Advances in unconventional computing

Free ebooks ==> www.Ebook777.com Emergence, Complexity and Computation ECC Andrew Adamatzky Editor Advances in Unconventional Computing Volume 2: Prototypes, Models and Algorithms Emergence, Complexity and Computation Volume 23 Series editors Ivan Zelinka, Technical University of Ostrava, Ostrava, Czech Republic e-mail: ivan.zelinka@vsb.cz Andrew Adamatzky, University of the West of England, Bristol, UK e-mail: adamatzky@gmail.com Guanrong Chen, City University of Hong Kong, Hong Kong, China e-mail: eegchen@cityu.edu.hk Editorial Board Ajith Abraham, MirLabs, USA Ana Lucia C Bazzan, Universidade Federal Rio Grande Sul, Porto Alegre, RS, Brazil Juan C Burguillo, University of Vigo, Spain Sergej Čelikovský, Academy of Sciences of the Czech Republic, Czech Republic Mohammed Chadli, University of Jules Verne, France Emilio Corchado, University of Salamanca, Spain Donald Davendra, Technical University of Ostrava, Czech Republic Andrew Ilachinski, Center for Naval Analyses, USA Jouni Lampinen, University of Vaasa, Finland Martin Middendorf, University of Leipzig, Germany Edward Ott, University of Maryland, USA Linqiang Pan, Huazhong University of Science and Technology, Wuhan, China Gheorghe Păun, Romanian Academy, Bucharest, Romania Hendrik Richter, HTWK Leipzig University of Applied Sciences, Germany Juan A Rodriguez-Aguilar, IIIA-CSIC, Spain Otto Rössler, Institute of Physical and Theoretical Chemistry, Tübingen, Germany Vaclav Snasel, Technical University of Ostrava, Czech Republic Ivo Vondrák, Technical University of Ostrava, Czech Republic Hector Zenil, Karolinska Institute, Sweden About this Series The Emergence, Complexity and Computation (ECC) series publishes new developments, advancements and selected topics in the fields of complexity, computation and emergence The series focuses on all aspects of reality-based computation approaches from an interdisciplinary point of view especially from applied sciences, biology, physics, or chemistry It presents new ideas and interdisciplinary insight on the mutual intersection of subareas of computation, complexity and emergence and its impact and limits to any computing based on physical limits (thermodynamic and quantum limits, Bremermann’s limit, Seth Lloyd limits…) as well as algorithmic limits (Gödel’s proof and its impact on calculation, algorithmic complexity, the Chaitin’s Omega number and Kolmogorov complexity, non-traditional calculations like Turing machine process and its consequences,…) and limitations arising in artificial intelligence field The topics are (but not limited to) membrane computing, DNA computing, immune computing, quantum computing, swarm computing, analogic computing, chaos computing and computing on the edge of chaos, computational aspects of dynamics of complex systems (systems with self-organization, multiagent systems, cellular automata, artificial life,…), emergence of complex systems and its computational aspects, and agent based computation The main aim of this series it to discuss the above mentioned topics from an interdisciplinary point of view and present new ideas coming from mutual intersection of classical as well as modern methods of computation Within the scope of the series are monographs, lecture notes, selected contributions from specialized conferences and workshops, special contribution from international experts More information about this series at http://www.springer.com/series/10624 Andrew Adamatzky Editor Advances in Unconventional Computing Volume 2: Prototypes, Models and Algorithms 123 Editor Andrew Adamatzky Unconventional Computing Centre University of the West of England Bristol UK ISSN 2194-7287 ISSN 2194-7295 (electronic) Emergence, Complexity and Computation ISBN 978-3-319-33920-7 ISBN 978-3-319-33921-4 (eBook) DOI 10.1007/978-3-319-33921-4 Library of Congress Control Number: 2016940327 © Springer International Publishing Switzerland 2017 This work is subject to copyright All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed The use of general descriptive names, registered names, trademarks, service marks, etc in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer International Publishing AG Switzerland Preface Unconventional computing is a science in flux What is unconventional today will be conventional tomorrow Designs being standard in the past are seen now as a novelty Unconventional computing is a niche for interdisciplinary science, cross-bred of computer science, physics, mathematics, chemistry, electronic engineering, biology, material science and nanotechnology The aims were to uncover and exploit principles and mechanisms of information processing in and functional properties of physical, chemical and living systems to develop efficient algorithms, design optimal architectures and manufacture working prototypes of future and emergent computing devices I invited world’s