title: Modelling amorphous computations with transcription networks.
abstract: The power of electronic computation is due in part to the development of modular gate structures that can be coupled to carry out sophisticated logical operations and whose performance can be readily modelled. However, the equivalences between electronic and biochemical operations are far from obvious. In order to help cross between these disciplines, we develop an analogy between complementary metal oxide semiconductor and transcriptional logic gates. We surmise that these transcriptional logic gates might prove to be useful in amorphous computations and model the abilities of immobilized gates to form patterns. Finally, to begin to implement these computations, we design unique hairpin transcriptional gates and then characterize these gates in a binary latch similar to that already demonstrated by Kim et al. (Kim, White & Winfree 2006 Mol. Syst. Biol. 2, 68 (doi:10.1038/msb4100099)). The hairpin transcriptional gates are uniquely suited to the design of a complementary NAND gate that can serve as an underlying basis of molecular computing that can output matter rather than electronic information.
authors.affiliation: Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, USA.
authors.forename: Zack Booth
authors.initials: ZB
authors.lastname: Simpson
authors.forename: Timothy L
authors.initials: TL
authors.lastname: Tsai
authors.forename: Nam
authors.initials: N
authors.lastname: Nguyen
authors.forename: Xi
authors.initials: X
authors.lastname: Chen
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Ellington
mesh_terms: D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D039301:Computers, Molecular; D004247:DNA / Q000235:genetics; D004563:Electrochemistry / Q000379:methods; D053263:Gene Regulatory Networks; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009991:Oscillometry / Q000379:methods; D010087:Oxides / Q000737:chemistry; D011401:Promoter Regions, Genetic; D012666:Semiconductors; D012984:Software; D014158:Transcription, Genetic
chemical_list: D010087:Oxides; D004247:DNA