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Simulations of Computing by Self-Assembly

Winfree, Erik (1998) Simulations of Computing by Self-Assembly. California Institute of Technology . (Unpublished) http://resolver.caltech.edu/CaltechCSTR:1998.22

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Abstract

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)
Group:Computer Science Technical Reports
Record Number:CaltechCSTR:1998.22
Persistent URL:http://resolver.caltech.edu/CaltechCSTR:1998.22
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
Collection:CaltechCSTR
Deposited By: Imported from CaltechCSTR
Deposited On:16 Apr 2003
Last Modified:26 Dec 2012 14:13

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