arXiv subjects
Publications and source records attributed to Andrew Adamatzky.
A cellular automaton collider is a finite state machine build of rings of one-dimensional cellular automata. We show how a computation can be performed on the collider by exploiting interactions between gliders (particles, localisations). The constructions proposed are based on universality of elementary cellular automaton rule 110, cyclic tag systems, supercolliders, and computing on rings.
A fluidic one-bit half-adder is made of five channels which intersect at a junction. Two channels are inputs, two channels are outputs and one channel is the drain. The channels direct fluid from input fragments to output fragments and the streams of fluid interact at the junctions. Binary signals are represented by water droplets introduced in the input channels: presence of a droplet in an input or output segments symbolises logical {\sc True}, absence --- {\sc False}. The droplets travel along channels by following a path of least resistance unless deflected at the junction. We demonstrate the function of the half-adder in both computer modelling and laboratory experiments, and propose a design of a one-bit full adder based on simulation.
We overview experimental laboratory prototypes of maze solvers. We speculate that all maze solvers implement Lee algorithm by first developing a gradient of values showing a distance from any site of the maze to the destination site and then tracing a path from a given source site to the destination site. All prototypes approximate a set of many-source-one-destination paths using resistance, chemical and temporal gradients. They trace a path from a given source site to the destination site using electrical current, fluidic, growth of slime mould, Marangoni flow, crawling of epithelial cells, excitation waves in chemical medium, propagating crystallisation patterns. Some of the prototypes visualise the path using a stream of dye, thermal camera or glow discharge; others require a computer to extract the path from time lapse images of the tracing. We discuss the prototypes in terms of speed, costs and durability of the path visualisation.
Actin is a globular protein which forms long polar filaments in eukaryotic. The actin filaments play roles of cytoskeleton, motility units , information processing and learning. We model actin filament as a double chain of finite state machines, nodes, which take states `0' and `1'. The states are abstractions of absence and presence of a sub-threshold charge on an actin units corresponding to the nodes. All nodes update their state in parallel in discrete time. A node updates its current state depending on states of two closest neighbours in the node chain and two closest neighbours in the complementary chain. Previous models of actin automata considered momentary state transitions of nodes. We enrich the actin automata model by assuming that states of nodes depends not only on the current states of neighbouring node but also on their past states. Thus, we assess the effect of memory of past states on the dynamics of acting automata. We demonstrate in computational experiments that memory slows down propagation of perturbations, decrease entropy of space-time patterns generated, transforms travelling localisations to stationary oscillators, and stationary oscillations to still patterns.
Slime mould \emph{Physarum polycephalum} is a large single cell capable for 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 the Physarum became a swiss knife of the unconventional computing: give the slime mould a problem it will solve it. We provide a concise summary of what exact computing and sensing operations are implemented with live slime mould. The Physarum devices range from morphological processors for computational geometry to experimental archeology tools, from self-routing wires to memristors, from devices approximating a shortest path to analog physical models of space exploration.
Slime mould Physarum polycephalum is a single cell visible by unaided eye. Let the slime mould span two electrodes with a single protoplasmic tube: if the tube is heated to approximately 40°C, the electrical resistance of the protoplasmic tube increases from 3 MΩ to approximatively 10'000 MΩ. The organism's resistance is not proportional nor correlated to the temperature of its environment. Slime mould can therefore not be considered as a thermistor but rather as a thermic switch. We employ the P. polycephalum thermic switch to prototype hybrid electrical analog summator, NAND gates, and cascade the gates into Flip-Flop latch. Computing operations performed on this bio-hybrid computing circuitry feature high repeatability, reproducibility and comparably low propagation delays
The manipulation of biological substrates is becoming more popular route towards generating novel computing devices. Physarum polycephalum is used as a model organism in biocomputing because it can create `wires' for use in hybrid circuits; programmable growth by manipulation through external stimuli and the ability withstanding a current and its tolerance to hybridisation with a variety of nano/microparticles. Lettuce seedlings have also had previous interest invested in them for generating plant wires, although currently there is little information as to their suitability for such applications. In this study both P. polycephalum and Lettuce seedlings were hybridised with gold nanoparticles - functionalised and unfunctionalised - to explore their uptake, toxicological effects and, crucially, any alterations in electrical properties they bestow upon the organisms. Using various microscopy techniques it was shown that P. polycephalum and lettuce seedlings are able to internalize nanoparticles and assemble them in vivo, however some toxicological effects were observed. The electrical resistance of both lettuce seedlings and P. polycephalum was found to decrease, the most significant reduction being with lettuce seedlings whose resistance reduced from 3MOhms to 0.5MOhms. We conclude that gold is a suitable nanomaterial for biohybridisation specifically in creating conductive pathways for more efficient biological wires in self-growing hybrid circuitry.
