Chemical complexity: Spontaneous and engineered structures

Pattern Formation in Catalytic H2 Oxidation on Rh: Zooming in by Correlative Microscopy

Spatio-temporal nonuniformities in H₂ oxidation on individual Rh(h k l) domains of a polycrystalline Rh foil were studied in the 10^–6 mbar pressure range by photoemission electron microscopy (PEEM), X-ray photoemission electron microscopy (XPEEM), and low-energy electron microscopy (LEEM). The latter two were used for in situ correlative microscopy to zoom in with significantly higher lateral resolution, allowing detection of an unusual island-mediated oxygen front propagation during kinetic transitions. The origin of the island-mediated front propagation was rationalized by model calculations based on a hybrid approach of microkinetic modeling and Monte Carlo simulations.

Information processing in tree networks of excitable elements

We study the collective response of small random tree networks of diffusively coupled excitable elements to stimuli applied to leaf nodes. Such networks model the morphology of certain sensory neurons that possess branched myelinated dendrites with excitable nodes of Ranvier at every branch point and at leaf nodes. Leaf nodes receive random inputs along with a stimulus and initiate action potentials that propagate through the tree. We quantify the collective response registered at the central node using mutual information. We show that in the strong-coupling limit, the statistics of the number of nodes and leaves determines the mutual information. At the same time, the collective response is insensitive to particular node connectivity and distribution of stimulus over leaf nodes. However, for intermediate coupling, the mutual information may strongly depend on the stimulus distribution among leaf nodes. We identify a mechanism behind the competition of leaf nodes that leads to nonmonotonous dependence of mutual information on coupling strength. We show that a localized stimulus given to a tree branch can be occluded by the background firing of unstimulated branches, thus suppressing mutual information. Nonetheless, the mutual information can be enhanced by a proper stimulus localization and tuning of coupling strength.

Emergent stochastic oscillations and signal detection in tree networks of excitable elements

We study the stochastic dynamics of strongly-coupled excitable elements on a tree network. The peripheral nodes receive independent random inputs which may induce large spiking events propagating through the branches of the tree and leading to global coherent oscillations in the network. This scenario may be relevant to action potential generation in certain sensory neurons, which possess myelinated distal dendritic tree-like arbors with excitable nodes of Ranvier at peripheral and branching nodes and exhibit noisy periodic sequences of action potentials. We focus on the spiking statistics of the central node, which fires in response to a noisy input at peripheral nodes. We show that, in the strong coupling regime, relevant to myelinated dendritic trees, the spike train statistics can be predicted from an isolated excitable element with rescaled parameters according to the network topology. Furthermore, we show that by varying the network topology the spike train statistics of the central node can be tuned to have a certain firing rate and variability, or to allow for an optimal discrimination of inputs applied at the peripheral nodes.

Chemical communication and dynamics of droplet emulsions in networks of Belousov-Zhabotinsky micro-oscillators produced by microfluidics

Chemical communication leading to synchronization and collective behaviour of dynamic elements, such as cell colonies, is a widespread phenomenon with biological, physical and chemical importance. Such synchronization between elements proceeds via chemical communication by emmision, interdiffusion and reception of specific messenger molecules. On a lab scale, these phenomena can be modeled by encapsulating an oscillating chemical reaction, which serves as a signal (information) sender/receiver element, inside microcompartments such as droplet emulsions, liposomes and polymersomes. Droplets can thus be regarded as single units, able to generate chemical messengers that diffuse in the environment and hence can interact with other compartments. The Belousov-Zhabotinsky (BZ) reaction is a well-known chemical oscillator largely used as a model for complex nonlinear phenomena, including chemical, physical and biological examples. When the BZ-reaction is encapsulated inside microcompartments, its chemical intermediates can serve as messengers by diffusing among different microcompartments, to trigger specific reactions leading to a collective behavior between the elements. The geometry and constitution of the diffusion pathways play an important role in governing the collective behaviour of the system. In this context, microfluidics is not only a versatile tool for mastering the encapsulation process of the BZ-reaction in monodisperse microcompartments, but also for creating geometries and networks with well defined boundaries. The individual compartments can be engineered with selected properties using different surfactants in the case of simple emulsions, or with specific membrane properties in the case of liposomes. Furthermore, it enables the arrangement of these microcompartments in various geometric configurations, where the diffusive coupling pathways between individual compartments are both spatially and chemically well-defined. In this tutorial paper, we review a number of articles reporting various approaches to generate networks of compartmentalized Belousov-Zhabotinsky (BZ) chemical oscillators using microfluidics. In contrast to biological cellular networks, the dynamical characteristics of the BZ-reaction is well-known and, when confined in microcompartments arranged in different configurations with a pure interdiffusive coupling, these communicative microreactors can serve to mimic various types of bio-physical networks, aiding to comprehend the concept of chemical communication.

