Gallery of studied systems

The systems studied with the oxDNA or oxRNA model with the links to the respective papers provided below:

DNA systems

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  DNA nanotweezers

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  Burnt bridges motor

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  Two-footed DNA walker

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  Single stranded pulling

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  Kissing hairpins (studied with the average model and the sequence-dependent model)

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  Loop sequence effects on melting temperatures of hairpins

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  Heterogeneous stacking transition in single strands

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  Duplex fraying

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  Biophysics of strand displacement

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  Overstretching

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  DNA Cruciforms

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  Hybridization kinetics

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  Plectonemes

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  Gels made of tetravalent DNA nanostars

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  Nematic phases formed by short DNA duplexes

RNA systems

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  Pseudoknot folding thermodynamics

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  Kissing complex

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  Nanoring

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  Hairpin unzipping