Papers by Andrew Adamatzky
Emergence, complexity and computation, Jul 27, 2016
Many forms of unconventional computing, i.e., massively parallel non-linear computers, can be rea... more Many forms of unconventional computing, i.e., massively parallel non-linear computers, can be realised through simulated evolution. That is, the behaviour of non-linear media can be controlled automatically and the structural design of the media optimized through the nature-inspired machine learning approach. This chapter describes work using the Belousov–Zhabotinsky reaction as a non-linear chemical medium in which to realise computation. A checkerboard image comprising of varying light intensity cells is projected onto the surface of a catalyst-loaded gel resulting in rich spatio-temporal chemical wave behaviour. Cellular automata are evolved to control the chemical activity through dynamic adjustment of the light intensity, implementing a number of Boolean functions in both simulation and experimentation.
Emergence, complexity and computation, Oct 27, 2017
Many forms of unconventional computing, i.e., massively parallel computers which exploit the non-... more Many forms of unconventional computing, i.e., massively parallel computers which exploit the non-linear material properties of their substrate, can be realised through simulated evolution. That is, the behaviour of non-linear media can be controlled automatically and the structural design of the media optimized through the nature-inspired machine learning approach. This chapter describes work using the Belousov-Zhabotinsky reaction as a non-linear chemical medium in which to realise computation. Firstly, aspects of the basic structure of an experimental chemical computer are evolved to implement two Boolean logic functions through a collision-based scheme. Secondly, a controller is evolved to dynamically affect the rich spatio-temporal chemical wave behaviour to implement three Boolean functions, in both simulation and experimentation.
arXiv (Cornell University), Mar 16, 2014
Physarum polycephalum is a macroscopic single celled plasmodial slime mould. We employ plasmodial... more Physarum polycephalum is a macroscopic single celled plasmodial slime mould. We employ plasmodial phototactic responses to construct laboratory prototypes of NOT and NAND logical gates with electrical inputs/outputs and optical coupling; the slime mould plays dual roles of computing device and electrical conductor. Slime mould logical gates are fault tolerant and resettable. The results presented here advance our understanding of how biological computing substrates may be manipulated to implement logical operations and demonstrate the feasibility of integrating living substrates into silicon hardware.
The plasmodium of the slime mould Physarum polycephalum has recently received sig-nificant attent... more The plasmodium of the slime mould Physarum polycephalum has recently received sig-nificant attention for its value as a highly malleable amorphous computing substrate. In laboratory-based experiments, micro- and nanoscale artificial circuit components were introduced into the P. polycephalum plasmdodium to investigate the electrical prop-erties and computational abilities of hybridised slime mould. It was found through a combination of imaging techniques and electrophysiological measurements that P. poly-cephalum is able to internalise a range of electrically active nanoparticles, assemble them in vivo and distribute them around the plasmodium. Hybridised plasmodium is able to form biomorphic mineralised networks, both inside the living plasmodium and the empty trails left in its wake by taxis, both of which facilitate the transmission of electricity. Hy-bridisation also alters the bioelectrical activity of the plasmodium and likely influences its information processing capabilities...
Natural Computing Series, 2018
Slime mould Physarum polycephalum is a large single cell capable of distributed sensing, concurre... more Slime mould Physarum polycephalum is a large single cell capable of distributed sensing, concurrent information processing, parallel computation, and decentralised actuation. The ease of culturing and experimenting with Physarum makes this slime mould an ideal substrate for real-world implementations of unconventional sensing and computing devices. In the last decade Physarum has become a popular inspiration for mathematical and algorithmic models and philosophical concepts of unconventional computing: give the slime mould a problem and it will solve it. We provide a concise summary of computing and sensing operations implemented with live slime mould and evaluate the feasibility of slime mould-based computing. 8.1 Overview Research in unconventional, or nature-inspired, computing aims to uncover novel principles of efficient information processing and computation in physical, chemical and biological systems, to develop novel non-standard algorithms and computing architectures, and also to implement conventional algorithms in non-silicon, or wet, substrates. This emerging field of science and engineering is predominantly occupied by theoretical research, e.g. quantum computation, membrane computing and dynamical systems computing. 8.1.1 Why slime mould computers? Despite the profound potential offered by unconventional computing, only a handful of experimental prototypes are reported so far, for example gasdischarge analog path finders; maze-solving micro-fluidic circuits; geomet-111
Advances in Physarum Machines, 2016
Being a living substrate the slime mould does not halt its behaviour when a task is solved but of... more Being a living substrate the slime mould does not halt its behaviour when a task is solved but often continues foraging the space thus masking the solution found. We propose to use temporal changes in compressibility of the slime mould patterns as indicators of the halting of the computation. Compressibility of a pattern characterises the pattern's morphological diversity, i.e. a number of different local configurations. At the beginning of computation the slime explores the space thus generating less compressible patterns. After gradients of attractants and repellents are detected the slime spans data sites with its protoplasmic network and retracts scouting branches, thus generating more compressible patterns. We analyse the feasibility of the approach on results of laboratory experiments and computer modelling.