Delayed feedback induced multirhythmicity in the oscillatory electrodissolution of copper

Occurrence of bi- and trirhythmicities (coexistence of two or three stable limit cycles, respectively, with distinctly different periods) has been studied experimentally by applying delayed feedback control to the copper-phosphoric acid electrochemical system oscillating close to a Hopf bifurcation point under potentiostatic condition. The oscillating electrode potential is delayed by τ and the difference between the present and delayed values is fed back to the circuit potential with a feedback gain K. The experiments were performed by determining the period of current oscillations T as a function of (both increasing and decreasing) τ at several fixed values of K. With small delay times, the period exhibits a sinusoidal type dependence on τ. However, with relatively large delays (typically τ ≫ T) for each feedback gain K, there exists a critical delay τcrit above which birhythmicity emerges. The experiments show that for weak feedback, Kτcrit is approximately constant. At very large delays, the dynamics becomes even more complex, and trirhythmicity could be observed. Results of numerical simulations based on a general kinetic model for metal electrodissolution were consistent with the experimental observations. The experimental and numerical results are also interpreted by using a phase model; the model parameters can be obtained from experimental data measured at small delay times. Analytical solutions to the phase model quantitatively predict the parameter regions for the appearance of birhythmicity in the experiments, and explain the almost constant value of Kτcrit for weak feedback.

Spatially organized partial synchronization through the chimera mechanism in a network of electrochemical reactions

Detailed experimental and numerical results are presented about the pattern formation mechanism of spatially organized partially synchronized states in a networked chemical system with oscillatory metal dissolution. Numerical simulations of the reaction system are used to identify experimental conditions (heterogeneity, network topology, and coupling time-scale) under which the chemical reactions, which take place in a network, are split into coexisting coherent and incoherent domains through the chimera mechanism. Experiments are carried out with a network of twenty electrodes arranged in a ring with seven nearest neighbor couplings in both directions along the ring. The patterns are characterized by analyzing the oscillation frequencies and entrainments to the mean field of the phases of oscillations. The chimera state forms from two domains of elements: the chimera core in which the elements have identical frequencies and are entrained to their corresponding mean field and the chimera shell where the elements exhibit desynchrony with each other and the mean field. The experiments point out the importance of low level of heterogeneities (e.g., surface conditions) and optimal level of coupling strength and time-scale as necessary components for the realization of the chimera state. For systems with large heterogeneities, a 'remnant' chimera state is identified where the pattern is strongly affected by the presence of frequency clusters. The exploration of dynamical features with networked reactions could open up ways for identification of novel types of patterns that cannot be observed with reaction diffusion systems (with localized interactions) or with reactions under global constraints, coupling, or feedback.

Spatially distributed current oscillations with electrochemical reactions in microfluidic flow cells

The formation of spatiotemporal patterns is investigated by using a chemical reaction on the surface of a high-aspect-ratio metal electrode positioned in a flow channel. A partial differential equation model is formulated for nickel dissolution in sulfuric acid in a microfluidic flow channel. The model simulations predict oscillatory patterns that are spatially distributed on the electrode surface; the downstream portion of the metal surface exhibits large-amplitude, nonlinear oscillations of dissolution rates, whereas the upstream portion displays small-amplitude, harmonic oscillations with a phase delay. The features of the dynamical response can be interpreted by the dependence of local dynamics on the widely varying surface conditions and the presence of strong coupling. The patterns can be observed for both contiguous and segmented metal surfaces. The existence of spatially distributed current oscillations is confirmed in experiments with Ni electrodissolution in a microfluidic device. The results show the impact of a widely heterogeneous environment on the types of patterns of chemical reaction rates.

