Joseph M. Schaeffer

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Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representation and(More)
Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple(More)
All Rights Reserved iii Acknowledgements Thanks to my advisor Erik Winfree, for his enthusiasm, expertise, and encouragement. The models presented here are due in a large part to helpful discussions with Niles Pierce, Loving, did summer research projects based on Multistrand and in the process helped build and shape the simulator. There are many people who(More)
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