Leeches are fascinating creatures: they have simple modular nervous circuitry m yet exhibit a rich spectrum of behavioural modes. Leeches could be ideal blue-prints for designing flexible soft robots which are modular, multi-functional, fault-tolerant, easy to control, capable for navigating using optical, mechanical and chemical sensorial inputs, have autonomous inter-segmental coordination and adaptive decision-making. With future designs of leech-robots in mind we study how leeches behave in geometrically constrained spaces. Core results of the paper deal with leeches exploring a row of rooms arranged along a narrow corridor. In laboratory experiments we find that rooms closer to ends of the corridor are explored by leeches more often than rooms in the middle of the corridor. Also, in series of scoping experiments, we evaluate leeches capabilities to navigating in mazes towards sources of vibration and chemo-attraction. We believe our results lay foundation for future developments of robots mimicking behaviour of leeches.
Safe evacuation of people from building and outdoor environments, and search and rescue operations, always will remain actual in course of all socio-technological developments. Modern facilities offer a range of automated systems to guide residents towards emergency exists. The systems are assumed to be infallible. But what if they fail? How occupants not familiar with a building layout will be looking for exits in case of very limited visibility where tactile sensing is the only way to assess the environment? Analogous models of human behaviour, and socio-dynamics in general, are provided to be fruitful ways to explore alternative, or would-be scenarios. Crowd, or a single person, dynamics could be imitated using particle systems, reaction-diffusion chemical medium, electro-magnetic fields, or social insects. Each type of analogous model offer unique insights on behavioural patterns of natural systems in constrained geometries. In this particular paper we have chosen leeches to analyse patterns of exploration. Reasons are two-fold. First, when deprived from other stimuli leeches change their behavioural modes in an automated regime in response to mechanical stimulation. Therefore leeches can give us invaluable information on how human beings might behave under stress and limited visibility. Second, leeches are ideal blueprints of future soft-bodied rescue robots. Leeches have modular nervous circuitry with a rich behavioral spectrum. Leeches are multi-functional, fault-tolerant with autonomous inter-segment coordination and adaptive decision-making. We aim to answer the question: how efficiently a real building can be explored and whether there any dependencies on the pathways of exploration and geometrical complexity of the building. In our case studies we use templates made on the floor plan of real building.
Purpose: Protoplasmic tubes of Physarum polycephalum, also know as Physarum Wires (PW), have been previously suggested as novel bio- electronic components. Until recently, practical examples of electronic circuits using PWs have been limited. These PWs have been shown to be self repairing, offering significant advantage over traditional electronic components. This article documents work performed to produce practical circuits using PWs. Method: We have demonstrated through manufacture and testing of hybrid circuits that PWs can be used to produce a variety of practical electronic circuits. A purality of different applications of PWs have been tested to show the universality of PWs in analogue and digital electronics. Results: Voltage dividers can be produced using a pair of PWs in series with an output voltage accurate to within 12%. PWs can also transmit analogue and digital data with a frequency of up to 19 kHz, which with the addition of a buffer, can drive high current circuits. We have demonstrated that PWs can last approximately two months, a 4 fold increase on previous literature. Protoplasmic tubes can be modified with the addition of conductive or magnetic nano-particles to provide changes in functionality. Conclusion This work has documented novel macro-scale data transmission through biological material; it has advanced the field of bio-electronics by providing a cheap and easy to grow conducting bio-material which may be used in future hybrid electronic technology.
