Complex dynamics in a two-enzyme reaction network with substrate competition

Pore-Forming Toxin-Driven Recovery of Peroxidase-Mimicking Activity in Biomass Channels for Label-Free Electrochemical Bacteria Sensing

The development of sensitive, selective, and rapid methods to detect bacteria in complex media is essential to ensuring human health. Virulence factors, particularly pore-forming toxins (PFTs) secreted by pathogenic bacteria, play a crucial role in bacterial diseases and serve as indicators of disease severity. In this study, a nanochannel-based label-free electrochemical sensing platform was developed for the detection of specific pathogenic bacteria based on their secreted PFTs. In this design, wood substrate channels were functionalized with a Fe-based metal-organic framework (FeMOF) and then protected with a layer of phosphatidylcholine (PC)-based phospholipid membrane (PM) that serves as a peroxidase mimetic and a channel gatekeeper, respectively. Using Staphylococcus aureus (S. aureus) as the model bacteria, the PC-specific PFTs secreted by S. aureus perforate the PM layer. Now exposed to the FeMOF, uncharged 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) molecules in the electrolyte undergo oxidation to cationic products (ABTS•+). The measured transmembrane ionic current indicates the presence of S. aureus and methicillin-resistant S. aureus (MRSA) with a low detection limit of 3 cfu mL-1. Besides excellent specificity, this sensing approach exhibits satisfactory performance for the detection of target bacteria in the complex media of food.

Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems

The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.

Multiple iodide autocatalysis paths of chemo-hydrodynamical patterns in the Briggs-Rauscher reaction

Autocatalytic feedback is often regarded as the core step for the chemo-hydrodynamical patterns in the nonlinear reaction system. The Briggs-Rauscher (BR) reaction shows sequential chemo-hydrodynamical patterns with three states, i.e. labyrinth, high iodine state, and rotating dendritic patterns. The short-lived labyrinth patterns, depending on [Mn²⁺]₀, the ratio of [CH₂(COOH)₂]₀ and [KIO₃]₀ and light intensities, result from iodide autocatalytic loop, which has three paths (involving Mn²⁺-induced radical reactions, the oxidation of iodomalonic compounds, and light-induced radical reactions, respectively). The high iodine state appears in a high ratio of [CH₂(COOH)₂]₀ and [KIO₃]₀, relating to the autocatalytic path involving the oxidation of iodomalonic compounds. The light-induced radical autocatalytic path can act as a convenient control parameter to modulate the patterns in the first stage by increasing the iodine radicals. The dendritic patterns in the third stage result from the Marangoni effect caused by the evaporation of the solutions and reactions between H₂O₂ and iodine-containing species, which is independent of [CH₂(COOH)₂]₀ and [Mn²⁺]₀. This work contributes to a better understanding of the complex spatiotemporal patterns in the chemo-hydrodynamical system.

Orbiting Self-Organization of Filament-Tethered Surface-Active Droplets

Dissipative chemical systems hold the potential to enable life-like behavior in synthetic matter, such as self-organization, motility, and dynamic switching between different states. Here, out-of-equilibrium self-organization is demonstrated by interconnected source and drain droplets at an air-water interface, which display dynamic behavior due to a hydrolysis reaction that generates a concentration gradient around the drain droplets. This concentration gradient interferes with the adhesion of self-assembled amphiphile filaments that grow from a source droplet. The chemical gradient sustains a unique orbiting of the drain droplet, which is proposed to be driven by the selective adhesion of the filaments to the front of the moving droplet, while filaments approaching from behind are destabilized upon contact with the hydrolysis product in the trail of the droplet. Potential applications are foreseen in the transfer of chemical signals amongst communicating droplets in rearranging networks, and the implementation of chemical reactions to drive complex positioning routines in life-like systems.

Determination of monophenolase activity based on backpropagation neural network analysis of three-dimensional fluorescence spectroscopy

Tyrosinase is pivotal for melanin formation. Measuring monophenolase activity is of great importance for both fundamental research and industrial applications. For the first time, a backpropagation (BP) artificial neural network with three-dimensional fluorescence spectroscopy was applied for the real-time determination of tyrosinase monophenolase activity. Principal component analysis (PCA) was utilized for the dimension reduction of three-dimensional fluorescence data. The four principal components served as inputs for the neural network. Network parameters were optimized using a genetic algorithm (GA). BP learning algorithm was applied to train the network model to determine tyrosine levels in a binary mixture containing tyrosine and L-DOPA without any chemical separation. The time course of tyrosine consumption by monophenolase was determined to calculate the initial velocity of the enzymatic reaction. The limit of detection of the monophenolase assay was 0.0615 U·mL^-1. This combined strategy of PCA, GAs, and BP artificial neural networks for three-dimensional fluorescence spectroscopy was efficient for the real-time and in-situ determination of monophenolase activity in a cascade reaction.

