Kalpana Mahalingam

Bio: Kalpana Mahalingam is an academic researcher from Indian Institute of Technology Madras. The author has contributed to research in topics: Palindrome & Combinatorics on words. The author has an hindex of 11, co-authored 62 publications receiving 436 citations. Previous affiliations of Kalpana Mahalingam include University of Western Ontario & University of South Florida.

Watson-Crick Jumping Finite Automata

Abstract: In this paper, we introduce a new automata called Watson-Crick jumping finite automata, working on tapes which are double stranded sequences of symbols, similar to that of a Watson-Crick automata. This automata scans the double stranded sequence in a discontinuous manner (i.e.) after reading a double stranded string, the automata can jump over some subsequence and continue scanning, depending on the rule. We define some variants of such automata and compare the languages accepted by these variants with the language classes in Chomsky hierarchy. We also investigate some closure properties.

On the Maximum Number of Distinct Palindromic Sub-arrays

Abstract: We investigate the maximum number of distinct palindromic sub-arrays in a two-dimensional finite word over a finite alphabet \(\varSigma \). For any finite array in \(\varSigma ^{m\times n}\), we find an upper bound for the number of distinct palindromic sub-arrays and improve it by giving a tight bound on the maximum number of distinct palindromes in an array in \(\varSigma ^{2\times n}\) for \(|\varSigma |=2\). We then, propose a better upper bound for any finite array in \(\varSigma ^{m\times n}\).

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA

Abstract: Digital production, transmission and storage have revolutionized how we access and use information but have also made archiving an increasingly complex task that requires active, continuing maintenance of digital media. This challenge has focused some interest on DNA as an attractive target for information storage because of its capacity for high-density information encoding, longevity under easily achieved conditions and proven track record as an information bearer. Previous DNA-based information storage approaches have encoded only trivial amounts of information or were not amenable to scaling-up, and used no robust error-correction and lacked examination of their cost-efficiency for large-scale information archival. Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information of 5.2 × 10(6) bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade.

Molecular Biology of the Gene.

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Discrete Applied Mathematics

Abstract: : Significant progress has been made with solution of location problems and in preprocessing and decomposition for discrete optimization. There has also been research on the application of techniques from combinational optimization to nonlinear problems.

Computation in Living Cells: Gene Assembly in Ciliates

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Watson---Crick palindromes in DNA computing

Abstract: 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 catenation and insertion. We obtain some properties that link the WK palindromes to classical notions such as that of primitive words. For example we show that the set of WK-palindromic words that cannot be written as the product of two nonempty WK-palindromes equals the set of primitive WK-palindromes. We also investigate various simultaneous Watson---Crick conjugate equations of words and show that the equations have, in most cases, only Watson---Crick palindromic solutions. Our results hold for more general functions, such as arbitrary morphic and antimorphic involutions.