Constructive Algebraic Topology

The classical ``computation'' methods in Algebraic Topology most often work by means of highly infinite objects and in fact +are_not+ constructive. Typical examples are shown to describe the nature of the problem. The Rubio-Sergeraert solution for Constructive Algebraic Topology is recalled. This is not only a theoretical solution: the concrete computer program +Kenzo+ has been written down which precisely follows this method. This program has been used in various cases, opening new research subjects and producing in several cases significant results unreachable by hand. In particular the Kenzo program can compute the first homotopy groups of a simply connected +arbitrary+ simplicial set.Comment: 24 pages, background paper for a plenary talk at the EACA Congress of Tenerife, September 199

Cinnamons: A Computation Model Underlying Control Network Programming

We give the easily recognizable name "cinnamon" and "cinnamon programming" to a new computation model intended to form a theoretical foundation for Control Network Programming (CNP). CNP has established itself as a programming paradigm combining declarative and imperative features, built-in search engine, powerful tools for search control that allow easy, intuitive, visual development of heuristic, nondeterministic, and randomized solutions. We define rigorously the syntax and semantics of the new model of computation, at the same time trying to keep clear the intuition behind and to include enough examples. The purposely simplified theoretical model is then compared to both WHILE-programs (thus demonstrating its Turing-completeness), and the "real" CNP. Finally, future research possibilities are mentioned that would eventually extend the cinnamon programming into the directions of nondeterminism, randomness, and fuzziness.Comment: 7th Intl Conf. on Computer Science, Engineering & Applications (ICCSEA 2017) September 23~24, 2017, Copenhagen, Denmar

Intrinsic Universality in Self-Assembly

We show that the Tile Assembly Model exhibits a strong notion of universality where the goal is to give a single tile assembly system that simulates the behavior of any other tile assembly system. We give a tile assembly system that is capable of simulating a very wide class of tile systems, including itself. Specifically, we give a tile set that simulates the assembly of any tile assembly system in a class of systems that we call \emph{locally consistent}: each tile binds with exactly the strength needed to stay attached, and that there are no glue mismatches between tiles in any produced assembly. Our construction is reminiscent of the studies of \emph{intrinsic universality} of cellular automata by Ollinger and others, in the sense that our simulation of a tile system $T$ by a tile system $U$ represents each tile in an assembly produced by $T$ by a $c \times c$ block of tiles in $U$, where $c$ is a constant depending on $T$ but not on the size of the assembly $T$ produces (which may in fact be infinite). Also, our construction improves on earlier simulations of tile assembly systems by other tile assembly systems (in particular, those of Soloveichik and Winfree, and of Demaine et al.) in that we simulate the actual process of self-assembly, not just the end result, as in Soloveichik and Winfree's construction, and we do not discriminate against infinite structures. Both previous results simulate only temperature 1 systems, whereas our construction simulates tile assembly systems operating at temperature 2

Self-Assembly of Infinite Structures

We review some recent results related to the self-assembly of infinite structures in the Tile Assembly Model. These results include impossibility results, as well as novel tile assembly systems in which shapes and patterns that represent various notions of computation self-assemble. Several open questions are also presented and motivated

Elements of a Theory of Simulation

Unlike computation or the numerical analysis of differential equations, simulation does not have a well established conceptual and mathematical foundation. Simulation is an arguable unique union of modeling and computation. However, simulation also qualifies as a separate species of system representation with its own motivations, characteristics, and implications. This work outlines how simulation can be rooted in mathematics and shows which properties some of the elements of such a mathematical framework has. The properties of simulation are described and analyzed in terms of properties of dynamical systems. It is shown how and why a simulation produces emergent behavior and why the analysis of the dynamics of the system being simulated always is an analysis of emergent phenomena. A notion of a universal simulator and the definition of simulatability is proposed. This allows a description of conditions under which simulations can distribute update functions over system components, thereby determining simulatability. The connection between the notion of simulatability and the notion of computability is defined and the concepts are distinguished. The basis of practical detection methods for determining effectively non-simulatable systems in practice is presented. The conceptual framework is illustrated through examples from molecular self-assembly end engineering.Comment: Also available via http://studguppy.tsasa.lanl.gov/research_team/ Keywords: simulatability, computability, dynamics, emergence, system representation, universal simulato