This collection includes most of the ASU Theses and Dissertations from 2011 to present. ASU Theses and Dissertations are available in downloadable PDF format; however, a small percentage of items are under embargo. Information about the dissertations/theses includes degree information, committee members, an abstract, supporting data or media.
In addition to the electronic theses found in the ASU Digital Repository, ASU Theses and Dissertations can be found in the ASU Library Catalog.
Dissertations and Theses granted by Arizona State University are archived and made available through a joint effort of the ASU Graduate College and the ASU Libraries. For more information or questions about this collection contact or visit the Digital Repository ETD Library Guide or contact the ASU Graduate College at gradformat@asu.edu.
Nucleic acid nanotechnology is a field of nanoscale engineering where the sequences of deoxyribonucleicacid (DNA) and ribonucleic acid (RNA) molecules are carefully designed to create self–assembled nanostructures with higher spatial resolution than is available to top–down fabrication methods. In the 40 year history
of the field, the structures created have scaled…
Nucleic acid nanotechnology is a field of nanoscale engineering where the sequences of deoxyribonucleicacid (DNA) and ribonucleic acid (RNA) molecules are carefully designed to create self–assembled nanostructures with higher spatial resolution than is available to top–down fabrication methods. In the 40 year history
of the field, the structures created have scaled from small tile–like structures constructed from a few hundred
individual nucleotides to micron–scale structures assembled from millions of nucleotides using the technique
of “DNA origami”. One of the key drivers of advancement in any modern engineering field is the parallel
development of software which facilitates the design of components and performs in silico simulation of the
target structure to determine its structural properties, dynamic behavior, and identify defects. For nucleic acid
nanotechnology, the design software CaDNAno and simulation software oxDNA are the most popular choices
for design and simulation, respectively. In this dissertation I will present my work on the oxDNA software
ecosystem, including an analysis toolkit, a web–based graphical interface, and a new molecular visualization
tool which doubles as a free–form design editor that covers some of the weaknesses of CaDNAno’s lattice–based design paradigm. Finally, as a demonstration of the utility of these new tools I show oxDNA simulation
and subsequent analysis of a nanoscale leaf–spring engine capable of converting chemical energy into dynamic motion. OxDNA simulations were used to investigate the effects of design choices on the behavior of
the system and rationalize experimental results.
