Pseudoknots in a Homopolymer

Details Pseudoknots in a Homopolymer Pseudoknots in a Homopolymer

2003-12-19

arxiv.org/abs/cond-mat/0312515v1

Phys. Rev. E 70, 011802 (2004)

Physics

Condensed Matter

Statistical Mechanics

submitted to PRE

Scientific paper

10.1103/PhysRevE.70.011802

After a discussion of the definition and number of pseudoknots, we reconsider the self-attracting homopolymer paying particular attention to the scaling of the number of pseudoknots at different temperature regimes in two and three dimensions. Although the total number of pseudoknots is extensive at all temperatures, we find that the number of pseudoknots forming between the two halves of the chain diverges logarithmically at (in both dimensions) and below (in 2d only) the theta-temparature. We later introduce a simple model that is sensitive to pseudoknot formation during collapse. The resulting phase diagram involves swollen, branched and collapsed homopolymer phases with transitions between each pair.

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