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- Natasa Jonoska, Kalpana Mahalingam
- DNA
- 2003

- Lila Kari, Kalpana Mahalingam
- DNA
- 2006

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… (More)

- Natasa Jonoska, David Kephart, Kalpana Mahalingam
- GECCO Late Breaking Papers
- 2002

- Lila Kari, Kalpana Mahalingam
- DNA
- 2007

This paper is a theoretical study of notions in combinatorics of words motivated by information being encoded as DNA strands in DNA computing. We generalize the classical notions of conjugacy and commutativity of words to incorporate the notion of an involution function, a formalization of the Watson-Crick complementarity of DNA single-strands. We define… (More)

- Lila Kari, Kalpana Mahalingam
- Natural Computing
- 2009

This paper provides an overview of existing approaches to encoding information on DNA strands for biocomputing, with a focus on the notion of Watson–Crick (WK) palindromes. We obtain a closed form for, as well as several properties of WK palindromes: The set of WK-palindromes is dense, context-free, but not regular, and is in general not closed under… (More)

- Natasa Jonoska, Kalpana Mahalingam, Junghuei Chen
- Natural Computing
- 2004

For an involution θ : Σ* → Σ* over a finite alphabet Σ we consider involution codes: θ-infix, θ-comma-free, θ-k -codes and θ-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… (More)

- Natasa Jonoska, Lila Kari, Kalpana Mahalingam
- Fundam. Inform.
- 2006

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… (More)

- BORDERED WORDS, Lila Kari, Kalpana Mahalingam
- 2006

In this paper we study a generalization of the classical notions of bordered and unbordered words. A nonempty word is called bordered if it has a proper prefix which is also a suffix of that word. A nonempty word is called unbordered if it is not bordered. We extend the notion of bordered and unbordered words to incorporate the notion of an involution… (More)

- Daniela Genova, Kalpana Mahalingam
- TPNC
- 2012

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… (More)

- Lila Kari, Kalpana Mahalingam
- Int. J. Found. Comput. Sci.
- 2007

In this paper we study a generalization of the classical notions of bordered and unbordered words, motivated by DNA computing. DNA strands can be viewed as finite strings over the alphabet {A, G, C, T}, and are used in DNA computing to encode information. Due to the fact that A is Watson-Crick complementary to T and G to C, DNA single strands that are… (More)