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Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands


Schaeffer, Joseph Malcolm (2013) Stochastic Simulation of the Kinetics of Multiple Interacting Nucleic Acid Strands. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/JEBY-6X69.


DNA nanotechnology is an emerging field which utilizes the unique structural properties of nucleic acids in order to build nanoscale devices, such as logic gates, motors, walkers, and algorithmic structures. Predicting the structure and interactions of a DNA device requires good modeling of both the thermodynamics and the kinetics of the DNA strands within the system. The kinetics of a set of DNA strands can be modeled as a continuous time Markov process through the state space of all secondary structures. The primary means of exploring the kinetics of a DNA system is by simulating trajectories through the state space and aggregating data over many such trajectories.

We expand on previous work by extending the thermodynamics and kinetics models to handle multiple strands in a fixed volume, and show that the new models are consistent with previous models. We developed data structures and algorithms that allow us to take advantage of local properties of secondary structure, improving the efficiency of the simulator so that we can handle larger systems. The new kinetic parameters in our model were calibrated by analyzing simulator results on experimental systems that measure basic kinetic rates of various processes. Finally, we apply the new simulator to explore a case study on toehold-mediated four-way branch migration.

Item Type:Thesis (Dissertation (Ph.D.))
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:
  • Winfree, Erik (chair)
  • Pierce, Niles A.
  • Umans, Christopher M.
  • Barr, Alan H.
  • Bruck, Jehoshua
Defense Date:28 September 2012
Funding AgencyGrant Number
National Science FoundationDMS-0506468
National Science FoundationCCF-0832824
Gordon and Betty Moore FoundationCaltech Programmable Molecular Technology Initiative
Record Number:CaltechTHESIS:02042013-110332492
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:7460
Deposited By: Joseph Schaeffer
Deposited On:14 Feb 2013 22:07
Last Modified:03 Oct 2019 23:58

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