20,827 research outputs found
On the Properties of Language Classes Defined by Bounded Reaction Automata
Reaction automata are a formal model that has been introduced to investigate
the computing powers of interactive behaviors of biochemical reactions([14]).
Reaction automata are language acceptors with multiset rewriting mechanism
whose basic frameworks are based on reaction systems introduced in [4]. In this
paper we continue the investigation of reaction automata with a focus on the
formal language theoretic properties of subclasses of reaction automata, called
linearbounded reaction automata (LRAs) and exponentially-bounded reaction
automata (ERAs). Besides LRAs, we newly introduce an extended model (denoted by
lambda-LRAs) by allowing lambda-moves in the accepting process of reaction, and
investigate the closure properties of language classes accepted by both LRAs
and lambda-LRAs. Further, we establish new relationships of language classes
accepted by LRAs and by ERAs with the Chomsky hierarchy. The main results
include the following : (i) the class of languages accepted by lambda-LRAs
forms an AFL with additional closure properties, (ii) any recursively
enumerable language can be expressed as a homomorphic image of a language
accepted by an LRA, (iii) the class of languages accepted by ERAs coincides
with the class of context-sensitive languages.Comment: 23 pages with 3 figure
A simple model of the Belousov-Zhabotinsky reaction from first principles
The Belousov-Zhabotinsky (BZ) reaction is an example of a temporally oscillating chemical
reaction. An unusual and interesting feature of the reaction is that as it progresses on a twodimensional
plate, self-organized spirals are formed. Many computer models have been constructed
of the BZ reaction to simulate the evolution of these spirals. The models typically use
cellular automata to allow progression of a wavefront through a notional substrate. Usually a
single substrate is used with somewhat arbitrary transference rules. Here it is shown that cellular
automata models of BZ spirals can be created by using a very simple set of equations based
on a three substrate model with close connection to reaction-diffusion models, more closely resembling
the actual BZ reaction. Source code for the model is given in the Processing language
Reaction Automata
Reaction systems are a formal model that has been introduced to investigate
the interactive behaviors of biochemical reactions. Based on the formal
framework of reaction systems, we propose new computing models called reaction
automata that feature (string) language acceptors with multiset manipulation as
a computing mechanism, and show that reaction automata are computationally
Turing universal. Further, some subclasses of reaction automata with space
complexity are investigated and their language classes are compared to the ones
in the Chomsky hierarchy.Comment: 19 pages, 6 figure
Evolving localizations in reaction-diffusion cellular automata
We consider hexagonal cellular automata with immediate cell neighbourhood and
three cell-states. Every cell calculates its next state depending on the
integral representation of states in its neighbourhood, i.e. how many
neighbours are in each one state. We employ evolutionary algorithms to breed
local transition functions that support mobile localizations (gliders), and
characterize sets of the functions selected in terms of quasi-chemical systems.
Analysis of the set of functions evolved allows to speculate that mobile
localizations are likely to emerge in the quasi-chemical systems with limited
diffusion of one reagent, a small number of molecules is required for
amplification of travelling localizations, and reactions leading to stationary
localizations involve relatively equal amount of quasi-chemical species.
Techniques developed can be applied in cascading signals in nature-inspired
spatially extended computing devices, and phenomenological studies and
classification of non-linear discrete systems.Comment: Accepted for publication in Int. J. Modern Physics
A New Class of Cellular Automata for Reaction-Diffusion Systems
We introduce a new class of cellular automata to model reaction-diffusion
systems in a quantitatively correct way. The construction of the CA from the
reaction-diffusion equation relies on a moving average procedure to implement
diffusion, and a probabilistic table-lookup for the reactive part. The
applicability of the new CA is demonstrated using the Ginzburg-Landau equation.Comment: 4 pages, RevTeX 3.0 , 3 Figures 214972 bytes tar, compressed,
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Exploring the concept of interaction computing through the discrete algebraic analysis of the Belousov–Zhabotinsky reaction
Interaction computing (IC) aims to map the properties of integrable low-dimensional non-linear dynamical systems to the discrete domain of finite-state automata in an attempt to reproduce in software the self-organizing and dynamically stable properties of sub-cellular biochemical systems. As the work reported in this paper is still at the early stages of theory development it focuses on the analysis of a particularly simple chemical oscillator, the Belousov-Zhabotinsky (BZ) reaction. After retracing the rationale for IC developed over the past several years from the physical, biological, mathematical, and computer science points of view, the paper presents an elementary discussion of the Krohn-Rhodes decomposition of finite-state automata, including the holonomy decomposition of a simple automaton, and of its interpretation as an abstract positional number system. The method is then applied to the analysis of the algebraic properties of discrete finite-state automata derived from a simplified Petri net model of the BZ reaction. In the simplest possible and symmetrical case the corresponding automaton is, not surprisingly, found to contain exclusively cyclic groups. In a second, asymmetrical case, the decomposition is much more complex and includes five different simple non-abelian groups whose potential relevance arises from their ability to encode functionally complete algebras. The possible computational relevance of these findings is discussed and possible conclusions are drawn
Reaction-diffusion fronts with inhomogeneous initial conditions
Properties of reaction zones resulting from A+B -> C type reaction-diffusion
processes are investigated by analytical and numerical methods. The reagents A
and B are separated initially and, in addition, there is an initial macroscopic
inhomogeneity in the distribution of the B species. For simple two-dimensional
geometries, exact analytical results are presented for the time-evolution of
the geometric shape of the front. We also show using cellular automata
simulations that the fluctuations can be neglected both in the shape and in the
width of the front.Comment: 11 pages, 3 figures, submitted to J. Phys.
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