Sensing the distance to a source of periodic oscillations in a nonlinear chemical medium with the output information coded in frequency of excitation pulses

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.

Minimum size for a nanoscale temperature discriminator based on a thermochemical system

What are the limits of size reduction for information processing devices based on chemical reactions? In this paper, we partially answer this question. We show that a thermochemical system can be used to design a discriminator of the parameters associated with oscillations of the ambient temperature. Depending on the amplitude and frequency of the oscillations, the system exhibits sharp transitions between different types of its time evolutions. This phenomenon can be used to discriminate between different parameter values describing the oscillating environment. We investigate the reliability of the thermochemical discriminator as a function of the number of molecules involved in the reactions. A stochastic model of chemical reactions and heat exchange with the neighborhood, in which the number of molecules explicitly appears, is introduced. For the selected values of the parameters, thermochemical discriminators operating with less than 10(5) molecules appear to be unreliable.

Understanding Networks of Computing Chemical Droplet Neurons Based on Information Flow

In this paper, we present general methods that can be used to explore the information processing potential of a medium composed of oscillating (self-exciting) droplets. Networks of Belousov–Zhabotinsky (BZ) droplets seem especially interesting as chemical reaction-diffusion computers because their time evolution is qualitatively similar to neural network activity. Moreover, such networks can be self-generated in microfluidic reactors. However, it is hard to track and to understand the function performed by a medium composed of droplets due to its complex dynamics. Corresponding to recurrent neural networks, the flow of excitations in a network of droplets is not limited to a single direction and spreads throughout the whole medium. In this work, we analyze the operation performed by droplet systems by monitoring the information flow. This is achieved by measuring mutual information and time delayed mutual information of the discretized time evolution of individual droplets. To link the model with reality, we use experimental results to estimate the parameters of droplet interactions. We exemplarily investigate an evolutionary generated droplet structure that operates as a NOR gate. The presented methods can be applied to networks composed of at least hundreds of droplets.

Chemical computing with reaction-diffusion processes

Chemical reactions are responsible for information processing in living organisms. It is believed that the basic features of biological computing activity are reflected by a reaction-diffusion medium. We illustrate the ideas of chemical information processing considering the Belousov-Zhabotinsky (BZ) reaction and its photosensitive variant. The computational universality of information processing is demonstrated. For different methods of information coding constructions of the simplest signal processing devices are described. The function performed by a particular device is determined by the geometrical structure of oscillatory (or of excitable) and non-excitable regions of the medium. In a living organism, the brain is created as a self-grown structure of interacting nonlinear elements and reaches its functionality as the result of learning. We discuss whether such a strategy can be adopted for generation of chemical information processing devices. Recent studies have shown that lipid-covered droplets containing solution of reagents of BZ reaction can be transported by a flowing oil. Therefore, structures of droplets can be spontaneously formed at specific non-equilibrium conditions, for example forced by flows in a microfluidic reactor. We describe how to introduce information to a droplet structure, track the information flow inside it and optimize medium evolution to achieve the maximum reliability. Applications of droplet structures for classification tasks are discussed.

Time-dependent wave selection for information processing in excitable media

We demonstrate an improved technique for implementing logic circuits in light-sensitive chemical excitable media. The technique makes use of the constant-speed propagation of waves along defined channels in an excitable medium based on the Belousov-Zhabotinsky reaction, along with the mutual annihilation of colliding waves. What distinguishes this work from previous work in this area is that regions where channels meet at a junction can periodically alternate between permitting the propagation of waves and blocking them. These valvelike areas are used to select waves based on the length of time that it takes waves to propagate from one valve to another. In an experimental implementation, the channels that make up the circuit layout are projected by a digital projector connected to a computer. Excitable channels are projected as dark areas and unexcitable regions as light areas. Valves alternate between dark and light: Every valve has the same period and phase, with a 50% duty cycle. This scheme can be used to make logic gates based on combinations of or and and-not operations, with few geometrical constraints. Because there are few geometrical constraints, compact circuits can be implemented. Experimental results from an implementation of a four-bit input, two-bit output integer square root circuit are given.

Spatiotemporal dynamics of glycolytic waves provides new insights into the interactions between immobilized yeast cells and gels

The immobilization of cells or enzymes is a promising tool for the development of biosensors, yet the interactions between the fixative materials and the cells are not fully understood, especially with respect to their impact on both cell metabolism and cell-to-cell signaling. We show that the spatiotemporal dynamics of waves of metabolic synchronization of yeast cells provides a new criterion to distinguish the effect of different gels on the cellular metabolism, which otherwise could not be detected. Cells from the yeast Saccharomyces carlsbergensis were immobilized into agarose gel, silica gel (TMOS), or a mixture of TMOS and alginate. We compared these immobilized cells with respect to their ability to generate temporal, intracellular oscillations in glycolysis as well as propagating, extracellular synchronization waves. While the temporal dynamics, as measured by the period and the number of oscillatory cycles, was similar for all three immobilized cell populations, significant differences have been observed with respect to the shape of the waves, wave propagation direction and velocity in the three gel matrices used.