Spatially organized dynamical states in chemical oscillator networks: synchronization, dynamical differentiation, and chimera patterns

Dynamical processes in many engineered and living systems take place on complex networks of discrete dynamical units. We present laboratory experiments with a networked chemical system of nickel electrodissolution in which synchronization patterns are recorded in systems with smooth periodic, relaxation periodic, and chaotic oscillators organized in networks composed of up to twenty dynamical units and 140 connections. The reaction system formed domains of synchronization patterns that are strongly affected by the architecture of the network. Spatially organized partial synchronization could be observed either due to densely connected network nodes or through the 'chimera' symmetry breaking mechanism. Relaxation periodic and chaotic oscillators formed structures by dynamical differentiation. We have identified effects of network structure on pattern selection (through permutation symmetry and coupling directness) and on formation of hierarchical and 'fuzzy' clusters. With chaotic oscillators we provide experimental evidence that critical coupling strengths at which transition to identical synchronization occurs can be interpreted by experiments with a pair of oscillators and analysis of the eigenvalues of the Laplacian connectivity matrix. The experiments thus provide an insight into the extent of the impact of the architecture of a network on self-organized synchronization patterns.

Dynamics of electrochemical oscillators with electrode size disparity: asymmetrical coupling and anomalous phase synchronization

Experiments are carried out in dual electrode oscillatory Ni electrodissolution in which the two electrodes have different surface areas. The transition to phase synchronization is analyzed as asymmetrical coupling strength, induced by placing a cross resistance between the electrodes, is varied. It is shown that because of nonisochronicity (phase shear, i.e., strong dependence of period on amplitude) of the oscillators, anomalous phase synchronization effects can be observed: advanced/delayed synchronization and, to a lesser extent, frequency difference enhancement. The type of synchronization is strongly affected by the underlying heterogeneities of the oscillators; in the experiments with a slow driver (large surface area) electrode the synchronization is advanced, with a fast driver electrode the synchronization is delayed with respect to symmetrical coupling. The findings thus reveal that the interplay of asymmetrical coupling with the types of inherent heterogeneities plays an important role for the interpretation of size effects in the dynamical behavior of a nonlinear chemical reaction.

Targeting characteristic wave properties in reaction-diffusion systems by optimization of external forcing

We consider the targeted manipulation of reaction-diffusion waves by optimization of an external forcing parameter. As an example, we present numerical results for the FitzHugh-Nagumo system exploiting model-based optimization capable of targeting characteristic wave properties such as wavelength, shape, and propagation speed by spatiotemporally controlling electric current. The conceptual basis of our approach is optimal control of periodic orbits in a wave-variable coordinate system. The results are transferred back to the partial differential equation context and validated in numerical simulations. The whole procedure is applicable to any reaction-diffusion model.

Hydrothermal and Structural Chemistry of the Zinc(II)- and Cadmium(II)-1,2,4-Triazolate Systems

Hydrothermal reactions of 1,2,4-triazole with zinc and cadmium salts have yielded 10 structurally unique materials of the M(II)/trz/Xn- system, with M(II)=Zn and Cd and Xn-=F-, Cl-, Br-, I-, OH-, NO3-, and SO(4)2- (trz=1,2,4-triazolate). Of the zinc-containing phases, [Zn(trz)2] (1), [Zn2(trz)3(OH)].3H2O (3.3H2O), and [Zn2(trz)(SO4)(OH)] (4) are three-dimensional, while [Zn(trz)Br] (2) is two-dimensional. All six cadmium phases, [Cd3(trz)3F2(H2O)].2.75H2O (5.2.75H2O), [Cd2(trz)2Cl2(H2O)] (6), [Cd3(trz)3Br3] (7), [Cd2(trz)3I] (8), [Cd3(trz)5(NO3)(H2O)].H2O (9.H2O), and [Cd8(trz)4(OH)2(SO4)5(H2O)] (10), are three-dimensional. In all cases, the anionic components Xn- participate in the framework connectivity as bridging ligands. The structural diversity of these materials is reflected in the variety of coordination polyhedra displayed by the metal sites: tetrahedral; trigonal bipyramidal; octahedral. Structures 3, 5, and 7-9 exhibit two distinct polyhedral building blocks. The materials are also characterized by a range of substructural components, including trinuclear and tetranuclear clusters, adamantoid cages, chains, layers, and complex frameworks.

