title: Healing assessment of tile sets for error tolerance in DNA self-assembly.
abstract: An assessment of the effectiveness of healing for error tolerance in DNA self-assembly tile sets for algorithmic/nano-manufacturing applications is presented. Initially, the conditions for correct binding of a tile to an existing aggregate are analysed using a Markovian approach; based on this analysis, it is proved that correct aggregation (as identified with a so-called ideal tile set) is not always met for the existing tile sets for nano-manufacturing. A metric for assessing tile sets for healing by utilising punctures is proposed. Tile sets are investigated and assessed with respect to features such as error (mismatched tile) movement, punctured area and bond types. Subsequently, it is shown that the proposed metric can comprehensively assess the healing effectiveness of a puncture type for a tile set and its capability to attain error tolerance for the desired pattern. Extensive simulation results are provided.
authors.affiliation: Department of ECE, Northeastern University, Boston, MA 02115, USA. masoud@ece.neu.edu
authors.forename: M
authors.initials: M
authors.lastname: Hashempour
authors.forename: Z
authors.initials: Z
authors.lastname: Mashreghian Arani
authors.forename: F
authors.initials: F
authors.lastname: Lombardi
mesh_terms: D003198:Computer Simulation; D003460:Crystallization / Q000379:methods*; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D049329:Nanostructures / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D004247:DNA