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From Sequence to Function through Secondary Structure Kinetics of RNA and DNA


Meruelo, Alejandro Daniel (2006) From Sequence to Function through Secondary Structure Kinetics of RNA and DNA. Senior thesis (Major), California Institute of Technology. doi:10.7907/4bxt-wa89.


A number of efforts to determine function from sequence of RNA and DNA have been made with varying success. Here we study the determination of function from sequence of DNA and RNA through their secondary structure kinetics, specifically the series of transitions between secondary structures. This series of transitions or microscopic structure can be described by a system of ordinary differential equations that can be approximating using balanced truncation to determine the macroscopic structure. By doing so, we have been able to identify signature topological features of microscopic structure and mathematically characterize the corresponding classes of macroscopic structure. Thus we are now able to take large, complex systems, reduce them, and understand their behavior. In the future, we hope to be able to identify small microscopic changes that lead to large macroscopic changes and possibly phasetransition like conditions between secondary states. Ultimately, this may lead to the development of a secondary-structure kinetics theory describing how one or more strands of DNA pair with one another to form different secondary structures and its potential future experimental verification.

Item Type:Thesis (Senior thesis (Major))
Subject Keywords:Physics
Degree Grantor:California Institute of Technology
Division:Physics, Mathematics and Astronomy
Major Option:Physics
Thesis Availability:Withheld
Research Advisor(s):
  • Mabuchi, Hideo
Thesis Committee:
  • None, None
Defense Date:8 May 2006
Record Number:CaltechTHESIS:02132018-142852598
Persistent URL:
Meruelo, Alejandro Daniel0000-0001-6087-1818
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:10718
Deposited By: Joy Painter
Deposited On:13 Feb 2018 23:49
Last Modified:20 May 2020 19:22

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