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.

Original languageEnglish (US)
Title of host publicationDNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers
Pages90-101
Number of pages12
DOIs
StatePublished - Nov 27 2009
Event14th International Meeting on DNA Computing, DNA14 - Prague, Czech Republic
Duration: Jun 2 2008Jun 9 2008

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume5347 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other14th International Meeting on DNA Computing, DNA14
CountryCzech Republic
CityPrague
Period6/2/086/9/08

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Keywords

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

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

Cite this

Williams, S., Lund, K., Lin, C., Wonka, P., Lindsay, S., & Yan, H. (2009). Tiamat: A three-dimensional editing tool for complex DNA structures. In DNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers (pp. 90-101). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 5347 LNCS). https://doi.org/10.1007/978-3-642-03076-5_8