Computing Arithmetic Functions Using Immobilised Enzymatic Reaction Networks

Living systems use enzymatic reaction networks to process biochemical information and make decisions in response to external or internal stimuli. Herein, we present a modular and reusable platform for molecular information processing using enzymes immobilised in hydrogel beads and compartmentalised in a continuous stirred tank reactor. We demonstrate how this setup allows us to perform simple arithmetic operations, such as addition, subtraction and multiplication, using various concentrations of substrates or inhibitors as inputs and the production of a fluorescent molecule as the readout.

Cold Nanozyme for Precise Enzymatic Antitumor Immunity

Precise catalysis is pursued for the biomedical applications of artificial enzymes. It is feasible to precisely control the catalysis of artificial enzymes via tunning the temperature-dependent enzymatic kinetics. The safety window of cold temperatures (4-37 °C) for the human body is much wider than that of thermal temperatures (37-42 °C). Although the development of cold-activated artificial enzymes is promising, there is currently a lack of suitable candidates. Herein, a cold-activated artificial enzyme is presented with Bi₂Fe₄O₉ nanosheets (NSs) as a paradigm. The as-obtained Bi₂Fe₄O₉ NSs possess glutathione oxidase (GSHOx)-like activity under cold temperature due to their pyroelectricity. Bi₂Fe₄O₉ NSs trigger the cold-enzymatic death of tumor cells via apoptosis and ferroptosis, and minimize the off-target toxicity to normal tissues. Moreover, an interventional device is fabricated to intelligently and remotely control the enzymatic activity of Bi₂Fe₄O₉ NSs on a smartphone. With Bi₂Fe₄O₉ NSs as an in situ vaccine, systemic antitumor immunity is successfully activated to suppress tumor metastasis and relapse. Moreover, blood biochemistry analysis and histological examination indicate the high biosafety of Bi₂Fe₄O₉ NSs for in vivo applications. This cold nanozyme provides a strategy for cancer vaccines, which can benefit the precise control over catalytic nanomedicines.

Influence of Oxygen on Chemoconvective Patterns in the Iodine Clock Reaction

There is increasing interest in using chemical clock reactions to drive material formation; however, these reactions are often subject to chemoconvective effects, and control of such systems remains challenging. Here, we show how the transfer of oxygen at the air-water interface plays a crucial role in the spatiotemporal behavior of the iodine clock reaction with sulfite. A kinetic model was developed to demonstrate how the reaction of oxygen with sulfite can control a switch from a low-iodine to high-iodine state under well-stirred conditions and drive the formation of transient iodine gradients in unstirred solutions. In experiments in thin layers with optimal depths, the reaction couples with convective instability at the air-water interface forming an extended network-like structure of iodine at the surface that develops into a spotted pattern at the base of the layer. Thus, oxygen drives the spatial separation of iodine states essential for patterns in this system and may influence pattern selection in other clock reaction systems with sulfite.

Spatial programming of self-organizing chemical systems using sustained physicochemical gradients from reaction, diffusion and hydrodynamics

Living organisms employ chemical self-organization to build structures, and inspire new strategies to design synthetic systems that spontaneously take a particular form, via a combination of integrated chemical reactions, assembly pathways and physicochemical processes. However, spatial programmability that is required to direct such self-organization is a challenge to control. Thermodynamic equilibrium typically brings about a homogeneous solution, or equilibrium structures such as supramolecular complexes and crystals. This perspective addresses out-of-equilibrium gradients that can be driven by coupling chemical reaction, diffusion and hydrodynamics, and provide spatial differentiation in the self-organization of molecular, ionic or colloidal building blocks in solution. These physicochemical gradients are required to (1) direct the organization from the starting conditions (e.g. a homogeneous solution), and (2) sustain the organization, to prevent it from decaying towards thermodynamic equilibrium. We highlight four different concepts that can be used as a design principle to establish such self-organization, using chemical reactions as a driving force to sustain the gradient and, ultimately, program the characteristics of the gradient: (1) reaction-diffusion coupling; (2) reaction-convection; (3) the Marangoni effect and (4) diffusiophoresis. Furthermore, we outline their potential as attractive pathways to translate chemical reactions and molecular/colloidal assembly into organization of patterns in solution, (dynamic) self-assembled architectures and collectively moving swarms at the micro-, meso- and macroscale, exemplified by recent demonstrations in the literature.

Self-Organization Emerging from Marangoni and Elastocapillary Effects Directed by Amphiphile Filament Connections

Self-organization of meso- and macroscale structures is a highly active research field that exploits a wide variety of physicochemical phenomena, including surface tension, Marangoni flow, and (elasto)capillary effects. The release of surface-active compounds generates Marangoni flows that cause repulsion, whereas capillary forces attract floating particles via the Cheerios effect. Typically, the interactions resulting from these effects are nonselective because the gradients involved are uniform. In this work, we unravel the mechanisms involved in the self-organization of amphiphile filaments that connect and attract droplets floating at the air-water interface, and we demonstrate their potential for directional gradient formation and thereby selective interaction. We simulate Marangoni flow patterns resulting from the release and depletion of amphiphile molecules by source and drain droplets, respectively, and we predict that these flow patterns direct the growth of filaments from the source droplets toward specific drain droplets, based on their amphiphile depletion rate. The interaction between such droplets is then investigated experimentally by charting the flow patterns in their surroundings, while the role of filaments in source-drain attraction is studied using microscopy. Based on these observations, we attribute attraction of drain droplets and even solid objects toward the source to elastocapillary effects. Finally, the insights from our simulations and experiments are combined to construct a droplet-based system in which the composition of drain droplets regulates their ability to attract filaments and as a consequence be attracted toward the source. Thereby, we provide a novel method through which directional attraction can be established in synthetic self-organizing systems and advance our understanding of how complexity arises from simple building blocks.

