Searcharxiv⌕ Search

arXiv subjects

Andrew Adamatzky

Publications and source records attributed to Andrew Adamatzky.

At least 145 records · Page 8Linked to original sources
arXiv2015

On the role of the plasmodial cytoskeleton in facilitating intelligent behaviour in slime mould Physarum polycephalum

The plasmodium of slime mould Physarum polycephalum behaves as an amorphous reaction-diffusion computing substrate and is capable of apparently intelligent behaviour. But how does intelligence emerge in an acellular organism? Through a range of laboratory experiments, we visualise the plasmodial cytoskeleton, a ubiquitous cellular protein scaffold whose functions are manifold and essential to life, and discuss its putative role as a network for transducing, transmitting and structuring data streams within the plasmodium. Through a range of computer modelling techniques, we demonstrate how emergent behaviour, and hence computational intelligence, may occur in cytoskeletal communications networks. Specifically, we model the topology of both the actin and tubulin cytoskeletal networks and discuss how computation may occur therein. Furthermore, we present bespoke cellular automata and particle swarm models for the computational process within the cytoskeleton and observe the incidence of emergent patterns in both. Our work grants unique insight into the origins of natural intelligence; the results presented here are therefore readily transferable to the fields of natural computation, cell biology and biomedical science. We conclude by discussing how our results may alter our biological, computational and philosophical understanding of intelligence and consciousness.

cs.ET↗
arXiv2014

Physarum Chip: Developments in growing computers from slime mould

The Phychip project is a collaborative European research initiative to design and implement computation using the organism Physarum polycephalum; it is funded by the Seventh Framework Programme (FP7) by the European Commission within CORDIS and the FET Proactive scheme. Included in this presentation are details the development of a Physarum based biosensor and biological logic gate, offering significant advancements in the respective fields. The work demonstrates the first steps towards Physarum computation and practical Physarum Biosensor; subsequent work will focus on development of a hybrid electronic-Physarum device capable of implementing computation.

cs.ET↗
arXiv2014

Complete Characterization of Structure of Rule 54

The dynamics of rule 54 one-dimensional two-state cellular automaton (CA) are a discrete analog of a space-time dynamics of excitations in nonlinear active medium with mutual inhibition. A cell switches its state 0 to state 1 if one of its two neighbors is in state 1 (propagation of a perturbation) and a cell remains in state 1 only if its two neighbors are in state 0. A lateral inhibition is because a 1-state neighbor causes a 1-state cell to switch to state 0. The rule produces a rich spectrum of space-time dynamics, including gliders and glider guns just from four primitive gliders. We construct a catalogue of gliders and describe them by tiles. We calculate a subset of regular expressions $Ψ_{R54}$ to encode gliders. The regular expressions are derived from de Bruijn diagrams, tile-based representation of gliders, and cycle diagrams sometimes. We construct an abstract machine that recognizes regular expressions of gliders in rule 54 and validate $Ψ_{R54}$. We also propose a way to code initial configurations of gliders to depict any type of collision between the gliders and explore self-organization of gliders, formation of larger tiles, and soliton-like interactions of gliders and computable devices.

nlin.CG↗
arXiv2014

Actin automata: Phenomenology and localizations

Actin is a globular protein which forms long filaments in the eukaryotic cytoskeleton, whose roles in cell function include structural support, contractile activity to intracellular signalling. We model actin filaments as two chains of one-dimensional binary-state semi-totalistic automaton arrays to describe hypothetical signalling events therein. Each node of the actin automaton takes state `0' (resting) or `1' (excited) and updates its state in discrete time depending on its neighbour's states. We analyse the complete rule space of actin automata using integral characteristics of space-time configurations generated by these rules and compute state transition rules that support travelling and mobile localizations. Approaches towards selection of the localisation supporting rules using the global characteristics are outlined. We find that some properties of actin automata rules may be predicted using Shannon entropy, activity and incoherence of excitation between the polymer chains. We also show that it is possible to infer whether a given rule supports travelling or stationary localizations by looking at ratios of excited neighbours are essential for generations of the localizations. We conclude by applying biomolecular hypotheses to this model and discuss the significance of our findings in context with cell signalling and emergent behaviour in cellular computation.

