Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time

We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by biology's fantastic ability to assemble biomolecules that form systems with complicated structure and dynamics, from molecular motors that walk on rigid tracks and proteins that dynamically alter the structure of the cell during mitosis, to embryonic development where large-scale complicated organisms efficiently grow from a single cell. Using this active self-assembly model, we show how to efficiently self-assemble shapes and patterns from simple monomers. For example, we show how to grow a line of monomers in time and number of monomer states that is merely logarithmic in the length of the line. Our main results show how to grow arbitrary connected two-dimensional geometric shapes and patterns in expected time that is polylogarithmic in the size of the shape, plus roughly the time required to run a Turing machine deciding whether or not a given pixel is in the shape. We do this while keeping the number of monomer types logarithmic in shape size, plus those monomers required by the Kolmogorov complexity of the shape or pattern. This work thus highlights the efficiency advantages of active self-assembly over passive self-assembly and motivates experimental effort to construct general-purpose active molecular self-assembly systems

Preparing sparse solvers for exascale computing.

Sparse solvers provide essential functionality for a wide variety of scientific applications. Highly parallel sparse solvers are essential for continuing advances in high-fidelity, multi-physics and multi-scale simulations, especially as we target exascale platforms. This paper describes the challenges, strategies and progress of the US Department of Energy Exascale Computing project towards providing sparse solvers for exascale computing platforms. We address the demands of systems with thousands of high-performance node devices where exposing concurrency, hiding latency and creating alternative algorithms become essential. The efforts described here are works in progress, highlighting current success and upcoming challenges. This article is part of a discussion meeting issue 'Numerical algorithms for high-performance computational science'

Distributed Decision Through Self-Synchronizing Sensor Networks in the Presence of Propagation Delays and Nonreciprocal Channels

In this paper we propose and analyze a distributed algorithm for achieving globally optimal decisions, either estimation or detection, through a self-synchronization mechanism among linearly coupled integrators initialized with local measurements. We model the interaction among the nodes as a directed graph with weights dependent on the radio interface and we pose special attention to the effect of the propagation delays occurring in the exchange of data among sensors, as a function of the network geometry. We derive necessary and sufficient conditions for the proposed system to reach a consensus on globally optimal decision statistics. One of the major results proved in this work is that a consensus is achieved for any bounded delay condition if and only if the directed graph is quasi-strongly connected. We also provide a closed form expression for the global consensus, showing that the effect of delays is, in general, to introduce a bias in the final decision. The closed form expression is also useful to modify the consensus mechanism in order to get rid of the bias with minimum extra complexity.Comment: Conference paper. Journal version submitted to IEEE Transactions on Signal Processing, January 10, 2007. Paper accepted for the publication on the VIII IEEE Workshop on Signal Processing Advances in Wireless Communications, (SPAWC 2007), January 22, 200

Towards formal models and languages for verifiable Multi-Robot Systems

Incorrect operations of a Multi-Robot System (MRS) may not only lead to unsatisfactory results, but can also cause economic losses and threats to safety. These threats may not always be apparent, since they may arise as unforeseen consequences of the interactions between elements of the system. This call for tools and techniques that can help in providing guarantees about MRSs behaviour. We think that, whenever possible, these guarantees should be backed up by formal proofs to complement traditional approaches based on testing and simulation. We believe that tailored linguistic support to specify MRSs is a major step towards this goal. In particular, reducing the gap between typical features of an MRS and the level of abstraction of the linguistic primitives would simplify both the specification of these systems and the verification of their properties. In this work, we review different agent-oriented languages and their features; we then consider a selection of case studies of interest and implement them useing the surveyed languages. We also evaluate and compare effectiveness of the proposed solution, considering, in particular, easiness of expressing non-trivial behaviour.Comment: Changed formattin