A Universal Semi-totalistic Cellular Automaton on Kite and Dart Penrose Tilings

In this paper we investigate certain properties of semi-totalistic cellular automata (CA) on the well known quasi-periodic kite and dart two dimensional tiling of the plane presented by Roger Penrose. We show that, despite the irregularity of the underlying grid, it is possible to devise a semi-totalistic CA capable of simulating any boolean circuit on this aperiodic tiling.Comment: In Proceedings AUTOMATA&JAC 2012, arXiv:1208.249

Fault Tolerance in Cellular Automata at Low Fault Rates

A commonly used model for fault-tolerant computation is that of cellular automata. The essential difficulty of fault-tolerant computation is present in the special case of simply remembering a bit in the presence of faults, and that is the case we treat in this paper. The conceptually simplest mechanism for correcting errors in a cellular automaton is to determine the next state of a cell by taking a majority vote among its neighbors (including the cell itself, if necessary to break ties). We are interested in which regular two-dimensional tessellations can tolerate faults using this mechanism, when the fault rate is sufficiently low. We consider both the traditional transient fault model (where faults occur independently in time and space) and a recently introduced combined fault model which also includes manufacturing faults (which occur independently in space, but which affect cells for all time). We completely classify regular two-dimensional tessellations as to whether they can tolerate combined transient and manufacturing faults, transient faults but not manufacturing faults, or not even transient faults.Comment: i+26 p

Proceedings of JAC 2010. Journées Automates Cellulaires

The second Symposium on Cellular Automata “Journ´ees Automates Cellulaires” (JAC 2010) took place in Turku, Finland, on December 15-17, 2010. The first two conference days were held in the Educarium building of the University of Turku, while the talks of the third day were given onboard passenger ferry boats in the beautiful Turku archipelago, along the route Turku–Mariehamn–Turku. The conference was organized by FUNDIM, the Fundamentals of Computing and Discrete Mathematics research center at the mathematics department of the University of Turku. The program of the conference included 17 submitted papers that were selected by the international program committee, based on three peer reviews of each paper. These papers form the core of these proceedings. I want to thank the members of the program committee and the external referees for the excellent work that have done in choosing the papers to be presented in the conference. In addition to the submitted papers, the program of JAC 2010 included four distinguished invited speakers: Michel Coornaert (Universit´e de Strasbourg, France), Bruno Durand (Universit´e de Provence, Marseille, France), Dora Giammarresi (Universit` a di Roma Tor Vergata, Italy) and Martin Kutrib (Universit¨at Gie_en, Germany). I sincerely thank the invited speakers for accepting our invitation to come and give a plenary talk in the conference. The invited talk by Bruno Durand was eventually given by his co-author Alexander Shen, and I thank him for accepting to make the presentation with a short notice. Abstracts or extended abstracts of the invited presentations appear in the first part of this volume. The program also included several informal presentations describing very recent developments and ongoing research projects. I wish to thank all the speakers for their contribution to the success of the symposium. I also would like to thank the sponsors and our collaborators: the Finnish Academy of Science and Letters, the French National Research Agency project EMC (ANR-09-BLAN-0164), Turku Centre for Computer Science, the University of Turku, and Centro Hotel. Finally, I sincerely thank the members of the local organizing committee for making the conference possible. These proceedings are published both in an electronic format and in print. The electronic proceedings are available on the electronic repository HAL, managed by several French research agencies. The printed version is published in the general publications series of TUCS, Turku Centre for Computer Science. We thank both HAL and TUCS for accepting to publish the proceedings.Siirretty Doriast

