Light and chemical oscillations: Review and perspectives

Living cells and biological mechanisms as prototypes for developing chemical artificial intelligence

Artificial Intelligence (AI) is having a revolutionary impact on our societies. It is helping humans in facing the global challenges of this century. Traditionally, AI is developed in software or through neuromorphic engineering in hardware. More recently, a brand-new strategy has been proposed. It is the so-called Chemical AI (CAI), which exploits molecular, supramolecular, and systems chemistry in wetware to mimic human intelligence. In this work, two promising approaches for boosting CAI are described. One regards designing and implementing neural surrogates that can communicate through optical or chemical signals and give rise to networks for computational purposes and to develop micro/nanorobotics. The other approach concerns "bottom-up synthetic cells" that can be exploited for applications in various scenarios, including future nano-medicine. Both topics are presented at a basic level, mainly to inform the broader audience of non-specialists, and so favour the rise of interest in these frontier subjects.

The Conformational Contribution to Molecular Complexity and Its Implications for Information Processing in Living Beings and Chemical Artificial Intelligence

This work highlights the relevant contribution of conformational stereoisomers to the complexity and functions of any molecular compound. Conformers have the same molecular and structural formulas but different orientations of the atoms in the three-dimensional space. Moving from one conformer to another is possible without breaking covalent bonds. The interconversion is usually feasible through the thermal energy available in ordinary conditions. The behavior of most biopolymers, such as enzymes, antibodies, RNA, and DNA, is understandable if we consider that each exists as an ensemble of conformers. Each conformational collection confers multi-functionality and adaptability to the single biopolymers. The conformational distribution of any biopolymer has the features of a fuzzy set. Hence, every compound that exists as an ensemble of conformers allows the molecular implementation of a fuzzy set. Since proteins, DNA, and RNA work as fuzzy sets, it is fair to say that life's logic is fuzzy. The power of processing fuzzy logic makes living beings capable of swift decisions in environments dominated by uncertainty and vagueness. These performances can be implemented in chemical robots, which are confined molecular assemblies mimicking unicellular organisms: they are supposed to help humans "colonise" the molecular world to defeat diseases in living beings and fight pollution in the environment.

Light induced spiking of proteinoids

Proteinoids, or thermal proteins, are produced by heating amino acids to their melting point and initiating polymerisation to produce polymeric chains. In aqueous solutions proteinoids swell into hollow microspheres. These microspheres produce endogenous burst of electrical potential spikes and change patterns of their electrical activity in response to illumination. We report results on a detailed investigation on the effects of white cold light on the spiking of proteinoids. We study how different types and intensities of light determine proteinoids' spiking amplitude, period, and pattern. The results of this study will be utilised to evaluate proteinoids for their potential as optical sensors and their application in unconventional computing.

A Role for Bottom-Up Synthetic Cells in the Internet of Bio-Nano Things?

The potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) is discussed. In particular, this perspective paper focuses on the growing interest in networks of biological and/or artificial objects at the micro- and nanoscale (cells and subcellular parts, microelectrodes, microvessels, etc.), whereby communication takes place in an unconventional manner, i.e., via chemical signaling. The resulting "molecular communication" (MC) scenario paves the way to the development of innovative technologies that have the potential to impact biotechnology, nanomedicine, and related fields. The scenario that relies on the interconnection of natural and artificial entities is briefly introduced, highlighting how Synthetic Biology (SB) plays a central role. SB allows the construction of various types of SCs that can be designed, tailored, and programmed according to specific predefined requirements. In particular, "bottom-up" SCs are briefly described by commenting on the principles of their design and fabrication and their features (in particular, the capacity to exchange chemicals with other SCs or with natural biological cells). Although bottom-up SCs still have low complexity and thus basic functionalities, here, we introduce their potential role in the IoBNT. This perspective paper aims to stimulate interest in and discussion on the presented topics. The article also includes commentaries on MC, semantic information, minimal cognition, wetware neuromorphic engineering, and chemical social robotics, with the specific potential they can bring to the IoBNT.

The Versatile Photo-Thermal Behaviour of a 2-Hydroxyazobenzene

Photochromic compounds are employed in implementing neuron surrogates. They will boost the development of neuromorphic engineering in wetware. In this work, the photochromic behaviours of (E)-3,4,6-trichloro-2-(p-diazenil)-phenol (t-DZH) and its conjugated phenoxide base (t-DZ) have been investigated experimentally in three different media: (1) pure acetonitrile, (2) in water and acetonitrile mixed in a 1/1 volume ratio, and (3) in an aqueous micellar solution of 3-(N,N-Dimethylmyristylammonio)propanesulfonate (SB3-14). The analysis of the spectral and kinetic features of t-DZH and t-DZ has been supported by quantum-mechanical DFT calculations, the maximum entropy method, and the determination of their colourability (C). The versatility of t-DZH and t-DZ makes them promising molecular probes of micro-environments and potential ingredients of photochemical oscillators required for implementing pacemaker neurons capable of communicating through optical signals in wetware.