A Bayesian Approach to Extracting Kinetic Information from Artificial Enzymatic Networks

In order to create artificial enzymatic networks capable of increasingly complex behavior, an improved methodology in understanding and controlling the kinetics of these networks is needed. Here, we introduce a Bayesian analysis method allowing for the accurate inference of enzyme kinetic parameters and determination of most likely reaction mechanisms, by combining data from different experiments and network topologies in a single probabilistic analysis framework. This Bayesian approach explicitly allows us to continuously improve our parameter estimates and behavior predictions by iteratively adding new data to our models, while automatically taking into account uncertainties introduced by the experimental setups or the chemical processes in general. We demonstrate the potential of this approach by characterizing systems of enzymes compartmentalized in beads inside flow reactors. The methods we introduce here provide a new approach to the design of increasingly complex artificial enzymatic networks, making the design of such networks more efficient, and robust against the accumulation of experimental errors.

Cascade reaction networks within audible sound induced transient domains in a solution

Spatiotemporal control of chemical cascade reactions within compartmentalized domains is one of the difficult challenges to achieve. To implement such control, scientists have been working on the development of various artificial compartmentalized systems such as liposomes, vesicles, polymersomes, etc. Although a considerable amount of progress has been made in this direction, one still needs to develop alternative strategies for controlling cascade reaction networks within spatiotemporally controlled domains in a solution, which remains a non-trivial issue. Herein, we present the utilization of audible sound induced liquid vibrations for the generation of transient domains in an aqueous medium, which can be used for the control of cascade chemical reactions in a spatiotemporal fashion. This approach gives us access to highly reproducible spatiotemporal chemical gradients and patterns, in situ growth and aggregation of gold nanoparticles at predetermined locations or domains formed in a solution. Our strategy also gives us access to nanoparticle patterned hydrogels and their applications for region specific cell growth.

Real-Time Monitoring of Dynamic Microbial Fe(III) Respiration Metabolism with a Living Cell-Compatible Electron-Sensing Probe

Monitoring microbial metabolism is vital for biomanufacturing processes optimization. However, it remains a grand challenge to offer insight into microbial metabolism due to particularly complex and dynamic processes. Here, we report an electron-sensing probe Zn₂ GeO₄ :Mn@Fe³⁺ for real-time and dynamic monitoring of Fe(III) respiration metabolism. The quenched persistent luminescence of Zn₂ GeO4:Mn@Fe³⁺ is recovered when Fe³⁺ accepted electrons from the dynamic Fe(III) respiration metabolism, enabling the real-time monitoring of microbial metabolism. The probe shows the capability to verify the role of related biomolecules in microbial Fe(III) respiration metabolism, to track the dynamic Fe(III) respiration metabolic response to environmental stress and microbial co-culture interactions. Furthermore, the Zn₂ GeO₄ :Mn@Fe³⁺ probe provides guidance for improving biosynthesis efficiency by monitoring Fe redox recycling in microbial co-culture.

Resonant amplification of enzymatic chemical oscillations by oscillating flow

Using theory and simulation, we analyzed the resonant amplification of chemical oscillations that occur due to externally imposed oscillatory fluid flows. The chemical reactions are promoted by two enzyme-coated patches located sequentially on the inner surface of a pipe that transports the enclosed chemical solution. In the case of diffusion-limited systems, the period of oscillations in chemical reaction networks is determined by the rate of the chemical transport, which is diffusive in nature and, therefore, can be effectively accelerated by the imposed fluid flows. We first identify the natural frequencies of the chemical oscillations in the unperturbed reaction-diffusion system and, then, use the frequencies as a forcing input to drive the system to resonance. We demonstrate that flow-induced resonance can be used to amplify the amplitude of the chemical oscillations and to synchronize their frequency to the external forcing. In particular, we show that even 10% perturbations in the flow velocities can double the amplitude of the resulting chemical oscillations. Particularly, effective control can be achieved for the two-step chemical reactions where during the first half-period, the fluid flow accelerates the chemical flux toward the second catalytic patch, while during the second half-period, the flow amplifies the flux to the first patch. The results can provide design rules for regulating the dynamics of coupled reaction-diffusion processes and can facilitate the development of chemical reaction networks that act as chemical clocks.

