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

  • Ho-Lin Chen
  • Ming-Yang Kao
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6518)


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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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Ho-Lin Chen
    • 1
    • 2
  • Ming-Yang Kao
    • 1
    • 2
  1. 1.Center for Mathematics of InformationCalifornia Institute of TechnologyPasadenaUSA
  2. 2.Department of Electrical Engineering and Computer ScienceNorthwestern UniversityEvanstonUSA

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