2003/12/19 by Alkan Kabakçıoğlu, A. Kabakcioglu, Attilio L. Stella +1 · 11 citations
Biochemistry, Genetics and Molecular Biology · Chemistry · Mathematics · Physics and Astronomy · #Chemistry #Force Microscopy Techniques and Applications #Geometry #Mathematics #Phase (matter) #Phase diagram #Physics #Protein Structure and Dynamics #Pseudoknot #Quantum mechanics #Scaling #Simple (philosophy) #Statistical physics #Theoretical and Computational Physics #Thermodynamics #cond-mat.soft #cond-mat.stat-mech
paper · pdf · doi:10.1103/physreve.70.011802
published in Physical Review E 70(1), 011802 (American Physical Society) · submitted to PRE
arxiv created 2003/12/19 · openalex publication_date 2004/07/20 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/05
After a discussion of the definition and number of pseudoknots, we reconsider the self-attracting homopolymer paying particular attention to the scaling of the pseudoknot number (Npk) at different temperature regimes in two and three dimensions. We find that, although the total number of pseudoknots is extensive at all temperatures, the number of those forming between the two halves of the chain diverges logarithmically at (both dimensions) and below (two dimensions only) the theta temperature. We later introduce a simple model that emphasizes the role of pseudoknot formation during collapse. The resulting phase diagram involves swollen, branched, and collapsed homopolymer phases with transitions between each pair.