Cross β amyloid assemblies as complex catalytic machinery

How modern enzymes evolved as complex catalytic machineries to facilitate diverse chemical transformations is an open question for the emerging field of systems chemistry. Inspired by Nature's ingenuity in creating complex catalytic structures for exotic functions, short peptide-based cross β amyloid sequences have been shown to access intricate binding surfaces demonstrating the traits of extant enzymes and proteins. Based on their catalytic proficiencies reported recently, these amyloid assemblies have been argued as the earliest protein folds. Herein, we map out the recent progress made by our laboratory and other research groups that demonstrate the catalytic diversity of cross β amyloid assemblies. The important role of morphology and specific mutations in peptide sequences has been underpinned in this review. We have divided the feature article into different sections where examples from biology have been covered demonstrating the mechanism of extant biocatalysts and compared with recent works on cross β amyloid folds showing covalent catalysis, aldolase, hydrolase, peroxidase-like activities and complex cascade catalysis. Beyond equilibrium, we have extended our discussion towards transient catalytic amyloid phases mimicking the energy driven cytoskeleton polymerization. Finally, a future outlook has been provided on the way ahead for short peptide-based systems chemistry approaches that can lead to the development of robust catalytic networks with improved enzyme-like proficiencies and higher complexities. The discussed examples along with the rationale behind selecting specific amino acids sequence will benefit readers to design systems for achieving catalytic reactivity similar to natural complex enzymes.

Construction of Peroxidase-like Metal-Organic Frameworks in TiO2 Nanochannels: Robust Free-Standing Membranes for Diverse Target Sensing

The high cost and easy denaturation of natural enzymes under environmental conditions hinder their practical usefulness in sensing devices. In this study, peroxidase (POD)-like metal-organic frameworks (MOFs) were in situ grown in the nanochannels of an anodized TiO₂ membrane (TiO₂NM) as an electrochemical platform for multitarget sensing. By directly using a nanochannel wall as the precursor of metal nodes, Ti-MOFs were in situ derived on the nanochannel wall. Benefitting from the presence of bipyridine groups on the ligands, the MOFs in the nanochannels provide plenty of sites for Fe³⁺ anchoring, thus endowing the resulting membrane (named as Fe³⁺:MOFs/TiO₂NM) with remarkable POD-like activity. Such Fe³⁺-induced POD-like activity is very sensitive to thiol-containing molecules owing to the strong coordination effect of thiols on Fe³⁺. Most importantly, the POD-like activity of nanochannels can be in situ characterized by the current-potential (I-V) properties via catalyzing the oxidation of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonate) (ABTS) substrate to the corresponding positively charged product ABTS^•+. As a proof-of-concept application, the free-standing POD-like membranes were applied as a label-free assay in sensing cysteine, as well as monitoring acetylcholinesterase (AChE) activity through the generated thiol-containing product. Furthermore, based on the toxicity effect of organophosphorus (OP) compounds on AChE, the robust membranes were successfully utilized to evaluate the toxicity of diverse OP compounds. The POD-like nanochannels open up an innovative way to expand the application of nanochannel-based electrochemical sensing platforms in drug inspection, food safety, and environmental pollution.

Glucose-oxidase like catalytic mechanism of noble metal nanozymes

Au nanoparticles (NPs) have been found to be excellent glucose oxidase mimics, while the catalytic processes have rarely been studied. Here, we reveal that the process of glucose oxidation catalyzed by Au NPs is as the same as that of natural glucose oxidase, namely, a two-step reaction including the dehydrogenation of glucose and the subsequent reduction of O₂ to H₂O₂ by two electrons. Pt, Pd, Ru, Rh, and Ir NPs can also catalyze the dehydrogenation of glucose, except that O₂ is preferably reduced to H₂O. By the electron transfer feature of noble metal NPs, we overcame the limitation that H₂O₂ must be produced in the traditional two-step glucose assay and realize the rapid colorimetric detections of glucose. Inspired by the electron transport pathway in the catalytic process of natural enzymes, noble metal NPs have also been found to mimic various enzymatic electron transfer reactions including cytochrome c, coenzymes as well as nitrobenzene reductions.

Chemically-powered swimming and diffusion in the microscopic world

The past decade has seen intriguing reports and heated debates concerning the chemically-driven enhanced motion of objects ranging from small molecules to millimetre-size synthetic robots. These objects, in solutions in which chemical reactions were occurring, were observed to diffuse (spread non-directionally) or swim (move directionally) at rates exceeding those expected from Brownian motion alone. The debates have focused on whether observed enhancement is an experimental artefact or a real phenomenon. If the latter were true, then we would also need to explain how the chemical energy is converted into mechanical work. In this Perspective, we summarize and discuss recent observations and theories of active diffusion and swimming. Notably, the chemomechanical coupling and magnitude of diffusion enhancement are strongly size-dependent and should vanish as the size of the swimmers approaches the molecular scale. We evaluate the reliability of common techniques to measure diffusion coefficients and finish by considering the potential applications and chemical to mechanical energy conversion efficiencies of typical nanoswimmers and microswimmers.

pH Feedback Lifecycles Programmed by Enzymatic Logic Gates Using Common Foods as Fuels

Artificial temporal signaling systems, which mimic living out-of-equilibrium conditions, have made large progress. However, systems programmed by enzymatic reaction networks in multicomponent and unknown environments, and using biocompatible components remain a challenge. Herein, we demonstrate an approach to program temporal pH signals by enzymatic logic gates. They are realized by an enzymatic disaccharide-to-monosaccharide-to-sugar acid reaction cascade catalyzed by two metabolic chains: invertase-glucose oxidase and β-galactosidase-glucose oxidase, respectively. Lifetimes of the transient pH signal can be programmed from less than 15 min to more than 1 day. We study enzymatic kinetics of the reaction cascades and reveal the underlying regulatory mechanisms. Operating with all-food grade chemicals and coupling to self-regulating hydrogel, our system is quite robust to work in a complicated medium with unknown components and in a biocompatible fashion.

