Molecular dynamics studies of knotted polymers

Molecular dynamics calculations have been used to explore the influence of knots on the strength of a polymer strand. In particular, the mechanism of breaking 3₁, 4₁, 5₁, and 5₂ prime knots has been studied using two very different models to represent the polymer: (1) the generic coarse-grained (CG) bead model of polymer physics and (2) a state-of-the-art machine learned atomistic neural network (NN) potential for polyethylene derived from electronic structure calculations. While there is a broad overall agreement between the results on the influence of the pulling rate on chain rupture based on the CG and atomistic NN models, for the simple 3₁ and 4₁ knots, significant differences are found for the more complex 5₁ and 5₂ knots. Notably, in the latter case, the NN model more frequently predicts that these knots can break not only at the crossings at the entrance/exit but also at one of the central crossing points. The relative smoothness of the CG potential energy surface also leads to stabilization of tighter knots compared to the more realistic NN model.