Chemical Memory with Discrete Turing Patterns Appearing in the Glycolytic Reaction.

Memory is an essential element in information processing devices. We investigated a network formed by just three interacting nodes representing continuously stirred tank reactors (CSTRs) in which the glycolytic reaction proceeds as a potential realization of a chemical memory unit. Our study is based on the 2-variable computational model of the reaction. The model parameters were selected such that the system has a stable limit cycle and several distinct, discrete Turing patterns characterized by stationary concentrations at the nodes. In our interpretation, oscillations represent a blank memory unit, and Turing patterns code information. The considered memory can preserve information on one of six different symbols. The time evolution of the nodes was individually controlled by the inflow of ATP. We demonstrate that information can be written with a simple and short perturbation of the inflow. The perturbation applies to only one or two nodes, and it is symbol specific. The memory can be erased with identical inflow perturbation applied to all nodes. The presented idea of pattern-coded memory applies to other reaction networks that allow for discrete Turing patterns. Moreover, it hints at the experimental realization of memory in a simple system with the glycolytic reaction.

New types of complex motion of a simple camphor boat.

We discuss the motion of a rectangular camphor boat, considering the position of a camphor pill in relation to the boat's stern as the control parameter. The boat moves because the pill releases surface active molecules that decrease the surface tension and support the motion. We introduce a new experimental system in which the boat rotates on a long arm around the axis located at the centre of a Petri dish; thus, the motion is restricted to a circle and can be studied under stationary conditions for a long time. The experiments confirmed two previously reported modes of motion: continuous motion when the pill was located at the boat edge and pulsating (intermittent) motion if it was close to the boat centre (Suematsu et al., J. Phys. Chem. C, 2010, 114(21), 9876-9882). For intermediate pill locations, we observed a new, unreported type of motion characterised by oscillating speed (i.e. oscillating motion). Different modes of motion can be observed for the same pill location. The experimental results are qualitatively confirmed using a simple reaction-diffusion model of the boat evolution used in the above-mentioned paper.

Information Processing Using Networks of Chemical Oscillators.

I believe the computing potential of systems with chemical reactions has not yet been fully explored. The most common approach to chemical computing is based on implementation of logic gates. However, it does not seem practical because the lifetime of such gates is short, and communication between gates requires precise adjustment. The maximum computational efficiency of a chemical medium is achieved if the information is processed in parallel by different parts of it. In this paper, I review the idea of computing with coupled chemical oscillators and give arguments for the efficiency of such an approach. I discuss how to input information and how to read out the result of network computation. I describe the idea of top-down optimization of computing networks. As an example, I consider a small network of three coupled chemical oscillators designed to differentiate the white from the red points of the Japanese flag. My results are based on computer simulations with the standard two-variable Oregonator model of the oscillatory Belousov−Zhabotinsky reaction. An optimized network of three interacting oscillators can recognize the color of a randomly selected point with >98% accuracy. The presented ideas can be helpful for the experimental realization of fully functional chemical computing networks.

Dynamic ordering caused by a source-sink relation between two droplets.

Two droplets composed of different chemicals, 1-decanol and liquid paraffin, floating on the water surface show characteristic co-responsive behavior. The presence of two different types of droplets in the system imposes an asymmetry that would not be possible with single droplets alone. The self-propulsion and interactions between droplets appear because surface active 1-decanol molecules provided by the source are absorbed by the paraffin sink thus generating an asymmetric surface tension gradient. This source-sink relation between droplets stabilizes and enhances the self-propulsion, and leads to a variety of dynamic structures including oscillations in the inter-droplet distance. We found that the character of time evolution also depends on the concentration of dye, Sudan Black B, initially used just to stain the decanol droplet. A simple mathematical model explains the transition between the stationary state and the oscillations as a Hopf bifurcation.

Complexity and bifurcations in the motion of a self-propelled rectangle confined in a circular water chamber.

We consider the motion of a self-propelled object of rectangular shape inside a circular water chamber. The mathematical model of self-motion includes equations for the orientation and location of the rectangle and reaction-diffusion equation with an effective diffusion coefficient for the time evolution of the surface concentration of active molecules. Numerical simulations of motion were performed for different values of the ratio between the supply rate S and the evaporation rate a of active molecules. Treating S0 = S/a as a control parameter, we found the critical behavior in variables characterizing the trajectory and identified different types of motion. If the value of S0 is small, the rectangle rests at the chamber center. For larger S0, a reciprocal motion during which the rectangle passes through the center is observed. At yet higher supply rates, the star-polygonal motion appears, and the trajectory remains at a distance from the chamber center. In the experiments with a rectangle made of camphor-camphene-polypropylene plastic moving in a Petri dish, we observed the transition from the star-polygonal motion to the reciprocal motion in time. This transition can be understood on the basis of the developed model if we assume that the supply rate decreases in time.