leading scientists and academicians to describe their vision of unconventional computing and to highlight most promising directions of future research in the field Their response was overwhelmingly enthusiastic: over fifty chapters were submitted spanning almost all fields of natural and engineering sciences Unable to fit over one and half thousands pages into one volume, I grouped the chapters as “theoretical” and “practical” By “theoretical”, I mean constructs and algorithms which have no immediate application domain and not solve any concrete problems, yet they make a solid mathematical or philosophical foundation to unconventional computing “Practical” includes experimental laboratory implementations and algorithms solving actual problems Such a division is biased by my personal vision of the field and should not be taken as an absolute truth The first volume brings us mind-bending revelations from gurus in computing and mathematics The topics covered are computability, (non-)universality and complexity of computation; physics of computation, analogue and quantum computing; reversible and asynchronous devices; cellular automata and other mathematical machines; P-systems and cellular computing; infinity and spatial computation; and chemical and reservoir computing As a dessert, we have two vibrant memoirs by founding fathers of the field The second volume is a tasty blend of experimental laboratory results, modelling and applied computing Emergent molecular computing is presented by enzymatic logical gates and circuits, and DNA nanodevices Reaction–diffusion chemical v vi Preface computing is exemplified by logical circuits in Belousov–Zhabotinsky medium and geometrical computation in precipitating chemical reactions Logical circuits realised with solitons and impulses in polymer chains show advances in collision-based computing Photochemical and memristive devices give us a glimpse into hot topics of novel hardware Practical computing is represented by algorithms of collective and immune-computing and nature-inspired optimisation Living computing devices are implemented in real and simulated cells, regenerating organisms, plant roots and slime mould Musical biocomputing and living architectures make the ending of our unconventional journey non-standard The chapters are self-contained No background knowledge is required to enjoy the book Each chapter is a treatise of marvellous ideas Open the book at a random page and start reading Abandon all stereotypes, conventions and rules Enter the stream of unusual Even a dead fish can go with the flow You can too Bristol, UK March 2016 Andrew Adamatzky Contents Implementing Molecular Logic Gates, Circuits, and Cascades Using DNAzymes Matthew R Lakin, Milan N Stojanovic and Darko Stefanovic Enzyme-Based Reversible Logic Gates Operated in Flow Cells Evgeny Katz and Brian E Fratto Modeling and Modifying Response of Biochemical Processes for Biocomputing and Biosensing Signal Processing Sergii Domanskyi and Vladimir Privman Sensing Parameters of a Time Dependent Inflow with an Enzymatic Reaction Jerzy Gorecki, Joanna N Gorecka, Bogdan Nowakowski, Hiroshi Ueno, Tatsuaki Tsuruyama and Kenichi Yoshikawa 29 61 85 Combinational Logic Circuit Based on BZ Reaction 105 Mingzhu Sun and Xin Zhao Associative Memory in Reaction-Diffusion Chemistry 141 James Stovold and Simon O’Keefe Calculating Voronoi Diagrams Using Chemical Reactions 167 Ben De Lacy Costello and Andrew Adamatzky Light-Sensitive Belousov–Zhabotinsky Computing Through Simulated Evolution 199 Larry Bull, Rita Toth, Chris Stone, Ben De Lacy Costello and Andrew Adamatzky On Synthesis and Solutions of Nonlinear Differential Equations—A Bio-Inspired Approach 213 Ivan Zelinka vii viii Contents 10 Marangoni Flow Driven Maze Solving 237 Kohta Suzuno, Daishin Ueyama, Michal Branicki, Rita Tóth, Artur Braun and István Lagzi 11 Chemotaxis and Chemokinesis of Living and Non-living Objects 245 Jitka Čejková, Silvia Holler, To Quyen Nguyenová, Christian Kerrigan, František Štěpánek and Martin M Hanczyc 12 Computing with Classical Soliton Collisions 261 Mariusz H Jakubowski, Ken Steiglitz and Richard Squier 13 Soliton-Guided Quantum Information Processing 297 Ken Steiglitz 14 Models of Computing on Actin Filaments 309 Stefano Siccardi and Andrew Adamatzky 15 Modeling DNA Nanodevices Using Graph Rewrite Systems 347 Reem Mokhtar, Sudhanshu Garg, Harish Chandran, Hieu Bui, Tianqi Song and John Reif 16 Computational Matter: Evolving Computational Functions in Nanoscale Materials 397 Hajo Broersma, Julian F Miller and Stefano Nichele 17 Unconventional Computing Realized with Hybrid Materials Exhibiting the PhotoElectrochemical Photocurrent Switching (PEPS) Effect 429 Kacper Pilarczyk, Przemysław Kwolek, Agnieszka Podborska, Sylwia Gawęda, Marek Oszajca and Konrad Szaciłowski 18 Organic Memristor Based Elements for Bio-inspired Computing 469 Silvia Battistoni, Alice