Computational exploration of helical polymer geometry, folding, and structural stability.
Williams, Matthew John
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This computational study aims at a better understanding of structure formation processes in helical polymers. For this purpose, parallel tempering Monte Carlo simulations were preformed using a generic coarse-grained model. Structural conformations exhibit helical order with tertiary structural organizations including single helices, multiple helical segments organized into bundles, and disorganized helical arrangements. We compare helical structure formation for flexible and semiflexible polymers. For each model, we analyze low-energy structural geometries, structural stability, and folding dynamics. This exploration lends insight into the restricted flexibility of biological polymers such as double-stranded DNA and proteins. Additionally, the influence of substrate adsorption on helical structures and stability is investigated in detail.