The Concilium of Information Processing Networks of Chemical Oscillators for Determining Drug Response in Patients With Multiple Myeloma.

It can be expected that medical treatments in the future will be individually tailored for each patient. Here we present a step towards personally addressed drug therapy. We consider multiple myeloma treatment with drugs: bortezomib and dexamethasone. It has been observed that these drugs are effective for some patients and do not help others. We describe a network of chemical oscillators that can help to differentiate between non-responsive and responsive patients. In our numerical simulations, we consider a network of 3 interacting oscillators described with the Oregonator model. The input information is the gene expression value for one of 15 genes measured for patients with multiple myeloma. The single-gene networks optimized on a training set containing outcomes of 239 therapies, 169 using bortezomib and 70 using dexamethasone, show up to 71% accuracy in differentiating between non-responsive and responsive patients. If the results of single-gene networks are combined into the concilium with the majority voting strategy, then the accuracy of predicting the patient's response to the therapy increases to ∼ 85%.

Computing With Networks of Chemical Oscillators and its Application for Schizophrenia Diagnosis.

Chemical reactions are responsible for information processing in living organisms, yet biomimetic computers are still at the early stage of development. The bottom-up design strategy commonly used to construct semiconductor information processing devices is not efficient for chemical computers because the lifetime of chemical logic gates is usually limited to hours. It has been demonstrated that chemical media can efficiently perform a specific function like labyrinth search or image processing if the medium operates in parallel. However, the number of parallel algorithms for chemical computers is very limited. Here we discuss top-down design of such algorithms for a network of chemical oscillators that are coupled by the exchange of reaction activators. The output information is extracted from the number of excitations observed on a selected oscillator. In our model of a computing network, we assume that there is an external factor that can suppress oscillations. This factor can be applied to control the nodes and introduce input information for processing by a network. We consider the relationship between the number of oscillation nodes and the network accuracy. Our analysis is based on computer simulations for a network of oscillators described by the Oregonator model of a chemical oscillator. As the example problem that can be solved with an oscillator network, we consider schizophrenia diagnosis on the basis of EEG signals recorded using electrodes located at the patient's scalp. We demonstrated that a network formed of interacting chemical oscillators can process recorded signals and help to diagnose a patient. The parameters of considered networks were optimized using an evolutionary algorithm to achieve the best results on a small training dataset of EEG signals recorded from 45 ill and 39 healthy patients. For the optimized networks, we obtained over 82% accuracy of schizophrenia detection on the training dataset. The diagnostic accuracy can be increased to almost 87% if the majority rule is applied to answers of three networks with different number of nodes.

A camphene-camphor-polymer composite material for the production of superhydrophobic absorbent microporous foams.

In a recently published paper (doi.org/10.3390/molecules26113116) on self-propelled motion of objects on the water surface, we described a novel surface-active plastic material obtained by dissolution of camphor and polypropylene in camphene at 250 [Formula: see text]C. The material has wax-like mechanical properties, can be easily formed to any moldable shape, and allows for longer and more stable self-propelled motion if compared with pure camphor or pure camphene or of a camphene-camphor wax. Here we use scanning electron microscopy to visualize and characterize the microporous structure of the solid polypropylene foam formed in the plastic for different polypropylene contents. The topology of foams remaining in the material after camphor and camphene molecules have been removed through evaporation or dissolution is similar to polypropylene foams obtained using thermally-induced phase separation. We show that the foams have a superhydrophobic surface but strongly absorb non-polar liquids, and suggest an array of potential scientific and industrial applications.

A Perfect Plastic Material for Studies on Self-Propelled Motion on the Water Surface.

We describe a novel plastic material composed of camphene, camphor, and polypropylene that seems perfectly suited for studies on self-propelled objects on the water surface. Self-motion is one of the attributes of life, and chemically propelled objects show numerous similarities with animated motion. One of important questions is the relationship between the object shape and its motility. In our previous paper, {R. Löffler et al. PCCP, 2019, 21, 24852-24856}, we presented a novel hybrid material, obtained from the solution of camphor in camphene, that allowed making objects of various shapes. This hybrid material has wax-like mechanical properties, but it has a very high tackiness. Here, we report that a small amount of polypropylene removed this undesirable feature. We investigated the properties of camphor-camphene-polypropylene plastic by performing the statistical analysis of a pill trajectory inside a Petri dish and compared them with those of camphor-camphene wax. The plastic showed the stable character of motion for over an hour-long experiment. The surface activity of objects made of plastic did not significantly depend on the weight ratios of the compounds. Such a significant increase in usefulness came from the polypropylene, which controlled the dissipation of camphor and camphene molecules.

