Oscillatory Reaction Research Articles

Photochemically Triggered and Autonomous Oscillatory pH-Modulated Transient Assembly/Disassembly of DNA Microdroplet Coacervates.

The assembly of pH-responsive DNA-based, phase-separated microdroplets (MDs) coacervates, consisting of frameworks composed of Y-shaped nucleic acid modules crosslinked by pH-responsive strands, is introduced. The phase-separated MDs reveal dynamic pH-stimulated switchable or oscillatory transient depletion and reformation. In one system, a photoisomerizable merocyanine/spiropyran photoacid is used for the light-induced pH switchable modulation of the reaction medium between the values pH=6.0-4.4. The dynamic transient photochemically-induced switchable depletion/reformation of phase-separated MDs, follows the rhythm of pH changes in solution. In a second system, the Landolt oscillatory reaction mixture pH 7.5→4.2→7.5 is applied to stimulate the oscillatory depletion/reformation of the MDs. The autonomous dynamic oscillation of the assembly/disassembly of the MDs follows the oscillating pH rhythm of the reaction medium.

Photochemically Triggered and Autonomous Oscillatory pH‐Modulated Transient Assembly/Disassembly of DNA Microdroplet Coacervates

AbstractThe assembly of pH‐responsive DNA‐based, phase‐separated microdroplets (MDs) coacervates, consisting of frameworks composed of Y‐shaped nucleic acid modules crosslinked by pH‐responsive strands, is introduced. The phase‐separated MDs reveal dynamic pH‐stimulated switchable or oscillatory transient depletion and reformation. In one system, a photoisomerizable merocyanine/spiropyran photoacid is used for the light‐induced pH switchable modulation of the reaction medium between the values pH=6.0–4.4. The dynamic transient photochemically‐induced switchable depletion/reformation of phase‐separated MDs, follows the rhythm of pH changes in solution. In a second system, the Landolt oscillatory reaction mixture pH 7.5→4.2→7.5 is applied to stimulate the oscillatory depletion/reformation of the MDs. The autonomous dynamic oscillation of the assembly/disassembly of the MDs follows the oscillating pH rhythm of the reaction medium.

The Bray–Liebhafsky Oscillatory Reaction as a Chemosensor for Benzenediols

Benezediols are widely used in different areas of industry, thus identification and quantification of benzenediols is of utmost importance due to their toxicity and high environmental abundance. In this work, benzenediol isomers (pyrocatechol, resorcinol, and hydroquinone) were investigated by using the Bray–Liebhafsky (BL) oscillatory reaction. All three isomers exhibit different behavior in the BL reaction, which renders the BL system applicable as a chemosensor. The period between the fifth and sixth oscillation, the amplitude of the sixth oscillation and in the case of hydroquinone, the emergence of a new oscillation in the BL reaction were selected as the parameters used for the identification and quantification of these isomers. Furthermore, electron paramagnetic resonance spectroscopy and DFT calculations were performed in order to provide insights into the mechanism of benzenediols reactions with the BL system.

Mathematical modelling of a self-oscillating catalytic reaction in a flow reactor

The article is devoted to the analysis of possible spatiotemporal kinetic structures that can arise during catalytic oxidation reactions on metal surfaces at atmospheric pressure. The catalytic oscillatory reaction in a flow reactor is modeled using a 1D system of equations of the reaction–diffusion–convection type. The STM type oscillatory reaction model of catalytic oxidation is used as a kinetic model. The obtained results of mathematical modelling show the decisive influence of an axial mixing in the reactor on the development of spatiotemporal structures. It is also shown that, depending on the ratio of adsorption constants of reacting species, three different isothermal spatiotemporal structures can arise, namely a spatially inhomogeneous stationary state, regular and aperiodic “breathing structures”.

Sinusoidal control strategy applied to continuous stirred‐tank reactors: Asymptotic and exponential convergence

AbstractThe main goal of this proposal is to present a class of nonlinear controllers for regulation and set point changes in continuous chemical reactors. The proposed control law has in its mathematical structure a proportional term of the regulation error to provide closed‐loop stability and a sinusoidal term, which can compensate for the nonlinearities of the plant. The closed‐loop stability of the plant is demonstrated via Lyapunov analysis, which reveals an asymptotic convergence of the control output to the required set points. Furthermore, the analysis of the regulation error's dynamic under the considered assumptions leads us to conclude that exponential stability is also reached. The controller is implemented via numerical experiments in two examples to generalize the applicability of the proposed approach by considering continuous stirred‐tank reactors models. The first case considers autocatalytic chemical oscillatory reactions that induce chaotic behaviour. For the second case, a process of acetone, butanol, and ethanol (ABE) fermentation through Clostridium acetobutylicum is considered. The proposed strategy shows an adequate performance because it can reach the required set point without long time settings and overshoot. A comparison with a smooth sliding‐mode and a standard proportional‐integral (PI) controller indicates the advantages of the proposed control approach.

