Modeling diffusional transport in the interphase cell nucleus
| Autor: | Chen-Xu Wu, Holger Merlitz, Jörg Langowski, Annika Wedemeier |
|---|---|
| Rok vydání: | 2007 |
| Předmět: |
Cell Nucleus
Models Molecular Persistence length Physics Discretization Interphase cell nucleus FOS: Physical sciences General Physics and Astronomy Computational Physics (physics.comp-ph) Random walk Models Biological Chromatin Protein Transport Chain length Models Chemical Biological Physics (physics.bio-ph) Lattice (order) Adjacency list Computer Simulation Physics - Biological Physics Statistical physics Physical and Theoretical Chemistry Physics - Computational Physics Interphase Self-avoiding walk |
| Zdroj: | The Journal of Chemical Physics. 127:045102 |
| ISSN: | 1089-7690 0021-9606 |
| DOI: | 10.1063/1.2753158 |
| Popis: | In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles, a random walk chain model, and a self avoiding random walk chain model with persistence length. By comparing a discrete and a continuous version of the random walk chain model, we demonstrate that lattice discretization does not alter particle diffusion. The influence of the 3D geometry of the fiber network on the particle diffusion is investigated in detail, while varying occupation volume, chain length, persistence length and walker size. It is shown that adjacency of the monomers, the excluded volume effect incorporated in the self avoiding random walk model, and, to a lesser extent, the persistence length, affect particle diffusion. It is demonstrated how the introduction of the effective chain occupancy, which is a convolution of the geometric chain volume with the walker size, eliminates the conformational effects of the network on the diffusion, i.e., when plotting the diffusion coefficient as a function of the effective chain volume, the data fall onto a master curve. 9 pages, 8 figures |
| Databáze: | OpenAIRE |
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