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

P. Sauer, Hong Liang Cui, Nadrian Seeman

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

Abstract

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
Pages428-431
Number of pages4
Volume1
ISBN (Print)0780379764
DOIs
StatePublished - 2003
Event2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003 - San Francisco, United States
Duration: Aug 12 2003Aug 14 2003

Other

Other2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003
CountryUnited States
CitySan Francisco
Period8/12/038/14/03

Fingerprint

Photonic crystals
DNA
deoxyribonucleic acid
photonics
Fabrication
Crystals
fabrication
Molecules
Energy gap
crystals
molecules
Permittivity
Thermodynamics
strands
X rays
Wavelength
rods
Water
grids
inclusions

Keywords

  • Crystalline materials
  • Dielectric materials
  • DNA
  • 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

Cite this

Sauer, P., Cui, H. L., & Seeman, N. (2003). Design tools for the fabrication of a photonic crystal based on DNA junctions. In 2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003 - Proceedings (Vol. 1, pp. 428-431). [1231810] IEEE Computer Society. https://doi.org/10.1109/NANO.2003.1231810

Design tools for the fabrication of a photonic crystal based on DNA junctions. / Sauer, P.; Cui, Hong Liang; Seeman, Nadrian.

2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003 - Proceedings. Vol. 1 IEEE Computer Society, 2003. p. 428-431 1231810.

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

Sauer, P, Cui, HL & Seeman, N 2003, Design tools for the fabrication of a photonic crystal based on DNA junctions. in 2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003 - Proceedings. vol. 1, 1231810, IEEE Computer Society, pp. 428-431, 2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003, San Francisco, United States, 8/12/03. https://doi.org/10.1109/NANO.2003.1231810
Sauer P, Cui HL, Seeman N. Design tools for the fabrication of a photonic crystal based on DNA junctions. In 2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003 - Proceedings. Vol. 1. IEEE Computer Society. 2003. p. 428-431. 1231810 https://doi.org/10.1109/NANO.2003.1231810
Sauer, P. ; Cui, Hong Liang ; Seeman, Nadrian. / Design tools for the fabrication of a photonic crystal based on DNA junctions. 2003 3rd IEEE Conference on Nanotechnology, IEEE-NANO 2003 - Proceedings. Vol. 1 IEEE Computer Society, 2003. pp. 428-431
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abstract = "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.",
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