Blurb and Data Appendix.
Blurb and Mathematica notebooks.
Blurb and sequence designer and data.
Blurb and simulation models.
Manuscript and supporting information:
Blurb and
paper and
supplementary info;
MATLAB raw data and plotting functions.
Nano Letters manuscript and supporting information:
Blurb and
paper
pupplementary info.
PLoS Biology on-line version, paper and supporting information:
Blurb and
(SierpinskiDNA_PLoS2004.pdf, 4.6 MB)
(SierpinskiDNA_supp_PLoS2004.pdf, 1.8 MB)
Two videos patched together from multiple AFM frames. The first shows an aggregate of many small, imperfect
algorithmic crystals, zooming in from a 25 um to a 25 nm field of view. The second shows a large crystal grown
from a nucleating strand, illustrating how the "Sierpinski" pattern degrades with distance from the nucleating
boundary as more and more assembly errors are made.
(SierpinskiDNA_PowersOfTwo.mpeg, 18.1 MB)
(SierpinskiDNA_Decorrelation.mpeg, 2.4 MB)
Information for the molecular models and simulation scripts:
NAMOT models of molecules used [[ to be added soon ]]
Xgrow Tile Assembly Model tile sets [[ to be added soon ]]
JACS "ASAP" On-line version, paper and supporting information:
Blurb and
(tubes_JACS_published.pdf, 892KB)
(tubes_supp_JACS_published.pdf, 5.5MB)
Two videos showing dynamics of tubes on mica, seen by AFM, and one visuallization of a proposed 3D model:
(normal_tubes_AFM_movie.mpg, 4.5MB)
(normal_tubes_3D_model.mpg, 10.7MB)
(flipped_tubes_AFM_movie.mpg, 4.9MB)
Information for the proposed 3D model:
NAMOT models of molecules used [[ to be added soon ]]
RasMol scripts [[ to be added soon ]]
PyMol scripts [[ to be added soon ]]
Final revision for publication in LNCS "DNA Computers 9":
Blurb and paper
(.ps, 49MB),
(.pdf, 2.1 MB).
Paper as submitted to DNA9:
(.ps, 48MB),
(.ps.gz, 8.1 MB).
The Xgrow Tile Assembly Model simulator.
Xgrow tile files used.
NAMOT - Nucleic Acid Modeling Tool.
NAMOT models of molecules used.
Simulation Scripts (MATLAB).
Double boundary tile image used to make length histograms shown in the paper (coming soon).
Final revision for publication in LNCS "DNA Computers 9":
Blurb and paper
(.ps, 18MB),
(.pdf, 2.0 MB).
[Note: Typo in Fig 7b: "FC" on the left should be "FM".]
The Xgrow Tile Assembly Model simulator.
Xgrow tile files used.
MATLAB scripts for kinetic trapping models and
data from Xgrow simulations, including a
shell script for running the simulations.