The slime mould Physarum polycephalum is known to construct proto- plasmic transport networks which approximate proximity graphs by forag- ing for nutrients during its plasmodial life cycle stage. In these networks, nodes are represented by nutrients and edges are represented by proto- plasmic tubes. These networks have been shown to be efficient in terms of length and resilience of the overall network to random damage. However relatively little research has been performed in the potential for Physarum transport networks to approximate the overall shape of a dataset. In this paper we distinguish between connectivity and shape of a planar point dataset and demonstrate, using scoping experiments with plasmodia of P. polycephalum and a multi-agent model of the organism, how we can gen- erate representations of the external and internal shapes of a set of points. As with proximity graphs formed by P. polycephalum, the behaviour of the plasmodium (real and model) is mediated by environmental stimuli. We further explore potential morphological computation approaches with the multi-agent model, presenting methods which approximate the Convex Hull and the Concave Hull. We demonstrate how a growth parameter in the model can be used to transition between Convex and Concave Hulls. These results suggest novel mechanisms of morphological computation mediated by environmental stimuli.
Computing devices are composed of spatial arrangements of simple funda- mental logic gates. These gates may be combined to form more complex adding circuits and, ultimately, complete computer systems. Implementing classical adding circuits using unconventional, or even living substrates such as slime mould Physarum polycephalum, is made difficult and often impracti- cal by the challenges of branching fan-out of inputs and regions where circuit lines must cross without interference. In this report we explore whether it is possible to avoid spatial propagation, branching and crossing completely in the design of adding circuits. We analyse the input and output patterns of a single-bit full adder circuit. A simple quantitative transformation of the input patterns which considers the total number of bits in the input string allows us to map the respective input combinations to the correct outputs patterns of the full adder circuit, reducing the circuit combinations from a 2:1 mapping to a 1:1 mapping. The mapping of inputs to outputs also shows an incremental linear progression, suggesting its implementation in a range of physical systems. We demonstrate an example implementation, first in simulation, inspired by self-oscillatory dynamics of the acellular slime mould Physarum polycephalum. We then assess the potential implementation using plasmodium of slime mould itself. This simple transformation may enrich the potential for using unconventional computing substrates to implement digital circuits.
Actin is a globular protein which forms long polar filaments in the eukaryotic cytoskeleton. Actin networks play a key role in cell mechanics and cell motility. They have also been implicated in information transmission and processing, memory and learning in neuronal cells. The acting filaments have been shown to support propagation of voltage pulses. Here we apply a coupled nonlinear transmission line model of actin filaments to study interactions between voltage pulses. By assigning a logical {\sc Truth} to the presence of a voltage pulses in a given location of the actin filament, and {\sc False} to the pulse's absence we represent digital information transmission along these filaments. When two pulses, representing Boolean values of input variables, interact, then they can facilitate or inhibit further propagation of each other. We explore this phenomenon to construct Boolean logical gates and a one-bit half-adder with interacting voltage pulses. We discuss implications of these findings on cellular process and technological applications.
A sub-excitable BZ medium responds to asymmetric local perturbation by producing travelling localised excitation wave-fragments, distant relatives of dissipative solitons. The size and life span of an excitation wave-fragment depend on the illumination level of the medium. Under the right conditions the wave-fragments conserve their shape and velocity vectors for extended time periods. We interpret the wave-fragments as values of Boolean variables. When two or more wave-fragments collide they annihilate or merge into a new wave-fragment. States of the logic variables, represented by the wave-fragments, are changed in the result of the collision between the wave-fragments. Thus, a logical gate is implemented. Several theoretical designs and experimental laboratory implementations of Boolean logic gates have been proposed in the past but little has been done cascading the gates into binary arithmetical circuits. We propose a unique design of a binary one-bit full adder based on a fusion gate. A fusion gate is a two-input three-output logical device which calculates conjunction of the input variables and conjunction of one input variable with negation of another input variable. The gate is made of three channels: two channels cross each other at an angle, third channel starts at the junction. The channels contain BZ medium. When two excitation wave-fragments, travelling towards each other along input channels, collide at the junction they merge into a single wave-front travelling along the third channel. If there is just one wave-front in the input channel, the front continues its propagation undisturbed. We make a one-bit full adder by cascading two fusion gates. We show how to cascade the adder blocks into a many-bit full adder. We evaluate feasibility of our designs by simulating evolution of excitation in the gates and adders using numerical integration of Oregonator equations.
