Characterizing DNA Bonding via Trajectories.

Dr. Michael Domaratzki Computer Science Acadia University Wolfville, NS

DEPARTMENT SEMINAR DATE: Friday, March 3, 2006 TIME: 3:30 pm PLACE: Thorvaldson 271 *** Everyone is welcome ***

Abstract

The design of DNA code words is an important challenge in DNA computing. The ability of two strands to bond forms the basis for DNA computing and therefore the ability to specify the bonding that should and should not occur in a set of single-stranded DNA is crucial. This specification of bonding patterns should be done in as general a way as possible to encourage re-usability of results.

In this talk, we describe the use of DNA trajectories as a specification for the bonding between DNA strands. We consider decidability questions--can we decide whether a set of DNA strands satisfies a specification?--as well as problems of equivalence. This last problem leads to interesting formal characterizations of the concepts of rotation of bonds and of weakening of bonding between strands.

About the speaker

Mike Domaratzki received his Ph.D. in Computer Science from Queen's University in 2004. He also holds M.Math (2001) and B.Math (1999) degrees from the University of Waterloo. His research interests include molecular computing, theory of computing, bio-informatics and enumeration. Mike is currently an Assistant Professor in the Jodrey School of Computer Science at Acadia University in Wolfville, NS.

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