Buoyancy-Driven Chemohydrodynamic Patterns in A + B → Oscillator Two-Layer Stratifications

Chemohydrodynamic patterns due to the interplay of buoyancy-driven instabilities and reaction-diffusion patterns are studied experimentally in a vertical quasi-two-dimensional reactor in which two solutions A and B containing separate reactants of the oscillating Belousov-Zhabotinsky system are placed in contact along a horizontal contact line where excitable or oscillating dynamics can develop. Different types of buoyancy-driven instabilities are selectively induced in the reactive zone depending on the initial density jump between the two layers, controlled here by the bromate salt concentration. Starting from a less dense solution above a denser one, two possible differential diffusion instabilities are triggered depending on whether the fast diffusing sulfuric acid is in the upper or lower solution. Specifically, when the solution containing malonic acid and sulfuric acid is stratified above the one containing the slow-diffusing bromate salt, a diffusive layer convection (DLC) instability is observed with localized convective rolls around the interface. In that case, the reaction-diffusion wave patterns remain localized above the initial contact line, scarcely affected by the flow. If, on the contrary, sulfuric acid diffuses upward because it is initially dissolved in the lower layer, then a double-diffusion (DD) convective mode develops. This triggers fingers across the interface that mix the reactants such that oscillatory dynamics and rippled waves develop throughout the whole reactor. If the denser solution is put on top of the other one, then a fast developing Rayleigh-Taylor (RT) instability induces fast mixing of all reactants such that classical reaction-diffusion waves develop later on in the convectively mixed solutions.

The Boundary between Two Modes of Gas Evolution: Oscillatory (H2 and O2) and Conventional Redox (O2 Only), in the Hydrocarbon/H2O2/Cu(II)/CH3CN System

During the oxidation of hydrocarbons using hydrogen peroxide solutions, the evolution of gaseous oxygen is a side and undesirable process, in which the consumption of the oxidizer is not associated with the formation of target products. Therefore, no attention is paid to the systematic study of the chemical composition of the gas and the mechanisms of its formation. Filling this gap, the authors discovered a number of new, previously unidentified, interesting facts concerning both gas evolution and the oxidation of hydrocarbons. In a 33% H2O2/Cu2Cl4·2DMG/CH3CN system, where DMG is dimethylglyoxime (Butane-2,3-dione dioxime), and is at 50 °C, evidence of significant evolution of gaseous hydrogen, along with the evolution of gaseous oxygen was found. In the authors’ opinion, which requires additional verification, the ratio of gaseous hydrogen and oxygen in the discussed catalytic system can reach up to 1:1. The conditions in which only gaseous oxygen is formed are selected. Using a number of oxidizable hydrocarbons with the first adiabatic ionization potentials (AIPs) of a wide range of values, it was found that the first stage of such a process of evolving only gaseous oxygen was the single electron transfer from hydrogen peroxide molecules to trinuclear copper clusters with the formation, respectively, of hydrogen peroxide radical cations H2O2•+ and radical anions Cu3Cl5•− (AIP = 5 eV). When the conditions for the implementation of such a single electron transfer mechanism are exhausted, the channel of decomposition of hydrogen peroxide molecules into gaseous hydrogen and oxygen is switched on, which is accompanied by the transition of the system to an oscillatory mode of gas evolution. In some cases, the formation of additional amounts of gaseous products is provided by the catalytically activated decomposition of water molecules into hydrogen and oxygen after the complete consumption of hydrogen peroxide molecules in the reaction of gaseous oxygen evolution. The adiabatic electron affinity of various forms of copper molecules involved in chemical processes is calculated by the density functional theory method.

Neural network and decision tree-based machine learning tools to analyse the anion-responsive behaviours of emissive Ru(ii)–terpyridine complexes

Artificial neural network, adaptive neuro-fuzzy inference and decision tree regression are implemented to analyse the anion-responsive behaviours of emissive Ru(ii)–terpyridine complexes.