Derivation of a quantitative minimal model from a detailed elementary-step mechanism supported by mathematical coupling analysis

Accurate experimental data increasingly allow the development of detailed elementary-step mechanisms for complex chemical and biochemical reaction systems. Model reduction techniques are widely applied to obtain representations in lower-dimensional phase space which are more suitable for mathematical analysis, efficient numerical simulation, and model-based control tasks. Here, we exploit a recently implemented numerical algorithm for error-controlled computation of the minimum dimension required for a still accurate reduced mechanism based on automatic time scale decomposition and relaxation of fast modes. We determine species contributions to the active (slow) dynamical modes of the reaction system and exploit this information in combination with quasi-steady-state and partial-equilibrium approximations for explicit model reduction of a novel detailed chemical mechanism for the Ru-catalyzed light-sensitive Belousov-Zhabotinsky reaction. The existence of a minimum dimension of seven is demonstrated to be mandatory for the reduced model to show good quantitative consistency with the full model in numerical simulations. We derive such a maximally reduced seven-variable model from the detailed elementary-step mechanism and demonstrate that it reproduces quantitatively accurately the dynamical features of the full model within a given accuracy tolerance.

Electrolyte diodes with weak acids and bases. I. Theory and an approximate analytical solution

Until now acid-base diodes and transistors applied strong mineral acids and bases exclusively. In this work properties of electrolyte diodes with weak electrolytes are studied and compared with those of diodes with strong ones to show the advantages of weak acids and bases in these applications. The theoretical model is a one dimensional piece of gel containing fixed ionizable groups and connecting reservoirs of an acid and a base. The electric current flowing through the gel is measured as a function of the applied voltage. The steady-state current-voltage characteristic (CVC) of such a gel looks like that of a diode under these conditions. Results of our theoretical, numerical, and experimental investigations are reported in two parts. In this first, theoretical part governing equations necessary to calculate the steady-state CVC of a reverse-biased electrolyte diode are presented together with an approximate analytical solution of this reaction-diffusion-ionic migration problem. The applied approximations are quasielectroneutrality and quasiequilibrium. It is shown that the gel can be divided into an alkaline and an acidic zone separated by a middle weakly acidic region. As a further approximation it is assumed that the ionization of the fixed acidic groups is complete in the alkaline zone and that it is completely suppressed in the acidic one. The general solution given here describes the CVC and the potential and ionic concentration profiles of diodes applying either strong or weak electrolytes. It is proven that previous formulas valid for a strong acid-strong base diode can be regarded as a special case of the more general formulas presented here.

Annihilation of limit-cycle oscillations by identification of critical perturbing stimuli via mixed-integer optimal control

We present a novel model-based mixed-integer optimal control method to automatically identify the strength and timing of critical external stimuli leading to the transient annihilation of limit-cycle oscillators. Biochemical oscillators of this type play a central role in regulating cellular rhythms. Their specific manipulation is a promising perspective to control biological functions by drugs and tailored treatment strategies. We demonstrate our new optimal control approach in an application to a biochemical model for oscillatory calcium signal transduction.

Real-time nonlinear feedback control of pattern formation in (bio)chemical reaction-diffusion processes: a model study

Theoretical and experimental studies related to manipulation of pattern formation in self-organizing reaction-diffusion processes by appropriate control stimuli become increasingly important both in chemical engineering and cellular biochemistry. In a model study, we demonstrate here exemplarily the application of an efficient nonlinear model predictive control (NMPC) algorithm to real-time optimal feedback control of pattern formation in a bacterial chemotaxis system modeled by nonlinear partial differential equations. The corresponding drift-diffusion model type is representative for many (bio)chemical systems involving nonlinear reaction dynamics and nonlinear diffusion. We show how the computed optimal feedback control strategy exploits the system inherent physical property of wave propagation to achieve desired control aims. We discuss various applications of our approach to optimal control of spatiotemporal dynamics.

