Tiamat: A Three-Dimensional Editing Tool for Complex DNA Structures

  • Sean Williams
  • Kyle Lund
  • Chenxiang Lin
  • Peter Wonka
  • Stuart Lindsay
  • Hao Yan
Conference paper

DOI: 10.1007/978-3-642-03076-5_8

Volume 5347 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
Williams S., Lund K., Lin C., Wonka P., Lindsay S., Yan H. (2009) Tiamat: A Three-Dimensional Editing Tool for Complex DNA Structures. In: Goel A., Simmel F.C., Sosík P. (eds) DNA Computing. DNA 2008. Lecture Notes in Computer Science, vol 5347. Springer, Berlin, Heidelberg

Abstract

We present the development of a new graphical user interface driven molecular modeling, editing and visualization tool called Tiamat. Tiamat addresses the challenge of how to efficiently model large and complex DNA nanostructures. We describe the three major components of our system. First, we discuss design guidelines and data structures that form the basis of flexible and large-scale editing. Second, we explain a semi-automatic sequence generator that combines user input with random sequence generation to efficiently label the molecules in the DNA structure. Third, we outline the visualization techniques including a simplification algorithm that are used to render large designs. The results demonstrate how Tiamat was used to generate large and complex designs.

Keywords

Structural DNA nanotechnology DNA tile 3D DNA structure display DNA sequence design 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Sean Williams
    • 1
  • Kyle Lund
    • 2
    • 4
  • Chenxiang Lin
    • 2
    • 4
  • Peter Wonka
    • 3
  • Stuart Lindsay
    • 2
    • 4
    • 5
  • Hao Yan
    • 2
    • 4
  1. 1.Department of Computer ScienceUniversity of CaliforniaDavis
  2. 2.Center for Single Molecule Biophysics, The Biodesign InstituteArizona State UniversityTempe
  3. 3.School of Computing and InformaticsArizona State UniversityTempe
  4. 4.Department of Chemistry and BiologyArizona State UniversityTempe
  5. 5.Department of Physics and AstronomyArizona State UniversityTempe