ArXiv, 2017
The slime mould Physarum polycephalum has been used in developing unconventional computing device... more The slime mould Physarum polycephalum has been used in developing unconventional computing devices for in which the slime mould played a role of a sensing, actuating, and computing device. These devices treated the slime mould rather as an active living substrate yet the slime mould is a self-consistent living creature which evolved for millions of years and occupied most part of the world, but in any case, that living entity did not own true cognition, just automated biochemical mechanisms. To "rehabilitate" the slime mould from the rank of a purely living electronics element to a "creature of thoughts" we are analyzing the cognitive potential of P. polycephalum. We base our theory of minimal cognition of the slime mould on a bottom-up approach, from the biological and biophysical nature of the slime mould and its regulatory systems using frameworks suh as Lyon's biogenic cognition, Muller, di Primio-Lengeler\'s modifiable pathways, Bateson's "p...
Biosystems, 2020
A fungal colony maintains its integrity via flow of cytoplasm along mycelium network. This flow, ... more A fungal colony maintains its integrity via flow of cytoplasm along mycelium network. This flow, together with possible coordination of mycelium tips propagation, is controlled by calcium waves and associated waves of electrical potential changes. We propose that these excitation waves can be employed to implement a computation in the mycelium networks. We use FitzHugh-Nagumo model to imitate propagation of excitation in a single colony of Aspergillus niger. Boolean values are encoded by spikes of extracellular potential. We represent binary inputs by electrical impulses on a pair of selected electrodes and we record responses of the colony from sixteen electrodes. We derive sets of two-inputs-on-output logical gates implementable the fungal colony and analyse distributions of the gates.
Langmuir, 2019
Neuromorphic computing devices attempt to emulate features of biological nervous systems through ... more Neuromorphic computing devices attempt to emulate features of biological nervous systems through mimicking the properties of synapses toward implementing the emergent properties of their counterparts, such as learning. Inspired by recent advances in the utilization of liquid marbles (LMs, microliter quantities of fluid coated in hydrophobic powder) for the creation of unconventional computing devices, we describe the development of LMs with neuromorphic properties through the use of copper coatings and 1.0 mg mL −1 carbon nanotube (CNT)-containing fluid cores. Experimentation was performed through sandwiching the LMs between two cup-style electrodes and stimulating them with repeated dc pulses at 3.0 V. Our results demonstrate that "entrainment" of CNT-filled copper LMs via periodic pulses can cause their electrical resistance to rapidly switch between high to low resistance profiles upon inverting the polarity of stimulation: the reduction in resistance between high and low profiles was approximately 88% after two rounds of entrainment. This effect was found to be reversible through reversion to the original stimulus polarity and was strengthened by repeated experimentation, as evidenced by a mean reduction in time to switching onset of 43%. These effects were not replicated in nanotube solutions not bound inside LMs. Our electrical characterization also reveals that nanotube-filled LMs exhibit pinched loop hysteresis IV profiles consistent with the description of memristors. We conclude by discussing the applications of this technology to the development of unconventional computing devices and the study of emergent characteristics in biological neural tissue.
We exploit chemo- and galvanotactic behaviour ofParamecium caudatumto design a hybrid device that... more We exploit chemo- and galvanotactic behaviour ofParamecium caudatumto design a hybrid device that allows for controlled uptake, transport and deposition of environmental micro- and nanoparticulates in an aqueous medium. Manipulation of these objects is specific, programmable and parallel. We demonstrate how device operation and output interpretation may be automated via a DIY low-cost fluorescence spectrometer, driven by a microprocessor board. The applications of the device presented range from collection and detoxification of environmental contaminants (e.g. nanoparticles), to micromixing, to natural expressions of computer logic.
