Chemical reaction-diffusion implementation of finding the shortest paths in a labyrinth

Towards proteinoid computers. Hypothesis paper

Proteinoids - thermal proteins - are produced by heating amino acids to their melting point and initiation of polymerisation to produce polymeric chains. Proteinoids swell in aqueous solution into hollow microspheres. The proteinoid microspheres produce endogenous burst of electrical potential spikes and change patterns of their electrical activity in response to illumination. The microspheres can interconnect by pores and tubes and form networks with a programmable growth. We speculate on how ensembles of the proteinoid microspheres can be developed into unconventional computing devices.

A programmable chemical computer with memory and pattern recognition

Current computers are limited by the von Neumann bottleneck, which constrains the throughput between the processing unit and the memory. Chemical processes have the potential to scale beyond current computing architectures as the processing unit and memory reside in the same space, performing computations through chemical reactions, yet their lack of programmability limits them. Herein, we present a programmable chemical processor comprising of a 5 by 5 array of cells filled with a switchable oscillating chemical (Belousov-Zhabotinsky) reaction. Each cell can be individually addressed in the 'on' or 'off' state, yielding more than 2.9 × 10¹⁷ chemical states which arise from the ability to detect distinct amplitudes of oscillations via image processing. By programming the array of interconnected BZ reactions we demonstrate chemically encoded and addressable memory, and we create a chemical Autoencoder for pattern recognition able to perform the equivalent of one million operations per second.

A brief history of liquid computers

A substrate does not have to be solid to compute. It is possible to make a computer purely from a liquid. I demonstrate this using a variety of experimental prototypes where a liquid carries signals, actuates mechanical computing devices and hosts chemical reactions. We show hydraulic mathematical machines that compute functions based on mass transfer analogies. I discuss several prototypes of computing devices that employ fluid flows and jets. They are fluid mappers, where the fluid flow explores a geometrically constrained space to find an optimal way around, e.g. the shortest path in a maze, and fluid logic devices where fluid jet streams interact at the junctions of inlets and results of the computation are represented by fluid jets at selected outlets. Fluid mappers and fluidic logic devices compute continuously valued functions albeit discretized. There is also an opportunity to do discrete operation directly by representing information by droplets and liquid marbles (droplets coated by hydrophobic powder). There, computation is implemented at the sites, in time and space, where droplets collide one with another. The liquid computers mentioned above use liquid as signal carrier or actuator: the exact nature of the liquid is not that important. What is inside the liquid becomes crucial when reaction-diffusion liquid-phase computing devices come into play: there, the liquid hosts families of chemical species that interact with each other in a massive-parallel fashion. I shall illustrate a range of computational tasks, including computational geometry, implementable by excitation wave fronts in nonlinear active chemical medium. The overview will enable scientists and engineers to understand how vast is the variety of liquid computers and will inspire them to design their own experimental laboratory prototypes. This article is part of the theme issue 'Liquid brains, solid brains: How distributed cognitive architectures process information'.

Towards fungal computer

We propose that fungi Basidiomycetes can be used as computing devices: information is represented by spikes of electrical activity, a computation is implemented in a mycelium network and an interface is realized via fruit bodies. In a series of scoping experiments, we demonstrate that electrical activity recorded on fruits might act as a reliable indicator of the fungi's response to thermal and chemical stimulation. A stimulation of a fruit is reflected in changes of electrical activity of other fruits of a cluster, i.e. there is distant information transfer between fungal fruit bodies. In an automaton model of a fungal computer, we show how to implement computation with fungi and demonstrate that a structure of logical functions computed is determined by mycelium geometry.

On Emulation of Flueric Devices in Excitable Chemical Medium

Flueric devices are fluidic devices without moving parts. Fluidic devices use fluid as a medium for information transfer and computation. A Belousov-Zhabotinsky (BZ) medium is a thin-layer spatially extended excitable chemical medium which exhibits travelling excitation wave-fronts. The excitation wave-fronts transfer information. Flueric devices compute via jets interaction. BZ devices compute via excitation wave-fronts interaction. In numerical model of BZ medium we show that functions of key flueric devices are implemented in the excitable chemical system: signal generator, and, xor, not and nor Boolean gates, delay elements, diodes and sensors. Flueric devices have been widely used in industry since late 1960s and are still employed in automotive and aircraft technologies. Implementation of analog of the flueric devices in the excitable chemical systems opens doors to further applications of excitation wave-based unconventional computing in soft robotics, embedded organic electronics and living technologies.

Binary full adder, made of fusion gates, in a subexcitable Belousov-Zhabotinsky system

In an excitable thin-layer Belousov-Zhabotinsky (BZ) medium a localized perturbation leads to the formation of omnidirectional target or spiral waves of excitation. A subexcitable BZ medium responds to asymmetric local perturbation by producing traveling localized 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. I 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. I 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 the conjunction of the input variables and the conjunction of one input variable with the negation of another input variable. The gate is made of three channels: two channels cross each other at an angle, a third channel starts at the junction. The channels contain a BZ medium. When two excitation wave-fragments, traveling towards each other along input channels, collide at the junction they merge into a single wave-front traveling along the third channel. If there is just one wave-front in the input channel, the front continues its propagation undisturbed. I make a one-bit full adder by cascading two fusion gates. I show how to cascade the adder blocks into a many-bit full adder. I evaluate the feasibility of my designs by simulating the evolution of excitation in the gates and adders using the numerical integration of Oregonator equations.

Where and how could intentional programs be generated in the brain?

Based on glial-neuronal interaction a formalism (negative language) for the generation of intentional programs is proposed. An intentional program generates a specific multirelational structure in an inner or outer appropriate environment according to the principle of feasibility. After description of the glial spatio-temporal boundary-setting function in its interaction with the neuronal system, it is hypothesized that intentional programs may be generated in glial networks (syncytia) in line with the formalism of negative language. Gap junctions are interpreted as multirelational negation operators, generating cycles in a permutation system. These cycles could represent intentional programs that can either be realized or not in neuronal networks embodying a permutation system. The feasibility of these intentional programs is essentially dependent on appropriate environmental information. Since the realization of intentional programs in neuronal networks allows high degrees of freedom, the problem of free will is tackled, as well. Free will is defined as the subjective freedom to choose between the inner determination of intentional programs and the overdetermination of their feasibility in an appropriate environment. Finally, the possible implementation of the proposed brain model in robot brains is briefly discussed.

Experimental logical gates in a reaction-diffusion medium: the XOR gate and beyond

We exploit the particulars of diffusive wave front interactions in certain types of two-reactant reaction-diffusion medium to construct a laboratory prototype of an XOR gate. In the design, the values of the logic variables are represented by the presence or absence of a precipitate, "wires" are constructed of a substrate loaded gel, and the computation is based on diffusive wave dynamics. We also discuss implementation of AND gate and study a three-valued composition, derived from the gate dynamic, and discuss possible logics that could be derived from this composition.

Roots and promises of chemical-based computing

General principles of information processing by chemical-based biomolecular systems (pseudobiological information processing paradigm) are discussed. These principles include very large scale parallelism of information processing, high behavioral complexity, complementarity of information features, self-organization, and multilevel architecture. Chemical-based information processing devices using these principles seem to be able to solve effectively problems of high computational complexity.