Knot spectrum of confined self-avoiding rings(Knots and soft-matter physics: Topology of polymers and related topics in physics, mathematics and biology)

Abstract

Advanced stochastic sampling techniques are used to probe the configuration space of self-avoiding flexible rings subject to spatial confinement. The sampled ring conformations are next processed by algorithms that exactly classify knots in rings that are not excessively confined. The physical parameters of the rings, i.e. contour length, bending rigidity and steric hindrance, are properly chosen to mimic the properties of DNA of the P4 bacteriophage, while the radius of the smallest sphere used to confine the model rings is about 2.5 times larger than the P4 capsid radius. By comparing the computed knot spectrum with the P4 one we establish that the consideredmodel correctly predicts an increase of the occurrence of chiral knots with progressive confinement but does not account for the bias of torus versus twist knots observed in P4 experiments.