The DNA and Natural Algorithms Group:

"Two Computational Primitives for Algorithmic Self-Assembly: Copying and Counting"

Nano Letters manuscript and supporting information:
(binary_counters_NanoLetters2005.pdf, 515 KB)
(binary_counter_supp_NanoLetters.pdf, 622 KB)

"Algorithmic Self-Assembly of DNA Sierpinski Triangles"

PLoS Biology on-line version, paper and supporting information:
(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 ]]

"Design and Characterization of Programmable DNA Nanotubes"

JACS "ASAP" On-line version, paper and supporting information:
(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 ]]

"One Dimensional Boundaries for DNA Tile Self-Assembly"

Final revision for publication in LNCS "DNA Computers 9": (.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).

"Proofreading Tile Sets: Error Correction for Algorithmic Self-Assembly"

Final revision for publication in LNCS "DNA Computers 9": (.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.