Knots in open Polymers

• W. Humphrey, A. Dalke and K. Schulten, Molec. Graphics 14, 33-38 (1996). [VMD (Visual Molecular Dynamics)]

Qualitative results for polymers in   coil (swollen),   globule (compact),  and   confined  sates.

• Knots are rare in the swollen phase (1% for 3000 CH2)
  • but common in a dense phases (80% for 3000 CH2)  [supporting data]
• Knots are tight in the swollen phase
  • but loose in a dense phases   [supporting data]

Biopolymers:

• Knots are rare for DNA in good solvent  (0.5%-4% for 10000 base pairs)
• Knots are also rare in globular proteins   (~1% - 230/24937 in a sampling of PDB structures)
  • The most interesting new knot we found is a 52  for the protein Ubiquitin Hydrolase

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