Gallery of studied systems

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

DNA systems

• 
  DNA nanotweezers
• 
  Burnt bridges motor
• 
  Two-footed DNA walker
• 
  Single stranded pulling
• 
  Kissing hairpins (studied with the average model and the sequence-dependent model)
• 
  Loop sequence effects on melting temperatures of hairpins
• 
  Heterogeneous stacking transition in single strands
• 
  Duplex fraying
• 
  Biophysics of strand displacement
• 
  Overstretching
• 
  DNA Cruciforms
• 
  Hybridization kinetics
• 
  Plectonemes
• 
  Gels made of tetravalent DNA nanostars
• 
  Nematic phases formed by short DNA duplexes

RNA systems

• 
  Pseudoknot folding thermodynamics
• 
  Kissing complex
• 
  Nanoring
• 
  Hairpin unzipping