Near-Infrared Photo-controlled Permeability of a Biomimetic Polymersome with Sustained Drug Release and Efficient Tumor Therapy

Synthetic polymersomes have structure similarity to bio-vesicles and could disassemble in response to stimuli for "on-demand" release of encapsulated cargos. Though widely applied as a drug delivery carrier, the burst release mode with structure complete destruction is usually taken for most responsive polymersomes, which would shorten the effective drug reaction time and impair the therapeutic effect. Inspired by the cell organelles' communication mode via regulating membrane permeability for transportation control, we highlight here a biomimetic polymersome with sustained drug release over a specific period of time via near-infrared (NIR) pre-activation. The polymersome is prepared by the self-assembling amphiphilic diblock copolymer P(OEGMA-co-EoS)-b-PNBOC and encapsulates the hypoxia-activated prodrug AQ4N and upconversion nanoparticle (PEG-UCNP) in its hydrophilic centric cavity. Thirty minutes of NIR pre-activation triggers cross-linking of NBOC and converts the permeability of the polymersome with sustained AQ4N release until 24 h after the NIR pre-activation. The photosensitizer EoS is activated and aggravates environmental hypoxic conditions during a sustained drug release period to boost the AQ4N therapeutic effect. The combination of sustained drug release with concurrent hypoxia intensification results in a highly efficient tumor therapeutic effect both intracellularly and in vivo. This biomimetic polymersome will provide an effective and universal tumor therapeutic approach.

Complex Cascade Reaction Networks via Cross β Amyloid Nanotubes

Biocatalytic reaction networks integrate complex cascade transformations via spatial localization of multiple enzymes confined within the cellular milieu. Inspired by nature's ingenuity, we demonstrate that short peptide-based cross-β amyloid nanotubular hybrids can promote different kinds of cascade reactions, from simple two-step, to multistep, to complex convergent cascades. The compartmentalizing ability of paracrystalline cross-β phases was utilized to colocalize sarcosine oxidase (SOX) and hemin as an artificial peroxidase. Further, the catalytic potential of the amyloid nanotubes with ordered arrays of imidazoles were used as hydrolase mimic. The SOX-hemin amyloid nanohybrids featuring a single extant enzyme could integrate different logic networks to access complex digital designs with the help of three concatenated AND gates and biologically relevant stimuli as inputs.

The impact of geometrical confinement in a slab on the behavior of tracer particles near active glucose oxidase micropump

Patches of surface-immobilized and catalytically active enzyme, immersed into a solution with the corresponding substrate, induce flow in the solution. Such systems are currently investigated as a promising direction in the development of self-powered micropumps that could operate autonomously within microfluidic devices. Here, we investigate the influence of confinement, within a slab of height H, on the response exhibited by silica tracer particles sedimented near a chemically active glucose oxidase patch which is immersed into a glucose solution of very low ionic strength. Irrespective of the value H, within the range explored in this study, a region depleted of tracers forms around the patch. When H is not much larger than the radius of the patch, the rate of growth of the depletion zone depends on H; somewhat surprisingly, this dependence is influenced by the glucose concentration. The results are discussed within the context of a simple model for a chemically active patch.

Autonomous mesoscale positioning emerging from myelin filament self-organization and Marangoni flows

Out-of-equilibrium molecular systems hold great promise as dynamic, reconfigurable matter that executes complex tasks autonomously. However, translating molecular scale dynamics into spatiotemporally controlled phenomena emerging at mesoscopic scale remains a challenge-especially if one aims at a design where the system itself maintains gradients that are required to establish spatial differentiation. Here, we demonstrate how surface tension gradients, facilitated by a linear amphiphile molecule, generate Marangoni flows that coordinate the positioning of amphiphile source and drain droplets floating at air-water interfaces. Importantly, at the same time, this amphiphile leads, via buckling instabilities in lamellar systems of said amphiphile, to the assembly of millimeter long filaments that grow from the source droplets and get absorbed at the drain droplets. Thereby, the Marangoni flows and filament organization together sustain the autonomous positioning of interconnected droplet-filament networks at the mesoscale. Our concepts provide potential for the development of non-equilibrium matter with spatiotemporal programmability.