Scientific Reports, 2019
As the extent to which aquatic environments are polluted with nano-scale objects is becoming know... more As the extent to which aquatic environments are polluted with nano-scale objects is becoming known, we are presented with an urgent need to study their effects on various forms of life and to clear and/or detoxify them. A range of methods exist to these ends, but a lack of inter-study comparability arising from an absence of experimental standardisation impedes progress. Here we present experiments that demonstrate measurement of orchestrated uptake and clearance of two environmentally-relevant nano- and micromaterials by a model aquatic microoraganism, Paramecium caudatum. Experiments were based on a simple, modular, multi-chamber platform that permits standardised control of organism behaviour and measurement of variables relevant to the study of nanotoxicology, including nanomaterial chemotaxis assays, bioaccumulation and deleterious effects on cell motility systems. Uptake of internalised materials may be estimated through the addition of a low-cost fluorescence spectrometer. P....
Biomimetics, 2018
The aquatic unicellular organism Paramecium caudatum uses cilia to swim around its environment an... more The aquatic unicellular organism Paramecium caudatum uses cilia to swim around its environment and to graze on food particles and bacteria. Paramecia use waves of ciliary beating for locomotion, intake of food particles and sensing. There is some evidence that Paramecia pre-sort food particles by discarding larger particles, but intake the particles matching their mouth cavity. Most prior attempts to mimic cilia-based manipulation merely mimicked the overall action rather than the beating of cilia. The majority of massive-parallel actuators are controlled by a central computer; however, a distributed control would be far more true-to-life. We propose and test a distributed parallel cilia platform where each actuating unit is autonomous, yet exchanging information with its closest neighboring units. The units are arranged in a hexagonal array. Each unit is a tileable circuit board, with a microprocessor, color-based object sensor and servo-actuated biomimetic cilia actuator. Localize...
Journal of Membrane Computing, 2019
P-systems are abstract computational models inspired by the phospholipid bilayer membranes genera... more P-systems are abstract computational models inspired by the phospholipid bilayer membranes generated by biological cells. Illustrated here is a mechanism by which recursive liposome structures (multivesicular liposomes) may be experimentally produced through electroformation of dipalmitoylphosphatidylcholine films for use in 'real' P-systems. We first present the electroformation protocol and microscopic characterisation of incident liposomes towards estimating the size of computing elements, level of internal compartment recursion, fault tolerance and stability. Following, we demonstrate multiple routes towards embedding symbols, namely modification of swelling solutions, passive diffusion, and microinjection. Finally, we discuss how computing devices based on P-systems can be produced and their current limitations.
Langmuir : the ACS journal of surfaces and colloids, Feb 20, 2018
Liquid marbles (LMs) have recently attracted interest for use as cargo carriers in digital microf... more Liquid marbles (LMs) have recently attracted interest for use as cargo carriers in digital microfluidics and have successfully been implemented as signal carriers in collision-based unconventional computing circuits. Both application domains require LMs to roll over substantial distances and to survive a certain number of collisions without degrading. To evaluate the lifetime of LMs being subjected to movement and impact stresses, we have selected four types of coating to investigate: polytetrafluoroethylene (PTFE), ultrahigh density polyethylene (PE), Ni, and a mixture of Ni with PE (Ni-PE). Hierarchies of robustness have been constructed which showed that pure PE LMs survived the longest when stationary and in motion. Pure PTFE LMs were shown to be the least resilient to multiple impacts. The PTFE coating provided minimal protection against evaporative losses for small LM volumes (2 and 5 μL) however, larger LMs (10 μL) were shown to have good evaporative stabilities when stationa...
Bio Systems, Jan 8, 2018
The slime mould Physarum polycephalum has been used in developing unconventional computing device... more The slime mould Physarum polycephalum has been used in developing unconventional computing devices for in which the slime mould played a role of a sensing, actuating, and computing device. These devices treated the slime mould rather as an active living substrate yet the slime mould is a self-consistent living creature which evolved for millions of years and occupied most part of the world, but in any case, that living entity did not own true cognition, just automated biochemical mechanisms. To "rehabilitate" the slime mould from the rank of a purely living electronics element to a "creature of thoughts" we are analyzing the cognitive potential of P. polycephalum. We base our theory of minimal cognition of the slime mould on a bottom-up approach, from the biological and biophysical nature of the slime mould and its regulatory systems using frameworks suh as Lyons biogenic cognition, Muller, di Primio-Lengelerś modifiable pathways, Bateson's "patterns tha...