Dimonte and Victor Erokhin 19 Memristors in Unconventional Computing: How a Biomimetic Circuit Element Can be Used to Do Bioinspired Computation 497 Ella Gale 20 Nature-Inspired Computation: An Unconventional Approach to Optimization 543 Xin-She Yang 21 On Hybrid Classical and Unconventional Computing for Guiding Collective Movement 561 Jeff Jones Free ebooks ==> www.Ebook777.com Contents ix 22 Cellular Automata Ants 591 Nikolaos P Bitsakidis, Nikolaos I Dourvas, Savvas A Chatzichristofis and Georgios Ch Sirakoulis 23 Rough Set Description of Strategy Games on Physarum Machines 615 Krzysztof Pancerz and Andrew Schumann 24 Computing a Worm: Reverse-Engineering Planarian Regeneration 637 Daniel Lobo and Michael Levin 25 An Integrated In Silico Simulation and Biomatter Compilation Approach to Cellular Computation 655 Savas Konur, Harold Fellermann, Larentiu Marian Mierla, Daven Sanassy, Christophe Ladroue, Sara Kalvala, Marian Gheorghe and Natalio Krasnogor 26 Plant Roots as Excellent Pathfinders: Root Navigation Based on Plant Specific Sensory Systems and Sensorimotor Circuits 677 Ken Yokawa and František Baluška 27 Soft Plant Robotic Solutions: Biological Inspiration and Technological Challenges 687 B Mazzolai, V Mattoli and L Beccai 28 Thirty Seven Things to Do with Live Slime Mould 709 Andrew Adamatzky 29 Experiments in Musical Biocomputing: Towards New Kinds of Processors for Audio and Music 739 Eduardo Reck Miranda and Edward Braund 30 Immunocomputing and Baltic Indicator of Global Warming 763 Alexander O Tarakanov and Alla V Borisova 31 Experimental Architecture and Unconventional Computing 773 Rachel Armstrong Index 805 www.Ebook777.com 798 R Armstrong 31.13 Urban Applications We are now living at the time of the Anthropocene [18] an era in Earth’s history where human activity is considered to be shaping geological events Since our cities are so large—occupying around % of the Earth’s land surface [41]—even small changes in their environmental performance may bring significant benefits to our ecosystems Through experimental architectural methods, we can consider how a lifelike materiality for cities conferred by using dissipative structures may provide a different platform for human development than industrial processes The 21st century is the age of the megacity These are metropolitan edifices have already sprung that now house more than 10 million inhabitants and appear ‘endless’ as they stretch over hundreds of square kilometers Yet, through our own design and engineering practices, the materiality of our living spaces is in conflict with the needs of their inhabitants Scarce drinking water is used to flush excrement Fertile soils are being scorched by intense agricultural practices and the produce transported hundreds of miles to provide the illusion of abundance within our urban deserts, which offer little or no fertility of their own, since they are largely devoid of fertile soils Above these metropolitan colossuses the skies are choking with invisible toxins and beyond them, their waste is stretched out into oceans of particulate plastics This scenario demands practical and theoretical research on living materials and technology that builds towards a scenario where architecture not only deals with the manufacturing of objects but also choreographs the flow of matter through our living spaces This may be concentrated in technologized sites that operate as architectural ‘organs’, such as algae bioreactors, which possess unique physiologies that shape the character and performance of spaces If living materials can be practically realized within our buildings, the fabric of our homes and cities may be enabled to perform the equivalent work to machines by orchestrating the molecular flow of matter through our most intimate environments For example, architectural organs may provide biomass for food and fuel—or produce low-level lighting through bioluminescence They could be situated in under used and under imagined spaces such as cavity walls within our homes, or be on proud display like the designs as in Philip’s Microbial home, which is fuelled by the actions of microorganisms [35] In this scenario, our cities will not be imagined as Le Corbusier’s machines for living in [17]—but as ecologies for thriving in— where each city possesses a unique urban metabolism that arises from its natural and architectural physiologies Working with the programmability of dissipative structures brings Nature right into our living spaces in ways that could make our homes more resilient and attractive Yet this is not fiction—such systems are already being developed for installation in the modern built environment We’re already tapping into this relationship between natural systems and machines using renewables—and now, unconventional computing creates the possibility of orchestrating the performance of micro agricultures that may help