Diffusion-driven instabilities in the BT-GN oscillatory carbonylation reaction network.

This study explores the role of diffusion in creating instabilities in the Bruk Temkin-Gorodsky Novakovic (BT-GN) oscillatory carbonylation reaction network. Stoichiometric network analysis and numerical methods revealed the presence of two destabilizing feedback cycles responsible for these instabilities. Analysis of a spatially uniform system showed that the saddle-node bifurcation can be simulated within the reaction network. The introduction of diffusion results in two types of instabilities: one occurs when a spatially uniform system is already unstable, leading to a reaction-diffusion front; and another involves diffusion-driven instabilities where introducing diffusion destabilizes a stable spatially uniform system. Slower PdI2 diffusion plays a key role in inducing these instabilities. Equations describing conditions for the emergence of the instabilities in both cases were derived.

Influence of L-tyrosine on dynamics of Bray-Liebhafsky oscillatory reaction in batch reactor. Experimental investigation and numerical modeling

The impact of L-tyrosine on the dynamics of the Bray-Liebhafsky (BL) oscillatory reaction was investigated both experimentally and numerically. The study focused on the examination of the sensitivity of the BL reaction to L-tyrosine perturbation. The results obtained indicated possible pathways of influence. Simulations were carried out with and without L-tyrosine. The interaction of L-tyrosine with the BL reaction system was tested with two possible reactions.

Design principles and control of non-cooperative oscillatory enzymatic reactions

Oscillatory phenomena are often observed in enzyme systems due to feedback regulation, with a classic motif for persistent oscillation being a three-component negative feedback loop. Delay and high cooperativity are proposed as essential for the oscillation in these motifs. This study focuses on designing and optimizing oscillatory biochemical reactions using three-node enzymatic networks without cooperativity. Our findings revealed that improving the specificity constant – the so-called kinetic efficiency – and selecting the optimal topology can greatly increase the probability and frequency of oscillation in biochemical reactions. Inspired by pharmacology, various moderators were utilized to enhance the specificity constant, demonstrating how various oscillatory regimes can be reached with a given topology.

Complex chemical reaction networks for future information processing.

Tackling the increasing energy demand of our society is one of the key challenges today. With the rise of artificial intelligence, information and communication technologies started to substantially contribute to this alarming trend and therefore necessitate more sustainable approaches for the future. Brain-inspired computing paradigms represent a radically new and potentially more energy-efficient approach for computing that may complement or even replace CMOS in the long term. In this perspective, we elaborate on the concepts and properties of complex chemical reaction networks (CRNs) that may serve as information-processing units based on chemical reactions. The computational capabilities of simpler, oscillatory chemical reactions have already been demonstrated in scenarios ranging from the emulation of Boolean gates to image-processing tasks. CRNs offer higher complexity and larger non-linearity, potentially at lower energy consumption. Key challenges for the successful development of CRN-based computers are associated with their specific physical implementations, operability, and readout modalities. CRNs are sensible to various reaction triggers, and provide multiple and interlinked reaction pathways and a diverse compound space. This bears a high potential to build radically new hardware and software concepts for energy-efficient computing based on neuromorphic architectures-with computing capabilities in real-world applications yet to be demonstrated.

Theoretical study of the O(3P) + CN(X2Σ+) → CO(X1Σ+) + N(2D)/N(4S) reactions.

