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Simulations of Computing by Self-Assembly

Winfree, Erik (1998) Simulations of Computing by Self-Assembly. California Institute of Technology , Pasadena, CA. (Unpublished)

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Winfree (1996) proposed a Turing-universal model of DNA self-assembly. In this abstract model, DNA double-crossover molecules self-assemble to form an algorithmically-patterned two-dimensional lattice. Here, we develop a more realistic model based on the thermodynamics and kinetics of oligonucleotide hydridization. Using a computer simulation, we investigate what physical factors influence the error rates, i.e., when the more realistic model deviates from the ideal of the abstract model. We find, in agreement with rules of thumb for crystal growth, that the lowest error rates occur at the melting temperature when crystal growth is slowest, and that error rates can be made arbitrarily low by decreasing concentration and increasing binding strengths.

Item Type:Report or Paper (Technical Report)
Winfree, Erik0000-0002-5899-7523
Additional Information:© 1998 California Institute of Technology. May 31, 1998. I am deeply grateful for stimulating discussions, suggestions, questions, and technical help from John Hopfield, Sanjoy Mahajan, Paul Rothemund, Len Adleman, John Reif, and James Wetmur. All errors, whatever their rate may be, are mine. MATLAB 5.2 code for running the simulations and reproducing all the figures in this paper may be obtained from the author. This work has been supported by the National Institute for Mental Health (Training Grant # 5 T32 MH 19138-07. General Motors' Technology Research Partnerships program, and by the Center for Neuromorphic Systems Engineering as a part of the National Science Foundation Engineering Research Center Program under grant EEC-9402726).
Group:Computer Science Technical Reports
Funding AgencyGrant Number
NIH Predoctoral Fellowship5 T32 MH 19138-07
General Motors Technology Research Partnerships ProgramUNSPECIFIED
Center for Neuromorphic Systems Engineering, CaltechUNSPECIFIED
Record Number:CaltechCSTR:1998.22
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Usage Policy:You are granted permission for individual, educational, research and non-commercial reproduction, distribution, display and performance of this work in any format.
ID Code:27062
Deposited By: Imported from CaltechCSTR
Deposited On:16 Apr 2003
Last Modified:03 Oct 2019 03:20

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