arXiv subjects

Andrew Adamatzky

Publications and source records attributed to Andrew Adamatzky.

At least 109 records · Page 6Linked to original sources

arXiv2018

On discovering functions in actin filament automata

We simulate an actin filament as an automaton network. Every atom takes two or three states and updates its state, in discrete time, depending on a ratio of its neighbours in some selected state. All atoms/automata simultaneously update their states by the same rule. Two state transition rules are considered. In semi-totalistic Game of Life like actin filament automaton atoms take binary states `0' and `1' and update their states depending on a ratio of neighbours in the state `1'. In excitable actin filament automaton atoms take three states: resting, excited and refractory. A resting atom excites if a ratio of its excited neighbours belong to some specified interval; transitions from excited state to refractory state and from refractory state to resting state are unconditional. In computational experiments we implement mappings of 8-bit input string to 8-bit output string via dynamics of perturbation/excitation on actin filament automata. We assign eight domains in an actin filament as I/O ports. To write {\sc True} to a port we perturb/excite a certain percentage of the nodes in the domain corresponding to the port. We read outputs at the ports after some time interval. A port is considered to be in a state {\sc True} if a number of excited nodes in the port's domain exceed a certain threshold. A range of eight-argument Boolean functions is uncovered in a series of computational trials when all possible configurations of eight-elements binary strings were mapped onto excitation outputs of the I/O domains.

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arXiv2018

Belousov-Zhabotinsky reaction in liquid marbles

This paper reports on a new method of encapsulating BZ solution droplets in a powder coating of either polyethylene (PE) or polytetrafluoroethylene (PTFE), to produce BZ liquid marbles (LMs). The BZ LMs have solid--liquid interfaces in contrast to the previously reported BZ encapsulation systems used to study pattern formations and wave transfers, such as BZ emulsions and BZ vesicles. All these systems are important to study as they can be seen as analogues for information transfer in excitable systems in nature. Due to the powder coating of the LMs, LMs do not wet the underlying substrate, making the LMs mobile, enabling them to be easily arranged in arrays. The preparation of complex LMs, containing an acidic oscillating solution, proves the resilience of LMs and their application in transporting a wide range of chemical cargoes and in playing a mediating role in chemical reactions. PTFE-coated LMs were harder to prepare and not as robust as PE-coated LMs, therefore oscillation studies of BZ LMs positioned in arrays only focused on PE-coated LMs. Sporadic transfer of excitation waves was observed between LMs placed in close proximity to each other in ordered and disordered arrays, suggesting the transfer of liquid species possibly arises from contact between imperfectly coated areas at the LM--LM interface or capillary action, where solution is actively transported to the marble surface through the coating. Propagation pathways of the excitation waves in both the disordered and ordered arrays of BZ LMs are reported. These results lay the foundations for future studies on information transmission and processing arrays of BZ LMs, in addition to observing BZ wave propagation in a LM and the effect of other physical stimuli such as heat, light and chemical environments on the dynamics of excitation in arrays of BZ Lms.

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arXiv2018

Logical Gates via Gliders Collisions

An elementary cellular automaton with memory is a chain of finite state machines (cells) updating their state simultaneously and by the same rule. Each cell updates its current state depending on current states of its immediate neighbours and a certain number of its own past states. Some cell-state transition rules support gliders, compact patterns of non-quiescent states translating along the chain. We present designs of logical gates, including reversible Fredkin gate and controlled NOT gate, implemented via collisions between gliders.

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arXiv2018

Excitable London: Street map analysis with Oregonator model

We explore geometry of London's streets using computational mode of an excitable chemical system, Belousov-Zhabotinsky (BZ) medium. We virtually fill in the streets with a BZ medium and study propagation of excitation waves for a range of excitability parameters, gradual transition from excitable to sub-excitable to non-excitable. We demonstrate a pruning strategy adopted by the medium with decreasing excitability when wider and ballistically appropriate streets are selected. We explain mechanics of streets selection and pruning. The results of the paper will be used in future studies of studying dynamics of cities with living excitable substrates.

