On the Decidability of Self-Assembly of Infinite Ribbons
FOCS '02 Proceedings of the 43rd Symposium on Foundations of Computer Science
Combining self-healing and proofreading in self-assembly
Natural Computing: an international journal
How crystals that sense and respond to their environments could evolve
Natural Computing: an international journal
Shape replication through self-assembly and RNase enzymes
SODA '10 Proceedings of the twenty-first annual ACM-SIAM symposium on Discrete Algorithms
Optimizing tile concentrations to minimize errors and time for DNA tile self-assembly systems
DNA'10 Proceedings of the 16th international conference on DNA computing and molecular programming
Simple evolution of complex crystal species
DNA'10 Proceedings of the 16th international conference on DNA computing and molecular programming
Complexity of graph self-assembly in accretive systems and self-destructible systems
Theoretical Computer Science
Programmable Control of Nucleation for Algorithmic Self-Assembly
SIAM Journal on Computing
Beyond biology: designing a new mechanism for self-replication and evolution at the nanoscale
Proceedings of the 13th annual conference on Genetic and evolutionary computation
Optimizing potential information transfer with self-referential memory
UC'06 Proceedings of the 5th international conference on Unconventional Computation
Complexity of graph self-assembly in accretive systems and self-destructible systems
DNA'05 Proceedings of the 11th international conference on DNA Computing
A self-assembly model of time-dependent glue strength
DNA'05 Proceedings of the 11th international conference on DNA Computing
Complexity of compact proofreading for self-assembled patterns
DNA'05 Proceedings of the 11th international conference on DNA Computing
Temperature 1 self-assembly: deterministic assembly in 3D and probabilistic assembly in 2D
Proceedings of the twenty-second annual ACM-SIAM symposium on Discrete Algorithms
Simple evolution of complex crystal species
Natural Computing: an international journal
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Is it possible to create a simple physical system that is capable of replicating itself? Can such a system evolve interesting behaviors, thus allowing it to adapt to a wide range of environments? This paper presents a design for such a replicator constructed exclusively from synthetic DNA. The basis for the replicator is crystal growth: information is stored in the spatial arrangement of monomers and copied from layer to layer by templating. Replication is achieved by fragmentation of crystals, which produces new crystals that carry the same information. Crystal replication avoids intrinsic problems associated with template-directed mechanisms for replication of one-dimensional polymers. A key innovation of our work is that by using programmable DNA tiles as the crystal monomers, we can design crystal growth processes that apply interesting selective pressures to the evolving sequences. While evolution requires that copying occur with high accuracy, we show how to adapt error-correction techniques from algorithmic self-assembly to lower the replication error rate as much as is required.