Showing papers by "Kalpana Mahalingam published in 2006"
05 Jun 2006
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.
Abstract: One of the main research topics in DNA computing is associated with the design of information encoding single or double stranded DNA strands that are “suitable” for computation. Double stranded or partially double stranded DNA occurs as a result of binding between complementary DNA single strands (A is complementary to T and C is complementary to G). This paper continues the study of the algebraic properties of DNA word sets that ensure that certain undesirable bonds do not occur. We formalize and investigate such properties of sets of sequences, e.g., where no complement of a sequence is a prefix or suffix of another sequence or no complement of a concatenation of n sequences is a subword of the concatenation of n + 1 sequences. The sets of code words that satisfy the above properties are called θ – prefix, θ-suffix and θ-intercode respectively, where θ is the formalization of the Watson-Crick complementarity. Lastly we develop certain methods of constructing such sets of DNA words with good properties and compute their informational entropy.
23 citations
Journal Article•
TL;DR: This paper studies a generalization of the classical notions of solid codes and comma-free codes: involution solid codes (θ-solid) and involution join codes ( θ-join), motivated by DNA strand design.
Abstract: In this paper we study a generalization of the classical notions of solid codes and comma-free codes: involution solid codes (0-solid) and involution join codes (0-join). These notions are motivated by DNA strand design where Watson-Crick complementarity can be formalized as an antimorphic involution. We investigate closure properties of these codes, as well as necessary conditions for 0-solid codes to be maximal. We show how the concept of 0-join can be utilized such that codes that are not themselves θ-comma free can be split into a union of subcodes that are θ-comma free.
9 citations
26 Jun 2006
TL;DR: In this article, a generalization of the classical notions of solid codes and comma-free codes, called involution solid codes (θ-solid) and involution join codes (ε-join), was proposed.
Abstract: In this paper we study a generalization of the classical notions of solid codes and comma-free codes: involution solid codes (θ-solid) and involution join codes (θ-join). These notions are motivated by DNA strand design where Watson-Crick complementarity can be formalized as an antimorphic involution. We investigate closure properties of these codes, as well as necessary conditions for θ-solid codes to be maximal. We show how the concept of θ-join can be utilized such that codes that are not themselves θ-comma free can be split into a union of subcodes that are θ-comma free.
3 citations