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arXiv2018

Modelling Microbial Fuel Cells using lattice Boltzmann methods

An accurate modelling of bio-electrochemical processes that govern Microbial Fuel Cells (MFCs) and mapping their behaviour according to several parameters will enhance the development of MFC technology and enable their successful implementation in well defined applications. The geometry of the electrodes is among key parameters determining efficiency of MFCs due to the formation of a biofilm of anodophilic bacteria on the anode electrode, which is a decisive factor for the functionality of the device. We simulate the bio-electrochemical processes in an MFC while taking into account the geometry of the electrodes. Namely, lattice Boltzmann methods are used to simulate the fluid dynamics and the advection-diffusion phenomena in the anode compartment. The model is verified on voltage and current outputs of a single MFC derived from laboratory experiments under continuous flow.

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arXiv2018

Simple networks on complex cellular automata: From de Bruijn diagrams to jump-graphs

We overview networks which characterise dynamics in cellular automata. These networks are derived from one-dimensional cellular automaton rules and global states of the automaton evolution: de Bruijn diagrams, subsystem diagrams, basins of attraction, and jump-graphs. These networks are used to understand properties of spatially-extended dynamical systems: emergence of non-trivial patterns, self-organisation, reversibility and chaos. Particular attention is paid to networks determined by travelling self-localisations, or gliders.

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arXiv2017

Cellular Automata Applications in Shortest Path Problem

Cellular Automata (CAs) are computational models that can capture the essential features of systems in which global behavior emerges from the collective effect of simple components, which interact locally. During the last decades, CAs have been extensively used for mimicking several natural processes and systems to find fine solutions in many complex hard to solve computer science and engineering problems. Among them, the shortest path problem is one of the most pronounced and highly studied problems that scientists have been trying to tackle by using a plethora of methodologies and even unconventional approaches. The proposed solutions are mainly justified by their ability to provide a correct solution in a better time complexity than the renowned Dijkstra's algorithm. Although there is a wide variety regarding the algorithmic complexity of the algorithms suggested, spanning from simplistic graph traversal algorithms to complex nature inspired and bio-mimicking algorithms, in this chapter we focus on the successful application of CAs to shortest path problem as found in various diverse disciplines like computer science, swarm robotics, computer networks, decision science and biomimicking of biological organisms' behaviour. In particular, an introduction on the first CA-based algorithm tackling the shortest path problem is provided in detail. After the short presentation of shortest path algorithms arriving from the relaxization of the CAs principles, the application of the CA-based shortest path definition on the coordinated motion of swarm robotics is also introduced. Moreover, the CA based application of shortest path finding in computer networks is presented in brief. Finally, a CA that models exactly the behavior of a biological organism, namely the Physarum's behavior, finding the minimum-length path between two points in a labyrinth is given.

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arXiv2017

Maze solvers demystified and some other thoughts

There is a growing interest towards implementation of maze solving in spatially-extended physical, chemical and living systems. Several reports of prototypes attracted great publicity, e.g. maze solving with slime mould and epithelial cells, maze navigating droplets. We show that most prototypes utilise one of two phenomena: a shortest path in a maze is a path of the least resistance for fluid and current flow, and a shortest path is a path of the steepest gradient of chemoattractants. We discuss that substrates with so-called maze-solving capabilities simply trace flow currents or chemical diffusion gradients. We illustrate our thoughts with a model of flow and experiments with slime mould. The chapter ends with a discussion of experiments on maze solving with plant roots and leeches which show limitations of the chemical diffusion maze-solving approach.

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arXiv2017

Slime mould: the fundamental mechanisms of cognition

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-Lengelerś modifiable pathways, Bateson's "patterns that connect" framework, Maturana's autopoetic network, or proto-consciousness and Morgan's Canon.

