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Optimizing Tile Concentrations to Minimize Errors and Time for DNA Tile Self-assembly Systems

Chen, Ho-Lin and Kao, Ming-Yang (2011) Optimizing Tile Concentrations to Minimize Errors and Time for DNA Tile Self-assembly Systems. In: DNA computing and molecular programming. Lecture Notes in Computer Science . No.6518. Springer , Berlin, pp. 13-24. ISBN 978-3-642-18304-1.

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DNA tile self-assembly has emerged as a rich and promising primitive for nano-technology. This paper studies the problems of minimizing assembly time and error rate by changing the tile concentrations because changing the tile concentrations is easy to implement in actual lab experiments. We prove that setting the concentration of tile T_i proportional to the square root of N_i where N_i is the number of times T_i appears outside the seed structure in the final assembled shape minimizes the rate of growth errors for rectilinear tile systems. We also show that t he same concentrations minimize the expected assembly time for a feasible class of tile systems. Moreover, for general tile systems, given tile concentrations, we can approximate the expected assembly time with high accuracy and probability by running only a polynomial number of simulations in the size of the target shape.

Item Type:Book Section
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Additional Information:© 2011 Springer-Verlag Berlin Heidelberg.
Series Name:Lecture Notes in Computer Science
Issue or Number:6518
Record Number:CaltechAUTHORS:20111006-080801531
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:27110
Deposited By: Tony Diaz
Deposited On:06 Oct 2011 15:45
Last Modified:03 Oct 2019 03:20

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