Improving Reliability in DNA based Computations with Applications to Cryptography

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.

Name thesis:degree_name

MS

Level thesis:degree_level

masters

Discipline thesis:degree_discipline

Engineering and Applied Science: Computer Engineering

Grantor dc:publisher

University of Cincinnati

Year dc:date

2012

Author dc:creator

• Mantha, Anusha

Contributors dc:contributor

• Purdy, Carla

• Computer Engineering

Statement dc:rights

• unrestricted
• This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws.

Language dc:language

English

Repository record dc:identifier

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

OAI identifier oai:identifier

oai:etd.ohiolink.edu:ucin1352992351