Difference between revisions of "Kinetic Tile Assembly Model (kTAM)"
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| − | In reality, DNA tile self-assembly is a more complicated process than that modeled by the [[Abstract Tile Assembly Model (aTAM) | aTAM]], and therefore a different model is required for a realistic simulation of the physical process of self-assembling DNA tiles. Whereas the aTAM is a great model for studying the capabilities and limitations of tile assembly, and for programming tile sets to understand issues related to computation and geometry, the '''kinetic Tile Assembly Model''' (kTAM) <ref name=Winf98 /> was developed as a more physically realistic model for laboratory settings, and considers the reversible nature of self-assembly, factoring in the rates of association and dissociation of basic molecular elements (so-called monomers, or tiles) within the original framework provided by the aTAM. The kTAM describes the dynamics of assembly according to a set of reversible chemical reactions: A tile can attach to an assembly anywhere that it makes even a weak bond, and any tile can dissociate from the assembly at a rate dependent on the total strength with which it adheres to the assembly. In this section, we first give a more formal definition of the kTAM, then describe the types of errors that it captures, and then discuss several results which have successfully demonstrated methods for reducing those errors. Techniques such as those discussed below have been responsible for a rapid and steady decline in the frequency of errors seen in laboratory experiments, plummeting from error rates of | + | In reality, DNA tile self-assembly is a more complicated process than that modeled by the [[Abstract Tile Assembly Model (aTAM) | aTAM]], and therefore a different model is required for a realistic simulation of the physical process of self-assembling DNA tiles. Whereas the aTAM is a great model for studying the capabilities and limitations of tile assembly, and for programming tile sets to understand issues related to computation and geometry, the '''kinetic Tile Assembly Model''' (kTAM) <ref name=Winf98 /> was developed as a more physically realistic model for laboratory settings, and considers the reversible nature of self-assembly, factoring in the rates of association and dissociation of basic molecular elements (so-called monomers, or tiles) within the original framework provided by the aTAM. The kTAM describes the dynamics of assembly according to a set of reversible chemical reactions: A tile can attach to an assembly anywhere that it makes even a weak bond, and any tile can dissociate from the assembly at a rate dependent on the total strength with which it adheres to the assembly. In this section, we first give a more formal definition of the kTAM, then describe the types of errors that it captures, and then discuss several results which have successfully demonstrated methods for reducing those errors. Techniques such as those discussed below have been responsible for a rapid and steady decline in the frequency of errors seen in laboratory experiments, plummeting from error rates of 10% per tile in 2004 <ref name=RothTriangles /> to only 0.13% by 2009 <ref name=OrigamiSeed />, and continuing to shrink. |
Revision as of 10:53, 22 May 2013
In reality, DNA tile self-assembly is a more complicated process than that modeled by the aTAM, and therefore a different model is required for a realistic simulation of the physical process of self-assembling DNA tiles. Whereas the aTAM is a great model for studying the capabilities and limitations of tile assembly, and for programming tile sets to understand issues related to computation and geometry, the kinetic Tile Assembly Model (kTAM) [1] was developed as a more physically realistic model for laboratory settings, and considers the reversible nature of self-assembly, factoring in the rates of association and dissociation of basic molecular elements (so-called monomers, or tiles) within the original framework provided by the aTAM. The kTAM describes the dynamics of assembly according to a set of reversible chemical reactions: A tile can attach to an assembly anywhere that it makes even a weak bond, and any tile can dissociate from the assembly at a rate dependent on the total strength with which it adheres to the assembly. In this section, we first give a more formal definition of the kTAM, then describe the types of errors that it captures, and then discuss several results which have successfully demonstrated methods for reducing those errors. Techniques such as those discussed below have been responsible for a rapid and steady decline in the frequency of errors seen in laboratory experiments, plummeting from error rates of 10% per tile in 2004 [2] to only 0.13% by 2009 [3], and continuing to shrink.
References
- ↑
Erik Winfree - Algorithmic Self-Assembly of DNA
- Ph.D. Thesis, California Institute of Technology , June 1998
- BibtexAuthor : Erik Winfree
Title : Algorithmic Self-Assembly of DNA
In : Ph.D. Thesis, California Institute of Technology -
Address :
Date : June 1998
- ↑
Rothemund, Paul W. K AND Papadakis, Nick AND Winfree, Erik - Algorithmic Self-Assembly of DNA Sierpinski Triangles
- ↑
Barish, Robert D., Schulman, Rebecca, Rothemund, Paul W. K., Winfree, Erik - {An information-bearing seed for nucleating algorithmic self-assembly}
- Proceedings of the National Academy of Sciences 106(15):6054--6059, @apr 2009
- http://dx.doi.org/10.1073/pnas.0808736106
BibtexAuthor : Barish, Robert D., Schulman, Rebecca, Rothemund, Paul W. K., Winfree, Erik
Title : {An information-bearing seed for nucleating algorithmic self-assembly}
In : Proceedings of the National Academy of Sciences -
Address :
Date : @apr 2009