us live in densely populated spaces in new ways Indeed, in the near future we are likely to see the rise of ‘smart green’ cities where—Nature and digital 31 Experimental Architecture and Unconventional Computing 799 Fig 31.15 Photograph Colt International Arup, SSC Gmbh BIQ house that houses microalgae in faỗade panels containing water They feed on sunlight and carbon dioxide to produce biomass that is collected, dried and burned back in the building to produce energy that offsets carbon emissions 800 R Armstrong information systems are brought together and work together ‘more’ with fewer resources—so that we can meet the needs of our urban populations differently A range of ambitious proposals is currently being tested in experimental contexts and in bespoke building installations that are setting new benchmarks for the next generation of ‘sustainable’ building designs For example, Astudio architects and Sustainable Now Technologies are constructing a bioprocessor for a 6th form college in Twickenham, as a next-generation ecological architecture The bioreactor system provided a focus for the school curriculum by generating outputs that could be used by the students For example, the biomass could be used as a fertilizer for green roofs and walls For example, the BIQ (Intelligent building) in Hamburg opened in November 2014 This apartment block has been constructed with watery facades that house microalgae, which produce biomass from sunlight and carbon dioxide and reduce energy consumption within the residential apartments by virtue of the thermalsolar effect (see Fig 31.15) While explorations such as living facades, are still very much at the experimental stage, they facilitate the convergence of different media so that the technological systems on which we currently rely, not inevitably damage our ecosystems, but may actually strengthen them Ultimately, by combining the self-organizing principles of dissipative structures with conventional technical platforms [40] may produce different kinds of environmental impacts in which the built and living environments mutually reinforce each other to produce a livelier planet 31.14 Conclusion Cross-disciplinary experimental platforms such as, experimental architecture may contribute to the development, pedagogy, social engagement and commercialization of unconventional computing In doing so, a future portfolio of unconventional computers may have significant impacts in underpinning new ways of living and working For example, it may be possible to use some of the strategies of the natural realm to directly address environmental challenges so that we no longer ‘mimic’ nature’s processes but directly apply its organizational ruleset In this way we may be able to go beyond performance limits of biological systems and generate new kinds of materials and spaces that have not yet been encountered For the lifelike qualities of materials at non-equilibrium states to reach a broader sphere of relevance to design and engineering practices, a toolset is needed that enables designers and engineers to compute with and directly manipulate them Experimental architecture works synergistically with unconventional computing to explore these possibilities While the relationships and the practice are not formalized, the juxtaposition between designled and scientific experiments has the potential to create propositions and contexts in which new kinds of computing and technical systems can be explored—both speculatively and practically These projects are not simply fictions but can be hypotheses that are iteratively examined and mapped out through drawings, models and prototypes 31 Experimental Architecture and Unconventional Computing 801 as potential trajectories These explorations may inform further design-led projects or even subsequent scientific experiments Since unconventional computing is an exploratory and creative practice, there are many points of synergy with experimental architecture Yet design disciplines not propose to produce scientific outcomes—or focus on empirical data—but nonetheless add to the field of knowledge by unfolding new possibilities and provoking further questions for exploration that may lead to new applications for science and technology Specifically, developments in the fields of physics and chemistry point towards the importance of dissipative structures in better understanding the organizational principles of living systems and how these may directly be applied to the practice of the built environment These have been discussed in this chapter as a potential platform for unconventional computing by applying experimental architecture to create an environment in which incomplete knowledge can be worked with intuitively and re-informed through design-led experiment Such explorations are complementary to the field of unconventional computing and opens up a space for articulating ideas