Biosystems, 2017
Motile cilia are cell-surface organelles whose purposes, in ciliated protists and certain ciliate... more Motile cilia are cell-surface organelles whose purposes, in ciliated protists and certain ciliated vertebrate epithelia, include generating fluid flow, sensing and substance uptake. Certain properties of cilia arrays, such as beating synchronisation and manipulation of external proximate particulate matter, are considered emergent, but remain incompletely characterised despite these phenomena having being the subject of extensive modelling. This study constitutes a laboratory experimental characterisation of one of the emergent properties of motile cilia: manipulation of adjacent particulates. The work demonstrates through automated videomicrographic particle tracking that interactions between microparticles and somatic cilia arrays of the ciliated model organism Paramecium caudatum constitute a form of rudimentary 'sorting'. Small particles are drawn into the organism's proximity by ciliainduced fluid currents at all times, whereas larger particles may be held immobile at a distance from the cell margin when the cell generates characteristic feeding currents in the surrounding media. These findings can contribute to the design and fabrication of biomimetic cilia, with potential applications to the study of ciliopathies.
Environment and Planning B: Urban Analytics and City Science, 2016
France has developed a high quality motorway system that has been rapidly rationalised and mature... more France has developed a high quality motorway system that has been rapidly rationalised and matured in the late 20th century yet has been founded on ancient, Roman infrastructures. The development of the motorway system is thus an iterative method associated with hierarchical ‘top-down’ processes taking into consideration factors such as population density, network demand, location of natural resources, civil engineering challenges and population growth. At the opposite extreme to this approach is the development of transport networks within simple biological systems which are typically decentralised, dynamic and emerge from simple, local and ‘bottom-up’ interactions. We examine the notion, and to what extent, that the structure of a complex motorway network could be predicted by the transport network of the single-celled slime mould Physarum polycephalum. This comparison is explored through its ability to ‘deduce’ the French motorway network in a series of analogue and digital exper...
Progress in biophysics and molecular biology, Jan 14, 2017
Unconventional computing is about breaking boundaries in thinking, acting and computing. Typical ... more Unconventional computing is about breaking boundaries in thinking, acting and computing. Typical topics of this non-typical field include, but are not limited to physics of computation, non-classical logics, new complexity measures, novel hardware, mechanical, chemical and quantum computing. Unconventional computing encourages a new style of thinking while practical applications are obtained from uncovering and exploiting principles and mechanisms of information processing in and functional properties of, physical, chemical and living systems; in particular, efficient algorithms are developed, (almost) optimal architectures are designed and working prototypes of future computing devices are manufactured. This article includes idiosyncratic accounts of 'unconventional computing' scientists reflecting on their personal experiences, what attracted them to the field, their inspirations and discoveries.
Scientific reports, 2017
Physarum Polycephalum is a single cell visible by unaided eye. This is a plasmodial, vegetative s... more Physarum Polycephalum is a single cell visible by unaided eye. This is a plasmodial, vegetative stage of acellular slime mould. This single cell has myriad of nuclei which contribute to a network of bio-chemical oscillators responsible for the slime mould's distributed sensing, concurrent information processing and decision making, and parallel actuation. When presented with a spatial configuration of sources of nutrients, the slime mould spans the sources with networks of its protoplasmic tube. These networks belong to a family of planar proximity graphs. The protoplasmic networks also show a degree of similarity to vehicular transport networks. Previously, we have shown that the foraging behaviour of the slime mould can be applied in archaeological research to complement and enhance conventional geographic information system tools. The results produced suffered from limitation of a flat substrate: transport routes imitated by the slime mould did not reflect patterns of elevati...
The nanotechnology revolution has allowed us to speculate on the possibilities of hybridising nan... more The nanotechnology revolution has allowed us to speculate on the possibilities of hybridising nanoscale materials with live substrates, yet significant doubt still remains pertaining to the effects of nanomaterials on biological matter. In this investigation we cultivate the ciliated protistic pond-dwelling microorganismParamecium caudatumin the presence of excessive quantities of magnetite nanoparticles in order to assess both potential beneficial applications for this technique as well as any deleterious effects on the organisms’ health. Our findings indicate that these nanoparticles are well-tolerated by paramecia, who were observed to consume in quantities exceeding 10% of their body volume: cultivation in the presence of magnetite nanoparticles does not alterP. caudatumcell volume, swim speed, growth rate or peak colony density and cultures may persist in nanoparticle-contaminated medium for many weeks. We demonstrate thatP. caudatumcells ingest starch coated magnetite nanopart...
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Papers by Andrew Adamatzky