Paper Type

Master's Thesis


College of Arts and Sciences

Degree Name

Master of Science in Mathematical Sciences (MS)


Mathematics & Statistics

NACO controlled Corporate Body

University of North Florida. Department of Mathematics and Statistics

First Advisor

Dr. Daniela Genova

Second Advisor

Dr. Michelle DeDeo

Third Advisor

Dr. Jae-Ho Lee

Department Chair

Dr. Richard Patterson

College Dean

Dr. George Rainbolt


Characterizing languages D that are maximal with the property that D* ⊆ S is an important problem in formal language theory with applications to coding theory and DNA codewords. Given a finite set of words of a fixed length S, the constraint, we consider its subword closure, S, the set of words whose subwords of that fixed length are all in the constraint. We investigate these maximal languages and present characterizations for them. These characterizations use strongly connected components of deterministic finite automata and lead to polynomial time algorithms for generating such languages. We prove that the subword closure S is strictly locally testable. Finally, we discuss applications to coding theory and encoding arbitrary blocks of information on DNA strands. This leads to very important applications in DNA codewords designed to obtain bond-free languages, which have been experimentally confirmed.