Audible sound-controlled spatiotemporal patterns in out-of-equilibrium systems

Naturally occurring spatiotemporal patterns typically have a predictable pattern design and are reproducible over several cycles. However, the patterns obtained from artificially designed out-of-equilibrium chemical oscillating networks (such as the Belousov-Zhabotinsky reaction for example) are unpredictable and difficult to control spatiotemporally, albeit reproducible over subsequent cycles. Here, we show that it is possible to generate reproducible spatiotemporal patterns in out-of-equilibrium chemical reactions and self-assembling systems in water in the presence of sound waves, which act as a guiding physical stimulus. Audible sound-induced liquid vibrations control the dissolution of atmospheric gases (such as O₂ and CO₂) in water to generate spatiotemporal chemical patterns in the bulk of the fluid, segregating the solution into spatiotemporal domains having different redox properties or pH values. It further helps us in the organization of transiently formed supramolecular aggregates in a predictable spatiotemporal manner.

Cross-β amyloid nanotubes for hydrolase-peroxidase cascade reactions

Herein, we report the catalytic potential of short peptide based cross-β amyloid nanotubes with surface exposed histidine capable of binding hemin and showing facile cascade reactions, playing the dual roles of hydrolases and peroxidases, two of the most important classes of enzymes in extant biology. The activity of these simple systems exceeded those of modern and larger proteins like cytochrome C and hemoglobin. Further, evidence suggested that these self-assembled nanotubes foreshadow the process of intermediate channeling, a feature seen in the case of advanced enzymes.

Covalent Catalysis by Cross β Amyloid Nanotubes

The binding pockets of extant enzymes feature precise positioning of amino acid residues that facilitate multiple complex transformations exploiting covalent and non-covalent interactions. Reversible covalent anchoring is extensively used as an efficient tool by Nature for activating modern enzymes such as esterases and dehydratases and also for proteins like opsins for the complex process of visual phototransduction. Here we construct paracrystalline amyloid surfaces through the self-propagation of short peptides which offer binding pockets exposed with arrays of imidazoles and lysines. As covalent catalysis is utilized by modern-day enzymes, these homogeneous amyloid nanotubes exploit Schiff imine formation via the exposed lysines to efficiently hydrolyze both activated and inactivated esters. Controls where lysines were mutated with charged residues accessed similar morphologies but did not augment the rate. The designed amyloid microphases thus foreshadow the generation of binding pockets of advanced proteins and have the potential to contribute to the development of functional materials.

Programming bulk enzyme heterojunctions for biosensor development with tetrahedral DNA framework

Protein-protein interactions are spatially regulated in living cells to realize high reaction efficiency, as seen in naturally existing electron-transfer chains. Nevertheless, arrangement of chemical/biochemical components at the artificial device interfaces does not possess the same level of control. Here we report a tetrahedral DNA framework-enabled bulk enzyme heterojunction (BEH) strategy to program the multi-enzyme catalytic cascade at the interface of electrochemical biosensors. The construction of interpenetrating network of BEH at the millimeter-scale electrode interface brings enzyme pairs within the critical coupling length (CCL) of ~10 nm, which in turn greatly improve the overall catalytic cascade efficiency by ~10-fold. We demonstrate the BEH generality with a range of enzyme pairs for electrochemically detecting clinically relevant molecular targets. As a proof of concept, a BEH-based sarcosine sensor enables single-step detection of the metabolic biomarker of sarcosine with ultrasensitivity, which hold the potential for precision diagnosis of early-stage prostate cancer.

Tetrahedral DNA framework-enabled bulk enzyme heterojunctions have been used to program biosensor interfaces. Here, the authors use DNA tetrahedrons to tether enzymes of an enzymatic cascade to gold electrodes, hence raising them over the bulk solution, which led to improved kinetics and sensitivity.

Lattice-Like DNA Tetrahedron Nanostructure as Scaffold to Locate GOx and HRP Enzymes for Highly Efficient Enzyme Cascade Reaction

In this work, the array arrangement of cascade enzymes was implemented by alternately and equidistantly anchoring two model enzymes glucose oxidase (GOx) and horseradish peroxidase (HRP) to the vertexes of rigid DNA tetrahedron units in lattice-like nucleic acid scaffold, in which the distance between any adjacent cascade enzymes had been regulated to the optimum for obtaining high enzyme cascade catalytic efficiency. Compared to the enzyme cascade system with no-array arrangement of cascade enzymes, the proposed enzyme cascade system allowed the intermediate H₂O₂ produced by GOx catalyzing substrate glucose to concurrently and equidistantly diffuse toward the four adjacent HRP enzyme surfaces. In this case, the invalid diffusion effect of intermediate H₂O₂ between cascade enzymes could be effectively avoided, thereby promoting the enzyme cascade reaction with high catalytic efficiency. The specific catalytic efficiency (k_cat/K_m) of the cascade enzyme system with array arrangement had been evaluated, which exhibited catalytic efficiency about 3.6 times higher than that of the randomly arranged cascade enzyme system. As a result, this strategy provided a new avenue for constructing a highly efficient enzyme cascade system with ultimate applications in biosynthesis, bioanalysis, and biodiagnostics.