and developing language protocols that are not dominated by industrial agendas and near to market objectives Instead researchers from across a spectrum of disciplines are enabled to engage imaginatively with the philosophy, theory and practice of knowledge acquisition in unconventional computing to develop its cultural relevance and continue to expand its frontiers in new directions The field of unconventional computing may ultimately wield significant influence on the fabrics that are unique to this planet and even collectively comprise a force capable of geoengineering-scale impacts We may see the advent of new kinds of Nature that are deeply entangled with the NBIC convergence Rather than the current practice of layering green vegetation over grey concrete [21], p 230 to achieve a new kind of urban ‘efficiency’—the ‘grey’ digital technologies of smart cities may be directly threaded into the green fibres of ‘sustainable’ living materials Out of these convergences alternative intelligences, gastrulating architectures, and production platforms for human development may begin to emerge with qualitatively different kinds of impacts that are similar to the natural realm Within these placental enfoldings new architectural strategies, programs and tactics are made available to experimental architects and urban designers, who use iterative, persistent experimentation to explore these spaces Rather than seeking atomic control of events, they embrace risk as a condition of existence and develop a broad palette of lively, multi materialities that incessantly coalesce to provoke new spatial experiences Unconventional computing may equip these designers with a new range of materials and technologies that can help them achieve these aims—fuzzy surfaces, cloudy vistas, fragile details, quantum logic, soft scaffoldings and all kinds of teratogenic in-betweens Such transgressive technical systems may infiltrate the spandrels between the mineralized bones of industrial construction [27] Yet these nascent landscapes and complex, fertile substrates not claim to provide totalizing solutions to the constantly unfolding multiplicities and challenges that we are facing Rather, they catalyse new opportunities for invention by providing an emerging palette of new possibilities and paradoxes from which we may birth new kinds of architectures In this way the built environment shares a common project with the 802 R Armstrong natural realm that can be shaped by human ethics through the production of life’s poetry and our mutual, continued survival into an ever-unfolding adjacent possible that is full of surprises References Adamatzky, A., De Lacy Costello, B.: Reaction-diffusion path planning in a hybrid chemical and cellular-automaton processors Chaos, Solitons Fract 16, 727–736 (2003) Adamatzky, A.De, Lacy Costello, B., Asai, T.: Reaction-Diffusion Computers Elsevier Science, London (2005) Adamatzky, A., Armstrong, R., Jones, J., Gunji, Y.K.: On creativity of slime mould Int J Gen Syst 42(5), 441–457 (2013) Adams, T.: The chemputer that could print out any drug The Observer (2012) www.guardian co.uk/science/2012/jul/21/chemputer-that-prints-out-drugs Accessed 19 Feb 2015 Armstrong, R.: 3D printing will destroy the world unless it tackles the 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Artificial Life XI MIT Press, Cambridge (2008) 52 WETFab : Event booklet School of Chemistry, University of Glasgow (24–25 Jan 2011) http:// www.chem.gla.ac.uk/cronin/files/news/WETFAB.pdf Accessed 26 Feb 2015 53 World Commission on Environment and Development Our Common Future Report of the World Commission on Environment and Development Published as Annex to General Assembly document A/42/427 (1987) www.un-documents.net/our-common-future.pdf Accessed 25 Feb 2015 54 Wolchover, N.: A new physics theory of life Quanta (22 Jan 2014) www.quantamagazine.org/ 20140122-a-new-physics-theory-of-life/ Accessed 10 Feb 2015 55 Woods, L.: War and Architecture Princeton Architectural Press, New York (1996) 56 Youde, K.: Unilever employees get taste of the future at Royal Society event (5 Nov 2013) www.citmagazine.com/article/1219480/unilever-employees-taste-future-royalsociety-event Accessed 28 Feb 2015 Index A Acidic hydrogel, 239 Actin, 309 automata, 312 Actuation, 688 Actuator, 692, 727 humidity-driven, 698 osmosis-based, 693 Adaptive behaviour, 688 Adder, 112, 115, 116 Alkaline solution, 239 Allosteric regulation, 87 α-shape, 716 Aluminium chloride, 168, 189, 191 Amoeboid robot, 731 Analogue cross point switches, 407 Analytic programming, 215 AND gate, 111, 206, 208, 209 multi-bit, 129 Ant colony optimization, 591, 592 ants, 594 artificial ants, 592 pheromones, 594 stigmergy, 594 Aptamers, 3, 19 Archeology, 714 Artificial evolution, 398 intelligence, 528, 639 life, 21, 22 Associative memory, 146 Attraction-based logical gates, 717 Automated guidance attractant stimuli, 577 