title: Permutation Machines.
abstract: We define a new inversion-based machine called a permuton of n genetic elements, which allows the n elements to be rearranged in any of the n·(n - 1)·(n - 2)···2 = n! distinct orderings. We present two design algorithms for architecting such a machine. We define a notion of a feasible design and use the framework to discuss the feasibility of the permuton architectures. We have implemented our design algorithms in a freely usable web-accessible software for exploration of these machines. Permutation machines could be used as memory elements or state machines and explicitly illustrate a rational approach to designing biological systems.
authors.affiliation: Department of Electrical and Computer Engineering, Boston University , Boston, Massachusetts 02215, United States.
authors.forename: Swapnil
authors.initials: S
authors.lastname: Bhatia
authors.affiliation: Department of Electrical and Computer Engineering, Duke University , Durham, North Carolina 27708, United States.
authors.forename: Craig
authors.initials: C
authors.lastname: LaBoda
authors.affiliation: Department of Developmental, Molecular, and Chemical Biology, Tufts University , Boston, Massachusetts 02155, United States.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Yanez
authors.affiliation: International Genetically Engineered Machine, Cambridge, Massachusetts 02139, United States.
authors.forename: Traci
authors.initials: T
authors.lastname: Haddock-Angelli
authors.affiliation: Department of Electrical and Computer Engineering, Boston University , Boston, Massachusetts 02215, United States.
authors.forename: Douglas
authors.initials: D
authors.lastname: Densmore
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D004247:DNA; D008957:Models, Genetic; D045522:Recombinases / Q000235:genetics / Q000378:metabolism; D012984:Software; D043324:beta-Fructofuranosidase / Q000235:genetics / Q000378:metabolism
chemical_list: D045522:Recombinases; D004247:DNA; D043324:beta-Fructofuranosidase
keywords: algorithm; feasible design; finite state machine; invertase; permutation