Physical Sciences and Mathematics Commons^™

Properties Of Graphs Used To Model Dna Recombination, Ryan Arredondo

USF Tampa Graduate Theses and Dissertations

A model for DNA recombination uses 4-valent rigid vertex graphs,

called assembly graphs. An assembly graph,

similarly to the projection of knots, can be associated with an

unsigned Gauss code, or double occurrence word.

We define biologically motivated reductions that act on double

occurrence words and, in turn, on their associated assembly graphs. For

every double occurrence word w there is a sequence of reduction

operations that may be applied to w so that what remains is the

empty word, [epsilon]. Then the nesting index of a word w,

denoted by NI(w), is defined to to be …