X-ray-Controlled Bilayer Permeability of Bionic Nanocapsules Stabilized by Nucleobase Pairing Interactions for Pulsatile Drug Delivery

The targeted and sustained drug release from stimuli-responsive nanodelivery systems is limited by the irreversible and uncontrolled disruption of the currently used nanostructures. Bionic nanocapsules are designed by cross-linking polythymine and photoisomerized polyazobenzene (PETAzo) with adenine-modified ZnS (ZnS-A) nanoparticles (NPs) via nucleobase pairing. The ZnS-A NPs convert X-rays into UV radiation that isomerizes the azobenzene groups, which allows controlled diffusion of the active payloads across the bilayer membranes. In addition, the nucleobase pairing interactions between PETAzo and ZnS-A prevent drug leakage during their in vivo circulation, which not only enhances tumor accumulation but also maintains stability. These nanocapsules with tunable permeability show prolonged retention, remotely controlled drug release, enhanced targeted accumulation, and effective antitumor effects, indicating their potential as an anticancer drug delivery system.

Glucose Oxidase Micropumps: Multi-Faceted Effects of Chemical Activity on Tracer Particles Near the Solid–Liquid Interface

We report the development of glucose oxidase pumps characterized by small lateral dimensions (≈200 μ m). We studied the effects of the activity of the enzyme pump on silica particles (“tracers”) sedimented around the enzyme pump/patch. Once the activity of the pump was turned on (i.e., the glucose substrate was added to the solution), in-plane motion of the tracers away from the enzyme patch, as well as the emergence of an in-plane region around the patch which was depleted by tracers, was observed. The lateral extent of this depletion zone increased in time at a rate dependent both on the glucose concentration and on the areal density of the enzyme in the patch. We argue that, when the tracers were very near the wall, their motion and the emergence of the depletion zone were most likely the result of diffusiophoresis and drag by osmotic flows induced at the wall, rather than that of drag by a solutal buoyancy driven convective flow. We infer that, for the glucose oxidase enzymatic pumps, bulk (solutal buoyancy), as previously reported, as well as surface (osmotic) driven flows coexist and have to be explicitly accounted for. It seems plausible to assume that this is the case in general for enzyme pumps, and these complementary effects should be considered in the design of applications, e.g., stirring or sensing inside microfluidic systems, based on such pumps.

Chemical Patterns in Autoxidations Catalyzed by Redox Dyes

We present simple and effective experiments to produce intricate chemical patterns from common chemicals in a classroom setting. Students selected an independent variable of their interest, designed their experiment, and investigated its effect on chemical patterns in a four-hour activity. Photographs and videos were taken, while the identity and the concentration of chemicals in the reaction mixture, the concentration of oxygen gas above the solution, the depth of the solution, the shape and the total area of container's cross section, and the temperature were varied. Students discussed their results and presented their investigation to the class. Our experiments enable students to conduct inquiries with open-ended discussion and also open possibilities for a chemical art competition.

Full-time dynamics of batch-wise enzymatic cycling system composed of two kinds of dehydrogenase mediated by NAD(P)H for mass production of chiral hydroxyl compounds

Enzymatic cycling system (coupled dehydrogenase-catalyzed biosystem being composed of two elementary enzymatic reactions mediated by NAD(P)H + NAD(P)⁺) is industrially attractive for reducing prochiral carbonyl compounds to the corresponding chiral hydroxyl compounds. The reaction rate equation of the batch-wise biosystem was generally derived by ordered Bi Bi mechanism of two-substrate enzyme reaction on several reasonable assumptions. The rate equations of the batch-wise biosystem was generalized by transforming them into the dimensionless forms. The dimensionless forms were solved numerically. It was revealed that the batch-wise biosystem was generally made up of unique 3 phases, i.e., phases I, II and III. Phase I was very short transient so that the biosystem entered rapidly phase II. In phase II the consumption rate dynamically balanced with its formation rate so that the concentration of NAD(P)H was invariable with time (and hence NAD(P)⁺ concentration was, too). Phase III was substrate-exhausting phase, and the coenzyme concentration became finally only [NAD(P)⁺] or only [NAD(P)H] depending on the initial molar ratio of the prochiral carbonyl compound to the substrate of the coenzyme regeneration reaction ( [Formula: see text] ) > or <1.0. In phases I and II the numerically calculated values of state variables were very close to the analytical but approximate ones. Preferable initial conditions of the batch-wise enzymatic cycling system, i.e., the initial coenzyme species = NAD(P)⁺ and [Formula: see text] , were proposed. As the main assumption irreversibility of the two elemental enzymatic reactions was discussed. Validity of the proposed rate equations was mentioned.

