Internal Diffusion-Limited Aggregation: Parallel Algorithms and Complexity

The computational complexity of internal diffusion-limited aggregation (DLA) is examined from both a theoretical and a practical point of view. We show that for two or more dimensions, the problem of predicting the cluster from a given set of paths is complete for the complexity class CC, the subset of P characterized by circuits composed of comparator gates. CC-completeness is believed to imply that, in the worst case, growing a cluster of size n requires polynomial time in n even on a parallel computer. A parallel relaxation algorithm is presented that uses the fact that clusters are nearly spherical to guess the cluster from a given set of paths, and then corrects defects in the guessed cluster through a non-local annihilation process. The parallel running time of the relaxation algorithm for two-dimensional internal DLA is studied by simulating it on a serial computer. The numerical results are compatible with a running time that is either polylogarithmic in n or a small power of n. Thus the computational resources needed to grow large clusters are significantly less on average than the worst-case analysis would suggest. For a parallel machine with k processors, we show that random clusters in d dimensions can be generated in O((n/k + log k) n^{2/d}) steps. This is a significant speedup over explicit sequential simulation, which takes O(n^{1+2/d}) time on average. Finally, we show that in one dimension internal DLA can be predicted in O(log n) parallel time, and so is in the complexity class NC

The Parallel Complexity of Coloring Games

International audienceWe wish to motivate the problem of finding decentralized lower-bounds on the complexity of computing a Nash equilibrium in graph games. While the centralized computation of an equilibrium in polynomial time is generally perceived as a positive result, this does not reflect well the reality of some applications where the game serves to implement distributed resource allocation algorithms, or to model the social choices of users with limited memory and computing power. As a case study, we investigate on the parallel complexity of a game-theoretic variation of graph coloring. These " coloring games " were shown to capture key properties of the more general welfare games and Hedonic games. On the positive side, it can be computed a Nash equilibrium in polynomial-time for any such game with a local search algorithm. However, the algorithm is time-consuming and it requires polynomial space. The latter questions the use of coloring games in the modeling of information-propagation in social networks. We prove that the problem of computing a Nash equilibrium in a given coloring game is PTIME-hard, and so, it is unlikely that one can be computed with an efficient distributed algorithm. The latter brings more insights on the complexity of these games

Parallel Computation Using Active Self-assembly

We study the computational complexity of the recently proposed nubots model of molecular-scale self-assembly. The model generalizes asynchronous cellular automaton to have non-local movement where large assemblies of molecules can be moved around, analogous to millions of molecular motors in animal muscle effecting the rapid movement of large arms and legs. We show that nubots is capable of simulating Boolean circuits of polylogarithmic depth and polynomial size, in only polylogarithmic expected time. In computational complexity terms, any problem from the complexity class NC is solved in polylogarithmic expected time on nubots that use a polynomial amount of workspace. Along the way, we give fast parallel algorithms for a number of problems including line growth, sorting, Boolean matrix multiplication and space-bounded Turing machine simulation, all using a constant number of nubot states (monomer types). Circuit depth is a well-studied notion of parallel time, and our result implies that nubots is a highly parallel model of computation in a formal sense. Thus, adding a movement primitive to an asynchronous non-deterministic cellular automation, as in nubots, drastically increases its parallel processing abilities

Diverse and robust molecular algorithms using reprogrammable DNA self-assembly

Molecular biology provides an inspiring proof-of-principle that chemical systems can store and process information to direct molecular activities such as the fabrication of complex structures from molecular components. To develop information-based chemistry as a technology for programming matter to function in ways not seen in biological systems, it is necessary to understand how molecular interactions can encode and execute algorithms. The self-assembly of relatively simple units into complex products is particularly well suited for such investigations. Theory that combines mathematical tiling and statistical–mechanical models of molecular crystallization has shown that algorithmic behaviour can be embedded within molecular self-assembly processes, and this has been experimentally demonstrated using DNA nanotechnology with up to 22 tile types. However, many information technologies exhibit a complexity threshold—such as the minimum transistor count needed for a general-purpose computer—beyond which the power of a reprogrammable system increases qualitatively, and it has been unclear whether the biophysics of DNA self-assembly allows that threshold to be exceeded. Here we report the design and experimental validation of a DNA tile set that contains 355 single-stranded tiles and can, through simple tile selection, be reprogrammed to implement a wide variety of 6-bit algorithms. We use this set to construct 21 circuits that execute algorithms including copying, sorting, recognizing palindromes and multiples of 3, random walking, obtaining an unbiased choice from a biased random source, electing a leader, simulating cellular automata, generating deterministic and randomized patterns, and counting to 63, with an overall per-tile error rate of less than 1 in 3,000. These findings suggest that molecular self-assembly could be a reliable algorithmic component within programmable chemical systems. The development of molecular machines that are reprogrammable—at a high level of abstraction and thus without requiring knowledge of the underlying physics—will establish a creative space in which molecular programmers can flourish

A Theory Of Strict P-Completeness

. A serious limitation of the theory of P-completeness is that it fails to distinguish between those P-complete problems that do have polynomial speedup on parallel machines from those that don't. We introduce the notion of strict P-completeness and develop tools to prove precise limits on the possible speedups obtainable for a number of Pcomplete problems. Key words. Parallel computation; P-completeness. Subject classifications. 68Q15, 68Q22. 1. Introduction A major goal of the theory of parallel computation is to understand how much speedup is obtainable in solving a problem on parallel machines over sequential machines. The theory of P-completeness has successfully classified many problems as unlikely to have polylog time algorithms on a parallel machine with a polynomial number of processors. However, the theory fails to distinguish between those P-complete problems that do have significant, polynomial speedup on parallel machines from those that don't. Yet this distinction is e..