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The multistrand simulator : stochastic simulation of the kinetics of multiple interacting DNA strands

Citation

Schaeffer, Joseph Malcolm (2012) The multistrand simulator : stochastic simulation of the kinetics of multiple interacting DNA strands. Master's thesis, California Institute of Technology. http://resolver.caltech.edu/CaltechTHESIS:02022012-143934605

Abstract

DNA has been used in vitro as a computational substrate due to programmable base-pairing interactions. This allows the construction of logic gates, self-assembled shapes, motors, walkers and other nanoscale devices comprised of DNA strands. These strands must be carefully designed in order to correctly perform their function, which requires effective models of the DNA system. The thermodynamics of multiple interacting DNA strands is a well-studied model which can make equilibrium predictions on these systems, but many devices operate far from equilibrium. The prediction of large non-equilibrium systems requires the simulation of a kinetics model, as these are both stochastic and computationally difficult to solve in an exact form. We developed the Multistrand kinetics simulator, which extends the previous work by expanding the kinetics model to handle multiple nucleic acid strands, as well as using optimized algorithms in order to speed up the simulations.

Item Type:Thesis (Master's thesis)
Subject Keywords:DNA nanotechnology; nucleic acid folding; stochastic simulation; continuous time Markov process; energy model; kinetics model; secondary structure;
Degree Grantor:California Institute of Technology
Division:Engineering and Applied Science
Major Option:Computer Science
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Winfree, Erik
Thesis Committee:
  • None, None
Defense Date:27 January 2012
Funders:
Funding AgencyGrant Number
National Science FoundationDMS-0506468
National Science FoundationCCF-0832824
Record Number:CaltechTHESIS:02022012-143934605
Persistent URL:http://resolver.caltech.edu/CaltechTHESIS:02022012-143934605
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:6807
Collection:CaltechTHESIS
Deposited By: Joseph Schaeffer
Deposited On:17 Feb 2012 21:38
Last Modified:26 Dec 2012 04:40

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PDF (Master's Thesis: Complete PDF (4Mb)) - Final Version
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PDF (Master's Thesis: Chapters 2-4 (System, Energy Model, Kinetics Model)) - Final Version
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PDF (Master's Thesis: Chapter 5 (The Simulator: Multistrand)) - Final Version
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PDF (Master's Thesis: Chapter 6 (Multistrand: Output and Analysis)) - Final Version
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PDF (Master's Thesis: Appendix A (Data Structures)) - Final Version
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PDF (Master's Thesis: Appendix B (Algorithms)) - Final Version
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PDF (Master's Thesis: Appendix C (Equivalence between Multistrand’s thermodynamics model and the NUPACK thermodynamics model)) - Final Version
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PDF (Master's Thesis: Appendix D (Strand Orderings for Pseudoknot-Free Representations)) - Final Version
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PDF (Master's Thesis: Bibliography) - Final Version
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PDF (Master's Thesis: Front and Introduction) - Final Version
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