cs.ET↗
arXiv2014

Designing Complex Dynamics in Cellular Automata with Memory

Since their inception at {\it Macy conferences} in later 1940s complex systems remain the most controversial topic of inter-disciplinary sciences. The term `complex system' is the most vague and liberally used scientific term. Using elementary cellular automata (ECA), and exploiting the CA classification, we demonstrate elusiveness of `complexity' by shifting space-time dynamics of the automata from simple to complex by enriching cells with {\it memory}. This way, we can transform any ECA class to another ECA class --- without changing skeleton of cell-state transition function --- and vice versa by just selecting a right kind of memory. A systematic analysis display that memory helps `discover' hidden information and behaviour on trivial --- uniform, periodic, and non-trivial --- chaotic, complex --- dynamical systems.

nlin.CG↗
arXiv2014

Slime Mould Logic Gates Based on Frequency Changes of Electrical Potential Oscillation

Physarum polycephalum is a large single amoeba cell, which in its plasmodial phase,forages and connects nearby food sources with protoplasmic tubes. The organism forages for food by growing these tubes towards detected food stuffs, this foraging behaviour is governed by simple rules of photoavoidance and chemotaxis. The electrical activity of the tubes oscillates, creating a peristaltic like action within the tubes, forcing cytoplasm along the lumen; the frequency of this oscillation controls the speed and direction of growth. External stimuli such as light and food cause changes in the oscillation frequency. We demonstrate that using these stimuli as logical inputs we can approximate logic gates using these tubes and derive combinational logic circuits by cascading the gates, with software analysis providing the output of each gate and determining the input of the following gate. Basic gates OR, AND and NOT were correct 90%, 77.8% and 91.7% of the time respectively. Derived logic circuits XOR, Half Adder and Full Adder were 70.8%, 65% and 58.8% accurate respectively. Accuracy of the combinational logic decreases as the number of gates is increased, however they are at least as accurate as previous logic approximations using spatial growth of Physarum polycephalum and up to 30 times as fast at computing the logical output. The results shown here demonstrate a significant advancement in organism-based computing, providing a solid basis for hybrid computers of the future.

cs.ET↗
arXiv2014

Slime Mould Memristors

In laboratory experiments we demonstrate that protoplasmic tubes of acellular slime mould \emph{Physarum polycephalum} show current versus voltage profiles consistent with memristive systems and that the effect is due to the living protoplasm of the mould. This complements previous findings on memristive properties of other living systems (human skin and blood) and contributes to development of self-growing bio-electronic circuits. Distinctive asymmetric $V$-$I$ curves which were occasionally observed when the internal current is on the same order as the driven current, are well-modelled by the concept of active memristors.

cs.ET↗
arXiv2014

Slime mould electronic oscillators

We construct electronic oscillator from acellular slime mould Physarum polycephalum. The slime mould oscillator is made of two electrodes connected by a protoplasmic tube of the living slime mould. A protoplasmic tube has an average resistance of 3~MOhm. The tube's resistance is changing over time due to peristaltic contractile activity of the tube. The resistance of the protoplasmic tube oscillates with average period of 73~sec and average amplitude of 0.6~MOhm. We present experimental laboratory results on dynamics of Physarum oscillator under direct current voltage up to 15~V and speculate that slime mould P. polycephalum can be employed as a living electrical oscillator in biological and hybrid circuits.

cs.ET↗
arXiv2014

A Physarum-Inspired Approach to Optimal Supply Chain Network Design at Minimum Total Cost with Demand Satisfaction

A supply chain is a system which moves products from a supplier to customers. The supply chains are ubiquitous. They play a key role in all economic activities. Inspired by biological principles of nutrients' distribution in protoplasmic networks of slime mould Physarum polycephalum we propose a novel algorithm for a supply chain design. The algorithm handles the supply networks where capacity investments and product flows are variables. The networks are constrained by a need to satisfy product demands. Two features of the slime mould are adopted in our algorithm. The first is the continuity of a flux during the iterative process, which is used in real-time update of the costs associated with the supply links. The second feature is adaptivity. The supply chain can converge to an equilibrium state when costs are changed. Practicality and flexibility of our algorithm is illustrated on numerical examples.

cs.NE↗
arXiv2014

Sensory fusion in Physarum polycephalum and implementing multi-sensory functional computation

Surface electrical potential and observational growth recordings were made of a protoplasmic tube of the slime mould Physarum polycephalum in response to a multitude of stimuli with regards to sensory fusion or multisensory integration. Each stimulus was tested alone and in combination in order to evaluate for the first time the effect that multiple stimuli have on the frequency of streaming oscillation. White light caused a decrease in frequency whilst increasing the temperature and applying a food source in the form of oat flakes both increased the frequency. Simultaneously stimulating P. polycephalum with light and oat flake produced no net change in frequency, while combined light and heat stimuli showed an increase in frequency smaller than that observed for heat alone. When the two positive stimuli, oat flakes and heat, were combined, there was a net increase in frequency similar to the cumulative increases caused by the individual stimuli. Boolean logic gates were derived from the measured frequency change.

