title: Logic circuits based on molecular spider systems.
abstract: Spatial locality brings the advantages of computation speed-up and sequence reuse to molecular computing. In particular, molecular walkers that undergo localized reactions are of interest for implementing logic computations at the nanoscale. We use molecular spider walkers to implement logic circuits. We develop an extended multi-spider model with a dynamic environment wherein signal transmission is triggered via localized reactions, and use this model to implement three basic gates (AND, OR, NOT) and a cascading mechanism. We develop an algorithm to automatically generate the layout of the circuit. We use a kinetic Monte Carlo algorithm to simulate circuit computations, and we analyze circuit complexity: our design scales linearly with formula size and has a logarithmic time complexity.
authors.affiliation: Department of Computer Science, University of New Mexico, United States.
authors.forename: Dandan
authors.initials: D
authors.lastname: Mo
authors.affiliation: Department of Computer Science, University of New Mexico, United States; Department of Chemical and Biological Engineering, University of New Mexico, United States; Center for Biomedical Engineering, University of New Mexico, United States.
authors.forename: Matthew R
authors.initials: MR
authors.lastname: Lakin
authors.affiliation: Department of Computer Science, University of New Mexico, United States; Center for Biomedical Engineering, University of New Mexico, United States. Electronic address: darko@cs.unm.edu.
authors.forename: Darko
authors.initials: D
authors.lastname: Stefanovic
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D039301:Computers, Molecular; D008128:Logic; D058615:Synthetic Biology / Q000379:methods
keywords: Localized signal transmission; Logic circuits; Molecular spiders; Parallel evaluation