Berlin 2008 – wissenschaftliches Programm
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BP: Fachverband Biologische Physik
BP 11: Transport Processes
BP 11.3: Vortrag
Dienstag, 26. Februar 2008, 15:45–16:00, C 243
Target Search on a Dynamic Polymer — •Thomas Schötz1, Richard Neher2, and Ulrich Gerland3 — 1Arnold Sommerfeld Center (ASC), LMU München, Germany — 2Kavli Institute for Theoretical Physics, University of California, Santa Barbara, USA — 3Institute for Theoretical Physics, University of Cologne, Germany
The diffusive search of a particle (protein) for a specific site on a heterogeneous polymer (DNA) is an interesting physics problem posed by the molecular biology of gene regulation. In the relevant limit where the DNA is in a compact conformation and the generic (electrostatic) attraction between the protein and DNA is strong, this search proceeds predominantly by local 1D sliding along the DNA and "hopping" to a different segment of the DNA, which is closeby in 3D space but may be distant along the contour. If the time between two hopping events is sufficiently long, such that the DNA conformations at subsequent events are uncorrelated, the dynamics of this search process can be described with the fractional Fokker-Planck-equation approach [Lomholt et al. PRL (2005)]. However, outside of this "annealed limit", the search dynamics changes drastically, as has been demonstrated in a study of the "quenched limit", i.e. the frozen polymer case [Sokolov et al. PRL (1997)]. In biological systems, typically neither of these limits is realized. Here, we study the full problem of the target search on a dynamic polymer. We observe a non-trivial crossover between the two limits, which is due to the breakdown of the correlations in the polymer conformations. We characterize these correlations and their effect on the transport in detail.