Neuromorphic computing is a brainlike information processing paradigm that requires adaptive learning mechanisms. A spiking neuro-evolutionary system is used for this purpose; plastic resistive memories are implemented as synapses in spiking neural networks. The evolutionary design process exploits parameter self-adaptation and allows the topology and synaptic weights to be evolved for each network in an autonomous manner. Variable resistive memories are the focus of this research; each synapse has its own conductance profile which modifies the plastic behaviour of the device and may be altered during evolution. These variable resistive networks are evaluated on a noisy robotic dynamic-reward scenario against two static resistive memories and a system containing standard connections only. Results indicate that the extra behavioural degrees of freedom available to the networks incorporating variable resistive memories enable them to outperform the comparative synapse types.
The giant single-celled amoeboid organism Physarum polycephalum constructs minimising transport networks but can also approximate the Voronoi diagram using two different mechanisms. In the first method Voronoi bisectors are rep- resented by deformation of a pre-existing plasmodial network by repellent sources acting as generating points. In the second method generating points act as inoculation sites for grow- ing plasmodia and Voronoi bisectors are represented by vacant regions before the plasmodia fuse. To explore the behaviour of minimising networks in the presence of repulsion fields we utilise a computational model of Physarum as a distributed virtual computing material. We characterise the different types of computational behaviours elicited by attraction and repulsion stimuli and demonstrate the approximation Voronoi diagrams using growth towards attractants, avoidance of repellents, and combinations of both. Approximation of Voronoi diagrams for point data sources, complex planar shapes and circle sets is demonstrated. By altering repellent con- centration we found that partition of data sources was maintained but the internal network connectivity was minimised by the contractile force of the transport network. To conclude, we find that the repertoire of unconventional computation methods is enhanced by the addition of stimuli presented by repellent fields, suggesting novel approaches to plane-division, packing, and minimisation problems.
True slime mould Physarum polycephalum approximates a range of complex computations via growth and adaptation of its proto- plasmic transport network, stimulating a large body of recent research into how such a simple organism can perform such complex feats. The properties of networks constructed by slime mould are known to be in- fluenced by the local distribution of stimuli within its environment. But can the morphological adaptation of slime mould yield any information about the global statistical properties of its environment? We explore this possibility using a particle based model of slime mould. We demonstrate how morphological adaptation in blobs of virtual slime mould may be used as a simple computational mechanism that can coarsely approx- imate statistical analysis, estimation and tracking. Preliminary results include the approximation of the geometric centroid of 2D shapes, ap- proximation of arithmetic mean from spatially represented sorted and unsorted data distributions, and the estimation and dynamical tracking of moving object position in the presence of noise contaminated input stimuli. The results suggest that it is possible to utilise collectives of very simple components with limited individual computational ability (for ex- ample swarms of simple robotic devices) to extract statistical features from complex datasets by means of material adaptation and sensorial fusion.
Using a particle model of Physarum displaying emer- gent morphological adaptation behaviour we demonstrate how a minimal approach to collective material computation may be used to transform and summarise properties of spatially represented datasets. We find that the virtual material relaxes more strongly to high-frequency changes in data which can be used for the smoothing (or filtering) of data by ap- proximating moving average and low-pass filters in 1D datasets. The relaxation and minimisation properties of the model enable the spatial computation of B-spline curves (approximating splines) in 2D datasets. Both clamped and unclamped spline curves, of open and closed shapes, can be represented and the degree of spline curvature corresponds to the relaxation time of the material. The material computation of spline curves also includes novel quasi-mechanical properties including unwind- ing of the shape between control points and a preferential adhesion to longer, straighter paths. Interpolating splines could not directly be ap- proximated due to the formation and evolution of Steiner points at nar- row vertices, but were approximated after rectilinear pre-processing of the source data. This pre-processing was further simplified by transform- ing the original data to contain the material inside the polyline. These exemplar results expand the repertoire of spatially represented uncon- ventional computing devices by demonstrating a simple, collective and distributed approach to data and curve smoothing.