Complexity of graph self-assembly in accretive systems and self-destructible systems
Self-assembly is a process in which small objects autonomously associate with each other to form larger complexes. It is ubiquitous in biological constructions at the cellular and molecular scale and has also been identified by nanoscientists as a fundamental method for building nano-scale structures. Recent years have seen convergent interest and efforts in studying self-assembly from mathematicians, computer scientists, physicists, chemists, and biologists. However most complexity theoretical studies of self-assembly utilize mathematical models with two limitations: (1) only attraction, while no repulsion, is studied; (2) only assembled structures of two dimensional square grids are studied. In this paper, we study the complexity of the assemblies resulting from the cooperative effect of repulsion and attraction in a more general setting of graphs. This allows for the study of a more general class of self-assembled structures than the previous tiling model. We define two novel assembly models, namely the accretive graph assembly model and the self-destructible graph assembly model, and identify a fundamental problem in them: the sequential construction of a given graph. We refer to it as the Accretive Graph Assembly Problem (AGAP) and the Self-Destructible Graph Assembly Problem (DGAP), in the respective models. Our main results are: (i) AGAP is NP-complete even if the maximum degree of the graph is restricted to 4 or the graph is restricted to be planar with maximum degree 5; (ii) counting the number of sequential assembly orderings that result in a target graph (#AGAP) is #P-complete; and (iii) DGAP is PSPACE-complete even if the maximum degree of the graph is restricted to 6 (this is the first PSPACE-complete result in self-assembly). We also extend the accretive graph assembly model to a stochastic model, and prove that determining the probability of a given assembly in this model is #P-complete. (C) 2010 Elsevier B.V. All rights reserved.
complexity graph self-assembly np-complete pspace-complete dna nanostrcture np