University of Arkansas Topology Seminar: 3/8/2018

Speaker: Matthew Patatiz

Title: Universal simulation of directed systems in the abstract Tile Assembly Model requires undirectedness

As a mathematical model of tile-based self-assembling systems, Winfree's abstract Tile Assembly Model (aTAM) has proven to be a remarkable platform for studying and understanding the behaviors and powers of self-assembling systems. Furthermore, as it is capable of Turing universal computation, the aTAM allows algorithmic self-assembly, in which the components can be designed so that the rules governing their behaviors force them to inherently execute prescribed algorithms as they combine. This power has yielded a wide variety of theoretical results in the aTAM utilizing algorithmic self-assembly to design systems capable of performing complex computations and forming extremely intricate structures. Adding to the completeness of the model, in FOCS 2012 the aTAM was shown to also be intrinsically universal, which means that there exists one single tile set such that for any arbitrary input aTAM system, that tile set can be configured into a "seed" structure which will then cause self-assembly using that tile set to simulate the input system, capturing its full dynamics modulo only a scale factor. However, the "universal simulator" of that result makes use of nondeterminism in terms of the tiles placed in several key locations when different assembly sequences are followed. This nondeterminism remains even when the simulator is simulating a system which is directed, meaning that it has exactly one unique terminal assembly and for any given location, no matter which assembly sequence is followed, the same tile type is always placed there. The question which then arose was whether or not that nondeterminism is fundamentally required, and if any universal simulator must in fact utilize more nondeterminism than directed systems when simulating them.

In this paper, we answer that question in the affirmative: the class of directed systems in the aTAM is not intrinsically universal, meaning there is no universal simulator for directed systems which itself is always directed. This result provides a powerful insight into the role of nondeterminism in self-assembly, which is itself a fundamentally nondeterministic process occurring via unguided local interactions. Furthermore, to achieve this result we leverage powerful results of computational complexity hierarchies, including tight bounds on both best and worst-case complexities of decidable languages, to tailor design systems with precisely controllable space resources available to computations embedded within them. We also develop novel techniques for designing systems containing subsystems with disjoint, mutually exclusive computational powers. The main result will be important in the development of future simulation systems, and the supporting design techniques and lemmas will provide powerful tools for the development of future aTAM systems as well as proofs of their computational abilities.