Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore

Abstract

The advent of solid state nanodevices allows for interrogating the physico-chemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been recently characterized by theoretical and computational studies of model polymer chains free from self-entanglement. However, sufficiently long equilibrated chains are necessarily knotted. The impact of such topological "defects" on the translocation process is largely unexplored, and is addressed in this study. By using Brownian dynamics simulations on a coarse-grained polyelectrolyte model we show that knots, despite being trapped at the pore entrance, do not "per se" cause the translocation process to jam. Rather, knots introduce an effective friction that increases with the applied force, and practically halts the translocation above a threshold force. The predicted dynamical crossover, which is experimentally verifiable, is of relevance in applicative contexts, such as DNA nanopore sequencing.

6 pages; 7 figures

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• Chirality modifies the interaction between knots
• On the factorization of composite polymer knots into separated prime components
• A principle for ideal torus knots
• Variational autoencoders understand knot topology
• Knotting of linear DNA in nano-slits and nano-channels: a numerical study