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The completion of the first draft of the human genome has led to an explosion of interest in genetics and molecular biology.The view of the genome as a network of interacting computational components is well-established, but researchers are now trying to reverse the analogy, by using living organisms to construct logic circuits.The potential applications for such technologies is huge, ranging from bio-sensors, through industrial applications to drug delivery and diagnostics.This book would be the first to deal with the implementation of this technology, describing several working experimental demonstrations using cells as components of logic circuits, building toward computers incorporating biological components in their functioning. ... Read more

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Table of contents for this book
Table of contents

Part I: Theoretical and Engineering Principles

1.An Introduction to Cellular Computing
Martyn Amos and Gerald Owenson

2.Proteins and Information Processing
Ray Paton, Michael Fisher, Grant Malcolm and Koichiro Matsuno

3.Enzyme Genetic Programming
Michael Lones and Andy Tyrell

4.Genetic Process Engineering
Ron Weiss, Thomas F. Knight Jr. and Gerald Sussman

5.The Device Science of Whole Cells as Components in Microscaleand Nanoscale Systems
Michael L. Simpson, Gary S. Sayler, et al.

Part II: Laboratory Experiments

6.The Enterococcus faecilis Information Gate
Kenichi Wakabayashi and Masayuki Yamamura

7.Cellular Computation and Communication Using Engineered Genetic Regulatory Networks
Ron Weiss, Thomas F. Knight Jr. and Gerald Sussman

8.The Biology of Integration of Cells in Microscale and Nanoscale Systems
Michael L. Simpson, Timothy E. McKnight, et al.

Part III: Computation in Ciliates

9.Encrypted Genes and Their Assembly in Ciliates
David M. Prescott and Grzegorz Rozenberg

10. Biocomputation in Ciliates
Lila Kari and Laura F. Landweber ... Read more

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Proceedings of the 4th International Workshop on Implementing Automata, WIA'99, held July 17-19, 2001 in Potsdam, Germany. Papers are devoted to issues of implementing automata of various types; parsing, finite languages, speech recognition, image and signal processing and systems analysis. Softcover. ... Read more

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This book constitutes the refereed proceedings of the Second International Conference on Language and Automata Theory and Applications, LATA 2008, held in Tarragona, Spain, in March 2008.

The 40 revised full papers presented were carefully reviewed and selected from 134 submissions. The papers deal with the various issues related to automata theory and formal languages.

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This book constitutes the thoroughly refereed post-proceedings of the 7th International Conference on Implementation and Application of Automata, CIAA 2002, held in Tours, France, in July 2002. The 28 revised full papers presented together with an invited paper and 4 short papers were carefully selected during two rounds of reviewing and revision. The topics addressed range from theoretical and methodological issues to automata applications in software engineering, natural language processing, speech recognition, and image processing, to new representations and algorithms for efficient implementation of automata and related structures. ... Read more

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This book constitutes the thoroughly refereed post-proceedings of the 6th International Conference on Implementation and Application of Automata, CIAA 2001, held in Pretoria, South Africa in July 2001.

The 23 revised full papers presented together with an invited paper were carefully selected during two rounds of reviewing and revision. The topics addressed from theoretical as well as application-oriented viewpoints range from foundational and methodological issues to novel applications in object-oriented modeling, finite transducers in natural language processing, and non-deterministic finite-state models in communication protocols. ... Read more

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Proceedings of the 5th International Conference, CIAA 2000, held July 24-25, 2000 in London, Ontario, Canada. Topics addressed from theoretical as well as application oriented viewpoints range from automata applications in software engineering to new representations and algorithms for efficient implementation of automata. Softcover. ... Read more

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Cellular Automata in Hyperbolic Spaces, Volume I: Theory introduces a hot topic in mathematics and computer science at the edge of hyperbolic geometry and cellular automata.

A hyperbolic space is a geometric model where through a given point there are two distinct parallels to a given line. A cellular automaton is a set of cells which are uniformly distributed in a space, connected locally and which update their states by the same rule.

Cellular Automata in Hyperbolic Spaces, Volume I: Theory presents novel results on location of tiles in many tilings of the hyperbolic place.These results are employed to implement emerging non-classical types of cellular automata and offer insights into accessing and transferring information in hyperbolic spaces.

Hyperbolic geometry is an essential part of theoretical astrophysics and cosmology; therefore ideas discussed in the book will play an important role in the theory of relativity.In addition to specialists in these traditional fields of application, many specialists in new domains are beginning to show a growing interest in hyperbolic geometry and cellular automata.This is especially the case in biology and computer science.

