Time-Complexity of Multilayered DNA Strand Displacement Circuits

  • Georg Seelig
  • David Soloveichik
Conference paper

DOI: 10.1007/978-3-642-10604-0_15

Volume 5877 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Seelig G., Soloveichik D. (2009) Time-Complexity of Multilayered DNA Strand Displacement Circuits. In: Deaton R., Suyama A. (eds) DNA Computing and Molecular Programming. DNA 2009. Lecture Notes in Computer Science, vol 5877. Springer, Berlin, Heidelberg

Abstract

Recently we have shown how molecular logic circuits with many components arranged in multiple layers can be built using DNA strand displacement reactions. The potential applications of this and similar technologies inspire the study of the computation time of multilayered molecular circuits. Using mass action kinetics to model DNA strand displacement-based circuits, we discuss how computation time scales with the number of layers. We show that depending on circuit architecture, the time-complexity does not necessarily scale linearly with the depth as is assumed in the usual study of circuit complexity. We compare circuits with catalytic and non-catalytic components, showing that catalysis fundamentally alters asymptotic time-complexity. Our results rely on simple asymptotic arguments that should be applicable to a wide class of chemical circuits. These results may help to improve circuit performance and may be useful for the construction of faster, larger and more reliable molecular circuitry.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Georg Seelig
    • 1
  • David Soloveichik
    • 2
  1. 1.University of WashingtonSeattleUSA
  2. 2.California Institute of TechnologyPasadenaUSA