Design tools for the fabrication of a photonic crystal based on DNA junctions

P. Sauer, Hong Liang Cui, N. C. Seeman

Research output: Chapter in Book/Report/Conference proceedingConference contribution


SEQUIN is a sequence design program used to create stable immobile DNA junctions. Several modifications to this program have been introduced that allow for the design of molecules containing multiple cross-overs on a single strand (ie. PX molecule) and molecules containing sticky-ends. There is also an inclusion of single mismatch pairing thermodynamics in the energy calculations and the addition of a graphical interface based on a two-dimensional grid with run time allocatable parameters. Using this program, a 2D photonic crystal can be designed. The structure of the crystal was modeled as cylindrical rods of water cut into a solid material with a dielectric constant equal to that of bulk DNA. The band gap for several variations of this crystal were calculated, all of which exist in the far UV to soft X-ray region. Current investigations include the possiblility of tiling together a superstructure for this 2D crystal in order to create a band gap at longer wavelengths.

Original languageEnglish (US)
Title of host publication2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003 - Proceedings
PublisherIEEE Computer Society
Number of pages4
ISBN (Electronic)0780379764
StatePublished - 2003
Event2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003 - San Francisco, United States
Duration: Aug 12 2003Aug 14 2003

Publication series

NameProceedings of the IEEE Conference on Nanotechnology
ISSN (Print)1944-9399
ISSN (Electronic)1944-9380


Other2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003
Country/TerritoryUnited States
CitySan Francisco


  • Crystalline materials
  • DNA
  • Dielectric materials
  • Fabrication
  • Photonic band gap
  • Photonic crystals
  • Sequences
  • Solid modeling
  • Structural rods
  • Thermodynamics

ASJC Scopus subject areas

  • Bioengineering
  • Electrical and Electronic Engineering
  • Materials Chemistry
  • Condensed Matter Physics


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