Length scale dependent elasticity in DNA from coarse-grained and all-atom models
| Autor: | Aderik Voorspoels, Enrico Carlon, Enrico Skoruppa, Jocelyne Vreede |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
Physics
Length scale Quantitative Biology::Biomolecules Base pair FOS: Physical sciences Biomolecules (q-bio.BM) DNA Molecular Dynamics Simulation Condensed Matter - Soft Condensed Matter 01 natural sciences Elasticity 010305 fluids & plasmas chemistry.chemical_compound chemistry Quantitative Biology - Biomolecules FOS: Biological sciences 0103 physical sciences Soft Condensed Matter (cond-mat.soft) Statistical physics DNA Conformations Elasticity (economics) Twist 010306 general physics Base Pairing |
| Popis: | The mechanical properties of DNA are typically described by elastic theories with purely local couplings (on-site models). We discuss and analyze coarse-grained (oxDNA) and all-atom simulations, which indicate that in DNA distal sites are coupled. Hence, off-site models provide a more realistic description of the mechanics of the double helix. We show that off-site interactions are responsible for a length scale dependence of the elasticity, and we develop an analytical framework to estimate bending and torsional persistence lengths in models including these interactions. Our simulations indicate that off-site couplings are particularly strong for certain degrees of freedom, while they are very weak for others. If stiffness parameters obtained from DNA data are used, the theory predicts large length scale dependent effects for torsional fluctuations and a modest effect in bending fluctuations, which is in agreement with experiments. 16 pages, 9 figures; video abstract at https://youtu.be/8FUdFw8IbuY |
| Databáze: | OpenAIRE |
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