The barrierless exothermic reactions between atomic oxygen and the cyano radical, O(3P) + CN(X2Σ+) → CO(X1Σ+) + N(2D)/N(4S), play a significant role in combustion, astrochemistry, and hypersonic environments. In this work, their dynamics and kinetics are investigated using both wave packet (WP) and quasi-classical trajectory (QCT) methods on recently developed potential energy surfaces of the 12A', 12A,″ and 14A″ states. The product state distributions in the doublet pathway obtained with the WP method for a few partial waves show extensive internal excitation in the CO product. This observation, combined with highly oscillatory reaction probabilities, signals a complex-forming mechanism. The statistical nature of the reaction is confirmed by comparing the WP results with those from phase space theory. The calculated rate coefficients using the WP (with a J-shifting approximation) and QCT methods exhibit agreement with each other near room temperature, 1.77 × 10-10 and 1.31 × 10-10cm3molecule-1s-1, but both are higher than the existing experimental results. The contribution of the quartet pathway is small at room temperature due to a small entrance channel bottleneck. The QCT rate coefficients are further compared with experimental results above 3000K, and the agreement is excellent.

Dynamical and computational analysis of fractional order mathematical model for oscillatory chemical reaction in closed vessels

One of the most fascinating chemical reactions is an oscillating one. The reactant and the autocatalyst are the two chemical species that are considered in this system. Firstly, we convert the oscillatory chemical reaction model into a fractional order oscillatory chemical reaction model for derivatives of arbitrary order provided in the sense of Caputo. The recommended methodology is centered on the shifted Jacobi collocation technique (JCT) and the shifted Jacobi operational matrix. In this work, we offer computational simulations of fractional order oscillatory chemical reaction models by using collocation technique and Newton polynomial interpolation (NPI) technique. The primary benefit of the collocation method is to study a general estimation for temporal and spatial discretizations. The numerical strategy also simplifies fractional differentiation equations (FDEs) by simplifying them into a simple issue that can be resolved by finding solutions to a few algebraic equations. We also present a comparison between the collocation and NPI techniques through the figures. The mathematical outcomes and data demonstrate that the offered strategy is an efficient procedure with outstanding reliability for resolving differential equations of arbitrary order. Some theorems related to the analysis of the collocation technique are also presented and explained here.

Chemical oscillation in ultracold chemistry

We demonstrate the occurrence of oscillatory reactions in the ultra-cold chemistry of atom-molecular Bose-Einstein condensate. Nonlinear oscillations in the mean-field dynamics occur for a specific range of elliptic modulus, giving rise to both in- and out-phase modulations in the atom-molecule population density. The reaction front velocity is found to be controlled by photoassociation, which also regulates the condensate density. Two distinct pairs of in-phase bright localized gap solitons are found as exact solutions, the existence of one of which necessarily requires a background. Cnoidal atomic density waves along with a plane-wave molecular motion are observed in both attractive and repulsive domains. The role of intra- and inter-species interactions on both existence and stability is explicated in the presence of photoassociation.

A nonlinear continuum framework for constitutive modeling of active polymer gels

Chemo-mechanical transduction is one of the key mechanisms that has formed the basis for designing bio-inspired self-driven synthetic systems from soft materials. Polymer hydrogels that use Belousov–Zhabotinsky (BZ) reaction are a unique class of dynamical reaction–diffusion (RD) systems that can continuously transduce internal chemical energy, from the reaction, to produce sustained mechanical work. In particular, BZ gels represent a complex nonlinear chemo-mechanical system, wherein, the autocatalytic oscillatory BZ reaction drives the rhythmic mechanical deformations through polymer-solvent inter–diffusion. The objective of our work is to develop a standardized finite element (FE) framework for chemically driven active hydrogels that captures nonlinear elastic deformations with limited chain extensibility. The distinguishing feature of our approach is that, unlike other approaches, it combines reaction kinetics, solvent transport, elastodynamics of the polymeric network, and polymer-solvent friction under a unified FE framework. Moreover, we adapt our approach to a specific case of BZ gels and capture their swelling-deswelling characteristics. We first implement our FE framework in MATLAB that subsequently, forms the basis for constructing a three-dimensional user element subroutine (3D-UEL) in ABAQUS. Ultimately, through our simulations, we are able to capture all the essential features of BZ gels that includes chemically driven mechanical deformations. In addition, we also demonstrate that our 3D-UEL efficiently captures the chemo-mechanical response of “stent-shaped” BZ gels–a non-standard 3D geometry. In essence, our FE approach not only allows us to simulate BZ gels but also provides a template for other active, dynamical, RD-based systems, driven by chemo-mechanical transduction, irrespective of internal or external mechanisms.

