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
The emerging discipline of biomolecular computation in the US
New Generation Computing
Molecular Assembly and Computation: From Theory to Experimental Demonstrations
ICALP '02 Proceedings of the 29th International Colloquium on Automata, Languages and Programming
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
Algorithmic self-assembly of dna
Algorithmic self-assembly of dna
The design of autonomous DNA nano-mechanical devices: Walking and rolling DNA
Natural Computing: an international journal
Compact error-resilient computational DNA tiling assemblies
DNA'04 Proceedings of the 10th international conference on DNA computing
Designs of autonomous unidirectional walking DNA devices
DNA'04 Proceedings of the 10th international conference on DNA computing
DNA'04 Proceedings of the 10th international conference on DNA computing
DNA13'07 Proceedings of the 13th international conference on DNA computing
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Self-assembly is the spontaneous self-ordering of substructures into superstructures, driven by the selective affinity of the substructures. Complementarity of DNA bases renders DNA an ideal material for programmable self-assembly of nanostructures. DNA self-assembly is the most advanced and versatile system that has been experimentally demonstrated 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 single strand “sticky ends” that complement the sticky ends of other DNA tiles, facilitating further assembly into larger structures known as DNA tiling lattices. In principle, DNA tiling assemblies can form any computable two or three-dimensional pattern, however complex, with the appropriate choice of the tiles' component DNA. Two-dimensional DNA tiling lattices composed of hundreds of thousands of tiles have been demonstrated experimentally. These assemblies can be used as programmable scaffolding to position molecular electronics and robotics components with precision and specificity, facilitating fabrication of complex nanoscale devices. We overview the evolution of DNA self-assembly techniques from pure theory, through simulation and design, and then to experimental practice. In particular, we begin with an overview of theoretical models and algorithms for DNA lattice self-assembly. Then we describe our software for the simulation and design of DNA tiling assemblies and DNA nano-mechanical devices. As an example, we discuss models, algorithms, and computer simulations for the key problem of error control in DNA lattice self-assembly. We then briefly discuss our laboratory demonstrations of DNA lattices and motors, including those using the designs aided by our software. These experimental demonstrations of DNA self-assemblies include the assembly of patterned objects at the molecular scale, the execution of molecular computations, and the autonomous DNA walking and computing devices.