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Our model consists of an unstructured knotted chain segment enclosed by two -hairpins. A force is applied at one end of the chain causing its translocation through a cylindrical pore of radius and length .
The time dependence of the position of the leading chain end measured along the pore axis for several translocation trajectories. The pore entrance corresponds to . The values of the force used are , 72, 90, and for the trajectories with no knot, and with the , , and knots, respectively.
An example of a translocation trajectory for a chain containing a knot: The time dependence of the position of the leading chain end and snapshots of the protein structure at different times.
The force dependence of the translocation rate (defined as the inverse mean translocation time). The straight lines are linear fits of the low-force data.
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