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Improving Reliability in DNA based Computations with Applications to Cryptography

Mantha, Anusha
http://rave.ohiolink.edu/etdc/view?acc_num=ucin1352992351

Abstract Details

2012, MS, University of Cincinnati, Engineering and Applied Science: Computer Engineering.
DNA computing has become an attractive alternative to traditional computing techniques due to the large storage capacity of DNA, massive parallelism and energy efficiency of the computations. However, since DNA computing is based on bio-molecular reactions, it is not error free. One of the main sources of these errors is false hybridizations between unintended sequences during the computation process. An efficient way to minimize these errors is through designing error-resistant DNA sequences. The DNA encoding problem is the design of DNA sequences in such a way that every DNA sequence hybridizes with its own complementary sequence during the computation process. In this thesis, the DNA encoding problem has been studied and approached using the simulated annealing algorithm. Several combinatorial constraints have been considered to optimize the DNA sequences so that they are resistant to false hybridizations during the computations. A cost function which captures the DNA design requirements has been developed and minimized using simulated annealing algorithm. Also, application of DNA computations to the field of cryptography has been studied. A new cryptographic algorithm based on linear self-assembly of DNA has been proposed in which the rate of hybridization errors could be controlled using the error-resistant DNA sequences generated using the simulated annealing algorithm in this work. A simulation framework to simulate the DNA cryptography algorithms has been developed using an object oriented approach. The DNA self assembly based cryptography algorithm developed in this work and an existing DNA cryptography algorithm based on polymerase chain reaction have been simulated and compared in terms of the implementation time complexity.
Carla Purdy, PhD (Committee Chair)
Raj Bhatnagar, PhD (Committee Member)
Wen Ben Jone, PhD (Committee Member)
99 p.
Computer Engineering

Recommended Citations

Citations

  • Mantha, A. (2012). Improving Reliability in DNA based Computations with Applications to Cryptography [Master's thesis, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1352992351

    APA Style (7th edition)

  • Mantha, Anusha. Improving Reliability in DNA based Computations with Applications to Cryptography. 2012. University of Cincinnati, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin1352992351.

    MLA Style (8th edition)

  • Mantha, Anusha. "Improving Reliability in DNA based Computations with Applications to Cryptography." Master's thesis, University of Cincinnati, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1352992351

    Chicago Manual of Style (17th edition)

ucin1352992351
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© 2012, all rights reserved.
This open access ETD is published by University of Cincinnati and OhioLINK.