2024/02/15 by Wolfhard Janke, Janke, Wolfhard, Suman Majumder +5
Engineering · #Advanced Theoretical and Applied Studies in Material Sciences and Geometry #FOS: Physical sciences #Soft Condensed Matter (cond-mat.soft)
paper · pdf · doi:10.48550/arxiv.2402.10147
openalex publication_date 2024/02/15 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that cover the whole range from flexible to stiff by conducting extensive replica-exchange Monte Carlo computer simulations. In the data analysis we focus on knotted conformations whose stability is shown to depend on the ratio rb/r\rm min with rb denoting the equilibrium bond length and r\rm min the distance of the strongest nonbonded interactions. For both models, our results provide evidence that at low temperatures for rb/r\rm min outside a small range around unity one always encounters knots as generic stable phases along with the usual frozen and bent-like structures. By varying the bending stiffness, we observe rather strong first-order-like structural transitions between the coexisting phases characterized by these geometrically different motifs. Through analyses of the energy distributions close to the transition point, we present exploratory estimates of the free-energy barriers between the coexisting phases.