-chemical mechanisms of structure formation and anticipate some biological consequences, with emphasis on electrostatic aspects.
Structure of DNA toroids and electrostatic attraction of DNA duplexes
- Andrey G. Cherstvy
- Physics, Chemistry
- 11 February 2005
DNA–DNA electrostatic attraction is considered as the driving force for the formation of DNA toroids in the presence of DNA condensing cations. This attraction comes from the DNA helical charge…
Le diagnostic foliaire en arboriculture: bilan de 20 ans d' étude
- J. Neyroud, S. Amiguet, Andrey G. Cherstvy, Ch. Evequoz
- Philosophy
- 2007
Cette etude evalue les resultats obtenus ces vingt dernieres annees par la technique du diagnostic foliaire en arboriculture. Des echantillons de reference de feuilles d'abricotier, de cerisier, de…
Protein--DNA interactions: reaching and recognizing the targets.
- Andrey G. Cherstvy, A. Kolomeisky, A. Kornyshev
- PhysicsJournal of Physical Chemistry B
- 31 July 2007
A theoretical approach is presented that describes some physical-chemical aspects of the target search and recognition of proteins and shows how the complementarity of the charge patterns on a target DNA sequence and on the protein may result in electrostatic recognition of a specific track on DNA and subsequent protein pinning.
Positively charged residues in DNA-binding domains of structural proteins follow sequence-specific positions of DNA phosphate groups.
- Andrey G. Cherstvy
- Biology, ChemistryJournal of Physical Chemistry B
- 2 April 2009
It is shown that positive amino acids on the proteins track sequence-specific positions of individual DNA phosphates, which can contribute to DNA recognition by DNA-binding proteins, which is governed for many DNA-protein complexes primarily by the hydrogen bond formation between protein residues and DNA bases.
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