Applications of Information Theory Methods for Evolutionary Optimization of Chemical Computers.

It is commonly believed that information processing in living organisms is based on chemical reactions. However, the human achievements in constructing chemical information processing devices demonstrate that it is difficult to design such devices using the bottom-up strategy. Here I discuss the alternative top-down design of a network of chemical oscillators that performs a selected computing task. As an example, I consider a simple network of interacting chemical oscillators that operates as a comparator of two real numbers. The information on which of the two numbers is larger is coded in the number of excitations observed on oscillators forming the network. The parameters of the network are optimized to perform this function with the maximum accuracy. I discuss how information theory methods can be applied to obtain the optimum computing structure.

How Does a Simple Network of Chemical Oscillators See the Japanese Flag?

Chemical computing is something we use every day (e.g., in the brain), but we can still not explore and master its potential in human-made experiments. It is expected that the maximum computational efficiency of a chemical medium can be achieved if information is processed in parallel by different parts of the medium. In this paper, we use computer simulations to explore the efficiency of chemical computing performed by a small network of three coupled chemical oscillators. We optimize the network to recognize the white and red regions of the Japanese flag. The input information is introduced as the inhibition times of individual oscillators, and the output information is coded in the number of activator maxima observed on a selected oscillator. We have used the Oregonator model to simulate the network time evolution and the evolutionary optimization to find the best network for the considered task. We have found that even a network of three interacting oscillators can recognize the color of a randomly selected point with 95% accuracy.

Inversion probability of three-bladed self-propelled rotors after forced stops of different durations.

We investigated self-propelled rotation of a symmetric three-bladed rotor on water under periodic halt and release operations. The rotation was driven by the difference in the surface tension around the blades of the rotor because camphor molecules developed from three camphor disks glued at the blade ends. Spontaneous inversion of rotation direction was observed after a forced stop of the rotor and the subsequent release. The probability of such inversion decreased with an increase in the halting time. The asymmetric distribution of camphor molecules around the blades was also inverted after the forced stop and the degree of asymmetry increased with an increase in the angular velocity characterizing the stationary rotation of the rotor. Our experimental results for rotors with different shapes indicate that there is a strong correlation between the stationary angular velocity of the rotor and the maximum time duration of the forced stop for which a high probability of inversion is observed.

On a simple model that explains inversion of a self-propelled rotor under periodic stop-and-release-operations.

We propose a simple mathematical model that describes the time evolution of a self-propelled object on a liquid surface using variables such as object location, surface concentration of active molecules, and hydrodynamic surface flow. The model is applied to simulate the time evolution of a rotor composed of a polygonal plate with camphor pills at its corners. We have qualitatively reproduced results of experiments, in which the inversion of rotational direction under periodic stop-and-release-operations was investigated. The model correctly describes the probability of the inversion as a function of the duration of the phase when the rotor is stopped. Moreover, the model allows to introduce the rotor asymmetry unavoidable in real experiments and study its influence on the studied phenomenon. Our numerical simulations have revealed that the probability of the inversion of rotational direction is determined by the competition among the transport of the camphor molecules by the flow, the intrinsic asymmetry of the rotor, and the noise amplitude.

A hybrid camphor-camphene wax material for studies on self-propelled motion.

A new material that combines the self-propelling properties of camphor with the malleability of camphene is reported. It has wax-like mechanical properties at room temperature and can be formed into required shapes. The speed of the self-propelled objects and the trajectory depend on the shape and camphor-camphene weight ratio.

Bifurcation in the angular velocity of a circular disk propelled by symmetrically distributed camphor pills.

We studied rotation of a disk propelled by a number of camphor pills symmetrically distributed at its edge. The disk was put on a water surface so that it could rotate around a vertical axis located at the disk center. In such a system, the driving torque originates from surface tension difference resulting from inhomogeneous surface concentration of camphor molecules released from the pills. Here, we investigated the dependence of the stationary angular velocity on the disk radius and on the number of pills. The work extends our previous study on a linear rotor propelled by two camphor pills [Y. Koyano et al., Phys. Rev. E 96, 012609 (2017)]. It was observed that the angular velocity dropped to zero after a critical number of pills was exceeded. Such behavior was confirmed by a numerical model of time evolution of the rotor. The model predicts that, for a fixed friction coefficient, the speed of pills can be accurately represented by a function of the linear number density of pills. We also present bifurcation analysis of the conditions at which the transition between a standing and a rotating disk appears.