classical computation component, 576 lost blob recovery mode, 585 momentum parameter, 574 novel properties, 582 repellent stimuli, 579 unconventional computation component, 576 B Bacteria, 19, 20 Badhamia utricularis, 615 Ballistic logical gates, 717 Baltic indicator, 763, 764, 767–771 Base stacking rule, 358 Base stacking with overhangs rule, 359 Bat algorithm, 551 Bayesian network, 732 Beam-splitter, 301–302 Belousov–Zhabotinsky reaction, 105, 144, 199 β-catenin, 639 Bilinear transformation, see linear fractional transformation Bin-packing, 401, 405, 414 Binary comparator, 117 decoder, 125 encoder, 122 Biocompilation, 660 Biocomputer, 740 Biocomputer music, 757 Biodetection, 19 Biodiesel, 729 Bioelectric field, 683 Bio-inspired game, 616 © Springer International Publishing Switzerland 2017 A Adamatzky (ed.), Advances in Unconventional Computing, Emergence, Complexity and Computation 23, DOI 10.1007/978-3-319-33921-4 805 806 Biological brain cells, 743 chemoattractants, 744 chemorepellents, 744 computation, 639 culturing methods, 746 information processing, phagocytosis, 745 Biomodel, 659 Bioparts, 656 Biosensors, Boolean logic, 473 Boron, 683 Brownian ratchet, 732 BZ reaction, 144 C Carbon nanotube composite, 402 Cartesian genetic programming, 407 Cell, 2, 517 Cell wall, 683 Cellular automata, 201, 202, 262–269, 421, 528, 591, 593, 741, 764, 770, 771 hyper-cellular automata ants, 600 long interaction rule, 601 Moore neighborhood, 593 Von Neumann neighborhood, 593 CGP, 407 Chaos, 509 Chemical diode, 108 process, 223 reaction networks, sensor, 724 Chemokinesis, 245, 248 Chemotaxis, 248 Chromosome, 399 Clustering, 591 discrete data tolerance, 599 identification, 611 seperation, 611 Coarse-grained modeling, 348 Cobaltous chloride, 177 Coincidence detector, 108, 129, 145 Collective movement, 561 cellular level, 562 closed loop methods, 573 hybrid control system, 576 non-living systems, 562 open loop methods, 571 population level, 562 robotics, 562 Index Collision in parity rule filter automata, 262 oblivious, 271 transactive, 271 Collision cycles, 285–291 control of, 288 FANOUT gate using, 289 multistable, 286 NAND gate using, 289 physical arrangement of, 287 state restoration of, 288 Colorimetric readouts, 17, 19 Colour sensor, 724 Combinational logic circuits, 111 Combinatorial optimization problems, 592 Comparator, 117, 119 Composition Rejection Method, 659 Computer controlled evolution, 398 Computer music, 741 acoustical quanta, 751 audio wires, 740, 754 biocomputer music, 757, 759 compositional tools, 751 electroacoustic music, 741 generative audio, 754 granular synthesis, 741, 751, 753 Markov chain, 759 MIDI, 751, 758 musification, 751 sequencer, 750 sonification, 758 step sequencers, 746 Concave hull, 716 Concurrent game, 616, 731 Confusion matrix, 409 Constraint satisfaction problems, Control, 226 Copper chloride, 168, 169, 176, 186, 187 Correlation Matrix Memory, 147 Cost function, 229 Cost funtion, 231 Coulomb blockade, 403, 422 Coupled oscillators, 731 Creativity, 730 Crossover, 546 Crossover structure, 110 Cuckoo search, 550 Current transient, 511 D Data mining, 543 Decanol droplet, 252 Index Decoder, 125 Delaunay triangulation, 716 Deoxyribozymes, see DNAzymes Development, 638 Differential evolution, 215, 551 Diffusio-phoresis, 250 Diffusive computation, 143 Digital acquisition card, 404 Diode, 108 Direct Method, 659 Directional coupler, 299 Discriminator, 88, 94 Distribution Gaussian distribution, 759 DNA, 142 8-17 motif, 15, 16 AND gates, 5–9, 13, 16, 18 ANDAND gates, 6, ANDANDNOT gates, 6, ANDNOT gates, 8, antiviral applications, 22 biodetection, 3, 19 biosensors, 20, 21 cancer therapy, 22 cascades, 2, 3, 8, 13, 16, 17, 19, 21 catalytic core, 3–7, 9, 14, 15 circular, 354 circularized, 19 clauses, cleavage reactions, 3–5, 7, 14, 15, 18, 21 deep circuits, 13–16, 18, 21 diagnostic applications, 18, 22 DNAzymes, 2–7, 9–22 E6 motif, 3, 5, 6, 16 graph, 353 graph notation, 353 inhibitors, 15, 16, 18–21 ligases, 13, 21 linear substrates, 3–8, 14, 17 logic gates, 2, 3, 7–14, 16, 19, 21 molecular automata, 2, 10, 12, 21 molecular beacons, 5, 7, 9, 12, 16, 19 multi-component assembly, multiple turnover, 4, 14, 21 nanodevice, 348 nanostructure, 348 non-circular, 354 NOT gates, 6, OR gates (implicit), oscillators, 17 parallel gate arrays, 2, 8–10, 12, 13, 16, 21 peroxidase-mimicking, 19 807 phosphodiesterases, 3, 13, 14, 21 strand graph, 354 structured substrates, 14–18, 21 substrate binding arms, 3–5, 7, 12, 14 therapeutic applications, 22 wide circuits, 9, 21 YES gates, 4, 5, 13, 16, 19 Domain binding rule, 357 Dynamical system, 548 Dynamics attractor, 647 bifurcation, 647 model, 646 systems, 638 trajectory, 646 E Electro-osmosis, 694 Elitism, 399 El Niño, 763, 764, 766, 767, 769–771 Emergence, 509 Energy generation, 729 Enzymatic reaction, 86, 90, 91, 96 Evacuation, 714 Evolutionary algorithm, 213, 234 computation, 642, 644 Evolutionary