Boolean Delay Equations: A simple way of looking at complex systems

Boolean Delay Equations (BDEs) are semi-discrete dynamical models with Boolean-valued variables that evolve in continuous time. Systems of BDEs can be classified into conservative or dissipative, in a manner that parallels the classification of ordinary or partial differential equations. Solutions to certain conservative BDEs exhibit growth of complexity in time. They represent therewith metaphors for biological evolution or human history. Dissipative BDEs are structurally stable and exhibit multiple equilibria and limit cycles, as well as more complex, fractal solution sets, such as Devil's staircases and ``fractal sunbursts``. All known solutions of dissipative BDEs have stationary variance. BDE systems of this type, both free and forced, have been used as highly idealized models of climate change on interannual, interdecadal and paleoclimatic time scales. BDEs are also being used as flexible, highly efficient models of colliding cascades in earthquake modeling and prediction, as well as in genetics. In this paper we review the theory of systems of BDEs and illustrate their applications to climatic and solid earth problems. The former have used small systems of BDEs, while the latter have used large networks of BDEs. We moreover introduce BDEs with an infinite number of variables distributed in space (``partial BDEs``) and discuss connections with other types of dynamical systems, including cellular automata and Boolean networks. This research-and-review paper concludes with a set of open questions.Comment: Latex, 67 pages with 15 eps figures. Revised version, in particular the discussion on partial BDEs is updated and enlarge

Proceedings of AUTOMATA 2010: 16th International workshop on cellular automata and discrete complex systems

International audienceThese local proceedings hold the papers of two catgeories: (a) Short, non-reviewed papers (b) Full paper

An Artistic Perspective on Distributed Computer Networks. Creativity in Human-Machine Systems

This thesis is written from an artistic perspective as a reflection on currently significant discussions in media theory, with a focus on the impact of technology on society. While mapping boundaries of contemporary art, post-digital art is considered the best for describing current discourses in media theory in the context of this research. Bringing into the discussion artworks by Martin Howse & Jonathan Kemp (2001-2008), Maurizio Bolognini (Bolognini 1988-present), and myself (mi_ga 2006), among many others, this research defines post-digital art, which in turn defines a complexity of interactions between elements of different natures, such as the living and non-living, human and machine, art and science. Within the analysis of P2P networks, I highlight Milgram's (1967) idea of six degrees of separation, which, at least from a speculative point of view, is interesting for the implementation of human-machine concepts in future technological developments. From this perspective, I argue that computer networks could, in the future, have more potential for merging with society if developed similarly to the computer routing scheme implemented in the Freenet distributed information storage and retrieval system. The thesis then describes my own artwork, 0.30402944246776265, including two newly developed plugins for the Freenet storage system; the first plugin is constructed to fulfill the idea of interacting elements of different natures (in this case, the WWW and Freenet), while the other plugin attempts to visualize data flow within the Freenet storage and retrieval system. All together, this paper proposes that a reconsideration of distributed and self-organized information systems, through an artistic and philosophical lens, can open up a space for the rethinking of the current integration of society and technology

Mathematical Modeling of Oxygen Transport, Cell Killing and Cell Decision Making in Photodynamic Therapy of Cancer

In this study we present a model of in vitro cell killing through type II Photodynamic Therapy (PDT) for simulation of the molecular interactions leading to cell death in time domain in the presence of oxygen transport within a spherical cell. By coupling the molecular kinetics to cell killing, we develop a modeling method of PDT cytotoxicity caused by singlet oxygen and obtain the cell survival ratio as a function of light fluence or initial photosensitizer concentration with different photon density or irradiance of incident light and other parameters of oxygen transport. A systems biology model is developed to account for the detailed molecular pathways induced by PDT treatment leading to cell killing. We derive a mathematical model of cell decision making through a binary cell fate decision scheme on cell death or survival, during and after PDT treatment, and we employ a rate distortion theory as the logical design for this decision making proccess to understand the biochemical processing of information by a cell. Rate distortion theory is also used to design a time dependent Blahut-Arimoto algorithm of three variables where the input is a stimulus vector composed of the time dependent concentrations of three PDT induced signaling molecules and the output reflects a cell fate decision. The concentrations of molecules involved in the biochemical processes are determined by a group of rate equations which produce the probability of cell survival or death as the output of cell decision. The modeling of the cell decision strategy allows quantitative assessment of the cell survival probability, as a function of multiple parameters and coefficients used in the model, which can be modified to account for heterogeneous cell response to PDT or other killing or therapeutic agents. The numerical results show that the present model of type II PDT yields a powerful tool to quantify various processes underlying PDT at the molecular and cellular levels and to interpret experimental results of in vitro cell studies. Finally, following an alternative approach, the cell survival probability is modeled as a predator - prey equation where predators are cell death signaling molecules and prey is the cell survival. The two models can be compared to each other as well as directly to the experimental results of measured molecular concentrations and cell survival ratios for optimization of models, to gain insights on in vitro cell studies of PDT.  Ph.D