cs.ET↗
arXiv2014

Towards slime mould electrical logic gates with optical coupling

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.

cs.ET↗
arXiv2014

Emergent Spiking in Non-Ideal Memristor Networks

Memristors have uses as artificial synapses and perform well in this role in simulations with artificial spiking neurons. Our experiments show that memristor networks natively spike and can exhibit emergent oscillations and bursting spikes. Networks of near-ideal memristors exhibit behaviour similar to a single memristor and combine in circuits like resistors do. Spiking is more likely when filamentary memristors are used or the circuits have a higher degree of compositional complexity (i.e. a larger number of anti-series or anti-parallel interactions). 3-memristor circuits with the same memristor polarity (low compositional complexity) are stabilised and do not show spiking behaviour. 3-memristor circuits with anti-series and/or anti-parallel compositions show richer and more complex dynamics than 2-memristor spiking circuits. We show that the complexity of these dynamics can be quantified by calculating (using partial auto-correlation functions) the minimum order auto-regression function that could fit it. We propose that these oscillations and spikes may be similar phenomena to brainwaves and neural spike trains and suggest that these behaviours can be used to perform neuromorphic computation.

cond-mat.mtrl-sci↗
arXiv2014

Does the D.C. Response of Memristors Allow Robotic Short-Term Memory and a Possible Route to Artificial Time Perception?

Time perception is essential for task switching, and in the mammalian brain appears alongside other processes. Memristors are electronic components used as synapses and as models for neurons. The d.c. response of memristors can be considered as a type of short-term memory. Interactions of the memristor d.c. response within networks of memristors leads to the emergence of oscillatory dynamics and intermittent spike trains, which are similar to neural dynamics. Based on this data, the structure of a memristor network control for a robot as it undergoes task switching is discussed and it is suggested that these emergent network dynamics could improve the performance of role switching and learning in an artificial intelligence and perhaps create artificial time perception.

cs.RO↗
arXiv2014

The Short-term Memory (D.C. Response) of the Memristor Demonstrates the Causes of the Memristor Frequency Effect

A memristor is often identified by showing its distinctive pinched hysteresis curve and testing for the effect of frequency. The hysteresis size should relate to frequency and shrink to zero as the frequency approaches infinity. Although mathematically understood, the material causes for this are not well known. The d.c. response of the memristor is a decaying curve with its own timescale. We show via mathematical reasoning that this decaying curve when transformed to a.c. leads to the frequency effect by considering a descretized curve. We then demonstrate the validity of this approach with experimental data from two different types of memristors.

cs.ET↗
arXiv2014

Is Spiking Logic the Route to Memristor-Based Computers?

Memristors have been suggested as a novel route to neuromorphic computing based on the similarity between neurons (synapses and ion pumps) and memristors. The D.C. action of the memristor is a current spike, which we think will be fruitful for building memristor computers. In this paper, we introduce 4 different logical assignations to implement sequential logic in the memristor and introduce the physical rules, summation, `bounce-back', directionality and `diminishing returns', elucidated from our investigations. We then demonstrate how memristor sequential logic works by instantiating a NOT gate, an AND gate and a Full Adder with a single memristor. The Full Adder makes use of the memristor's memory to add three binary values together and outputs the value, the carry digit and even the order they were input in.

cs.ET↗
arXiv2014

Boolean Logic Gates From A Single Memristor Via Low-Level Sequential Logic

By using the memristor's memory to both store a bit and perform an operation with a second input bit, simple Boolean logic gates have been built with a single memristor. The operation makes use of the interaction of current spikes (occasionally called current transients) found in both memristors and other devices. The sequential time-based logic methodology allows two logical input bits to be used on a one-port by sending the bits separated in time. The resulting logic gate is faster than one relying on memristor's state switching, low power and requires only one memristor. We experimentally demonstrate working OR and XOR gates made with a single flexible Titanium dioxide sol-gel memristor.

cs.ET↗
arXiv2014

Towards plant wires

In experimental laboratory studies we evaluate a possibility of making electrical wires from living plants. In scoping experiments we use lettuce seedlings as a prototype model of a plant wire. We approximate an electrical potential transfer function by applying direct current voltage to the lettuce seedlings and recording output voltage. We analyse oscillation frequencies of the output potential and assess noise immunity of the plant wires. Our findings will be used in future designs of self-growing wetware circuits and devices, and integration of plant-based electronic components into future and emergent bio-hybrid systems.

cs.ET↗