6533b870fe1ef96bd12d04fe
RESEARCH PRODUCT
Entropic Interactions between Two Knots on a Semiflexible Polymer.
Benjamin TrefzPeter VirnauFlorian C. RiegerJonathan Tammo SiebertStefanie StalterDavid Richardsubject
0301 basic medicinePolymers and PlasticsknotsThermal fluctuationsNanotechnology01 natural sciencesString (physics)Microscopic scaleArticlelcsh:QD241-44103 medical and health scienceschemistry.chemical_compoundKnot (unit)lcsh:Organic chemistry0103 physical sciences010306 general physicsTrefoilchemistry.chemical_classificationQuantitative Biology::Biomoleculesfree energy barriersStrain (chemistry)General ChemistryPolymerDNA030104 developmental biologyMonomerchemistryChemical physicsknots; DNA; free energy barriersdescription
Two knots on a string can either be separated or intertwined, and may even pass through each other. At the microscopic scale, such transitions may occur spontaneously, driven by thermal fluctuations, and can be associated with a topological free energy barrier. In this manuscript, we study the respective location of a trefoil ( 3 1 ) and a figure-eight ( 4 1 ) knot on a semiflexible polymer, which is parameterized to model dsDNA in physiological conditions. Two cases are considered: first, end monomers are grafted to two confining walls of varying distance. Free energy profiles and transition barriers are then compared to a subset of free chains, which contain exactly one 3 1 and one 4 1 knot. For the latter, we observe a small preference to form an intertwined state, which can be associated with an effective entropic attraction. However, the respective free energy barrier is so small that we expect transition events to occur spontaneously and frequently in polymers and DNA, which are highly knotted for sufficient strain lengths.
| year | journal | country | edition | language |
|---|---|---|---|---|
| 2017-02-01 | Polymers |