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.

On Derivation Languages of a Class of Splicing Systems

Abstract: Derivation languages are language theoretical tools that describe halting derivation processes of a generating device. We consider two types of derivation languages, namely Szilard and control languages for splicing systems where iterated splicing is done in non-uniform way defined by Mitrana, Petre and Rogojin in 2010. The families of Szilard (rules and labels are mapped in a one to one manner) and control (more than one rule can share the same label) languages generated by splicing systems of this type are then compared with the family of languages in the Chomsky hierarchy. We show that context-free languages can be generated as Szilard and control languages and any non-empty context-free language is a morphic image of the Szilard language of this type of system with finite set of rules and axioms. Moreover, we show that these systems with finite set of axioms and regular set of rules are capable of generating any recursively enumerable language as a control language.

Involution Solid and Join codes

Abstract: In this paper we study a generalization of the classical notions of solid codes and commafree codes: involution solid codes (t-solid) and involution join codes (t-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 t-solid codes to be maximal. We show how the concept of t-join can be utilized such that codes that are not themselves t-comma free can be split into a union of subcodes that are t-comma free.

Derivation Languages of Splicing P Systems

Abstract: Labelled splicing P systems are distributed parallel computing models, where sets of strings that evolve by splicing rules are labelled. In this work, we consider labelled splicing systems with the following modifications: (i) The strings in the membranes are present in arbitrary number of copies; (ii) the rules in the regions are finite in number. Results on the language family generated by the labelled splicing system in comparison with the language families of the Chomsky hierarchy, including recursively enumerable languages, are obtained, by involving only either one or two membranes in the P systems considered.

Two-Dimensional Digitized Picture Arrays and Parikh Matrices

Abstract: Parikh matrix mapping or Parikh matrix of a word has been introduced in the literature to count the scattered subwords in the word. Several properties of a Parikh matrix have been extensively investigated. A picture array is a two-dimensional connected digitized rectangular array consisting of a finite number of pixels with each pixel in a cell having a label from a finite alphabet. Here we extend the notion of Parikh matrix of a word to a picture array and associate with it two kinds of Parikh matrices, called row Parikh matrix and column Parikh matrix. Two picture arrays A and B are defined to be M-equivalent if their row Parikh matrices are the same and their column Parikh matrices are the same. This enables to extend the notion of M-ambiguity to a picture array. In the binary and ternary cases, conditions that ensure M-ambiguity are then obtained.

Watson-crick bordered words and their syntactic monoid

Abstract: DNA strands that, mathematically speaking, are finite strings over the alphabet {A, G, C, T} 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 Watson-Crick complementary can bind to each other or to themselves in either intended or unintended ways. One of the structures that is usually undesirable for biocomputation, since it makes the affected DNA string unavailable for future interactions, is the hairpin: If some subsequences of a DNA single string are complementary to each other, the string will bind to itself forming a hairpin-like structure. This paper studies a mathematical formalization of a particular case of hairpins, the Watson-Crick bordered words. A Watson-Crick bordered word is a word with the property that it has a prefix that is Watson-Crick complementary to its suffix. We namely study algebraic properties of Watson-Crick bordered and unbordered words. We also give a complete characterization of...

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.

Abstract: No wonder you activities are, reading will be always needed. It is not only to fulfil the duties that you need to finish in deadline time. Reading will encourage your mind and thoughts. Of course, reading will greatly develop your experiences about everything. Reading molecular biology of the gene is also a way as one of the collective books that gives many advantages. The advantages are not only for you, but for the other peoples with those meaningful benefits.

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.