Specific external forcing of spatiotemporal dynamics in reaction-diffusion systems

Self-organization behavior and in particular pattern forming spatiotemporal dynamics play an important role in far from equilibrium chemical and biochemical systems. Specific external forcing and control of self-organizing processes might be of great benefit in various applications ranging from technical systems to modern biomedical research. We demonstrate that in a cellular chemotaxis system modeled by one-dimensional reaction-diffusion equations particular forms of spatiotemporal dynamics can be induced and stabilized by controlling spatially distributed influx patterns of a chemical species as a function of time. In our model study we show that a propagating wave with certain shape and velocity and static symmetrical and asymmetrical patterns can be forced and manipulated by numerically computing open-loop optimal influx controls.

Electrolyte diodes and hydrogels: determination of concentration and pK value of fixed acidic groups in a weakly charged hydrogel

Current-voltage (CV) characteristics of polyvinyl alcohol (PVA)-glutardialdehyde hydrogel cylinders were measured in aqueous KCl solutions. To this end a new special apparatus was constructed where the gel cylinder connects two electrolyte reservoirs. The measured quantities are the electric current flowing through the gel and the potential difference between the two reservoirs. Concentration polarization near the gel-liquid interfaces is decreased considerably by applying an intense mechanical stirring in both reservoirs. Under these conditions below 1 V concentration polarization is negligible, and the CV curves are nearly straight lines. It was found that the gel applied here is a weakly charged anionic hydrogel. Concentration of fixed anions was determined from the slope of these lines measured in 0.001 and 0.01 molar KCl solutions. Fixed anion concentration of the same piece of gel was measured also with a different method, when the gel was used in an acid-base diode. In this case one reservoir contained 0.1 molar HCl, and the other 0.1 molar KOH. From the results of the two measurements, the concentration (4.45 x 10(-3) M) and the pK value (4.03) of the fixed acid groups responsible for the anionic character of the gel was calculated. The pK value is compatible with fixed carboxylic acid groups contaminating the PVA gel. Furthermore, concentration polarization phenomena in the boundary layers nearby the gel were studied in 0.001 M KCl solutions, measuring the diodelike CV characteristic of a gel cylinder, when stirring was applied only at one side of the gel. Boundary layers facing the cathode or the anode responded in a different way to stirring. The difference cannot be explained completely with the hypothesis of electroconvection suggested previously.

Manipulation of surface reaction dynamics by global pressure and local temperature control: a model study

Specific catalyst design and external manipulation of surface reactions by controlling accessible physical or chemical parameters may be of great benefit for improving catalytic efficiencies and energetics, product yield, and selectivities in the field of heterogeneous catalysis. Studying a realistic spatiotemporal one-dimensional model for CO oxidation on Pt(110) we demonstrate the value and necessity of mathematical modeling and advanced numerical methods for directed external multiparameter control of surface reaction dynamics. At the model stage we show by means of optimal control techniques that species coverages can be adjusted to desired values, aperiodic oscillatory behavior for distinct coupled reaction sites can be synchronized, and overall reaction rates can be optimized by varying the surface temperature in space and time and the CO and O2 gas phase partial pressure with time. The control aims are formulated as objective functionals to be minimized which contain a suitable mathematical formulation for the deviation from the desired system behavior. The control functions pCO(t) (CO partial pressure), pO2(t) (O2 partial pressure), and T(x,t) (surface temperature distribution) are numerically computed by a specially tailored optimal control method based on a direct multiple shooting approach which is suitable to cope with the highly nonlinear unstable mode character of the CO oxidation model.

Dynamic control and information processing in chemical reaction systems by tuning self-organization behavior

Specific external control of chemical reaction systems and both dynamic control and signal processing as central functions in biochemical reaction systems are important issues of modern nonlinear science. For example nonlinear input-output behavior and its regulation are crucial for the maintainance of the life process that requires extensive communication between cells and their environment. An important question is how the dynamical behavior of biochemical systems is controlled and how they process information transmitted by incoming signals. But also from a general point of view external forcing of complex chemical reaction processes is important in many application areas ranging from chemical engineering to biomedicine. In order to study such control issues numerically, here, we choose a well characterized chemical system, the CO oxidation on Pt(110), which is interesting per se as an externally forced chemical oscillator model. We show numerically that tuning of temporal self-organization by input signals in this simple nonlinear chemical reaction exhibiting oscillatory behavior can in principle be exploited for both specific external control of dynamical system behavior and processing of complex information.