Theses and Dissertations

Date of Award


Document Type


Degree Name

Master of Science (MS)



First Advisor

Dr. Andreas Hanke

Second Advisor

Dr. Ahmed Touhami

Third Advisor

Dr. Hyeongjun Kim


Denaturation of DNA means separation of dsDNA into ssDNA due to the breaking of hydrogen bond by the application of heat or another mechanical method to carry out the processes like translation,transcription, and replication. Single-molecule DNA stretching experiments displayed a force-induced transition at a force of 65pN for long dsDNA molecules. In these experiments, double stranded DNA molecules are stretched by a force applied to opposite ends of the DNA, e.g., in anatomic force microscope or an optical tweezers instrument. Here we study the thermal and force-induced denaturation of the helicoidal DNA bubble-in-the middle sequence by Monte-Carlo simulations technique. We applied periodic boundary conditions to avoid a large number of opening at the ends of the DNA molecules. Our goal is to quantitatively predict DNA melting curves for short DNA (10-100 sequence of base pairs) and to show that statistical physics can be used to understand the stretching behavior of short DNA oligomer. We compare the results of our simulations with the previously published experimental result for both thermal and mechanical DNA stretching.


Copyright 2019 Pawan Kumar Thapaliya. All Rights Reserved.

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