Generating DNA code words using forbidding and enforcing systems
Document Type
Conference Proceeding
Publication Date
11-6-2012
Subject Area
ARRAY(0x55a3f50159e0)
Abstract
Research in DNA computing was initiated by Leonard Adleman in 1994 when he solved an instance of an NP-complete problem solely by molecules. DNA code words arose in the attempt to avoid unwanted hybridizations of DNA strands for DNA based computations. Given a set of constraints, generating a large set of DNA strands that satisfy the constraints is an important problem in DNA computing. On the other hand, motivated by the non-determinism of molecular reactions, A. Ehrenfeucht and G. Rozenberg introduced forbidding and enforcing systems (fe-systems) as a model of computation that defines classes of languages based on two sets of constraints. We attempt to establish a connection between these two areas of research in natural computing by characterizing a variety of DNA codes that avoid certain types of cross hybridizations by fe-systems. We show that one fe-system can generate the entire class of DNA codes of a certain property, for example θ-k-codes, and confirm some properties of DNA codes through fe-systems. We generalize by fe-systems some known methods of generating good DNA code words which have been tested experimentally. © 2012 Springer-Verlag.
Publication Title
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume
7505 LNCS
First Page
147
Last Page
160
Digital Object Identifier (DOI)
10.1007/978-3-642-33860-1_13
ISSN
03029743
E-ISSN
16113349
ISBN
9783642338595
Citation Information
Genova, & Mahalingam, K. (n.d.). Generating DNA Code Words Using Forbidding and Enforcing Systems. In Theory and Practice of Natural Computing (pp. 147–160). Springer Berlin Heidelberg. https://doi.org/10.1007/978-3-642-33860-1_13