Artificial temperature-compensated biological clock using temperature-sensitive Belousov-Zhabotinsky gels

The circadian rhythm is a fundamental physiological function for a wide range of organisms. The molecular machinery for generating rhythms has been elucidated over the last few decades. Nevertheless, the mechanism for temperature compensation of the oscillation period, which is a prominent property of the circadian rhythm, is still controversial. In this study, we propose a new mechanism through a chemically synthetic approach (i.e., we realized temperature compensation by the Belousov-Zhabotinsky (BZ) gels). The BZ gels are prepared by embedding a metal catalyst of the BZ reaction into the gel polymer. We made the body of BZ gels using a temperature-sensitive polymer gel, which enabled temperature compensation of the oscillation by using temperature dependence of volume. Moreover, we constructed a simple mathematical model for the BZ oscillation in temperature-sensitive gels. The model can reproduce temperature compensation of BZ gels, even though all reactions are temperature sensitive according to the Arrhenius rule. Our finding hints that a soft body coupling may be underlying temperature-compensated biological functions, including circadian rhythms.

Modulation of spatiotemporal dynamics in the bromate–sulfite–ferrocyanide reaction system by visible light

We have carried out the first systematic study of the effects of visible light on the homogenous dynamics in the bromate–sulfite–ferrocyanide (BSF) reaction. Under flow conditions, the reaction system displayed photoinduction and photoinhibition behavior, and the oscillatory period decreased with the increase of light intensity, which is due to the fact that light irradiation mainly enhanced the negative process and affected the positive feedback. The light effect on positive and negative feedback is studied by analyzing the period length of pH increasing and decreasing in detail. With the increase of light intensity, the period length of pH increasing decreases monotonically, while the period length of pH decreasing changes nonmonotonically. These results suggest that light could be used as a powerful tool to control homogenous dynamics. Results obtained from numerical simulations are in good agreement with experimental data.

The BSF reaction system displayed photoinduction and photoinhibition behavior under flow conditions. The oscillatory period decreased as the light irradiation mainly enhanced the negative process and affected the positive feedback.

Ozone depletion due to dust release of iodine in the free troposphere

Iodine is an atmospheric trace element emitted from oceans that efficiently destroys ozone (O₃). Low O₃ in airborne dust layers is frequently observed but poorly understood. We show that dust is a source of gas-phase iodine, indicated by aircraft observations of iodine monoxide (IO) radicals inside lofted dust layers from the Atacama and Sechura Deserts that are up to a factor of 10 enhanced over background. Gas-phase iodine photochemistry, commensurate with observed IO, is needed to explain the low O₃ inside these dust layers (below 15 ppbv; up to 75% depleted). The added dust iodine can explain decreases in O₃ of 8% regionally and affects surface air quality. Our data suggest that iodate reduction to form volatile iodine species is a missing process in the geochemical iodine cycle and presents an unrecognized aeolian source of iodine. Atmospheric iodine has tripled since 1950 and affects ozone layer recovery and particle formation.

Light sensitive Belousov-Zhabotinsky medium accommodates multiple logic gates

Computational functionality has been implemented successfully on chemical reactions in living systems. In the case of Belousov-Zhabotinsky (BZ) reaction, this was achieved by using collision-based techniques and by exploiting the light sensitivity of BZ. In order to unveil the computational capacity of the light sensitive BZ medium and the possibility to implement re-configurable logic, the design of multiple logic gates in a fixed BZ reservoir was investigated. The three basic logic gates (namely NOT, OR and AND) were studied to prove the Turing completeness of the architecture. Namely, all possible Boolean functions can be implemented as a combination of these logic gates. Nonetheless, a more complicated logic function was investigated, aiming to illustrate further capabilities of a fixed size BZ reservoir. The experiments executed within this study were implemented with a Cellular Automata (CA)-based model of the Oregonator equations that simulate excitation and wave propagation on a light sensitive BZ thin film. Given that conventional or von Neumann architecture computations is proved possible on the proposed configuration, the next step would be the realization of unconventional types of computation, such as neuromorphic and fuzzy computations, where the chemical substrate may prove more efficient than silicon.

Towards Embedded Computation with Building Materials

We present results showing the capability of concrete-based information processing substrate in the signal classification task in accordance with in materio computing paradigm. As the Reservoir Computing is a suitable model for describing embedded in materio computation, we propose that this type of presented basic construction unit can be used as a source for “reservoir of states” necessary for simple tuning of the readout layer. We present an electrical characterization of the set of samples with different additive concentrations followed by a dynamical analysis of selected specimens showing fingerprints of memfractive properties. As part of dynamic analysis, several fractal dimensions and entropy parameters for the output signal were analyzed to explore the richness of the reservoir configuration space. In addition, to investigate the chaotic nature and self-affinity of the signal, Lyapunov exponents and Detrended Fluctuation Analysis exponents were calculated. Moreover, on the basis of obtained parameters, classification of the signal waveform shapes can be performed in scenarios explicitly tuned for a given device terminal.