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arXiv2017

Liquid Marble Interaction Gate for Collision-Based Computing

Liquid marbles are microlitre droplets of liquid, encapsulated by self-organised hydrophobic particles at the liquid/air interface. They offer an efficient approach for manipulating liquid droplets and compartmentalising reactions in droplets. Digital fluidic devices employing liquid marbles might benefit from having embedded computing circuits without electronics and moving mechanical parts (apart from the marbles). We present an experimental implementation of a collision gate with liquid marbles. Mechanics of the gate follows principles of Margolus' soft-sphere collision gate. Boolean values of the inputs are given by the absence (FALSE) or presence (TRUE) of a liquid marble. There are three outputs: two outputs are trajectories of undisturbed marbles (they only report TRUE when just one marble is present at one of the inputs), one output is represented by trajectories of colliding marbles (when two marbles collide they lose their horizontal momentum and fall), this output reports TRUE only when two marbles are present at inputs. Thus the gate implements AND and AND-NOT logical functions. We speculate that by merging trajectories representing AND-NOT output into a single channel one can produce a one-bit half-adder. Potential design of a one-bit full-adder is discussed, and the synthesis of both a pure nickel metal and hybrid nickel/polymer liquid marble is reported.

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arXiv2017

Computing via material topology optimisation

We construct logical gates via topology optimisation (aimed to solve a station problem of heat conduction) of a conductive material layout. Values of logical variables are represented high and low values of a temperature at given sites. Logical functions are implemented via the formation of an optimum layout of conductive material between the sites with loading conditions. We implement AND and XOR gates and a one-bit binary half-adder.

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arXiv2017

On dynamics of excitation in F-actin: automaton model

We represent a filamentous actin molecule as a graph of finite-state machines (F-actin automaton). Each node in the graph takes three states --- resting, excited, refractory. All nodes update their states simultaneously and by the same rule, in discrete time steps. Two rules are considered: threshold rule --- a resting node is excited if it has at least one excited neighbour and narrow excitation interval rule --- a resting node is excited if it has exactly one excited neighbour. We analyse distributions of transient periods and lengths of limit cycles in evolution of F-actin automaton, propose mechanisms for formation of limit cycles and evaluate density of information storage in F-actin automata.

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arXiv2017

Towards implementation of Cellular Automata in Microbial Fuel Cells

The Microbial Fuel Cell (MFC) is a bio-electrochemical transducer converting waste products into electricity using microbial communities. Cellular Automaton (CA) is a uniform array of finite-state machines that update their states in discrete time depending on states of their closest neighbors by the same rule. Arrays of MFCs could, in principle, act as massive-parallel computing devices with local connectivity between elementary processors. We provide a theoretical design of such a parallel processor by implementing CA in MFCs. We have chosen Conway's Game of Life as the 'benchmark' CA because this is the most popular CA which also exhibits an enormously rich spectrum of patterns. Each cell of the Game of Life CA is realized using two MFCs. The MFCs are linked electrically and hydraulically. The model is verified via simulation of an electrical circuit demonstrating equivalent behaviors. The design is a first step towards future implementations of fully autonomous biological computing devices with massive parallelism. The energy independence of such devices counteracts their somewhat slow transitions - compared to silicon circuitry - between the different states during computation.

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arXiv2017

Cellular non-nonlinear network model of microbial fuel cell

A cellular non-linear network (CNN) is a uniform regular array of locally connected continuous-state machines, or nodes, which update their states simultaneously in discrete time. A microbial fuel cell (MFC) is an electro-chemical reactor using the metabolism of bacteria to drive an electrical current. In a CNN model of the MFC, each node takes a vector of states which represent geometrical characteristics of the cell, like the electrodes or impermeable borders, and quantify measurable properties like bacterial population, charges produced and hydrogen ions concentrations. The model allows the study of integral reaction of the MFC, including temporal outputs, to spatial disturbances of the bacterial population and supply of nutrients. The model can also be used to evaluate inhomogeneous configurations of bacterial populations attached on the electrode biofilms.