Cellular Automata in Hyperbolic Spaces, Volume I, Theory is a unique work which skillfully hybridizes two differentdomains of geometry and computation in a way beneficial for mathematics, computer science and engineering.Interest in the concepts, and their possible implementations, contained in this outstanding treatise is sure to last for decades. ... Read more

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Cellular Automata in Hyperbolic Spaces Volume II: Implementation and Computations introduces the hot topic of mathematics and computer science at the edge of hyperbolic geometry and cellular automata. A hyperbolic space is a geometric model where, through a given point, there are two distinct parallels to a given line. A cellular automaton is a set of cells that are uniformly distributed in a space, connected locally and update which their states by the same rule.This volume advances the novel results presented in Volume 1 on a location of tiles in many tilings of the hyperbolic plane. These results are applied in further studies of cellular automata in non-traditional spaces. We discuss a wide range of applications from cell phones to the theoretical problems of tilings. Hyperbolic geometry is an essential part of theoretical astrophysics and cosmology; therefore ideas discussed in the book will play an important role in the theory of relativity.In addition to specialists of these traditional fields of application, many specialists in new domains are beginning to show a growing interest in both hyperbolic geometry and cellular automata. This is especially the case in biology and in computer science.Cellular Automata in Hyperbolic Spaces Volume II: Implementation and Computations skillfully hybridizes the different disciplines of geometry and computation and is certain to be beneficial in the fields of mathematics, computer science and engineering. An outstanding treatise of concepts and implementations, the book will prove to be relevant for decades.Contains ten pages of color plates ... Read more

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This book constitutes the refereed proceedings of the 9th International Conference on Cellular Automata for Research and Industry, ACRI 2010, held in Ascoli Piceno, Italy, in September 2010.The first part of the volume contains 39 revised papers that were carefully reviewed and selected from the main conference; they are organized according to six main topics: theoretical results on cellular automata, modeling and simulation with cellular automata, CA dynamics, control and synchronization, codes and cryptography with cellular automata, cellular automata and networks, as well as CA-based hardware. The second part of the volume comprises 35 revised papers dedicated to contributions presented during ACRI 2010 workshops on theoretical advances, specifically asynchronous cellular automata, and challenging application contexts for cellular automata: crowds and CA, traffic and CA, and the international workshop of natural computing. ... Read more

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Urban development and migration from rural to urban areas are impacting prime agricultural land and natural landscapes, particularly in the less developed countries. These phenomena will persist and require serious study by those monitoring global environmental change. To address this need, various models have been devised to analyze urbanization and the physical, socioeconomic, and institutional factors impacting urban development.

The most promising and rapidly developing of these paradigms take advantage of new Geographical Information System (GIS) technology. Modelling Urban Development with Geographical Information Systems and Cellular Automata presents one such cutting-edge model that is more than just predictive. It describes how the model simulates the urbanization process, and it provides theoretical context to promote understanding. Starting with a practical overview of the modelling techniques used in urban development research, the author focuses on the cellular automata model and its greatest strength – the incorporation of fuzzy set and fuzzy logic approaches through which urban development can be viewed as a spatially and temporally continuous process.

Real-Life Application to Develop Future Planning Methods
The text describes a landmark study underway, in which the fuzzy constrained cellular automata model has been implemented in a GIS environment to simulate urban development in Sydney, Australia. Featuring a survey of associated research and a geographical database for the Sydney simulation, this book answers many general "what if" questions for urban planners and details a new approach that they can adapt to their own testing and evaluation needs. This modeling method will provide researchers and planners with the means to not just predict population trends, but to better prepare for their consequences.

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Cellular operations will play a critical role in designing and programming nano-scale computers. In this book a cellular operation is defined as an operation which uses information within a neighborhood to perform either local or global computational tasks. Cellular operations can be used to solve complex and computation-intensive problems such as parallel learning. Cellular operations can also be used to simulate and explain different kinds of physical phenomena such as small-world phenomena.Since many cellular computational platforms, such as cellular automata and cellular neural networks are proven to be as universal as the Turing machine, cellular operations can be used to solve any computable problems in Turing sense. Therefore, a cellular computer based on cellular operations can serve as an all-purpose computer.The cellular image operators presented in this book can help the design of image processing tasks for different hardware platforms based on either CPU or cellular processors. This book also provides a powerful toolbox for designing cellular hardware platforms such as nano-scale array processors and VLSI array processors. On the one hand, this book can help physicists to understand how cellular automata and fuzzy cellular automata can be used to solve engineering problems. On the other hand, this book can help electrical engineers to design software for cellular computers based on either micro-electronics or nano-electronics. This book can also serve as a handbook of parallel image processing for experts from the image processing community. ... Read more

