The mechanical and structural properties of dsDNA have been successfully described by models with varying levels of complexity and coarse-graining schemes. Prior work has characterized local stacking/twist effects and force-torque phase diagrams under external constraints. However, the role of base-pairing and torsional elasticity in global morphological transitions remain poorly characterized in the absence of external constraints. Here we investigate the delicate balance required for the strength of base-pairing interactions and the twisting energy to preserve the double-helix structure in a model made up of two semiflexible chains. We found that the model exhibits several distinct morphological phases: flat, random coil, double-helix, and the unwound double-helix. We calculate the Gauss linking number to characterize transitions between these phases.
Macromolecular coil-to-helix transitions simultaneously modify local geometry and persistence length, driving complex changes in overall chain size. Here, we apply the wormlike (persistent) chain model to both coil and helical fragments to examine how the degree of helicity, θ, and average helical fragment length, kh,...
Karthik C Sinha, Alexey A. Gavrilov, Artem M. Rumyantsev· Journal of Chemical Physics· 1 citation
This work presents a minimal coarse-grained molecular dynamics model for the coil-helix transition in polymers. We demonstrate that the addition of a Morse potential to a freely jointed chain with volume and bond potentials is sufficient to reproduce the essential thermodynamic features of the transition. From the simu...
Karthik C Sinha, Alexey A. Gavrilov, Artem M. Rumyantsev· Journal of Chemical Physics· 1 citation
Collagen's triple helix structure is fundamental to the mechanical integrity of bodily tissues, and its stability is vital for optimal physiological function. While the stabilization mechanisms of simple, symmetric collagen homotrimers have been previously studied, the hydration dynamics of native-like collagen heterot...
Anand Balupuri, Dong-Hyun Son, Nam Sook Kang· Biopolymers· 0 citations
The structural feasibility of chain folding within an accepted cellulose-II structure is investigated in this study. We incorporate 3-residue and 5-residue folded glucosyl turns into a cellulose-II fibril crystal model to assess if the dominant structure can be retained. Ten candidate turn models were generated by meta...
Ling-Han Kong, S. J. Eichhorn, Richard A. Bryce· Biomacromolecules· 0 citations
Helical segments in polymer chains are often transient, finite, and dynamically evolving, yet their origin and stability remain incompletely understood. Here, we develop a minimal coarse-grained statistical-mechanical theory that explains how such "living helices" emerge in fluctuating polymer systems. Using a three-st...
Biman Bagchi· Journal of Chemical Physics· 0 citations
Abstract Many biomolecules and their synthetic counterparts preferentially assemble into double-helices with a preferred handedness and parallelism, such as all-antiparallel, right-handed double-helical polymorphs of DNA and RNA favored under ambient conditions by Watson–Crick duplexing. We analyze knots formed by doub...
S. Hyde, M. E. Evans, Callum A. R. Metzke et al.· PNAS Nexus· 0 citations
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