Influence of reaction-induced convection on quorum sensing in enzyme-loaded agarose beads

Quorum Sensing in Emulsion Droplet Swarms Driven by a Surfactant Competition System

Quorum sensing enables unicellular organisms to probe their population density and perform behavior that exclusively occurs above a critical density. Quorum sensing is established in emulsion droplet swarms that float at a water surface and cluster above a critical density. The design involves competition between 1) a surface tension gradient that is generated upon release of a surfactant from the oil droplets, and thereby drives their mutual repulsion, and 2) the release of a surfactant precursor from the droplets, that forms a strong imine surfactant which suppresses the surface tension gradient and thereby causes droplet clustering upon capillary (Cheerios) attraction. The production of the imine-surfactant depends on the population density of the droplets releasing the precursor so that the clustering only occurs above a critical population density. The pH-dependence of the imine-surfactant formation is exploited to trigger quorum sensing upon a base stimulus: dynamic droplet swarms are generated that cluster and spread upon spatiotemporally varying acid and base conditions. Next, the clustering of two droplet subpopulations is coupled to a chemical reaction that generates a fluorescent signal. It is foreseen that quorum sensing enables control mechanisms in droplet-based systems that display collective responses in contexts of, e.g., sensing, optics, or dynamically controlled droplet-reactors.

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.

Collective Behavior of Urease pH Clocks in Nano- and Microvesicles Controlled by Fast Ammonia Transport

The transmission of chemical signals via an extracellular solution plays a vital role in collective behavior in cellular biological systems and may be exploited in applications of lipid vesicles such as drug delivery. Here, we investigated chemical communication in synthetic micro- and nanovesicles containing urease in a solution of urea and acid. We combined experiments with simulations to demonstrate that the fast transport of ammonia to the external solution governs the pH-time profile and synchronizes the timing of the pH clock reaction in a heterogeneous population of vesicles. This study shows how the rate of production and emission of a small basic product controls pH changes in active vesicles with a distribution of sizes and enzyme amounts, which may be useful in bioreactor or healthcare applications.

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.

Autonomous Transient pH Flips Shaped by Layered Compartmentalization of Antagonistic Enzymatic Reactions

Transient signaling orchestrates complex spatiotemporal behaviour in living organisms via (bio)chemical reaction networks (CRNs). Compartmentalization of signal processing is an important aspect for controlling such networks. However, artificial CRNs mostly focus on homogeneous solutions to program autonomous self-assembling systems, which limits their accessible behaviour and tuneability. Here, we introduce layered compartments housing antagonistic pH-modulating enzymes and demonstrate that transient pH signals in a supernatant solution can be programmed based on spatial delays. This overcomes limitations of activity mismatches of antagonistic enzymes in solution and allows to flexibly program acidic and alkaline pH lifecycles beyond the possibilities of homogeneous solutions. Lag time, lifetime, and the pH minima and maxima can be precisely programmed by adjusting spatial and kinetic conditions. We integrate these spatially controlled pH flips with switchable peptides, furnishing time-programmed self-assemblies and hydrogel material system.

Size- and position-dependent bifurcations of chemical microoscillators in confined geometries

The present theoretical study deals with microparticles (beads) that contain an immobilized Belousov-Zhabotinsky (BZ) reaction catalyst. In the theoretical experiment, a BZ bead is immersed in a small water droplet that contains all of the BZ reaction reagents but no catalyst. Such heterogeneous reaction-diffusion BZ systems with the same BZ reactant concentrations demonstrate various dynamic modes, including steady state and low-amplitude, high-amplitude, and mixed-mode oscillations (MMOs). The emergence of such dynamics depends on the sizes of the bead and water droplet, as well as on the location of the bead inside the droplet. MMO emergence is explained by time-delayed positive feedback in combination with a canard phenomenon. If two identical BZ beads are immersed in the same droplet, many different dynamic modes including chaos are observed.