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arXiv · 1401.5932

Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects

Jaeoh Shin·Andrey G Cherstvy·Ralf Metzler
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Abstract

During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the dynamics and statistical behaviour of two flexible ring polymers in the presence of cylindrical confinement and crowding molecules. From extensive computer simulations we determine the degree of ring-ring overlap and the number of inter-monomer contacts for varying volume fractions $\phi$ of crowders. We also examine the entropic de-mixing of polymer rings in the presence of mobile crowders and determine the characteristic times of the internal polymer dynamics. Effects of the ring length on ring-ring overlap are also analysed. In particular, on systematic variation of the fraction of crowding molecules a $(1-\phi)$-scaling is found for the ring-ring overlap length along the cylinder axis, and a non-monotonic dependence of the 3D ring-ring contact number is predicted. Our results help to rationalise the implications of macromolecular crowding for circular DNA molecules in confined spaces inside bacteria as well as in localised cellular compartments inside eukaryotic cells.

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Jaeoh Shin, Andrey G Cherstvy, Ralf Metzler. 2014-01-23. Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects. https://doi.org/10.1088/1367-2630/16/5/053047

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