Tilings and patterns
The program-size complexity of self-assembled squares (extended abstract)
STOC '00 Proceedings of the thirty-second annual ACM symposium on Theory of computing
Combinatorial optimization problems in self-assembly
STOC '02 Proceedings of the thiry-fourth annual ACM symposium on Theory of computing
Elements of the Theory of Computation
Elements of the Theory of Computation
The emerging discipline of biomolecular computation in the US
New Generation Computing
Challenges and Applications for Self-Assembled DNA Nanostructures
DNA '00 Revised Papers from the 6th International Workshop on DNA-Based Computers: DNA Computing
String Tile Models for DNA Computing by Self-Assembly
DNA '00 Revised Papers from the 6th International Workshop on DNA-Based Computers: DNA Computing
Strict Self-assembly of Discrete Sierpinski Triangles
CiE '07 Proceedings of the 3rd conference on Computability in Europe: Computation and Logic in the Real World
Computability and Complexity in Self-assembly
CiE '08 Proceedings of the 4th conference on Computability in Europe: Logic and Theory of Algorithms
Strict self-assembly of discrete Sierpinski triangles
Theoretical Computer Science
Self-assembly of infinite structures: A survey
Theoretical Computer Science
Design, simulation, and experimental demonstration of self-assembled DNA nanostructures and motors
UPP'04 Proceedings of the 2004 international conference on Unconventional Programming Paradigms
A molecular solution for minimum vertex cover problem in tile assembly model
The Journal of Supercomputing
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While the topic of Molecular Computation would have appeared even a half dozen years ago to be purely conjectural, it now is an emerging subfield of computer science with the development of its theoretical basis and a number of moderate to large-scale experimental demonstrations. This paper focuses on a subarea of Molecular Computation known as DNA self-assembly. Self-assembly is the spontaneous self-ordering of substructures into superstructures driven by the selective affinity of the substructures. DNA provides a molecular scale material for effecting this programmable self-assembly, using the selective affinity of pairs of DNA strands to form DNA nanostructures. DNA self-assembly is the most advanced and versatile system known for programmable construction of patterned systems on the molecular scale. The methodology of DNA self-assembly begins with the synthesis of single-strand DNA molecules that self-assemble into macromolecular building blocks called DNA tiles. These tiles have sticky ends that match the sticky ends of other DNA tiles, facilitating further assembly into large structures known as DNA tiling lattices. In principal you can make the DNA tiling assemblies form any computable two-or three-dimensional pattern, however complex, with the appropriate choice of the tile's component DNA. This paper overviews the evolution of DNA self-assembly techniques from pure theory to experimental practice. We describe how some theoretical developments have made a major impact on the design of self-assembly experiments, as well as a number of theoretical challenges remaining in the area of DNA self-assembly. We descuss algorithms and software for the design, simulation and optimization of DNA tiling assemblies. We also describe the first experimental demonstrations of DNA self-assemblies that execute molecular computations and the assembly of patterned objects at the molecular scale. Recent experimental results indicate that this technique is scalable. Molecular imaging devices such as atomic force microscopes and transmission electron microscopes allow visualization of self-assembled two-dimensional DNA tiling lattices composed of hundreds of thousands of tiles. These assemblies can be used as scaffolding on which to position molecular electronics and robotics components with precision and specificity. The programmability lets this scaffolding have the patterning required for fabricating complex devices made of these components.