Targeting 3D Bladder Cancer Spheroids with Urease-Powered Nanomotors

Cancer is one of the main causes of death around the world, lacking efficient clinical treatments that generally present severe side effects. In recent years, various nanosystems have been explored to specifically target tumor tissues, enhancing the efficacy of cancer treatment and minimizing the side effects. In particular, bladder cancer is the ninth most common cancer worldwide and presents a high survival rate but serious recurrence levels, demanding an improvement in the existent therapies. Here, we present urease-powered nanomotors based on mesoporous silica nanoparticles that contain both polyethylene glycol and anti-FGFR3 antibody on their outer surface to target bladder cancer cells in the form of 3D spheroids. The autonomous motion is promoted by urea, which acts as fuel and is inherently present at high concentrations in the bladder. Antibody-modified nanomotors were able to swim in both simulated and real urine, showing a substrate-dependent enhanced diffusion. The internalization efficiency of the antibody-modified nanomotors into the spheroids in the presence of urea was significantly higher compared with antibody-modified passive particles or bare nanomotors. Furthermore, targeted nanomotors resulted in a higher suppression of spheroid proliferation compared with bare nanomotors, which could arise from the local ammonia production and the therapeutic effect of anti-FGFR3. These results hold significant potential for the development of improved targeted cancer therapy and diagnostics using biocompatible nanomotors.

Small molecule reaction networks that model the ROS dynamics of the rhizosphere

Molecules released by plants and bacteria form complex abiotic reaction diffusion networks that might regulate the ROS dynamics along the roots of the plants.

Using Chemical Pumps and Motors To Design Flows for Directed Particle Assembly

Mechanical and electrical pumps are conventionally used to drive fluid flow in microfluidic devices; these pumps require external power supplies, thus limiting the portability of the devices. Harnessing catalytic reactions in solution allows pumping to be shifted into the chemical realm and alleviates the need for extraneous equipment. Chemical "pumps" involve surface-bound catalytic patches that decompose dissolved reagents into the products of the reaction. The catalytic reactions thereby produce chemical gradients that in turn generate pronounced flow fields. Such chemically-generated flows can be harnessed to transport particles in the solution and regulate their self-organization into complex structures within confined chambers. The challenge, however, is determining the reactions and conditions that will yield "programmable" flows, which permit control over the structure formation. In this Account, we review our modeling efforts to design chemical pumps (and "motors") to regulate the motion and assembly of microscopic particles in solution. In the first scenario, microcapsules release reagents in a microchamber with stationary catalytic patches and thereby act as "fuel" for the microcapsules' self-sustained motion. As the reagent is consumed, the capsules aggregate into "colonies" on the catalyst-covered sites. The shape of the assembled colonies can be tailored by patterning the distribution of the catalyst on the surface. Hence, these chemical pumps can be utilized to regulate the autonomous motion and targeted delivery of microcarriers in microfluidic devices. Notably, this fundamental physicochemical mechanism could have played a role in the self-organization of early biological cells (protocells). In the second example, the catalysts are localized on mobile, active particles, which are called "motors". Reactants dispersed in the solution are decomposed at the surface of the motors and produce a convective flow that transports both the active particles and nearby passive, non-coated particles. Depending on the numbers of active and passive particles and the structure of the self-organized cluster, these assemblies can translate or spin and thus act as self-assembled "conveyor belts" or gears in the microchamber. The latter examples involve the formation of two-dimensional structures. In the final scenario, we devise a mechanism for assembling three-dimensional towerlike structures using microcapsules in solution. Here, chemicals diffusing from a central patch on a surface generate a radially directed flow along the surface toward the center. This toroidal roll of fluid lifts the capsules above the patch and draws out the cluster into a tower, whose structure can be tailored by varying the attractive capsule-capsule and capsule-surface interaction strengths. Hence, our method of flow-directed assembly can permit the growth of reconfigurable 3D structures from simple subunits. Taken together, these findings facilitate the fabrication of stand-alone microfluidic devices that autonomously perform multistage chemical reactions and assays for portable biomedical applications and act as small-scale factories to autonomously build microscale components.

Oscillations, travelling fronts and patterns in a supramolecular system

Supramolecular polymers, such as microtubules, operate under non-equilibrium conditions to drive crucial functions in cells, such as motility, division and organelle transport¹. In vivo and in vitro size oscillations of individual microtubules^2,3 (dynamic instabilities) and collective oscillations⁴ have been observed. In addition, dynamic spatial structures, like waves and polygons, can form in non-stirred systems⁵. Here we describe an artificial supramolecular polymer made of a perylene diimide derivative that displays oscillations, travelling fronts and centimetre-scale self-organized patterns when pushed far from equilibrium by chemical fuels. Oscillations arise from a positive feedback due to nucleation-elongation-fragmentation, and a negative feedback due to size-dependent depolymerization. Travelling fronts and patterns form due to self-assembly induced density differences that cause system-wide convection. In our system, the species responsible for the nonlinear dynamics and those that self-assemble are one and the same. In contrast, other reported oscillating assemblies formed by vesicles⁶, micelles⁷ or particles⁸ rely on the combination of a known chemical oscillator and a stimuli-responsive system, either by communication through the solvent (for example, by changing pH^7-9), or by anchoring one of the species covalently (for example, a Belousov-Zhabotinsky catalyst^6,10). The design of self-oscillating supramolecular polymers and large-scale dissipative structures brings us closer to the creation of more life-like materials¹¹ that respond to external stimuli similarly to living cells, or to creating artificial autonomous chemical robots¹².