Journal ArticleDOI
Involution codes: with application to DNA coded languages
TLDR
This work investigates conditions under which both X and X+ are same type of involutions codes, and general methods for generating such involution codes are given.Abstract:
For an involution ? : ?* ? ?* over a finite alphabet ? we consider involution codes: ?-infix, ?-comma-free, ?-k -codes and ?-subword-k-codes. These codes arise from questions on DNA strand design. We investigate conditions under which both X and X+ are same type of involution codes. General methods for generating such involution codes are given. The information capacity of these codes show to be optimized in most cases. A specific set of these codes was chosen for experimental testing and the results of these experiments are presented.read more
Citations
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Journal ArticleDOI
Watson---Crick palindromes in DNA computing
Lila Kari,Kalpana Mahalingam +1 more
TL;DR: An overview of existing approaches to encoding information on DNA strands for biocomputing, with a focus on the notion of Watson–Crick (WK) palindromes, and obtains a closed form for, as well as several properties of WK palINDromes.
Book ChapterDOI
DNA codes and their properties
Lila Kari,Kalpana Mahalingam +1 more
TL;DR: This paper continues the study of the algebraic properties of DNA word sets that ensure that certain undesirable bonds do not occur and develops certain methods of constructing such sets of DNA words with good properties and compute their informational entropy.
Journal ArticleDOI
Involutively bordered words
Lila Kari,Kalpana Mahalingam +1 more
TL;DR: This paper studies a mathematical formalization of a particular case of hairpins, the Watson-Crick bordered words, a word with the property that it has a prefix that is Watson- Crick complementary to its suffix.
Journal ArticleDOI
The syntactic monoid of hairpin-free languages
TL;DR: This paper gives a complete characterization of the syntactic monoid of the language consisting of all hairpin-free words over a given alphabet and illustrates it with an example using the DNA alphabet.
Journal ArticleDOI
On pseudoknot-bordered words and their properties
Lila Kari,Shinnosuke Seki +1 more
TL;DR: Pseudo-bordered words are studied, a mathematical formalization of pseudoknot-like inter- and intra-molecular structures motivated by biomolecular computing that model DNA or RNA strands that will be free of secondary structures.
References
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Book
An Introduction to Symbolic Dynamics and Coding
Douglas Lind,Brian Marcus +1 more
TL;DR: Requiring only a undergraduate knowledge of linear algebra, this first general textbook includes over 500 exercises that explore symbolic dynamics as a method to study general dynamical systems.
Book
DNA Computing: New Computing Paradigms
TL;DR: This book starts with an introduction to DNA computing, exploring the power of complementarity, the basics of biochemistry, and language and computation theory, and brings the reader to the most advanced theories develop thus far in this emerging research area.
Journal ArticleDOI
Formal language theory and DNA: an analysis of the generative capacity of specific recombinant behaviors.
TL;DR: This study initiates the formal analysis of the generative power of recombinational behaviors in general by means of a new generative formalism called a splicing system and a significant subclass of these languages, which are shown to coincide with a class of regular languages which have been previously studied in other contexts: the strictly locally testable languages.
Journal ArticleDOI
Solution of a 20-Variable 3-SAT Problem on a DNA Computer
Ravinderjit S. Braich,Nickolas Chelyapov,Cliff Johnson,Paul W. K. Rothemund,Leonard M. Adleman +4 more
TL;DR: A 20-variable instance of the NP-complete three-satisfiability (3-SAT) problem was solved on a simple DNA computer and may be the largest yet solved by nonelectronic means.