Method development and validation for total mercury determination in coke oven gas combining a trap sampling method with CVAAS detection.

Coke oven gas is one of the by-products of the coal coking process. It is used as a fuel in the coking plant, but also as a raw material in the chemical industry to produce methanol, syngas or environment-friendly, low-CO2 hydrogen fuel. Due to the reasons mentioned above, the knowledge of coke oven gas pollutants such as mercury is a key issue. To determine the mercury in the cleaned coke oven gas a trap sampling method combined with CVAAS mercury detection was developed, optimized and validated. In order to perform the sampling process the traps filled with activated carbon were used. The determination of mercury in the traps material was performed by means of an MA-2 mercury analyzer. During the optimization of the method one selected the trap material, sample volume and flow rate. The optimal volume of the coke oven gas sample was 3 dm3 and the flow rate was 18 dm3/h (per one trap). The developed method was validated according to the Eurachem recommendation and was applied to determine mercury in the clean coke oven gas. The coke oven gas sampling was performed in a coking plant in Poland. The average concentration of mercury in the clean coke oven gas was 3.2 ±â€¯0.3 µg/m3N (k = 2) for n = 18.

Period of Oscillatory Motion of a Camphor Boat Determined by the Dissolution and Diffusion of Camphor Molecules.

Here, we investigated the oscillatory motion of a camphor boat on water to clarify how the dynamics of camphor concentration profile determines the period of oscillation. The boat, which was made of a plastic plate and a camphor disk, was glued below the plate at a distance from the edge. The dependence of oscillation period on temperature and viscosity of the water phase was measured in experiments. We reproduced the experimental results by calculating the period of oscillatory motion by considering the experimental values of physicochemical parameters describing the time evolution of camphor concentration profile and the friction acting on a boat, such as diffusion and dissolution rates of camphor, viscosity of the water phase, and the threshold concentration of camphor necessary to accelerate the boat from the resting state. The increase in the period of oscillatory motion at low temperatures was explained by the reduced dissolution rate of camphor into the water phase.

Cancer classification with a network of chemical oscillators.

We discuss chemical information processing considering dataset classifiers formed with a network of interacting droplets. Our arguments are based on computer simulations of droplets in which a photosensitive variant of the Belousov-Zhabotinsky (BZ) reaction proceeds. By applying optical control we can adjust the time evolution of individual droplets and prepare the network to perform a specific computational task. We demonstrate that chemical classifiers made of droplets can be designed in computer simulations based on evolutionary algorithms. The mutual information between the dataset and the observed time evolution of droplets in the network is taken as the fitness function in the optimization process. We show that a classifier of the Wisconsin Breast Cancer Dataset made of a relatively small number of droplets can distinguish between malignant and benign forms of cancer with an accuracy exceeding 97%. The reliability of the optimized chemical classifiers of this dataset as a function of optimization time, number of droplets involved in data processing and the method of extracting the output information is discussed.

Unidirectional motion of a camphor disk on water forced by interactions between surface camphor concentration and dynamically changing boundaries.

We study the motion of a camphor disk on the water surface in a system with flexible boundaries. The boundaries can be dynamically modified by non-uniform surface tension resulting from the nonhomogeneous surface concentration of the camphor molecules dissipated by the disk. We investigate the geometry of the boundaries that forces unidirectional motion of the disk. The studied system can be regarded as a signal diode if the presence or absence of a camphor disk at a specific point is interpreted as the binary TRUE and FALSE variables. The diode can be incorporated into more complex devices, like a ring that imposes unidirectional rotation of camphor disks.

Chemical memory with states coded in light controlled oscillations of interacting Belousov-Zhabotinsky droplets.

The information storing potential of droplets, in which an oscillatory, photosensitive Belousov-Zhabotinsky (BZ) reaction proceeds, is investigated experimentally. We consider coupled oscillations in pairs and triplets of droplets. Droplets are surrounded by a solution of lipids in decane. Oscillations synchronize via diffusion of an activator through a lipid bilayer. The reaction in each droplet can be individually controlled by illumination with blue light through an optical fiber. We found that in pairs of BZ droplets, only the in-phase and the forcing oscillation modes are stable, however switching between these modes is not reliable. In triplets of droplets, switching between two different, stable rotational modes (clockwise and anticlockwise) can be easily implemented. Therefore, such a system is an excellent candidate for a light controlled, reliable, one bit chemical memory unit.