  Recent experiments demonstrated that knots in single DNA strands can be
formed by hydrodynamic compression in a nanochannel. In this letter, we further
elucidate the underlying molecular mechanisms by carrying out a compression
experiment in silico, where an equilibrated coarse-grained double-stranded DNA
confined in a square channel is pushed by a piston. The probability of forming
knots is a non-monotonic function of the persistence length and can be enhanced
significantly by increasing the piston speed. Under compression, knots are
abundant and delocalized due to a backfolding mechanism from which
chain-spanning loops emerge, while knots are less frequent and only weakly
localized in equilibrium. Our in silico study thus provides insights into the
formation, origin and control of DNA knots in nanopores.