algorithm, 398 Evolution-in-materio, 399 Exploitation, 544 F Fatty acid, 239 Fault tolerant graph, 732 Ferric chloride, 170, 173, 176, 177 Ferrous sulphate, 175, 178 Field–Koros–Noyes reaction, 107 Field-programmable, 731 Firefly algorithm, 549 First Reaction Method, 659 Fitness function, 399 Flatworms, 638 Flower pollination algorithm, 552 Fluid flow, 239 Fluorophores, 3, 4, 7, 9, 10, 16, 17, 20 Formal Verification, 660 Förster resonance energy transfer, FPGA, 399 Frequency based logical gates, 718 Frequency classification, 405 Full-adder, 317, 526 Function optimisation, 401, 405 808 G Gabriel graph, 716 Games strategies, 10, 12, 21 tic-tac-toe, 10–12 tit-for-tat, 12 Gap junctions, 639 Genes, 19, 20, 399 expression, 22 regulatory networks, 17 silencing, 22 Genetic algorithm, 398 logic gates, 661 networks, 656 operator, 546 programming, 215, 398 Genome, 213, 641 Genotype, 399 Global search, 553 Global warming, 763, 764, 768, 771 Gödel operator, 322 Gold nanoparticles, 402 Grammatical evolution, 215 Graph colouring, 405, 416 grammars, 350 rewriting, 350 rewriting rule, 355 rewriting system, 355 Gravity, 680 H Habituation, 506 Half-adder, 331 Hamiltonian, 335 path problem, 3, 142 Hamiltonian path problem, Hardware interface, 404 Heavy-tailed, 556 Hebbian learning, 470 High performance computing, 645 Hilbert space, 231, 232 Hopfield network, 142 Hull, 716 Hysteresis, 89, 93, 98 I Illusion, 728 Image processing, 145, 603 Index Immunocomputing, 763, 770, 771 Infobiotics workbench, 657 Information coded in oscillation type, 94, 99 Information encoding, 640 Information storage in DNA, Input-mapping, 400 In silico experiment, 646 In vitro evolution, Ionic conductivity, 326 Iterative maps, 548 K Kerr effect, 297 Kolmogorov–Uspensky machine, 720 L Ladder diagram, 628 Legendre equation, 298, 304–306 Levels of information, 640 Lévy distribution, 555 LFT, see linear fractional transformation Light, 681 Linear fractional transformation, 273 Liquid crystal, 399 Living cells, 656 Local search, 553 Logarithmic Direct Method, 659 Logic, 2, 22, 522 adder circuits, 2, 8, Boolean, 2, 3, 5, 7, 8, 10, 12, 13, 21 clauses, 13 digital, 1, disjunctive normal form, 8, 13 gates, 2, 5, 6, 404 literals, 7, 8, 13 XOR function, 8, Logical gate attraction-based, 717 ballistic, 717 frequency based, 718 micro-fluidic, 719 opto-electronics, 718 reversible, 732 Low-pass filter, 722, 731 Lower predecessor anticipation, 620 Łukasiewicz logic, 321, 322 M Machine learning, 405, 659 Magneto taxis, 250 Index Manakov system i operator in, 274 COPY gate in, 279 FANOUT gate in, 279 Move operator in, 275 NAND gate in, 280 NOT gate in, 279 ONE gate in, 279 state in, 273 time-gated, 277 universality of, 277–285 Manganese chloride, 175 MAP kinase cascades, 16 Marangoni flow, 239 Markov chain, 528 Mass migration, 713 Master Equation Method, 422 Material processors, 399 Maze, 238, 251, 710 Maze solving, 145 Mechanoreception, 701 MECOBO, 407 Membrane computing, 656 Memory, 501, 521 Memory cells, 151 Memristor, 469, 497, 506, 724, 756 aloe vera plants, 757 human blood, 757 human skin, 757 hysteresis, 756 memristive characteristics, 757 organic systems, 757 Metaheuristic, 557 Micro-Fluidic logical gates, 719 Microcontroller, 404 Microspheres, 13, 14 MIMO control, 229 Möbius transformation, see linear fractional transformation Molecular beacons, 4, computing, 2, 3, 7, 21 solution-phase, 8, 21 surface-bound, 21 walkers, Monte Carlo Methods, 422 Morphology, 638 Morse interaction potential, 335 Multi-armed bandit, 732 Multi-bit AND operation, 129 OR operation, 131 Multi-case routing, 732 809 Multi-chromosomal genotype, 413 Multi-electrode array (MEA), 743 Multiscale, 555 Multi-swarm, 550 Music, 528, 739, 754, 758, 759 generation, 730 industry, 739 Musical biocomputer, 740, 746 Mutation, 399, 546 N NAND gate, 206, 208, 209 Nano rod, 250 Nanodevice, 348 Nanomachines, Nanoparticle network, 402 Nanostructure, 348 Nash equilibrium, 624 Negative differential resistance (NDR), 419 Nematode, 682 Neoblasts, 642 Nervous system, 727 Network, 513, 517 Network optimisation, 732 Neural net, 528 Neural networks, 423 artificial, Neuromorphic computer, 501 Neuron, 502, 506 NLS, see nonlinear Schrödinger equation Non-enzymatic DNA graph rewriting rules, 357 Nonlinear Schrödinger equation, 269 cubic, 270 Manakov, 271 saturable, 271 NOT gate, 112, 132 Notum, 639 Nucleic acids, 2, catalytic, 2, complementary, 3–7, 15 denaturation, 20 DNA, 2, 3, 5, 21 double-stranded DNA, 19, 20 hairpins, 5, 13 hybridization, 3, 15, 16 oligonucleotides, 5, 8, 10, 19–21 plasmid DNA, 19, 20 RNA, 3, 21, 22 sequence design, 8, 12 toehold, 6, 13–15, 19, 20 810 O Octanol, 639 Oil droplet, 249 One-bit half-adder, 331 One-bit full-adder, 113 One-bit half-adder, 112 Ontology, 642 Optimised Direct Method, 659 Opto-Electronics logical gates, 718 OR gate, 111 multi-bit, 131 Ordinary differential equation, 231 Oregonator, 149 equation, 