Periodic perturbation of one of two identical chemical oscillators coupled via inhibition

We study perturbation with period T(p) of one of two model Belousov-Zhabotinsky chemical oscillators diffusively coupled through an inhibitory species. We find a variety of resonance regimes, characterized as N1:N2:n , where N1 (N2) and n are the numbers of spikes of the perturbed (unperturbed) oscillator and the external perturbation, respectively, per global period T(G). The resonance mode is determined primarily by the ratios T(p)/T0 and T(p)/T(C), where T0 and T(C) are the periods of a single oscillator and of two coupled antiphase oscillators, respectively (T(C)≅2T0 at large coupling strength). The period of the perturbed oscillator can be tuned over a wide range (from T0 to >10T0) by varying T(p) between T(C) and T0.

Unpinning of a spiral wave anchored around a circular obstacle by an external wave train: common aspects of a chemical reaction and cardiomyocyte tissue

It is well known that spiral waves are often stabilized by anchoring to a local heterogeneity ("pinning") and that such pinned waves are rather difficult to eliminate. In the present report, we show that pinned spiral waves can be eliminated through collision with a wave train arriving from the outer region, as confirmed in experiments on the Belousov-Zhabotinsky (BZ) reaction as well as in cardiomyocyte tissue culture. A numerical simulation using the Oregonator, a mathematical model for the BZ reaction, provides the parameter area for successful unpinning. The scenario of unpinning is discussed in terms of the dispersion relation of the wave train by taking into account the curvature effect of the excitation wave.

Onset of unidirectional pulse propagation in an excitable medium with asymmetric heterogeneity

Heterogeneity is one of the most important and ubiquitous types of external perturbations in dissipative systems. To know the behaviors of pulse waves in such media is closely related to studying the collision process between the pulse and the heterogeneity-induced-ordered pattern. In particular, we focus on unidirectional propagation of pulses in a medium with an asymmetric bump heterogeneity. This topic has attracted much interest recently with respect to potential computational aspects of chemical pulse propagation as well as with respect to pulse propagation in biological signal processing. We employ a three-component reaction-diffusion system with one activator and two inhibitor species to illustrate these issues. The reduced dynamics near a drift bifurcation describes the phenomena in the full partial differential equations by ordinary differential equations. Such a reduced dynamics is able to capture unidirectional propagation properties of pulses near an asymmetric heterogeneity in a qualitatively correct way. A remarkable feature is that such unidirectional behavior is linked to the imperfection of global bifurcation structure and the resulting asymmetric locations of critical points.

Implementation of glider guns in the light-sensitive Belousov-Zhabotinsky medium

In cellular automata models a glider gun is an oscillating pattern of nonquiescent states that periodically emits traveling localizations (gliders). The glider streams can be combined to construct functionally complete systems of logical gates and thus realize universal computation. The glider gun is the only means of ensuring the negation operation without additional external input and therefore is an essential component of a collision-based computing circuit. We demonstrate the existence of glider-gun-like structures in both experimental and numerical studies of an excitable chemical system-the light-sensitive Belousov-Zhabotinsky reaction. These discoveries could provide the basis for future designs of collision-based reaction-diffusion computers.

Survival versus collapse: abrupt drop of excitability kills the traveling pulse, while gradual change results in adaptation

Excitable media show changes in their basic characteristics that reflect temporal changes in the environment. In the photosensitive Belousov-Zhabotinsky (BZ) reaction, excitability is decreased by illumination. We found that a traveling pulse failed to propagate when a certain level of light intensity was switched on abruptly, but the pulse continued propagating when the light intensity reached the same level gradually. We investigated the mechanism of adaptation of pulse propagation to the change in light intensity using two mathematical models, the Oregonator model (a specific model for the photosensitive BZ reaction), and the FitzHugh-Nagumo model (a generic model for excitable media). The appearance of a characteristic such as adaptation is shown to be a general feature for a traveling pulse in excitable media.

Microchameleons: nonlinear chemical microsystems for amplification and sensing

In biological systems, the coupling of nonlinear biochemical kinetics and molecular transport enables functional sensing and "signal" amplification across many length scales. Drawing on biological inspiration, we describe how artificial reaction-diffusion (RD) microsystems can provide a basis for sensing applications, capable of amplifying micro- and nanoscopic events into macroscopic visual readouts. The RD applications reviewed here are based on a novel experimental technique, WETS for Wet Stamping, which offers unprecedented control over RD processes in microscopic and complex geometries. It is discussed how RD can be used to sense subtle differences in the thickness and/or absorptivity of thin absorptive films, amplify macromolecular phase transitions, detect the presence and quality of self-assembled monolayers, and provide dynamic spatiotemporal readouts of chemical "metabolites."