Experimental support for the model of Bray–Liebhafsky oscillatory reaction based on the heterogeneous effects

Participation of the heterogeneous effects in the Bray–Liebhafsky reaction. Content of the large bubbles in the mixture under fast and slow stirring rate with corresponding effects on oscillatory dynamics.

A 3D-printed oscillatory polymerase chain reaction system using a single heater

Nucleic acid amplification is a process that arises in all organisms. Polymerase chain reaction (PCR) is a standard laboratory nucleic acids amplification technology in vitro widely used in medical detection and biometric-related research. This device represents the first demonstration of 3D-printed oscillatory thermocycling within a portable PCR device. This study uses a single Peltier element to create the three temperature regions required for PCR. The overall control system uses an Arduino microcontroller with the advantages of easy development, abundant resources, and easy access to device software design. The sample-driving system integrated with the 3D printed object and the laser-cut acrylic component to achieve the linear reciprocating motion of the sample is conducive to the realisation of the portable design of the device. After system optimisation, the reaction tube moves from the denaturation zone to the aluminum block for cooling, and it moves to the groove of the denaturation zone from the annealing zone to accelerate the sample temperature rise. The time duration reduces from 180 s to 85 s to complete one thermal cycle. Combining the 5 mm instead of 3 mm thickness of the acrylic material and the configuration of the acrylic end exposed in the air creates a more significant temperature difference from 25 °C to 40 °C. Using this oscillatory PCR device, we successfully amplified a 219 bp PCR product of turmeric DNA after 30 thermal cycles within 50 min. The developed PCR device will cost less than $300 USD in our work. Compared with previous works, the cost of this research device is relatively low, and the total volume of the device is quite small. This work should be interesting to persons involved in diagnosing the infectious diseases of viruses and bacteria and identifying the fake healthy food in the low-cost bioreaction chambers in fields and remote areas.

Visualizing dynamic competitive adsorption processes between iodine and methyl iodide within single covalent organic framework crystals

Covalent organic frameworks (COFs) are important porous adsorbents for volatile iodine (I2) and methyl iodide (CH3I). In situ monitoring of the dynamic adsorption process of single COF crystals toward I2 and CH3I is a critical and fundamental issue for understanding the reaction mechanism and improving the sorption performance. Here, we report operando real-time dark-field optical microscopy (DFM) imaging of visually studying the dynamic adsorption behavior of LZU-111 (LZU=Lanzhou University) COFs in the I2/CH3I binary gaseous mixture at the single-crystal level. Time-lapse imaging shows that the uptake of CH3I and I2 results in the R intensity increase and B intensity decrease of the DFM images. Employing the R and B intensities as two indicators, we find an unusual blinking of R/B intensities from single LZU-111 crystals, which is attributed to the intermittent sorption-desorption processes of CH3I and I2 within the LZU-111 framework. The visualization of the dynamic reaction process provides clear evidence that the competitive adsorption between CH3I and I2 goes through a multi-time and oscillatory reaction pathway instead of a successive procedure. Combined with theoretical calculations, the difference in the migration capability and initial pressure is identified for initiating the intermittent blinking events.

Microdispersed Ti/B/N Materials Synthesized in Chain Reactions in Processes Initiated by Microwaves of a High-Power Gyrotron: Structure and Cytotoxicity

An original plasma-chemical facility has been developed at the Prokhorov General Physics Institute of the Russian Academy of Sciences based on the gyrotrons of the thermonuclear complex of the L-2 M/MIG-3 stellarator. The scope of its applications includes the synthesis of powders for new types of catalysts, the formation and doping of ceramics, and other applications. We have previously demonstrated that in specific conditions, chain oscillatory reactions can be initialized in the reactor by powerful microwave pulses of the gyrotron in mixtures of metal and dielectric powders, resulting in the formation of microdispersed materials with controllable physical and chemical properties. In such reactions, initiated in mixtures of Ti and B, BN powders in a series of particle samples with a developed surface have been obtained. The resulting materials have a heterogeneous composition and size distribution controlled by the synthesis conditions. Thus, the obtained structures exhibit repeatable characteristics attractive for numerous applications, from catalytic particle formation and reinforcement additives to biomedical materials. In order to analyze the hazardless of the materials, cytotoxicity tests were necessary. In this work, the methods for such an analysis have been applied. The study of the obtained samples for cytotoxicity against human cells (lines HEK293T, MCF7, A549, VA13) showed toxic effects only at concentrations of tens of mg/L and the absence of detectable toxic effects in bacterial system (E. coli). The low toxicity at the cellular level indicates the potential for the safe use of the proposed microstructures, but requires further testing of safety at the organism level.

