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Molecules Computing: Self-Assembled Nanostructures, Molecular Automata,and Chemical Reaction Networks


Soloveichik, David (2008) Molecules Computing: Self-Assembled Nanostructures, Molecular Automata,and Chemical Reaction Networks. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/ZGE0-AF38.


Many endeavors of molecular-level engineering either rely on biological material such as nucleic acids and restriction enzymes, or are inspired by biological processes such as self-assembly or cellular regulatory networks. This thesis develops theories on three such topics: self-assembled nanostructures, molecular automata, and chemical reaction networks. The abstractions and underlying methods of the theories presented herein are based on computer science and include Turing machines and circuits. Toward engineering self-assembled nanostructures, we create a theory of scale-free shapes in which the complexity of their self-assembly is connected to the shapes' descriptional complexity. Further, we study patterns in terms of whether they can be self-assembled robustly without an increase in scale to accommodate redundancy. We also describe a new method of ensuring resilience to more types of error simultaneously. Toward creating molecular automata we study the computational power of a restriction enzyme-based automaton. Toward designing chemical reaction networks, we develop a technique of storing and processing information in molecular counts, which is capable of achieving Turing universal computation. We also study the computational complexity of simulating stochastic chemical reaction networks and formally connect robustness and simulation efficiency. Lastly, we describe nucleic acid implementations of Boolean logic circuits and arbitrary mass-action kinetics. The three areas of this thesis are promising realizations of molecular-level engineering, and the theories presented here inform the range of possibility or delineate inherent difficulties in these areas.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:benenson automata; chemical kinetics; complexity of shapes; DNA nanotechnology; self-assembly; stochastic kinetics; tile-assembly
Degree Grantor:California Institute of Technology
Division:Engineering and Applied Science
Major Option:Computation and Neural Systems
Awards:Milton and Francis Clauser Doctoral Prize, 2008
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Winfree, Erik
Thesis Committee:
  • Abu-Mostafa, Yaser S. (chair)
  • Umans, Christopher M.
  • Winfree, Erik
  • Bruck, Jehoshua
  • Doyle, John Comstock
Defense Date:5 May 2008
Record Number:CaltechETD:etd-05292008-142339
Persistent URL:
Soloveichik, David0000-0002-2585-4120
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:2261
Deposited By: Imported from ETD-db
Deposited On:02 Jun 2008
Last Modified:31 Jan 2020 23:02

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