201 Oscillator, 722 Osmosis, 693 P PANI, 470 Parallel computer, 741 Parity function, 405, 411 rule filter automata, 262 Partial Propensities Direct Method, 659 Particle machine, 263–269 VLSI implementation of, 263 Particle swarm optimization, 549 Pathogen detection, 19 Patterning, 638, 641 PEDOT:PSS, 470 Penalty, 227 Perceptron, 476 Periodic inflow, 93, 99 Petri net, 628 Photon decoherence of, 306 guiding by soliton, 297–306 phase shifting of, 297–299, 303 phase shifting of), 303 transfer of, 299–301 trapping by soliton, 297–306 Physarum adaptive learning behaviour, 757 computation in, 563 external influence, 563 language, 628 logic, 731 memrstor, 757 oscillatory rhythm, 563 polycephalum, 142, 484, 563, 615, 740, 743, 744 Index protoplasmic tube, 754, 758 robotics applications, 563 Pixel traces, 150 Planaria, 638, 639 Plant, 678, 687 phototropism, 681 root, 678, 688 root-brain theory, 678 root cap, 682 root tip, 678 tropism, 678 Plant memory, 682 PM, see particle machine Polarization of photon, 299 of soliton, 298 Poly(3,4-ethylenedioxythiophene)polystyrene sulfonate, 470 Potassium ferricyanide, 169, 177, 178, 187 Predictive control, 226, 229 PRFA, see parity rule filter automata Price of programmability, 398 Probe, see soliton, as probe Proteins GFP-fusion proteins, 20 signaling cascades, 16, 21 Pseudo-DNA nanostructures, 351 Pump, see soliton, as pump Q Quantum cellular automata, 310 computing, 304 Quantum computing, 304 Qubit flying, 300, 304, 306 photon as carrier of, 297, 300 Quenchers, 3, 4, R Reactive oxygen species, 682 Reactor, 224, 226, 229 Recombination, 399 Regeneration, 638 Regulatory networks, 642 Remote toehold mediated strand displacement, 359 ReRAM, 498 Reverse engineering, 639, 642 Reversible logical gate, 732 Ribozymes, 21 self-replicating, 21 Index Riemann surface, 732 RLC line, 326 RNAi, 639 Robot, 530 control, 405 controller, 726 plant-inspired, 703 Root, 688, 689 Rough set, 616 Ruthenium catalyst, 144 S Schottky diode, 725 Schrödinger equation cubic nonlinear, 298 linear, 298 Sea surface temperature, 763, 766, 767, 771 Self-propelled systems, 248 Sensor chemical, 724 colour, 724 tactile, 723 SET, 403 Shapes, 638 Shor’s factorisation, 731 Shortest path, 240, 710, 711, 732 Signal amplification, propagation, 3, 13, 15, 17 Signalling networks, 656 Silver nitrate, 178 Simulated evolution, 201 Simulation of nanoparticle networks, 422 Single electron circuit, 731 transistor, 403 Skeletonisation, 174 Slime mould, 142, 251 Sodium hydroxide, 168, 189, 191 Soliton, 262–263, 269–291, 335 as photon guide, 297–306 as probe, 298 as pump, 298 dark, 304–306 envelope, 269 in automata, 262 induced waveguide of, 298–299, 304– 306 Manakov, 271 spatial, 298, 299 temporal, 298 Sorting Direct Method, 659 811 Space exploration, 715 Spanning tree, 712 Spike, 511, 521 Stand alone device, 402 Steiner tree, 731 Stochastic simulation algorithm, 659 Strand displacement, see Toehold-mediated strand displacement Strand displacement rule, 357 Supply chain design, 732 Surface tension, 239 Swarm intelligence, 689 Symbolic regression, 215, 234 Synthetic biology, 656 Systems biology, 17 T Tactile sensor, 723 Tanada effect, 683 Thin layer reactor, 144 Three-bit adder, 116 3-NLS, see nonlinear Schrödinger equation, cubic Time delay unit, 109 Toehold-mediated strand displacement, 6, 7, 13–17, 19, 20 Tone discriminator, 405 Towers of Hanoi, 711 Transistor, 726 Transition system, 619 Transport networks, 712 Travelling salesman problem (TSP), 401, 404, 711 Tree spanning, 712 Steiner, 731 Tug of war, 732 Turing machine, 397, 740 Two-bit adder, 115 comparator, 119 half-adder, 316 U Unmanned aerial vehicle, 528 Upper predecessor anticipation, 620 V Variable precision rough set model, 618 Virtual plasmodium, 565 amoeboid movement, 568 812 attractant stimuli, 568 cohesion, 566 oscillatory dynamics, 567 repellent stimuli, 568 scaling parameter, 566 Viruses dengue, 16, 18, 19 detection, 16, 19 serotypes, 16, 18 Index W Waveguide, see soliton, induced waveguide of Well-formed DNA graph, 354 degree, 354 in-degree, 354 out-degree, 354 vertex, 354 Wetware-silicon device, 743 Wire, 721 Worm, 638 Volatile, 679 Voltage divider, 725 Voronoi diagram, 145, 168, 715 X XOR gate, 112, 206, 208, 209 crystal growth, 176 generalised, 173 multiplicatively weighted, 176 Y Y-maze, 679 ... are (but not limited to) membrane computing, DNA computing, immune computing, quantum computing, swarm computing, analogic computing, chaos computing and computing on the edge of chaos, computational... input binding loop that detects the training inputs This allows a non-expert user to select the automaton’s strategy in a training phase that mimicks the real gameplay but using the training inputs... standpoint, the training inputs are simply an instance of “staging” the inputs to the system, although in the MAYA-III design the training inputs were designed with an additional overhanging toehold,