Role of Fast and Slow Inhibitors in Oscillatory Rhythm Design.

In biological or abiotic systems, rhythms occur, owing to the coupling between positive and negative feedback loops in a reaction network. Using the Semenov-Whitesides oscillatory network for thioester hydrolysis as a prototype, we experimentally and theoretically analyzed the role of fast and slow inhibitors in oscillatory reaction networks. In the presence of positive feedback, a single fast inhibitor generates a time delay, resulting in two saddle-node bifurcations and bistability in a continuously stirred tank reactor. A slow inhibitor produces a node-focus bifurcation, resulting in damped oscillations. With both fast and slow inhibitors present, the node-focus bifurcation repeatedly modulates the saddle-node bifurcations, producing stable periodic oscillations. These fast and slow inhibitions result in a pair of time delays between steeply ascending and descending dynamics, which originate from the positive and negative feedbacks, respectively. This pattern can be identified in many chemical relaxation oscillators and oscillatory models, e.g., the bromate-sulfite pH oscillatory system, the Belousov-Zhabotinsky reaction, the trypsin oscillatory system, and the Boissonade-De Kepper model. This study provides a novel understanding of chemical and biochemical rhythms and suggests an approach to designing such behavior.

Empirically developed model of the stirring-controlled Belousov–Zhabotinsky reaction

The Belousov–Zhabotinsky chemical reaction is famous for its oscillatory behavior occurring due to inherent physicochemical processes. Oscillations of the Belousov–Zhabotinsky reaction may be periodic or chaotic, depending on parameters, and these dynamics can be controlled by external impacts such as stirring. The complex behavior, the variability of the oscillatory modes, and controllability make the Belousov–Zhabotinsky reaction an important research subject in many fields of science, including various applications such as chemical computing or smart materials. One of the key limitations for the practical application of this oscillatory reaction is the absence of its exact mathematical model which can reproduce dynamics close to the real chemical process. This work aims to fill this gap by designing a novel model of the Belousov–Zhabotinsky reaction based on experimental data. To solve this task, we designed a complex experimental setup based on a photometric station with controllable stirring mechanisms. We performed two experiments in batch reactors (cuvettes). In the first experiment, we investigated how constant stirring with different rates affects the reaction behavior, and in the second experiment, we periodically stirred the reaction and observed its response. As a result, we found that chemical oscillations in the Belousov–Zhabotinsky reaction are in both cases chaotic, their amplitude depends on stirring more than their period does, and they are highly non-stationary: in the course of the reaction, their sensitivity to stirring decreases, so the oscillations remain controllable only during the first hour. Using a novel two-stage differential equation reconstruction approach, we managed to develop a complex of local dynamical models for the stirring-controlled BZ reaction with good correspondence to the empirical data. The presented models are more consistent with experimentally observed Belousov–Zhabotinsky dynamics than earlier models. The developed model can be used in various applications and extended to a wide class of controlled oscillatory reactions.

Addressing the Primary and Subharmonic Resonances of the Swing Equation

A research investigation is undertaken to gain a more comprehensive understanding of the primary and subharmonic resonances exhibited by the swing equation. The occurrence of the primary resonance is characterised by amplified oscillatory reactions, voltage instability, and the possibility for system failure. The phenomenon of subharmonic resonance arises when the frequency of disturbance is a whole-number fraction of the natural frequency. This results in the occurrence of low-frequency oscillations and the potential for detrimental effects on equipment. The objective of this study is to expand upon the current literature regarding the impacts of primary resonance and enhance comprehension of subharmonic resonance in relation to the stability of a specific power system model. The analytical and numerical tools are utilised to investigate the fundamental principles of this resonant-related problem, aiming to provide an effective control solution. This choice is driven by the model’s complex nonlinear dynamical behaviour, which offers valuable insights for further analysis. This analysis includes the Floquet Method, the Method of strained parameters, and the concept of tangent instability in order to provide an extension to existing literature relating to primary and subharmonic resonances, taking into account the dynamic and bifurcation characteristics of the swing equation. This objective will be achieved through the utilisation of both analytical and numerical methods, enabling the identification of specific indicators of chaos that can contribute to the safe operation of real-world scenarios.