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

  • Ho-Lin Chen
  • Ming-Yang Kao
Conference paper

DOI: 10.1007/978-3-642-18305-8_2

Volume 6518 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Chen HL., Kao MY. (2011) Optimizing Tile Concentrations to Minimize Errors and Time for DNA Tile Self-assembly Systems. In: Sakakibara Y., Mi Y. (eds) DNA Computing and Molecular Programming. DNA 2010. Lecture Notes in Computer Science, vol 6518. Springer, Berlin, Heidelberg

Abstract

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 Ti proportional to the square root of Ni where Ni is the number of times Ti 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