The DNA and Natural Algorithms Group:

Extra Supplementary Material for Papers


"Chemical Reaction Networks and Stochastic Local Search"

Erik Winfree (DNA25 2019).

Blurb and Mathematica notebooks.


"Diverse and robust molecular algorithms using reprogrammable DNA self-assembly"

Damien Woods, David Doty, Cameron Myhrvold, Joy Hui, Felix Zhou, Peng Yin, Erik Winfree (Nature 2019).

Blurb and sequence designer and data.


"DNA as a Universal Substrate for Chemical Kinetics"

David Soloveichik, Georg Seelig, Erik Winfree (Proceedings of the National Academy of Science 2010).

Blurb and simulation models.


"Construction of an in vitro bistable circuit from synthetic transcriptional switches"

Jongmin Kim, Kristin S. White, Erik Winfree (Molecular Systems Biology 2006).

Manuscript and supporting information:
Blurb and paper and supplementary info; MATLAB raw data and plotting functions.


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

Robert D. Barish, Paul W. K. Rothemund, Erik Winfree (Nano Letters 2005).  

Nano Letters manuscript and supporting information:
Blurb and paper
pupplementary info.


"Algorithmic Self-Assembly of DNA Sierpinski Triangles"

Paul W.K. Rothemund, Nick Papadakis, Erik Winfree (PLoS Biology 2004).  

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 ]]


"Design and Characterization of Programmable DNA Nanotubes"

Paul W.K. Rothemund, Axel Ekani-Nkodo, Nick Papadakis, Ashish Kumar, Deborah Kuchnir Fygenson, Erik Winfree (JACS 2004).  

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 ]]


"One Dimensional Boundaries for DNA Tile Self-Assembly"

Rebecca Schulman, Shaun Lee, Nick Papadakis, Erik Winfree (Proceedings of DNA Based Computers 9).  

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).


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

Erik Winfree and Renat Bekbolatov (Proceedings of DNA Based Computers 9).  

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.



Please see further information on our group's publications.