TY - GEN

T1 - Optimizing tile concentrations to minimize errors and time for DNA tile self-assembly systems

AU - Chen, Ho Lin

AU - Kao, Ming-Yang

PY - 2011

Y1 - 2011

N2 - 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 the 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.

AB - 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 the 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.

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U2 - 10.1007/978-3-642-18305-8_2

DO - 10.1007/978-3-642-18305-8_2

M3 - Conference contribution

AN - SCOPUS:79251552523

SN - 9783642183041

T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

SP - 13

EP - 24

BT - DNA Computing and Molecular Programming - 16th International Conference, DNA 16, Revised Selected Papers

T2 - 16th International Conference on DNA Computing and Molecular Programming, DNA 16

Y2 - 14 June 2010 through 17 June 2010

ER -