Localization dynamics in a binary two-dimensional cellular automaton: the Diffusion Rule

We study a two-dimensional cellular automaton (CA), called Diffusion Rule (DR), which exhibits diffusion-like dynamics of propagating patterns. In computational experiments we discover a wide range of mobile and stationary localizations (gliders, oscillators, glider guns, puffer trains, etc), analyze spatio-temporal dynamics of collisions between localizations, and discuss possible applications in unconventional computing.Comment: Accepted to Journal of Cellular Automat

Phenomenology of retained refractoriness: On semi-memristive discrete media

We study two-dimensional cellular automata, each cell takes three states: resting, excited and refractory. A resting cell excites if number of excited neighbours lies in a certain interval (excitation interval). An excited cell become refractory independently on states of its neighbours. A refractory cell returns to a resting state only if the number of excited neighbours belong to recovery interval. The model is an excitable cellular automaton abstraction of a spatially extended semi-memristive medium where a cell's resting state symbolises low-resistance and refractory state high-resistance. The medium is semi-memristive because only transition from high- to low-resistance is controlled by density of local excitation. We present phenomenological classification of the automata behaviour for all possible excitation intervals and recovery intervals. We describe eleven classes of cellular automata with retained refractoriness based on criteria of space-filling ratio, morphological and generative diversity, and types of travelling localisations

The Kinetic Basis of Self-Organized Pattern Formation

In his seminal paper on morphogenesis (1952), Alan Turing demonstrated that different spatio-temporal patterns can arise due to instability of the homogeneous state in reaction-diffusion systems, but at least two species are necessary to produce even the simplest stationary patterns. This paper is aimed to propose a novel model of the analog (continuous state) kinetic automaton and to show that stationary and dynamic patterns can arise in one-component networks of kinetic automata. Possible applicability of kinetic networks to modeling of real-world phenomena is also discussed.Comment: 8 pages, submitted to the 14th International Conference on the Synthesis and Simulation of Living Systems (Alife 14) on 23.03.2014, accepted 09.05.201

Two dimensional outflows for cellular automata with shuffle updates

In this paper, we explore the two-dimensional behavior of cellular automata with shuffle updates. As a test case, we consider the evacuation of a square room by pedestrians modeled by a cellular automaton model with a static floor field. Shuffle updates are characterized by a variable associated to each particle and called phase, that can be interpreted as the phase in the step cycle in the frame of pedestrian flows. Here we also introduce a dynamics for these phases, in order to modify the properties of the model. We investigate in particular the crossover between low- and high-density regimes that occurs when the density of pedestrians increases, the dependency of the outflow in the strength of the floor field, and the shape of the queue in front of the exit. Eventually we discuss the relevance of these results for pedestrians.Comment: 20 pages, 5 figures. v2: 16 pages, 5 figures; changed the title, abstract and structure of the paper. v3: minor change

DNA Computing by Self-Assembly

Information and algorithms appear to be central to biological organization and processes, from the storage and reproduction of genetic information to the control of developmental processes to the sophisticated computations performed by the nervous system. Much as human technology uses electronic microprocessors to control electromechanical devices, biological organisms use biochemical circuits to control molecular and chemical events. The engineering and programming of biochemical circuits, in vivo and in vitro, would transform industries that use chemical and nanostructured materials. Although the construction of biochemical circuits has been explored theoretically since the birth of molecular biology, our practical experience with the capabilities and possible programming of biochemical algorithms is still very young