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This volume arose from courses given at the Second School on Statistical Physics and Cooperative Systems, Santiago, Chile, December 1990. It contains a selection of survey papers on recent trends in the fields of statistical physics, automata networks and dynamical systems. The various papers included deal with topics such as chaotic systems, turbulence, transport, cellular automata, fractals, neural networks, optimization problems, and spin glasses. This work is aimed at mathematicians, physicists and engineers interested in cellular automata, dynamical systems, statistical physics and neural networks. ... Read more

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This volume contains the proceedings of the 14th Spring School of the LITP (Laboratoire d`Informatique Théorique et de Programmation, Université Paris VI-VII, CNRS) held May 12-16, 1986 in Argelès-Village on the French Catalan coast. This meeting was organized by C. Choffrut, M. Nivat, F. Robert, P. Sallé and gathered a hundred participants. The proceedings of the last two Spring Schools have already been published in this series and deal with "Automata on Infinite Words" (LNCS 192) and "Combinators and Functional Programming Languages" (LNCS 242). The purpose of this yearly meeting is to present the state of the art in a specific topic which has gained considerable maturity. The field chosen this year was the theory of automata networks. Though the content of this book is essentially restricted to computer science aspects of the topic, illustrations were given at the meeting on how the model of cellular automata could be used to solve problems in statistical, fluid and solid state mechanics. Applications to biology with growth models also exist. ... Read more

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Microporous materials such as zeolites are widely used in many different areas of application ranging from catalysis to molecular sieving. The spatial structure of a zeolite is made up of a static network of channels and cages able to host and exchange guest molecules. Exploiting the analogy with the discrete nature of Cellular Automata (CA), a probabilistic model has been developed to capture both static and transport properties of diffusing species in zeolites at a mesoscopic, coarse-grained level. This model focuses on the sensitivity of each cell (representing a zeolite pore) upon its instantaneous occupancy to mimic the effects of the guest-host and guest-guest interactions observed in real zeolites. Local partition functions and kinetic barriers are used to build up a simple and fast evolution rule allowing it to reproduce data from experimental data and/or atomistic simulations. With its local and parallel nature and its drastically reduced number of degrees of freedom, such an approach can be exploited to enlarge the scales of space and time in numerical simulations of diffusion in zeolites. ... Read more

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This book studies the relationship between automata and monadic second-order logic, focusing on classes of automata that describe the concurrent behavior of distributed systems. It provides a unifying theory of communicating automata and their logical properties. Based on Hanf's Theorem and Thomas's graph acceptors, it develops a result that allows characterization of many popular models of distributed computation in terms of the existential fragment of monadic second-order logic.

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Cancer cells display characteristic traits acquired in a step-wise manner during carcinogenesis. Some of these traits are autonomous growth, induction of angiogen- esis, invasion and metastasis. In this thesis, the focus is on one of the latest stages of tumor progression, tumor invasion. Tumor invasion emerges from the combined effect of tumor cell-cell and cell-microenvironment interactions, which can be studied with the help of mathematical analysis. Cellular automata (CA) can be viewed as simple models of self-organizing complex systems in which collective behavior can emerge out of an ensemble of many interacting "simple" components. In particular, we focus on an important class of CA, the so-called lattice-gas cellular automata (LGCA). Here, the principal tools of mathematical analysis of LGCA are the mean-field approximation and the corresponding Lattice Boltzmann equation. The main objective of this thesis is to investigate important aspects of tumor invasion, under the microscope of mathematical modeling and analysis: -Impact of the tumor environment -Effect of tumor cell proliferation and migration -Mechanisms of tumor invasion emergence -Computing in vivo tumor invasion ... Read more

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This book covers the basic and applied mathematics of locally interacting highly nonlinear multicomponent systems which have biological and technological applications including neural networks. It shows the behaviour which such systems can display and investigates both their abstract aspect and their applications to the problems of morphogenesis, neuronal activity and the theory of queues. Numerical and simulation results are appended wherever possible to the analyses. The subject lies at the intersection of many disciplines including mathematical physiology, statistical physics and deterministic cellular automata. Therefore, besides the cited applications, the theory is also of great relevance to the modelling of other biological, chemical, physical and socio-economic systems such as plant competition, genetics, enzymology and election voting. The book reviews the mathematical background and main results of the Russian school of investigators and broadens the co-operation between pure and applied mathematicians within biology, making it relevant to researchers working on nonlinear studies within both mathematics and science departments. ... Read more