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arXiv2017

Computers from plants we never made. Speculations

We discuss possible designs and prototypes of computing systems that could be based on morphological development of roots, interaction of roots, and analog electrical computation with plants, and plant-derived electronic components. In morphological plant processors data are represented by initial configuration of roots and configurations of sources of attractants and repellents; results of computation are represented by topology of the roots' network. Computation is implemented by the roots following gradients of attractants and repellents, as well as interacting with each other. Problems solvable by plant roots, in principle, include shortest-path, minimum spanning tree, Voronoi diagram, $α$-shapes, convex subdivision of concave polygons. Electrical properties of plants can be modified by loading the plants with functional nanoparticles or coating parts of plants of conductive polymers. Thus, we are in position to make living variable resistors, capacitors, operational amplifiers, multipliers, potentiometers and fixed-function generators. The electrically modified plants can implement summation, integration with respect to time, inversion, multiplication, exponentiation, logarithm, division. Mathematical and engineering problems to be solved can be represented in plant root networks of resistive or reaction elements. Developments in plant-based computing architectures will trigger emergence of a unique community of biologists, electronic engineering and computer scientists working together to produce living electronic devices which future green computers will be made of.

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arXiv2016

Fredkin and Toffoli gates implemented in Oregonator model of Belousov-Zhabotinsky medium

A thin-layer Belousov-Zhabotinsky (BZ) medium is a powerful computing device capable for implementing logical circuits, memory, image processors, robot controllers, and neuromorphic architectures. We design the reversible logical gates --- Fredkin gate and Toffoli gate --- in a BZ medium network of excitable channels with sub-excitable junctions. Local control of the BZ medium excitability is an important feature of the gates' design. A excitable thin-layer BZ medium responds to a localised perturbation with omnidirectional target or spiral excitation waves. A sub-excitable BZ medium responds to an asymmetric perturbation by producing travelling localised excitation wave-fragments similar to dissipative solitons. We employ interactions between excitation wave-fragments to perform computation. We interpret the wave-fragments as values of Boolean variables. A presence of a wave-fragment at a given site of a circuit represents logical truth, absence of the wave-fragment --- logical false. Fredkin gate consists of ten excitable channels intersecting at eleven junctions eight of which are sub-excitable. Toffoli gate consists of six excitable channels intersecting at six junctions four of which are sub-excitable. The designs of the gates are verified using numerical integration of two-variable Oregonator equations.

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arXiv2016

Generative complexity of Gray-Scott model

In the Gray-Scott reaction-diffusion system one reactant is constantly fed in the system, another reactant is reproduced by consuming the supplied reactant and also converted to an inert product. The rate of feeding one reactant in the system and the rate of removing another reactant from the system determine configurations of concentration profiles: stripes, spots, waves. We calculate the generative complexity --- a morphological complexity of concentration profiles grown from a point-wise perturbation of the medium --- of the Gray-Scott system for a range of the feeding and removal rates. The morphological complexity is evaluated using Shannon entropy, Simpson diversity, approximation of Lempel-Ziv complexity, and expressivity (Shannon entropy divided by space-filling). We analyse behaviour of the systems with highest values of the generative morphological complexity and show that the Gray-Scott systems expressing highest levels of the complexity are composed of the wave-fragments (similar to wave-fragments in sub-excitable media) and travelling localisations (similar to quasi-dissipative solitons and gliders in Conway's Game of Life).

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arXiv2016

On plant roots logical gates

Theoretical constructs of logical gates implemented with plant roots are morphological computing asynchronous devices. Values of Boolean variables are represented by plant roots. A presence of a plant root at a given site symbolises the logical {\sc True}, an absence the logical {\sc False}. Logical functions are calculated via interaction between roots. Two types of two-inputs-two-outputs gates are proposed: a gate $\langle x, y \rangle \rightarrow \langle xy, x+y \rangle$ where root apexes are guided by gravity and a gate $\langle x, y \rangle \rightarrow \langle \overline{x}y, x \rangle$ where root apexes are guided by humidity. We propose a design of binary half-adder based on the gates.

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