Joanna Natalia Gorecka

Information processing with structured excitable medium

There are many ways in which a nonlinear chemical medium can be used for information processing. Here we are concerned with an excitable medium and the straightforward method of information coding: a single excitation pulse represents a bit of information and a group of excitations forms a message. Our attention is focused on a specific type of nonhomogeneous medium that has an intentionally introduced geometrical structure of regions characterized by different excitability levels. We show that in information processing applications the geometry plays an equally important role as the dynamics of the medium and allows one to construct devices that perform complex signal processing operations even for a relatively simple kinetics of the reactions involved. In the paper we review a number of published chemical realizations of simple information processing devices like logical gates or memory cells and we show that by combining these devices as building blocks the medium can perform complex operations like for example counting of arriving excitations. We also present a new, simple realizations of chemical signal diode that transmits pulses in one direction only.

Realistic parameters for simple models of the Belousov-Zhabotinsky reaction.

We use experimental results to estimate the values of parameters of simple models describing the time evolution of the Belousov-Zhabotinsky reaction proceeding in droplets surrounded by hydrocarbons. The equations with fitted parameters correctly describe the period of oscillations for a large class of experimental conditions at which the reaction is performed.

Molecular dynamics simulations of nonequilibrium rate constant in a model exothermic reaction

Abstract In this Letter, we study the nonequilibrium effects which appear in a thermally activated exothermic reaction A + A →products using the molecular dynamics for reactive hard spheres. We have found that the rate constant is reduced with respect to its equilibrium value and the relative decrease of rate constant is similar to that observed for a thermoneutral reaction with the same activation energy. It is demonstrated that a simple phenomenology, which assumes a Maxwellian distribution of the energetic states for the reactant and for the system as a whole, gives a good estimation of the nonequilibrium rate constant.

On one dimensional chemical diode and frequency generator constructed with an excitable surface reaction

The oxidation of carbon monoxide on a Pt(110) surface is considered as a medium for chemical information processing in which bits of information are represented by traveling pulses of high oxygen coverage. Using numerical simulations for a model of CO oxidation we demonstrate that in such system one dimensional chemical signal diode can be realized by setting a proper profile of temperature. We also show that a pulse splitting can occur on a temperature inhomogeneity. The phenomenon of pulse splitting can be used to construct one dimensional generator of a train of pulses with adjustable frequency.

On the nonequilibrium effects in thermally activated reactions A+A⇌B+B⇌C+C

We study the nonequilibrium effects in an adiabatic system with thermally activated reactions A+A⇌B+B⇌C+C. The results of a simple phenomenological theory which assumes that temperatures of reagents may be different from the temperature of the system as a whole are compared with results of molecular dynamics simulations. We show that the nonequilibrium effects caused by one reaction may be magnified as well as reduced by the presence of the other processes. Good agreement between theory and simulations has been obtained.

Sensing Parameters of a Time Dependent Inflow with an Enzymatic Reaction

Functionality of living organisms is based on decision making. Chemical reactions stand behind information processing in biological systems. Therefore, it is interesting to consider reaction models that show ability to make decisions by evolving towards significantly different states, depending on conditions at which those reactions proceed. It has been recently demonstrated that a system exhibiting cooperative or sigmoidal response with respect to the input exhibits the potential to function as a discriminator of the amplitude or the frequency of its external periodic perturbation. Here we consider a few models of allosteric enzymatic reactions and discuss their applicability for sensing the frequency or the amplitude of the time dependent input in a form of reagent inflow. The output is coded in a product oscillation type. On the basis of numerical simulations we compare results for a full reaction model with its reduced, easier to analyze version.

Information Processing with Structured Chemical Excitable Medium

It is well known that an excitable medium can be used for information processing with pulses of excitation. In such medium messages can be coded or in the number of pulses or in the sequences of times separating subsequent excitations. Information is processed as the result of two major effects: interactions between pulses and interactions between a pulse and the environment. The properties of excitable medium provide us with a number of features remaining those characterizing biological information processing. For example, pulses of excitation appear as the result of an external stimulus and they can propagate in a homogeneous medium with a constant velocity and a stationary shape dissipating medium energy.

On the application of statistical physics for the description of nonequilibrium effects in chemical systems

In this paper we show how the methods of statistical physics may be applied to describe the nonequilibrium effects in systems with thermally activated reactions. A special attention is given to systems with multiple reactions, in which such effects are more important then in systems with a single reaction. Considering a model reaction scheme we demonstrate that a simple phenomenology, which associates different temperatures to different reagents, gives an accurate description of the nonequilibrium effects.

Distance and Direction Sensing with Excitable Chemical Medium

We demonstrate a strategy of sensing the distance between an observer and a small source of periodic oscillations in a nonlinear chemical medium. The information about the distance is returned in the firing numbers of pulses excited in the set of sensor channel. The same method can be also applied to recognize the direction of a train of plane excitation waves. The idea of chemical sensor is tested in simulations based on the Rovinsky-Zhabotinsky model and the results are confirmed by experiments with Belousov-Zhabotinsky reaction.