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Gel electrophoresis allows one to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots, being more compact, drift faster than simpler knots. Recent experiments have shown that the drift velocity dependence on the knot type is inverted when changing from low to high electric fields. We present a computer simulation on a lattice of...
Purpose: Trying to explain differences in gel migration of circular DNA molecules closed into various type of knots we related them to properties of ideal geometric forms of knots.Methods: The [ldquo ]ideal[rdquo ] geometric form of a given knot is defined as the shape of the corresponding knot made out of a tube with uniform thickness, whereby the volume of the tube reaches maximum for its fixed...
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